en Yuki Yamagata SSBD Ontology Emi Fujisawa Fangfang Wang Haruna Yamamoto Hiroya Itoga Koji Kyoda Miguel Miranda-Miranda Shuichi Onami Yasue Nakano Yukako Tohsato Yuki Yamagata The SSBD Ontology is an ontology of SSBD (https://ssbd.riken.jp). SSBD is a platform for sharing and reusing bioimaging data. SSBD:database is an added-value database for bioimages and biological dynamics data. It provides a rich set of open resources for analyzing microscopy images and qunatitative data of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Microscopy images and quantitative biological data are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations. image 2025-05-08 BFO OWL specification label Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label BFO OWL specification label BFO CLIF specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label BFO CLIF specification label An annotation property that represents an ID used in the NIH LINCS project. Oliver He, Jiangan Xie, Jie Zheng LINCS ID An annotation property that specifies an STR profile of a cell line cell. Yongqun He STR profile editor preferred label editor preferred term The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label example example of usage A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> IAO:0000112 uberon example_of_usage true example_of_usage example of usage example of usage in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status has curation status definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition textual definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> GROUP:OBI:<http://purl.obofoundry.org/obo/obi> IAO:0000116 uberon editor_note true editor_note editor note editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor term editor alternative label alternative term A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). alternative label alternative term alternative term definition source Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source definition source has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg IAO:0000232 uberon curator_notes true curator_notes curator note curator note curator notes term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg IAO:0000233 external uberon term_tracker_item true true term_tracker_item The 'tracker item' can associate a tracker with a specific ontology term. term tracker item term tracker item ontology term requester The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester is denotator type Relates an class defined in an ontology, to the type of it's denotator In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') Alan Ruttenberg is denotator type imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from imported from expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to expand expression to expand assertion to ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. Chris Mungall expand assertion to expand assertion to first order logic expression PERSON:Alan Ruttenberg first order logic expression antisymmetric property part_of antisymmetric property xsd:true Use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property OBO foundry unique label has ID digit count Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) Person:Alan Ruttenberg has ID digit count has ID range allocated Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300] Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms Person:Alan Ruttenberg has ID range allocated to has ID policy for Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg has ID policy for has ID prefix Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. Person:Alan Ruttenberg has ID prefix elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) has associated axiom(fol) is allocated id range Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" PERSON:Alan Ruttenberg Add as annotation triples in the granting ontology is allocated id range has ontology root term Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. Nicolas Matentzoglu IAO:0000700 external has_ontology_root_term true has_ontology_root_term has ontology root term has ontology root term preferred_root may be identical to A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. David Osumi-Sutherland #40 VFB Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. may be identical to has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI has axiom label term replaced by Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by term replaced by An alternative term used by the IEDB. IEDB alternative term This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. OBO Operations call logical characteristic of object property 'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. defined by construct temporal interpretation An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation temporal interpretation https://oborel.github.io/obo-relations/temporal-semantics/ https://code.google.com/p/obo-relations/wiki/ROAndTime https://github.com/oborel/obo-relations/wiki/ROAndTime A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. non-overlapping with shares no parts with Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171> CONSTRUCT { part_of: a owl:ObjectProperty . [ a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?x ; a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?y ] ] } WHERE { ?x mutually_spatially_disjoint_with: ?y . } RO:0002171 uberon mutually_spatially_disjoint_with true true mutually_spatially_disjoint_with mutually spatially disjoint with mutually spatially disjoint with https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. RO:0002174 uberon dubious_for_taxon true true dubious_for_taxon This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost this relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleost dubious for taxon dubious for taxon dubious_for_taxon An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. logical macro assertion http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/ A logical macro assertion whose domain is an IRI for a class The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL logical macro assertion on a class A logical macro assertion whose domain is an IRI for a property logical macro assertion on a property Used to annotate object properties to describe a logical meta-property or characteristic of the object property. logical macro assertion on an object property logical macro assertion on an annotation property relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' Chris Mungall is direct form of If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive A shortcut relationship that holds between two entities based on their identity criteria logical macro assertion involving identity A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds. in approximate one to one relationship with 'anterior end of organism' is-opposite-of 'posterior end of organism' 'increase in temperature' is-opposite-of 'decrease in temperature' x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). is opposite of true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation. cjm nominally disjoint with Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" cjm 2018-03-13T23:59:29+00:00 is directional form of cjm 2018-03-14T00:03:24+00:00 is negative form of part-of is homeomorphic for independent continuants. R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. cjm 2018-10-21T19:46:34+00:00 R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. is homeomorphic for An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. UBPROP:0000001 uberon external_definition true external_definition This annotation property may be replaced with an annotation property from an external ontology such as IAO external_definition A textual description of an axiom loss in this ontology compared to an external ontology. UBPROP:0000002 uberon axiom_lost_from_external_ontology true axiom_lost_from_external_ontology This annotation property may be replaced with an annotation property from an external ontology such as IAO axiom_lost_from_external_ontology Notes on the homology status of this class. UBPROP:0000003 uberon homology_notes true homology_notes This annotation property may be replaced with an annotation property from an external ontology such as IAO homology_notes UBPROP:0000004 uberon provenance_notes true provenance_notes provenance_notes An alternate comment for a class taken unmodified from an external source. Note that obo format only allows a single comment for a class, and does not provide a structured means of adding provenance info. UBPROP:0000005 uberon external_comment true external_comment This annotation property may be replaced with an annotation property from an external ontology such as IAO external_comment Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'. UBPROP:0000007 uberon has_relational_adjective true has_relational_adjective has_relational_adjective Notes on the how instances of this class vary across species. UBPROP:0000008 uberon taxon_notes true taxon_notes taxon_notes Notes on the evolved function of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000009 uberon function_notes true function_notes function_notes Notes on the structure, composition or histology of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000010 uberon structure_notes true structure_notes structure_notes Notes on the ontogenic development of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000011 uberon development_notes true development_notes development_notes Notes on how similar or equivalent classes are represented in other ontologies. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000012 uberon external_ontology_notes true external_ontology_notes external_ontology_notes Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000013 uberon terminology_notes true terminology_notes terminology_notes FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term UBPROP:0000202 uberon fma_set_term true fma_set_term fma_set_term Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity. http://purl.org/dc/elements/1.1/creator true dc-creator An entity primarily responsible for making the content of the resource. Creator creator Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. A date associated with an event in the life cycle of the resource. Date Date Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats). The physical or digital manifestation of the resource. Format Format The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a resource from which the present resource is derived. Source Source Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme. The topic of the content of the resource. Subject and Keywords Subject and Keywords Typically, a Title will be a name by which the resource is formally known. http://purl.org/dc/elements/1.1/title uberon dc-title true dc-title A name given to the resource. Title Title title Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity. An entity responsible for making contributions to the content of the resource. Contributor contributor description http://purl.org/dc/terms/license uberon dcterms-license true dcterms-license license consider Author of the class. created by created_by Date class was created. creation date creation_date ID of merged class. has_alternative_id An alternative label for a class or property which has a more general meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym has_broad_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/18 disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. Reference database or publication source. database_cross_reference has cross-reference An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. Exact synonym. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym has exact synonym has_exact_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym has_narrow_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has_obo_format_version Name space of the ontology. disease_ontology has_obo_namespace An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. Has related synonym. https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym has_related_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 An identifier for an individual entity. An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. id In subset. in_subset shorthand Comment. comment Is defined by. rdfs:isDefinedBy A human readable name for this class. label label http://www.w3.org/2000/01/rdf-schema#seeAlso seeAlso spatial uberon seeAlso true seeAlso see also A skos concept mapping used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably. has exact match http://xmlns.com/foaf/0.1/depicted_by uberon depicted_by true depicted_by depicted by http://xmlns.com/foaf/0.1/depiction uberon depiction true depiction depiction is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of BFO:0000050 external quality uberon part_of part_of part of http://www.obofoundry.org/ro/#OBO_REL:part_of https://wiki.geneontology.org/Part_of realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes preceded by X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X). x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 is preceded by takes place after external uberon preceded_by preceded_by preceded by preceded by preceded_by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 external uberon precedes precedes precedes precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in BFO:0000066 external occurs_in occurs_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in https://wiki.geneontology.org/Occurs_in The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. c = pattern in the ink b = paper + ink r = friend c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file. 8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy obsolete_specifically denotes true An information artifact IA mentions an entity E exactly when it has a component/part that denotes E 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity) 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition PERSON: Jonathan Rees Person: Alan Ruttenberg mentions Inverse of the relation 'mentions' 2022-01-28T07:20:08+00:00 mentioned by see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote obsolete_materially denotes true obsolete_describes true obsolete_represents true inverse of the relation 'denotes' Person: Jie Zheng, Chris Stoeckert, Mike Conlon denoted by relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point has coordinate unit label relates a process to a time-measurement-datum that represents the duration of the process Person:Alan Ruttenberg is duration of A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality. Person:Alan Ruttenberg Person:Bjoern Peters is quality specification of inverse of the relation of is quality specification of 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship Person:Alan Ruttenberg Person:Bjoern Peters quality is specified as relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken Alan Ruttenberg has time stamp relates a time stamped measurement datum to the measurement datum that was measured Alan Ruttenberg has measurement datum is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of is_specified_output_of is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of has organization member bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of RO:0000053 external uberon bearer_of bearer_of bearer of bearer of has characteristic participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in RO:0000056 external uberon participates_in participates_in participates in participates_in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 external has_participant has_participant has participant has participant this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality RO:0000086 uberon has_quality has_quality has quality has quality a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ location_of RO:0001015 location_of location of located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in http://www.obofoundry.org/ro/#OBO_REL:located_in RO:0001025 located_in located in https://wiki.geneontology.org/Located_in David Osumi-Sutherland <= Primitive instance level timing relation between events before or simultaneous with Relation between occurrents, shares start and end boundaries. x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. David Osumi-Sutherland RO:0002082 coincides_with is_equal_to simultaneous_with t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y). David Osumi-Sutherland starts_at_end_of A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. RO:0002087 directly preceded by is directly preceded by is immediately preceded by starts_at_end_of external uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by immediately preceded by immediately_preceded_by David Osumi-Sutherland ends_at_start_of meets RO:0002090 external immediately_precedes immediately_precedes X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes immediately precedes immediately_precedes David Osumi-Sutherland io X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) starts during David Osumi-Sutherland d during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during David Osumi-Sutherland o overlaps X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). ends during in taxon w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. RO:0002180 external uberon has_component has_component has component Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to Relation between occurrents, shares a start boundary with. inverse of starts with Chris Mungall Allen RO:0002223 uberon starts starts Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall started by RO:0002224 external uberon starts_with starts_with starts with starts with Relation between occurrents, shares an end boundary with. inverse of ends with Chris Mungall RO:0002229 finishes ends ends p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes RO:0002233 external has_input has_input has input has input https://wiki.geneontology.org/Has_input p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. Chris Mungall produces RO:0002234 external has_output has_output has output has output https://wiki.geneontology.org/Has_output q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of Chris Mungall inheres in part of characteristic of part of An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of has member is a mereological relation between a collection and an item. SIO RO:0002351 uberon has_member has_member has member Chris Mungall depends on inverse of has skeleton Chris Mungall RO:0002576 uberon skeleton_of skeleton_of skeleton of a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Melissa Haendel RO:0003000 external uberon produces produces Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces a produced_by b iff some process that occurs_in b has_output a. Melissa Haendel RO:0003001 external uberon produced_by produced_by produced by produced by produced_by p acts on population of c iff c' is a collection, has members of type c, and p has participant c pg 2020-06-08T17:21:33+00:00 RO:0012003 external acts_on_population_of acts_on_population_of acts on population of acts on population of Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. TODO: Add homeomorphy axiom ECO:0000041 SO:similar_to sameness similar to correspondence resemblance in similarity relationship with A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). has_high_plasma_membrane_amount A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). has_low_plasma_membrane_amount has_not_completed c site_of p if c is the bearer of a disposition that is realized by a process that has p as part. uberon capable_of_has_part site_of site_of uberon subdivision_of placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B subdivision of component of has SSBD core information has biosample information has concentration information has contrast enhancing method has dataset output has detection method has dimension information has fold dilution information has genetic information has illumination method has imaged parameter has imaging mehod recorded type has imaging method has imaging method total infornation has instrument information has license has MeSH ID has ome zarr information has project participant has project publications has reagent information has resolution enhancing method has sample preparation method has visualization method is about GO bp is about GO cc is about GO mf is about anatomical entity A (relation that relates an information artifact to a biological related entity such as organism, anatomical entity, cell, biological process. is about biological related is about cell is about cell line is about life cycle is about organism is about strain participates in project publications has measurement value has x coordinate value has z coordinate value has y coordinate value has dataset folder name date of opened has OME-NGFF version has PMID PubMed ID has ROR ID has address the particulars of the place where someone or an organization is situated. For now, this slot is a simple text "blob" containing all relevant details of the given location for fitness of purpose. For the moment, this "address" can include other contact details such as email and phone number(?). https://w3id.org/biolink/vocab/address has affiliation https://w3id.org/biolink/vocab/affiliation has axes has biosample variable has channel has concentration value has concentration value 2 has dataset download url https://w3id.org/biolink/vocab/dataset_download_url has dataset ID has dataset title has department name has description has DOI has extrinsic variable has family name has file format has first name has fold dilution has fold dilution 2 has ID A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI https://w3id.org/biolink/vocab/id has intrinsic variable hasJ-GLOBAL ID has laboratory name has metadata version has middle name has name A human-readable name for an attribute or entity. https://w3id.org/biolink/vocab/name has ORCID has organization name has organization url has personal ID has phone number has PMCID has project SID has project DOI has reagent name has reagent name 2 has reagent uri has reagent uri 2 has researchmap ID has s3 endpoint has size C has size T has size X has size Y has size Z has strain URL has thumbnail url has time interval has title name has time slice has total time frame has type https://w3id.org/biolink/vocab/type has unit has url This slot holds a string representation of a URL for an external resource about the node it is present on. Unlike an 'xref' that is primarily represented by a CURIE, this slot is intended to hold a full URL that can be used to directly access a resource. When linking to an external resource that cannot be represented by a unique CURIE, this slot should be used. However, when the intent is to link to the default URI expansion of a CURIE related to the node it is present on, the xref slot should be used instead. https://w3id.org/biolink/vocab/url has version has vizarr url has xref https://w3id.org/biolink/vocab/xref has e-mail Topical Descriptors indicate the subject of an indexed item such as a journal article. See D063926, 'Drug Hypersensitivity Syndrome', for an example. MeSH TopicalDescriptor APOLLO_SV:00000008 A planned process that has specified output a software product and that involves the creation of source code. Mathias Brochhausen William R. Hogan http://en.wikipedia.org/wiki/Software_development A planned process resulting in a software product involving the creation of source code. software development APOLLO_SV:00000032 A measurement datum that is the output of counting. Mathias Brochhausen A measurement datum that is the output of counting. count APOLLO_SV:00000522 software source code version control repository A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc. William R. Hogan Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based source code repository BFO:0000001 entity Entity entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) BFO:0000006 BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] BFO:0000009 an infinitely thin plane in space. the surface of a sphere-shaped part of space A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] two-dimensional spatial region A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] BFO:0000015 a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] BFO:0000018 A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] BFO:0000019 the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] BFO:0000023 John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] BFO:0000026 an edge of a cube-shaped portion of space. A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] one-dimensional spatial region A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] BFO:0000028 a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial region A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] CARO:0030000 biological entity CHEBI:15956 biotin An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. biotin CHEBI:16670 peptide Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. peptide CHEBI:23367 molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well molecular entity CHEBI:31624 fluorescein (lactone form) A xanthene dye that is highly fluorescent, detectable even when present in minute quantities. Used forensically to detect traces of blood, in analytical chemistry as an indicator in silver nitrate titrations and in microscopy. fluorescein (lactone form) CHEBI:33696 nucleic acid A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. nucleic acid CHEBI:33839 macromolecule CHEBI:37987 Cy3 dye Cy3 dye CHEBI:37989 Cy5 dye Cy5 dye CHEBI:42098 digoxigenin A hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta-, 12beta- and 14beta-positions. It has been isolated from the plant species of the genus Digitalis. digoxigenin CHEBI:51756 Alexa Fluor 532 Alexa Fluor 532 CHEBI:51760 Alexa Fluor 546 Alexa Fluor 546 CHEBI:52673 Alexa Fluor 555 A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate. Alexa Fluor 555 CLO:0000001 cell line cell A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture Yongqun He, Matthew Brush, Sirarat Sarntivijai, Alexander Diehl, Jie Zheng, Yu Lin, Bjoern Peters A 'cell line cell' is a part of a cell line established through the passaging/selection of a primary cultured cells or the experimental modification of an existing cell line. New types of cell line cells are established after sufficient passaging of a primary culture to establish a stable and homogenous population that qualifies as a line (typically 1-20 passages), or following some spontaneous or experimental modification that confers novel characteristics to an existing line. A cell line cell typically has mutations of five or more genes compared to the original cell that derives the cell line cell. Some gene mutations may turn on some oncogenes. Cell line cells can be in active culture, stored in a quiescent state for future use (e.g. frozen in liquid nitrogen), or applied in experimental procedures. cell line cell CLO:0000019 immortal cell line cell A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. Yongqun He, Matthew Brush, Allen Xiang, Asiyah Yu Lin, Sirarat Sarntivijai, James Malone, Jie Zheng, Tomasz Adamusiak continuous cell line cell permanent cell line cell immortal cell line cell CLO:0000076 a immortal contractile cell line cell that is derived from muscle cell ZX, YH immortal muscle cell line cell CLO:0000079 an immortal cell line cell that is derived from electrically active cell ZX, YH immortal electrically active cell line cell CLO:0000080 a immortal electrically active cell line cell that is derived from electrically responsive cell ZX, YH immortal electrically responsive cell line cell CLO:0000081 a immortal electrically responsive cell line cell that is derived from neuron ZX, YH immortal neuron cell line cell CLO:0000084 a immortal neuron cell line cell that is derived from peripheral neuron ZX, YH immortal peripheral neuron cell line cell CLO:0000093 a cell line that is derived from motile cell ZX, YH immortal motile cell line immortal motile cell line cell CLO:0000102 a immortal motile cell line that is derived from leukocyte ZX, YH immortal leukocyte cell line immortal leukocyte cell line cell CLO:0000107 a immortal leukocyte cell line that is derived from nongranular leukocyte ZX, YH immortal nongranular leukocyte cell line immortal nongranular leukocyte cell line cell CLO:0000108 a immortal nongranular leukocyte cell line that is derived from lymphocyte ZX, YH immortal lymphocyte cell line immortal lymphocyte cell line cell CLO:0000109 a immortal lymphocyte cell line that is derived from T cell ZX, YH immortal T cell line immortal T cell line cell CLO:0000110 a immortal T cell line that is derived from alpha-beta T cell ZX, YH immortal alpha-beta T cell line immortal alpha-beta T cell line cell CLO:0000113 a immortal alpha-beta T cell line that is derived from mature alpha-beta T cell ZX, YH immortal mature alpha-beta T cell line immortal mature alpha-beta T cell line cell CLO:0000114 a immortal mature alpha-beta T cell line that is derived from CD4-positive, CD25-positive, alpha-beta regulatory T cell ZX, YH immortal CD4-positive, CD25-positive, alpha-beta regulatory T cell line immortal CD4-positive, CD25-positive, alpha-beta regulatory T cell line cell CLO:0000115 a immortal CD4-positive, CD25-positive, alpha-beta regulatory T cell line that is derived from induced T-regulatory cell ZX, YH immortal induced T-regulatory cell line immortal induced T-regulatory cell line cell CLO:0000116 a immortal T cell line that is derived from mature T cell ZX, YH immortal mature T cell line immortal mature T cell line cell CLO:0000124 a immortal cell line cell that is derived from eukaryotic cell ZX, YH immortal eukaryotic cell line cell CLO:0000128 a immortal eukaryotic cell line that is derived from animal cell ZX, YH immortal animal cell line immortal animal cell line cell CLO:0000129 a immortal animal cell line that is derived from epithelial cell ZX, YH immortal epithelial cell line cell CLO:0000147 a immortal animal cell line that is derived from hematopoietic cell ZX, YH immortal hematopoietic cell line immortal hematopoietic cell line cell CLO:0000156 a immortal animal cell line that is derived from neural cell ZX, YH immortal neural cell line immortal neural cell line cell CLO:0000160 a immortal animal cell line that is derived from connective tissue cell ZX, YH immortal connective tissue cell line cell CLO:0000161 a immortal connective tissue cell line that is derived from fibroblast ZX, YH immortal fibroblast cell line immortal fibroblast cell line cell CLO:0000165 a cell line that is derived from nucleate cell ZX, YH immortal nucleate cell line immortal nucleate cell line cell CLO:0000166 a cell line that is derived from somatic cell ZX, YH immortal somatic cell line cell CLO:0000168 a immortal epithelial cell line cell that is derived from HeLa cell Yongqun He HeLa derived cell line cell CLO:0000182 An immortal fibroblast cell line cell that derives from arm. Yue Liu, Yongqun He immortal arm-derived fibroblast cell line cell CLO:0000220 An immortal cell line cell that derives from kidney. Yue Liu, Yongqun He immortal kidney-derived cell line cell CLO:0000243 An immortal cell line cell that derives from female gonad. Yue Liu, Yongqun He immortal female gonad-derived cell line cell CLO:0000271 An immortal cell line cell that derives from eye. Yue Liu, Yongqun He immortal eye-derived cell line cell CLO:0000283 An immortal epithelial cell line cell that derives from uterine cervix. Yue Liu, Yongqun He immortal uterine cervix-derived epithelial cell line cell CLO:0000527 An immortal female gonad-derived cell line cell that derives from Chinese hamster. Yue Liu, Yongqun He immortal Chinese hamster female gonad-derived cell line cell CLO:0000533 An immortal kidney-derived cell line cell that derives from vervet monkey. Yue Liu, Yongqun He immortal vervet monkey kidney-derived cell line cell CLO:0000563 An immortal epithelial cell line cell that derives from human. Yue Liu, Yongqun He immortal human epithelial cell line cell CLO:0000573 An immortal kidney-derived cell line cell that derives from dog. Yue Liu, Yongqun He immortal dog kidney-derived cell line cell CLO:0000581 An immortal muscle cell line cell that derives from mouse. Yue Liu, Yongqun He immortal mouse muscle cell line cell CLO:0000587 An immortal kidney-derived cell line cell that derives from human. Yue Liu, Yongqun He immortal human kidney-derived cell line cell CLO:0000636 An immortal uterine cervix-derived epithelial cell line cell that derives from human. Yue Liu, Yongqun He immortal human uterine cervix-derived epithelial cell line cell CLO:0000876 An immortal eye-derived cell line cell that derives from human. Yue Liu, Yongqun He immortal human eye-derived cell line cell CLO:0001230 293 293 HEK 293 cell HEK 293 HEK-293 Human Embryonic Kidney 293 WEB: http://hek293.com/ WEB: http://web.expasy.org/cellosaurus/CVCL_0045 WEB: https://www.atcc.org/Products/All/CRL-1573.aspx HEK293 ATCC: CRL-1573 BTO: BTO_0000007 EFO: EFO_0001182) RRID: CVCL_0045 CLO:0001401 4T1 4T1 cell ATCC: CRL-2539 CLO:0002462 CHO-K1 CHO-K1 cell ATCC: CCL-61 CLO:0002597 COS-7 COS-7 cell ATCC: CRL-1651 MeSH: D019556 CLO:0003696 HeLa S3 HeLa S3 cell ATCC: CCL-2.2 CLO:0003707 HEp-2 HEp-2 cell ATCC: CCL-23 CLO:0004290 hTERT RPE-1 disease: pigmented epithelium; immortalized with hTERT hTERT RPE-1 cell ATCC: CRL-4000 CLO:0007156 L1210 L1210 cell ATCC: CCL-219 CLO:0007665 MEF (C57BL/6) disease: feeder layer MEF (C57BL/6) cell ATCC: SCRC-1008 CLO:0037236 An immortal kidney-derived cell line cell that derives from human. Yue Liu, Yongqun He immortal human kidney-derived epithelial cell line cell CLO:0037237 Amelogenin: X; CSF1PO: 11,12; D13S317: 12; D16S539: 9; D18S51: 18; D21S11: 28,30.2; D3S1358: 15,17; D5S818: 8,9; D7S820: 11,12; D8S1179: 12,14; FGA: 23; Penta D: 9,10; Penta E: 7,15; TH01: 7,9.3; TPOX: 11; vWA: 16,19 293 293 HEK HEK 293 HEK-293 HEK293 WEB: http://hek293.com/ WEB: http://web.expasy.org/cellosaurus/CVCL_0045 WEB: https://www.atcc.org/Products/All/CRL-1573.aspx 293-derived cell ATCC: CRL-1573 RRID: CVCL_0045 CLO:0037271 'Tango cell' refers to one of many stable cell lines, all based on the parental line HEK293T, designed to work in a 'Tango beta-arrestin' recruitiment assay to measure receptor activation for more than 300 GPCRs. See PMID25895059 and https://pdspdb.unc.edu/prestotango/ BAO, YH http://www.ncbi.nlm.nih.gov/pubmed/25895059 https://pdspdb.unc.edu/prestotango/ https://www.ncbi.nlm.nih.gov/pubmed/18165312 Tango cell BTO: BAO_0030063 CLO:0037372 293 T 293-T 293T 293tsA1609neo HEK 293 T HEK-293-T HEK-293T HEK293T Hek 293T Human Embryonic Kidney 293T https://web.expasy.org/cellosaurus/CVCL_0063 HEK293T cell CVCL: CVCL_0063 CLO:0050871 A immortal mouse muscle cell line cell that has the characteristics: Said differentiate to myotubes, but need confirmation. Backup of ECA91031101. RIKEN Cell bank Team Yongqun He C2C12 RCB0987 Derived from tissue: muscle in animal: mouse, C3H. Register: ECACC RCB0987 cell CL:0000001 primary cultured cell A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged. primary cultured cell CL:0000010 cultured cell A cell in vitro that is or has been maintained or propagated as part of a cell culture. cell Note that this class was re-labeled to 'cultured cell' instead of 'cell line cell', as it intent was clarified to cover any cultured cells of multicellular and unicellular organisms. This includes cells actively being cultured, or cells that have been cultured but are stored in a quiescent state for future use. In having been cultured, cells must establish homeostasis and often replicate in a foreign environment. Accomodation of this stress initiates a selection of cells fit for such challenges, wherein necessary adaptive biochemical and.or genetic changes can occur. These changes can set them apart from the in vivo cells from which they derive, and such changes will typically accumulate and change over increasing time in culture. cultured cell CL:0000034 A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. CALOHA:TS-2086 FMA:63368 ZFA:0005957 animal stem cell This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’. stem cell CL:0000039 A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring. ZFA:0009016 Originally this term had some plant germ line cell children. germ line cell CL:0000048 A stem cell that can give rise to multiple lineages of cells. FMA:84789 ZFA:0009020 multi-fate stem cell multifate stem cell multipotent cell multipotent stem cell multi fate stem cell CL:0000066 A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. BTO:0000414 CALOHA:TS-2026 CARO:0000077 FBbt:00000124 FMA:66768 WBbt:0003672 ZFA:0009034 epitheliocyte epithelial cell https://www.swissbiopics.org/api/image/Epithelial_cells.svg CL:0000068 An epithelial cell that is part of a duct. ZFA:0009372 duct epithelial cell CL:0000076 Any epithelial cell that is part of some squamous epithelium. CALOHA:TS-1249 ZFA:0009039 squamous epithelial cell CL:0000081 A cell found predominately in the blood. FMA:62844 MESH:D001773 ZFA:0009044 blood cell CL:0000133 Ectoderm destined to be nervous tissue. ZFA:0009080 neurectoderm cell neurectodermal cell CL:0000134 A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs. BTO:0002625 BTO:0003298 FMA:70546 ZFA:0009081 bone marrow stromal cells colony-forming unit-fibroblast marrow stromal cells BMSC CFU-F MSC mesenchymal precursor cell mesenchymal progenitor cells mesenchymal stem cell mesenchymal stromal cell mesenchymal stromal cells stem cells, mesenchymal Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. mesenchymal stem cell https://github.com/obophenotype/cell-ontology/issues/474 CL:0000150 An epithelial cell, located in a gland, that is specialised for the synthesis and secretion of specific biomolecules, such as hormones, or mucous. CALOHA:TS-2085 FMA:86494 glandular epithelial cell glandular secretory epithelial cell CL:0000151 A cell that specializes in controlled release of one or more substances. BTO:0003659 FMA:86916 secretory cell CL:0000152 A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct. FMA:16014 ZFA:0009092 exocrine cell CL:0000154 Any secretory cell that is capable of some protein secretion. protein secreting cell CL:0000159 seromucus secreting cell CL:0000163 A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions. FMA:83809 ZFA:0009096 endocrinocyte endocrine cell CL:0000164 An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas. Enteroendocrine cells are a specialized subset of cells located within the epithelial lining of both the small and large intestines, as well as the stomach and pancreas. Constituting less than 1% of the total population of intestinal cells, they are differentiated from a common intestinal cell progenitor, thus sharing lineage with absorptive and goblet cells of the intestines. The distinct characteristic feature of an enteroendocrine cell is its inherent capacity to synthesize and secrete a plethora of gut hormones such as serotonin, somatostatin, neurotensin, cholecystokinin, secretin, gastric inhibitory peptide, motilin, and glucagon-like peptide-1. Integrated within this complex network of signaling agents, these substances control various aspects of the digestive system. Each enteroendocrine cell has its unique combination of hormones to release, determined by its position along the intestinal tract. Intriguingly, these hormones not only modulate local gut function, including motility, absorption and secretion, but also potentiate distant actions on other systems such as endocrine, nervous and immune and play a role in the feeling of satiety. The release of these hormones from enteroendocrine cells is a highly regulated and dynamic process. The cells are equipped with sensory receptors localized on its luminal side that respond to various stimuli, including changes in nutrient composition, chemical or mechanical changes in the gut lumen, or even signals arising from commensal microbiota. This sensory input stimulates a signaling cascade within the cell, culminating in the release of specific hormones into the interstitial fluid. These hormones then make their way into the bloodstream, acting on their respective target receptors to mediate their duties. The multifunctional characteristics of enteroendocrine cells make them crucial for maintaining gut homeostasis and the overall physiological well being of the body. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.) BTO:0003865 FMA:62930 MESH:D019858 ZFA:0009097 https://cellxgene.cziscience.com/cellguide/CL_0000164 enteroendocrine cell CL:0000167 Any secretory cell that is capable of some peptide hormone secretion. ZFA:0009100 peptide hormone secreting cell CL:0000168 Any secretory cell that is capable of some insulin secretion. BTO:0000783 ZFA:0009101 insulin secreting cell CL:0000170 A cell that secretes glucagon. FMA:84045 ZFA:0009103 glucagon-secreting cell glucagon secreting cell CL:0000172 Any secretory cell that is capable of some somatostatin secretion. ZFA:0009105 somatostatin secreting cell CL:0000211 A cell whose function is determined by the generation or the reception of an electric signal. ZFA:0009128 electrically active cell CL:0000213 A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism. ZFA:0009130 boundary cell lining cell CL:0000219 A cell that moves by its own activities. ZFA:0009136 motile cell CL:0000221 A cell of the outer of the three germ layers of the embryo. FMA:72549 ZFA:0009137 ectoderm cell ectodermal cell CL:0000222 A cell of the middle germ layer of the embryo. Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.) FMA:72554 ZFA:0009138 https://cellxgene.cziscience.com/cellguide/CL_0000222 mesoblast mesoderm cell mesodermal cell CL:0000223 A cell of the inner of the three germ layers of the embryo. FMA:72555 ZFA:0009139 endoderm cell endodermal cell CL:0000226 A cell with a single nucleus. single nucleate cell CL:0000234 Any cell capable of ingesting particulate matter via phagocytosis. BTO:0001044 FMA:83806 MESH:D010586 ZFA:0009140 phagocyte CL:0000255 Any cell that in taxon some Eukaryota. MESH:D005057 eukaryotic cell CL:0000313 Columnar glandular cell with irregular nucleus, copious granular endoplasmic reticulum and supranuclear granules. Secretes a watery fluid containing proteins known as serous fluid. BTO:0003687 FMA:62511 serous cell serous secreting cell CL:0000319 Any cell that is capable of some mucus secretion. BTO:0003689 ZFA:0009159 mucous cell mucus secreting cell CL:0000325 A cell that is specialised to accumulate a particular substance(s). stuff accumulating cell CL:0000329 Any cell that is capable of some oxygen transport. ZFA:0009164 oxygen accumulating cell CL:0000335 A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors. ZFA:0009166 mesenchyme condensation cell CL:0000352 A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation. epiblast cell CL:0000365 Diploid cell produced by the fusion of sperm cell nucleus and egg cell. zygote BTO:0000854 EHDAA2:0004546 FMA:72395 animal zygote CL:0000393 A cell whose function is determined by its response to an electric signal. ZFA:0009190 electrically responsive cell CL:0000412 A cell that contains more than two haploid sets of chromosomes. polyploid cell CL:0000518 A phagocyte in vertebrates that is able to phagocytosis. phagocyte (sensu Vertebrata) CL:0000540 The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. BTO:0000938 CALOHA:TS-0683 FBbt:00005106 FMA:54527 VHOG:0001483 WBbt:0003679 ZFA:0009248 nerve cell These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. neuron https://www.swissbiopics.org/api/image/Neuron_cells.svg CL:0000578 experimentally modified cell in vitro A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. cell This class has been re-labeled to imply reference only to in vitro experimentally modified cells, similarly, the definition has been slightly updated to reflect this. 'experimentally modified cell' refers only to cells in vitro, and not modified in vivo/in environment cells. There is currently no class representing unmodified in vitro cells (other than the parent 'cell in vitro'), or a class representing modified native cells. More granular subclassing of experimentally modified cell can be found in ReO. MHB 1.12.12 experimentally modified cell in vitro CL:0000586 The reproductive cell in multicellular organisms. BTO:0000535 NCIT:C12597 VHOG:0001534 WBbt:0006796 germ cell CL:0000622 A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus). Acinar cells are specialized exocrine gland cells that secrete specific enzymes and fluids to aid in digestion. Found primarily in the pancreas and salivary glands, the term acinar is derived from the Latin word 'acinus' which means 'grape'; this is because acinar cells are arranged in a grape-like cluster around small ducts, formulating an acinus structure. In the salivary glands, acinar cells secrete digestive enzymes as well as other substances such as mucus and water. These secretions service the initial stages of the digestive process, preparing the consumed food for onward digestion in the stomach and intestines by lubricating and partially breaking it down. In the pancreas, acinar cells are responsible for synthesizing and secreting a significant amount of digestive enzymes, such as trypsin, chymotrypsin, and amylase. These enzymes are stored in zymogen granules inside the acinar cells until they are dispatched into the small intestine. Once within the small intestine, they break down proteins, carbohydrates, and fats into substances that can be absorbed. This is vital to the effective and efficient digestion and absorption of nutrients from the food we consume. Acinar cells have high protein synthesis rates and are susceptible to accumulation of misfolded proteins; the subsequential induction of ER stress is thought to be involved in the development of pancreatitis, a serious inflammatory disease of the exocrine pancreas. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.) FMA:83625 MESH:D061354 ZFA:0009277 https://cellxgene.cziscience.com/cellguide/CL_0000622 acinic cell acinous cell acinar cell CL:0000696 A cell that stores and secretes pancreatic polypeptide hormone. PP cells, also known as pancreatic polypeptide cells (and previously called F cells or gamma cells), are enteroendocrine cells predominantly found in the islets of Langerhans in the head of the pancreas. They are one of the four main endocrine cell types present in the pancreatic islets, along with type A, B and D cells. PP cells are notable for their production of pancreatic polypeptide, an anorexigenic hormone that modulates food intake and energy homeostasis. By secreting pancreatic polypeptide, PP cells play a significant role in the management of both digestive and appetite regulation. Upon ingestion of food, there is a significant increase in the secretion of pancreatic polypeptide, which then reduces biliary secretion and helps slow down the movement of food through the digestive tract. This allows more time for digestion to take place and nutrients to be absorbed, promoting the efficient use of dietary intake. The pancreatic polypeptide further reduces appetite by interacting with the hypothalamus, the area of the brain responsible for control of hunger. Given their important role in digestion, malfunction or damage to PP cells can lead to a disturbance in the digestive process and contribute to some disease conditions. For example, an overproduction of pancreatic polypeptide can result in conditions such as pancreatic tumors and diabetes. Conversely, an under secretion might contribute to obesity due to impaired dietary control. Furthermore, PP cells may also play a role in the body's energy balance, suggesting their implication in conditions related to energy metabolism. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.) FMA:62938 FMA:83409 https://cellxgene.cziscience.com/cellguide/CL_0000696 type F enteroendocrine cell PP cell CL:0000723 A stem cell that can give rise to cell types of the body other than those of the germ-line. CALOHA:TS-2086 MESH:D053687 ZFA:0009307 somatic stem cell CL:0000988 A cell of a hematopoietic lineage. BTO:0000574 CALOHA:TS-2017 FMA:70366 FMA:83598 ZFA:0005830 haematopoietic cell haemopoietic cell hemopoietic cell hematopoietic cell CL:0001035 A connective tissue cell found in bone. Bone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes. The formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis. The primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage. A remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.) 2011-11-16T04:28:16+00:00 https://cellxgene.cziscience.com/cellguide/CL_0001035 bone cell CL:0002067 An enteroendocrine cell that produces glucagon. Type A enteroendocrine cells, also known as alpha cells or A cells, are a species of endocrine cells primarily located in the pancreatic islets of Langerhans; they have also been identified within the lining of the stomach. Functionally, these cells are pivotal in glucose metabolism and homeostasis, accounting for about 20% of the total population of cells in the pancreatic islets. The primary role of type A enteroendocrine cells involves the synthesis, storage, and secretion of the peptide hormone glucagon, which is critical in energy regulation throughout the body. In response to a decrease in blood glucose levels, the pancreatic A cells are stimulated to secrete glucagon into the bloodstream. Glucagon acts on its target cells, mainly in the liver, to stimulate glycogenolysis and gluconeogenesis processes, thereby increasing blood glucose levels back to normal. In this way, pancreatic A cells play an integral role in maintaining glucose homeostasis and preventing hypoglycemia. Pancreatic A cells also participate in the local regulation of islet activities as glucagon acts through glucagon receptors on A, B and D type cells within the islets. Recent studies have also shown that Pancreatic A cells play a role in the generation and regeneration of B type cells. Following beta cell injuries pancreatic A cells increase in numbers and produce Glucagon-like peptide-1 (GLP-1), which increases the proliferation and cytoprotection of beta cells. In response to extreme injury of B type cells pancreatic A cells can transform (transdifferentiate) into functioning B type cells. Until recently, glucagon has been considered a pancreas-specific hormone; however, extrapancreatic glucagon has been reported in patients who had undergone complete, and glucagon-positive cells been identified in the human stomach, indicating that Type A enteroendocrine cells are not restricted to the pancreas. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.) 2010-09-10T10:48:54+00:00 FMA:62939 https://cellxgene.cziscience.com/cellguide/CL_0002067 type A enteroendocrine cell CL:0002092 A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells. 2010-07-22T04:48:15+00:00 BTO:0004850 FMA:83621 MESH:D001854 MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense. bone marrow cell CL:0002242 A cell containing at least one nucleus. 2010-09-07T03:32:33+00:00 FMA:67513 nucleate cell CL:0002319 A cell that is part of the nervous system. 2010-09-15T01:34:57+00:00 CALOHA:TS-2040 FMA:70333 neural cell CL:0002320 A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. 2010-09-15T03:01:54+00:00 CALOHA:TS-2096 FMA:63875 MESH:D003239 ZFA:0009392 connective tissue cell CL:0002321 A cell of the embryo. Embryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. They are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. The balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.) 2010-09-15T03:39:21+00:00 CALOHA:TS-0263 FMA:82840 WBbt:0007028 ZFA:0007089 https://cellxgene.cziscience.com/cellguide/CL_0002321 embryonic cell (metazoa) CL:0002494 A cell located in the heart, including both muscle and non muscle cells. 2010-12-07T09:37:22+00:00 BTO:0001539 CALOHA:TS-0115 FMA:83808 FMA:84791 heart cell From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cardiocyte CL:0005026 Multi fate stem cell that gives rise to both hepatocytes and cholangiocytes as descendants. The term often refers to fetal precursors of hepatocytes (differently from 'hepatic stem cell', usually applied to the self-renewing pool of hepatocyte precursors in the adult liver). Hepatoblasts may also be endogenous, as some stem cells found in the liver come from the bone marrow via blood circulation. Hepatoblasts are immature precursor cells that predominate during the early stages of liver development, specifically in the embryonic phase of life. They first arise from the endoderm, one of the three primary germ layers in the very early embryo, and then differentiate into two distinct mature liver cell types - the hepatocytes and cholangiocytes. During liver organogenesis hepatoblasts proliferate and migrate into the septum transversum to form the liver bud. Proliferation and differentiation of these cells are regulated by several soluble factors, such as hepatocyte growth factor, which is a mitogen of both hepatoblasts and mature hepatocytes. As they start to differentiate into hepatocytes and cholangiocytes, the cells begin to express hepatic markers like albumin and alpha-fetoprotein. Although hepatoblasts are specified embryonic liver cells that are bipotential for hepatocytes and cholangiocytes, a subset of liver cells (called oval cells) has been identified in adults that express stem cell markers, such as CD133 and cKIT, and has been suggested to have the same potential as hepatoblasts to differentiate into hepatocytes and cholangiocytes. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.) https://cellxgene.cziscience.com/cellguide/CL_0005026 hepatoblast https://github.com/obophenotype/cell-ontology/issues/800 CL:0007001 Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized). 2012-06-15T02:51:27+00:00 scleroblast Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) skeletogenic cell CL:0008001 Any hematopoietic cell that is a precursor of some other hematopoietic cell type. hematopoietic precursor cell CL:0008019 A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration. mesenchyme cell mesenchymal cell CL:0011012 A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.) https://cellxgene.cziscience.com/cellguide/CL_0011012 neural crest cell CL:0011115 A cell that, by division or terminal differentiation, can give rise to other cell types. Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. precursor cell CL:1000600 Any cell that is part of some lower urinary tract. KUPO:0001115 lower urinary tract cell CL:1001319 Any cell that is part of some urinary bladder. KUPO:0001120 bladder cell CL:1001610 Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes. CALOHA:TS-2109 bone marrow hematopoietic cells bone marrow poietic cells bone marrow hematopoietic cell CL:1100001 An epithelial cell that is specialised for the synthesis and secretion of specific biomolecules. 2024-07-21T09:24:44+00:00 secretory epithelial cell image FBbi:00000002 chemically fixed tissue FBbi:00000002 image FBbi:00000003 coagulating-fixative fixed tissue FBbi:00000003 image FBbi:00000004 acetone fixed tissue FBbi:00000004 image FBbi:00000005 acrolein fixed tissue FBbi:00000005 image FBbi:00000006 ethanol fixed tissue FBbi:00000006 image FBbi:00000007 methanol fixed tissue FBbi:00000007 image FBbi:00000008 crosslinking-fixative fixed tissue FBbi:00000008 image EGS FBbi:00000009 ethylene glycol-bis-succinimidyl succinate fixed tissue FBbi:00000009 image FBbi:00000010 formaldehyde fixed tissue FBbi:00000010 image FBbi:00000011 glutaraldehyde fixed tissue FBbi:00000011 image FBbi:00000012 osmium tetroxide fixed tissue FBbi:00000012 image FBbi:00000013 cryofixed tissue FBbi:00000013 image FBbi:00000014 unfixed tissue FBbi:00000014 image FBbi:00000015 embedded tissue FBbi:00000015 image FBbi:00000016 tissue in plastic embedment FBbi:00000016 image FBbi:00000017 tissue in acrylic resin embedment FBbi:00000017 image FBbi:00000018 tissue in epoxy resin embedment FBbi:00000018 image FBbi:00000019 tissue in wax embedment FBbi:00000019 image FBbi:00000020 tissue in paraffin embedment FBbi:00000020 image FBbi:00000021 tissue in polyester wax embedment FBbi:00000021 image FBbi:00000022 tissue in polyethylene glycol embedment FBbi:00000022 image FBbi:00000023 unembedded tissue FBbi:00000023 image FBbi:00000024 whole mounted tissue FBbi:00000024 Unfixed fully hydrated tissue, typically employed to monitor dynamic changes in the living state. image live-cell imaging FBbi:00000025 living tissue FBbi:00000025 Unfixed fully hydrated tissue, typically employed to monitor dynamic changes in the living state. XX:ISBN978-087969683-2 image FBbi:00000026 sectioned tissue FBbi:00000026 image FBbi:00000027 cryostat-sectioned tissue FBbi:00000027 image FBbi:00000028 hand-sectioned tissue FBbi:00000028 image FBbi:00000029 microtome-sectioned tissue FBbi:00000029 image FBbi:00000030 vibratome-sectioned tissue FBbi:00000030 image FBbi:00000033 diagram FBbi:00000033 image FBbi:00000034 HA peptide tag FBbi:00000034 image FBbi:00000035 cresyl fast violet FBbi:00000035 Staining with an aqueous or alcoholic solution of eosin Y,colors eosinophilic structures in various shades of red, pink and orange. The eosinophilic structures are generally composed of intracellular or extracellular protein. The Lewy bodies and Mallory bodies are examples of eosinophilic structures. Most of the cytoplasm is eosinophilic. Red blood cells are stained intensely red. image FBbi:00000037 eosin FBbi:00000037 Staining with an aqueous or alcoholic solution of eosin Y,colors eosinophilic structures in various shades of red, pink and orange. The eosinophilic structures are generally composed of intracellular or extracellular protein. The Lewy bodies and Mallory bodies are examples of eosinophilic structures. Most of the cytoplasm is eosinophilic. Red blood cells are stained intensely red. Wikipedia:http://en.wikipedia.org/wiki/H%26E_stain image FBbi:00000038 ethidium bromide FBbi:00000038 image FBbi:00000039 fuchsin FBbi:00000039 image FBbi:00000040 giemsa FBbi:00000040 The staining method involves application of hemalum, which is a complex formed from aluminium ions and oxidized haematoxylin. This colors nuclei of cells (and a few other objects, such as keratohyalin granules) blue. The staining of nuclei by hemalum does not require the presence of DNA and is probably due to binding of the dye-metal complex to arginine-rich basic nucleoproteins such as histones. The mechanism is different from that of nuclear staining by basic (cationic) dyes such as thionine or toluidine blue. Staining by basic dyes is prevented by chemical or enzymatic extraction of nucleic acids. Such extractions do not prevent staining of nuclei by hemalum. image FBbi:00000041 hematoxylin FBbi:00000041 The staining method involves application of hemalum, which is a complex formed from aluminium ions and oxidized haematoxylin. This colors nuclei of cells (and a few other objects, such as keratohyalin granules) blue. The staining of nuclei by hemalum does not require the presence of DNA and is probably due to binding of the dye-metal complex to arginine-rich basic nucleoproteins such as histones. The mechanism is different from that of nuclear staining by basic (cationic) dyes such as thionine or toluidine blue. Staining by basic dyes is prevented by chemical or enzymatic extraction of nucleic acids. Such extractions do not prevent staining of nuclei by hemalum. Wikipedia:http://en.wikipedia.org/wiki/H%26E_stain image FBbi:00000042 methyl green FBbi:00000042 image FBbi:00000043 methyl violet FBbi:00000043 image FBbi:00000044 nitro blue tetrazolium chloride FBbi:00000044 image FBbi:00000045 nuclear fast red FBbi:00000045 image FBbi:00000046 orcein FBbi:00000046 image PI FBbi:00000047 propidium iodide FBbi:00000047 image FBbi:00000048 SYTOX Green FBbi:00000048 image FBbi:00000049 toluidine blue FBbi:00000049 image AO FBbi:00000051 acridine orange FBbi:00000051 image HO342 Hoechst 33342 FBbi:00000052 Hoechst 33342 FBbi:00000052 image FBbi:00000053 cationic colloidal gold FBbi:00000053 image Mitotracker X FBbi:00000054 CMX rosamine (Mitotracker Red) FBbi:00000054 image DiOC FBbi:00000055 DiOC6 (3,3'-dihexyloxacarbocyanine iodide) FBbi:00000055 image DAPI FBbi:00000056 4',6-diamidino-2-phenylindole (DAPI) FBbi:00000056 image FBbi:00000057 lucifer yellow FBbi:00000057 image FBbi:00000058 methylene blue FBbi:00000058 image FBbi:00000059 Nile blue A FBbi:00000059 image FBbi:00000060 Nile red FBbi:00000060 image FBbi:00000061 pyronine FBbi:00000061 image FBbi:00000062 rhodamine 123 FBbi:00000062 image FBbi:00000063 rhodamine B FBbi:00000063 image FBbi:00000064 SYTO Blue FBbi:00000064 image FBbi:00000065 SYTO Green FBbi:00000065 image FBbi:00000066 SYTO Orange FBbi:00000066 image FBbi:00000067 SYTO Red FBbi:00000067 image FBbi:00000068 YO-PRO-1 FBbi:00000068 image FBbi:00000073 taxol FBbi:00000073 image FBbi:00000076 genetically encoded enzyme FBbi:00000076 image lacZ, X-gal FBbi:00000077 beta-galactosidase FBbi:00000077 image GUS, X-gluc FBbi:00000078 beta-glucuronidase FBbi:00000078 image BFP FBbi:00000080 EBFP FBbi:00000080 image CFP FBbi:00000081 ECFP FBbi:00000081 image YFP FBbi:00000084 EYFP FBbi:00000084 image DsRed FBbi:00000085 DsRed FBbi:00000085 image FBbi:00000086 c-MYC peptide tag FBbi:00000086 image FBbi:00000087 FLAG peptide tag FBbi:00000087 visualization of the connected regions of a cell by filling with a label image FBbi:00000088 intracellular filling FBbi:00000088 Fully hydrated tissue rapidly frozen to produce vitrified water, and maintained continuously below the glass transition temperature of water (approximately -137 deg C jm 2010-03-07T02:05:48Z image tissue in amorphous ice embedment FBbi:00000089 tissue in vitreous ice embedment FBbi:00000089 Fully hydrated tissue rapidly frozen to produce vitrified water, and maintained continuously below the glass transition temperature of water (approximately -137 deg C PMID:3043536 image FBbi:00000090 fluor labeled RNA fill FBbi:00000090 image FBbi:00000091 5-SFX fluorescein RNA fill FBbi:00000091 image FBbi:00000092 X-rhodamine RNA fill FBbi:00000092 Tissue treated to make cell membranes permeable, typically for the purpose of allowing access by exogenous stains or substrates. jm 2010-03-07T02:26:37Z image FBbi:00000093 permeabilized tissue FBbi:00000093 image FBbi:00000094 fluor labeled protein fill FBbi:00000094 image FBbi:00000095 fluor conjugated actin fill FBbi:00000095 image FBbi:00000100 phalloidin FBbi:00000100 image FBbi:00000109 fluor conjugated tubulin fill FBbi:00000109 image FBbi:00000112 probe for lipid FBbi:00000112 image FBbi:00000113 DiA FBbi:00000113 image FBbi:00000114 DiD FBbi:00000114 image FBbi:00000115 DiI FBbi:00000115 image FBbi:00000116 DiO FBbi:00000116 image FBbi:00000117 DiR FBbi:00000117 image FBbi:00000118 miscellaneous fill FBbi:00000118 image Neurobiotin FBbi:00000119 biotin ethylenediamine fill FBbi:00000119 image FBbi:00000120 cobalt fill FBbi:00000120 image FBbi:00000121 silver-intensified cobalt fill FBbi:00000121 image FBbi:00000122 metabolically incorporated radioisotope FBbi:00000122 image FBbi:00000123 [14]C FBbi:00000123 image FBbi:00000124 [32]P FBbi:00000124 image FBbi:00000125 [33]P FBbi:00000125 image FBbi:00000126 [35]S FBbi:00000126 image FBbi:00000127 [3]H FBbi:00000127 image FBbi:00000128 vizualization of label conjugated to probe FBbi:00000128 tissue made permeable by the action of glycerol jm 2010-03-07T02:37:12Z image glycerinated tissue FBbi:00000129 glycerol permeabilized FBbi:00000129 image FBbi:00000130 labeled primary antibody FBbi:00000130 image FBbi:00000132 alkaline phosphatase FBbi:00000132 image FBbi:00000138 horseradish peroxidase FBbi:00000138 image FBbi:00000156 primary antibody plus labeled secondary antibody FBbi:00000156 image FBbi:00000158 acid phosphatase FBbi:00000158 image FBbi:00000176 esterase FBbi:00000176 image FBbi:00000178 glucose oxidase FBbi:00000178 image AMCA FBbi:00000191 aminomethylcoumarin FBbi:00000191 image FBbi:00000192 Cascade blue FBbi:00000192 image FBbi:00000202 gold FBbi:00000202 image FBbi:00000204 DNA probe FBbi:00000204 image FBbi:00000215 RNA probe FBbi:00000215 image FBbi:00000223 graphic illustration FBbi:00000223 image FBbi:00000224 computer graphic FBbi:00000224 image FBbi:00000225 black and white graphic FBbi:00000225 image FBbi:00000226 color graphic FBbi:00000226 image FBbi:00000227 grey scale graphic FBbi:00000227 image FBbi:00000228 camera lucida assisted graphic FBbi:00000228 image FBbi:00000229 free hand graphic FBbi:00000229 image FBbi:00000230 line art graphic FBbi:00000230 image FBbi:00000231 charcoal pencil graphic FBbi:00000231 image FBbi:00000232 colored pencil graphic FBbi:00000232 image FBbi:00000233 graphite pencil graphic FBbi:00000233 image black and white graphic FBbi:00000234 pen and ink graphic FBbi:00000234 image FBbi:00000235 painted graphic FBbi:00000235 image FBbi:00000236 acrylic painted graphic FBbi:00000236 image FBbi:00000237 oil painted graphic FBbi:00000237 image FBbi:00000238 pastel painted graphic FBbi:00000238 image FBbi:00000239 watercolor painted graphic FBbi:00000239 methods for imaging objects large enough to be observed by the unaided eye image FBbi:00000240 macroscopy FBbi:00000240 methods for forming images of objects too small to be observed with the unaided eye image FBbi:00000241 microscopy FBbi:00000241 image FBbi:00000243 bright-field microscopy FBbi:00000243 imaging with rejection of the unscattered illumination (removal of the zero order component of the diffracted wave) image FBbi:00000244 dark-field microscopy FBbi:00000244 image FBbi:00000247 phase contrast microscopy FBbi:00000247 image FBbi:00000248 polarization microscopy FBbi:00000248 image FBbi:00000249 time lapse microscopy FBbi:00000249 image FBbi:00000252 single-spot confocal microscopy FBbi:00000252 image FBbi:00000253 spinning disk confocal microscopy FBbi:00000253 image FBbi:00000254 two-photon laser scanning microscopy FBbi:00000254 image FBbi:00000255 multi-photon microscopy FBbi:00000255 image mode of electron microscopy FBbi:00000256 electron microscopy FBbi:00000256 image is formed by scanning the surface of the specimen with a beam of electrons in a raster pattern image FBbi:00000257 scanning electron microscopy (SEM) FBbi:00000257 image FBbi:00000258 transmission electron microscopy (TEM) FBbi:00000258 the scanning probe is maintained at a fixed distance above the surface e of the specimen by van der Waals forces image FBbi:00000259 atomic force microscopy FBbi:00000259 http://en.wikipedia.org/wiki/X-ray_microscope image FBbi:00000260 X-ray microscopy FBbi:00000260 image FBbi:00000261 montage FBbi:00000261 Membrane permeabilization by the action of ionic or non-ionic detergents jm 2010-03-07T02:37:21Z image FBbi:00000262 detergent permeabilized FBbi:00000262 permeabilization due to extraction of lipid from membranes by an organic solvent such as acetone or methanol. jm 2010-03-07T02:37:29Z image FBbi:00000263 solvent permeabilized FBbi:00000263 Saponin, a detergent-like molecule, preferentially forms holes in membranes that contain cholesterol. jm 2010-03-07T02:43:41Z image saponized tissue FBbi:00000264 saponin permeabilized FBbi:00000264 methods and devices used for capturing an image of a real object; distinct from images created by artwork jm 2010-03-09T09:57:38Z image photograph FBbi:00000265 recorded image FBbi:00000265 methods and devices used for creating images by some form of artwork, as distinct from capturing images by means of some recording device jm 2010-03-09T10:04:40Z image artwork drawing FBbi:00000266 portrayed image FBbi:00000266 A form of graphical illustration that changes with time to give a sense of motion or represent dynamic changes in the portrayal. jm 2010-03-09T10:12:11Z image FBbi:00000267 animation FBbi:00000267 jm 2010-03-09T10:46:27Z image FBbi:00000272 illumination by photons FBbi:00000272 jm 2010-03-09T10:46:27Z image FBbi:00000273 illumination by electrons FBbi:00000273 jm 2010-03-09T10:46:27Z image FBbi:00000274 illumination by acoustic waves FBbi:00000274 jm 2010-03-09T10:46:27Z image FBbi:00000275 illumination by neutrons FBbi:00000275 jm 2010-03-09T10:46:27Z image FBbi:00000276 illumination by ions FBbi:00000276 illumination that covers the entire field of view of the image-forming lens jm 2010-03-09T10:50:41Z image FBbi:00000277 widefield illumination FBbi:00000277 illumination restricted to a small portion of the field of view of the imaging lens; often one or more diffraction limited spots jm 2010-03-09T10:50:41Z image FBbi:00000278 narrowfield illumination FBbi:00000278 jm 2010-03-09T10:50:41Z image FBbi:00000279 coherent illumination FBbi:00000279 jm 2010-03-09T10:50:41Z image FBbi:00000280 incoherent illumination FBbi:00000280 jm 2010-03-09T10:50:41Z image FBbi:00000281 nearfield illumination FBbi:00000281 jm 2010-03-09T10:50:41Z image FBbi:00000282 farfield illumination FBbi:00000282 jm 2010-03-09T10:50:41Z image FBbi:00000283 continuous illumination FBbi:00000283 illumination that varies with time; often achieved with pulsed lasers for the purpose of generating very-high peak illumination power jm 2010-03-09T10:50:41Z image FBbi:00000284 pulsed illumination FBbi:00000284 jm 2010-03-09T10:50:41Z image FBbi:00000285 oblique illumination FBbi:00000285 illumination by a single spot of light that is scanned across the field of view jm 2010-03-09T10:51:29Z image FBbi:00000286 single point scanning FBbi:00000286 illumination by multiple points of light simultaneously jm 2010-03-09T10:51:29Z image FBbi:00000287 multiple point scanning FBbi:00000287 scanning by multiple points of light arising from pinholes in a spinning disk that is illuminated by a widefield source jm 2010-03-09T10:52:38Z image FBbi:00000288 spinning disk scanning FBbi:00000288 Multiple points of illumination generated by a fixed array of sources. jm 2010-03-09T10:52:38Z image FBbi:00000289 array scanning FBbi:00000289 illumination parallel or at small angles to the optical axis is attenuated or blocked by a stop jm 2010-03-09T11:04:14Z image FBbi:00000290 hollow-cone illumination FBbi:00000290 Illumination is distributed asymmetrically around the optic axis, typically achieved by a non-circular stop placed below the lower lens element and aperture of the condenser. jm 2010-03-09T11:04:14Z image FBbi:00000291 anaxial illumination FBbi:00000291 Illumination is distributed asymmetrically around the optic axis, typically achieved by a non-circular stop placed below the lower lens element and aperture of the condenser. : illumination restricted to angles that exceed the acceptance angle of the image-forming lens jm 2010-03-09T11:04:41Z image FBbi:00000292 darkfield illumination FBbi:00000292 illumination at angles less than the acceptance angle of the image-forming lens is attenuated by a filter to give a colored background of unscattered light; higher angle illumination may be filtered to give a contrasting color jm 2010-03-09T11:04:41Z image FBbi:00000293 Rheinberg illumination FBbi:00000293 jm 2010-03-09T11:33:49Z image FBbi:00000296 photodiode FBbi:00000296 jm 2010-03-09T11:33:49Z image FBbi:00000297 avalanche photodiode (APD) FBbi:00000297 jm 2010-03-09T11:33:49Z image FBbi:00000298 silicon intensified target tube (SIT) FBbi:00000298 jm 2010-03-09T11:33:49Z image FBbi:00000299 intensified SIT (ISIT) FBbi:00000299 jm 2010-03-09T11:33:49Z image FBbi:00000300 intensified CCD (ICCD) FBbi:00000300 jm 2010-03-09T11:33:49Z image FBbi:00000301 electron multiplying CCD (EMCCD) FBbi:00000301 jm 2010-03-09T11:33:49Z image FBbi:00000302 electron bombardment CCD (EBCCD) FBbi:00000302 jm 2010-03-09T11:33:49Z image FBbi:00000303 film FBbi:00000303 jm 2010-03-09T11:33:49Z image FBbi:00000305 piezo-electric device FBbi:00000305 jm 2010-03-09T12:45:35Z image FBbi:00000306 wide-field detection FBbi:00000306 jm 2010-03-09T12:45:35Z image FBbi:00000307 narrow-field detection FBbi:00000307 jm 2010-03-09T03:11:47Z image FBbi:00000308 absorption of illumination FBbi:00000308 jm 2010-03-09T03:11:47Z image FBbi:00000309 inelastic scattering FBbi:00000309 jm 2010-03-09T03:11:47Z image FBbi:00000310 elastic scattering FBbi:00000310 jm 2010-03-09T03:11:47Z image FBbi:00000311 refractive index FBbi:00000311 jm 2010-03-09T03:11:47Z image FBbi:00000312 optical path length gradient FBbi:00000312 jm 2010-03-09T03:11:47Z image FBbi:00000313 retardance FBbi:00000313 jm 2010-03-09T03:11:47Z image FBbi:00000314 stiffness FBbi:00000314 jm 2010-03-09T03:11:47Z image FBbi:00000315 electron density FBbi:00000315 jm 2010-03-09T03:11:47Z image FBbi:00000316 fluorescence emission FBbi:00000316 jm 2010-03-09T03:11:47Z image FBbi:00000317 sub-nanosecond time-resolved fluorescence emission) FBbi:00000317 jm 2010-03-09T03:11:47Z image FBbi:00000318 fluorescence polarization (polarization angle resolved fluorescence emission) FBbi:00000318 jm 2010-03-09T03:11:47Z image FBbi:00000319 chemical composition FBbi:00000319 jm 2010-03-09T03:11:47Z image FBbi:00000320 elevation FBbi:00000320 jm 2010-03-09T03:14:53Z image FBbi:00000322 optical method FBbi:00000322 jm 2010-03-09T03:14:53Z image FBbi:00000323 computational method FBbi:00000323 jm 2010-03-09T03:20:14Z image FBbi:00000324 in-focus phase contrast FBbi:00000324 jm 2010-03-09T03:20:14Z image FBbi:00000325 defocus phase contrast FBbi:00000325 jm 2010-03-09T03:20:14Z image FBbi:00000327 Hoffman modulation FBbi:00000327 jm 2010-03-09T03:20:14Z image FBbi:00000328 single sideband edge enhancement (SSBE) FBbi:00000328 jm 2010-03-09T03:20:14Z image FBbi:00000329 interference reflection contrast (IRM) FBbi:00000329 jm 2010-03-09T03:20:14Z image FBbi:00000330 interference contrast FBbi:00000330 jm 2010-03-09T03:20:14Z image FBbi:00000331 polarization contrast FBbi:00000331 jm 2010-03-09T03:24:02Z image FBbi:00000332 structured illumination microscopy (SIM) FBbi:00000332 jm 2010-03-09T03:24:02Z image FBbi:00000333 point-localization method FBbi:00000333 jm 2010-03-09T03:32:12Z image FBbi:00000335 PALM (photoactivation localization microscopy) FBbi:00000335 jm 2010-03-09T03:32:12Z image FBbi:00000336 STORM (stochastic optical reconstruction microscopy) FBbi:00000336 jm 2010-03-09T03:32:12Z image FBbi:00000337 FIONA (fluorescence imaging with one nanometer accuracy) FBbi:00000337 jm 2010-03-09T03:32:12Z image FBbi:00000338 DOPI (defocussed orientation and position imaging) FBbi:00000338 jm 2010-03-09T03:32:12Z image FBbi:00000339 PAINT (point accumulation for imaging in nanoscale topography) FBbi:00000339 structured illumination used at sufficiently high power to cause significant ground-state depletion of the imaged fluorophore, thus allowing for non-linear resolution enhancement jm 2010-03-09T03:32:29Z image FBbi:00000340 saturated structured-illumination microscopy (SSIM) FBbi:00000340 jm 2010-03-09T03:51:49Z image FBbi:00000341 UV/visible/IR illumination FBbi:00000341 jm 2010-03-09T03:51:49Z image FBbi:00000342 X-ray illumination FBbi:00000342 jm 2010-03-09T04:04:04Z image FBbi:00000343 microscopy with lenses FBbi:00000343 imaging by means of a physical probe that passes over the sample jm 2010-03-09T04:04:04Z image FBbi:00000344 scanning probe microscopy FBbi:00000344 jm 2010-03-09T04:18:03Z image mode of light microscopy FBbi:00000345 light microscopy FBbi:00000345 jm 2010-03-09T10:19:35Z image FBbi:00000347 scanning tunneling microscopy FBbi:00000347 jm 2010-03-09T10:19:35Z image FBbi:00000348 nearfield scanning optical microscopy (ANSOM) FBbi:00000348 Aperture-less NSOM. jm 2010-03-09T10:20:01Z image FBbi:00000349 ANSOM FBbi:00000349 jm 2010-03-09T10:23:41Z image FBbi:00000350 polarized light illumination FBbi:00000350 jm 2010-03-09T10:25:08Z image FBbi:00000351 orientation-independent polarization microscopy FBbi:00000351 jm 2010-03-09T10:27:11Z image FBbi:00000352 polarization-sensitive detection FBbi:00000352 Uses an objective with extra components to manipulate the wave front in the plane of the objective aperture. jm 2010-03-09T10:41:27Z image FBbi:00000353 modified objective lens FBbi:00000353 a computational method that is linear in the mathematical sense, meaning that image intensity is conserved and the data remain suitable for all quantitative analyses jm 2010-03-09T11:09:35Z image FBbi:00000354 linear method FBbi:00000354 computational method that are mathematically non-linear; image intensity is not conserved, and the data are in general not suitable for quantitative analyses of pixel values jm 2010-03-09T11:09:35Z image FBbi:00000355 non-linear method FBbi:00000355 jm 2010-03-09T11:10:59Z image FBbi:00000356 Wiener filter FBbi:00000356 jm 2010-03-09T11:10:59Z image FBbi:00000357 3D-deconvolution FBbi:00000357 jm 2010-03-09T11:11:56Z image FBbi:00000358 no-neighbors deblurring FBbi:00000358 jm 2010-03-09T11:11:56Z image FBbi:00000359 nearest-neighbors deblurring FBbi:00000359 jm 2010-03-09T11:19:41Z image FBbi:00000360 constrained iterative deconvolution FBbi:00000360 jm 2010-03-09T11:19:41Z image FBbi:00000361 maximum likelihood deconvolution FBbi:00000361 jm 2010-03-09T11:19:41Z image FBbi:00000362 blind deconvolution FBbi:00000362 jm 2010-03-09T11:19:42Z image FBbi:00000363 exhaustive photon reassignment FBbi:00000363 Fluorescence loss in photobleaching; a method of determining whether two populations of fluorophore are in diffusive communication with one another by observing the decrease in brightness of one population when the other population is subjected to continuous photobleaching. jm 2010-03-11T10:09:33Z image FBbi:00000365 FLIP FBbi:00000365 Fluorescence loss in photobleaching; a method of determining the rate and extent of exchange between a localized population of fluorophore and a non-localized diffusible pool, by observing the rate of recovery of brightness of the localized population after photobleaching. jm 2010-03-11T10:09:33Z image FBbi:00000366 FRAP FBbi:00000366 Fluorescence loss in photobleaching; a method of determining the rate and extent of exchange between a localized population of fluorophore and a non-localized diffusible pool, by observing the rate of recovery of brightness of the localized population after photobleaching. XX:-new-dbxref- jm 2010-03-11T10:09:33Z image FBbi:00000368 FLIM FBbi:00000368 single (or selective) plane illumination. jm 2010-03-11T10:09:33Z image FBbi:00000369 SPIM FBbi:00000369 coherent Raman anti-Stokes microscopy jm 2010-03-11T10:13:20Z image FBbi:00000370 CARS FBbi:00000370 optical coherence tomography; an interferometric method of imaging using back-scattered photons (elastic scattering) jm 2010-03-11T10:32:19Z image FBbi:00000371 OCT FBbi:00000371 image created using the electrons generated by ionization of a sample due to inelastic scattering of the primary beam of radiation jm 2010-03-12T08:34:44Z image FBbi:00000372 secondary_electron imaging FBbi:00000372 imaged formed using electrons undergoing elastic scattering at very high angles, with emission of characteristic X-rays jm 2010-03-12T08:40:37Z image FBbi:00000373 back-scattered_electron imaging FBbi:00000373 jm 2010-03-12T08:54:56Z image FBbi:00000374 detection of photons FBbi:00000374 jm 2010-03-12T08:54:56Z image FBbi:00000375 detection of electrons FBbi:00000375 jm 2010-03-12T08:54:56Z image FBbi:00000376 detection of acoustic waves FBbi:00000376 jm 2010-03-12T08:54:56Z image FBbi:00000377 detection of current induced in the specimen FBbi:00000377 jm 2010-03-12T08:55:29Z image FBbi:00000378 detection of UV/visible/IR photons FBbi:00000378 jm 2010-03-12T08:55:29Z image FBbi:00000379 detection of X-ray photons FBbi:00000379 jm 2010-03-12T09:12:36Z image FBbi:00000380 scanning-transmission electron microscopy FBbi:00000380 jm 2010-03-12T09:16:40Z image EFTEM energy filtered TEM ESI electron spectroscopic imaging FBbi:00000381 EELS imaging FBbi:00000381 jm 2010-03-12T09:16:40Z image FBbi:00000382 EDAX imaging FBbi:00000382 Illumination used for the purpose of inducing some observable change in the specimen during the course of an imaging session. This illumination may or may not be the same as the illumination used for imaging. Typically used in conjunction with live-cell imaging jm 2010-03-12T09:32:53Z image FBbi:00000383 specimen_modifying_illumination FBbi:00000383 jm 2010-03-12T10:06:46Z image FBbi:00000384 photo-bleaching illumination FBbi:00000384 jm 2010-03-12T10:06:46Z image FBbi:00000385 photo-ablation illumination FBbi:00000385 jm 2010-03-12T10:06:46Z image FBbi:00000386 photo-switching illumination FBbi:00000386 jm 2010-03-12T10:06:46Z image FBbi:00000387 photo-activation illumination FBbi:00000387 jm 2010-03-12T10:06:46Z image FBbi:00000388 uncaging illumination FBbi:00000388 jm 2010-03-12T10:06:46Z image FBbi:00000389 trapping illumination FBbi:00000389 jm 2010-03-12T10:06:46Z image FBbi:00000390 emission-depletion illumination FBbi:00000390 illumination in the shape of a thin line that is swept over the field of view jm 2010-03-12T10:31:26Z image FBbi:00000391 slit-scanning illumination FBbi:00000391 illumination and detection via a thin slit jm 2010-03-12T10:32:36Z image FBbi:00000392 slit-scan confocal microscopy FBbi:00000392 Fixed array of sources focused to an array of spots that is swept over the specimen in raster fashion jm 2010-03-12T10:35:43Z image FBbi:00000393 array-scan confocal microscopy FBbi:00000393 jm 2010-03-12T10:39:24Z image FBbi:00000394 spot detector FBbi:00000394 jm 2010-03-12T10:39:24Z image FBbi:00000395 area detector FBbi:00000395 methods of visualization that differentiate between different regions or surfaces of the specimen based on contiguity jm 2010-03-14T08:38:50Z image FBbi:00000396 visualization of contiguous regions FBbi:00000396 methods of visualization that differentiate regions of the specimen on the basis of their chemical properties jm 2010-03-14T08:38:50Z image FBbi:00000397 visualization by chemical attribute FBbi:00000397 visualization by depositing a label on the surface of a specimen uniformly (plating), or from a particular direction so that surface topography becomes visible (shadowing) jm 2010-03-14T08:44:06Z image FBbi:00000398 shadowing and plating FBbi:00000398 visualization by exclusion of a stain in which the specimen is immersed; compare with "positive staining. jm 2010-03-14T08:44:06Z image FBbi:00000399 negative staining FBbi:00000399 jm 2010-03-14T09:07:35Z image FBbi:00000400 sequence-specific nucleic acid probe FBbi:00000400 jm 2010-03-14T09:07:35Z image FBbi:00000401 antibody FBbi:00000401 jm 2010-03-14T09:07:35Z image FBbi:00000402 lectin FBbi:00000402 jm 2010-03-14T09:07:35Z image FBbi:00000403 small-molecule probe FBbi:00000403 jm 2010-03-14T10:42:36Z image FBbi:00000404 fluorescent dextran fill FBbi:00000404 jm 2010-03-14T10:54:20Z image FBbi:00000405 fluorescent protein tag FBbi:00000405 jm 2010-03-14T09:25:57Z image FBbi:00000406 probes for nucleic acid FBbi:00000406 jm 2010-03-14T11:10:25Z image FBbi:00000407 small genetically encoded tag FBbi:00000407 jm 2010-03-14T09:25:57Z image FBbi:00000408 probe for protein FBbi:00000408 jm 2010-03-14T09:25:57Z image FBbi:00000409 organelle-specific probe FBbi:00000409 jm 2010-03-14T09:26:11Z image FBbi:00000410 macromolecular probe FBbi:00000410 jm 2010-03-14T09:28:19Z image FBbi:00000411 probe for mitochondria FBbi:00000411 jm 2010-03-14T09:28:19Z image FBbi:00000412 probe for endoplasmic reticulum FBbi:00000412 jm 2010-03-14T09:28:19Z image FBbi:00000413 probe for Golgi FBbi:00000413 jm 2010-03-14T09:28:19Z image FBbi:00000414 probe for lysosomes FBbi:00000414 jm 2010-03-15T11:51:34Z image positive staining FBbi:00000415 stain with broad specificity FBbi:00000415 jm 2010-03-14T11:12:03Z image FBbi:00000416 tetracysteine tag FBbi:00000416 jm 2010-03-14T09:33:18Z image FBbi:00000417 Hoechst 33258 FBbi:00000417 jm 2010-03-14T11:12:03Z image FBbi:00000418 genetically encoded biotin tag FBbi:00000418 jm 2010-03-17T01:55:02Z image FBbi:00000419 freeze_fracture/freeze_etch FBbi:00000419 jm 2010-03-17T01:59:59Z image FBbi:00000420 fluorescent protein derived from Aequorea victoria FBbi:00000420 jm 2010-03-14T09:33:53Z image FBbi:00000421 membrane-permeant probe FBbi:00000421 jm 2010-03-14T09:33:53Z image FBbi:00000422 membrane impermeant probe FBbi:00000422 jm 2010-03-14T09:42:34Z image FBbi:00000423 acridine homodimer FBbi:00000423 jm 2010-03-14T09:42:34Z image FBbi:00000424 7-amino-actinomycin D FBbi:00000424 jm 2010-03-14T09:48:57Z image FBbi:00000425 conconavalin A FBbi:00000425 jm 2010-03-14T09:48:57Z image FBbi:00000426 wheat germ agglutinin FBbi:00000426 jm 2010-03-14T09:48:57Z image FBbi:00000427 Phaseolus vulgaris lectin PHA-L) FBbi:00000427 jm 2010-03-14T09:48:57Z image FBbi:00000428 Arachis hypogaea (PNA) FBbi:00000428 jm 2010-03-14T09:48:57Z image FBbi:00000429 Helix pomatia agglutinin FBbi:00000429 jm 2010-03-14T09:48:57Z image FBbi:00000430 soybean agglutinin FBbi:00000430 jm 2010-03-14T09:48:57Z image FBbi:00000431 cholera toxin B FBbi:00000431 jm 2010-03-14T09:52:30Z image FBbi:00000432 peptide-nucleic acid probe FBbi:00000432 jm 2010-03-17T01:59:59Z image FBbi:00000433 fluorescent protein derived from Anthozoa FBbi:00000433 jm 2010-03-17T01:59:59Z image FBbi:00000434 optical highlighter FBbi:00000434 jm 2010-03-17T02:01:22Z image FBbi:00000435 Blue fluorescent protein from Aequorea victoria FBbi:00000435 jm 2010-03-17T02:01:22Z image FBbi:00000436 Cyan fluorescent protein from Aequorea FBbi:00000436 jm 2010-03-17T02:01:22Z image FBbi:00000437 Green fluorescent protein from Aequorea FBbi:00000437 jm 2010-03-14T10:15:00Z image FBbi:00000438 DiIC16 FBbi:00000438 jm 2010-03-14T10:22:41Z image FBbi:00000440 Alexa Fluor 488 FBbi:00000440 jm 2010-03-14T10:22:41Z image FBbi:00000441 Alexa Fluor 546 FBbi:00000441 jm 2010-03-14T10:22:41Z image FBbi:00000442 Alexa Fluor 568 FBbi:00000442 jm 2010-03-14T10:22:41Z image FBbi:00000443 Alexa Fluor 555 FBbi:00000443 jm 2010-03-14T10:22:41Z image FBbi:00000444 Alexa Fluor 594 FBbi:00000444 jm 2010-03-14T10:22:41Z image FBbi:00000445 Alexa Fluor 610 FBbi:00000445 jm 2010-03-14T10:22:41Z image FBbi:00000446 Alexa Fluor 633 FBbi:00000446 jm 2010-03-14T10:22:41Z image FBbi:00000447 Alexa Fluor 647 FBbi:00000447 jm 2010-03-14T10:22:41Z image FBbi:00000448 Cy2 FBbi:00000448 jm 2010-03-14T10:22:41Z image FBbi:00000449 Cy3 FBbi:00000449 jm 2010-03-14T10:22:41Z image FBbi:00000450 Cy5 FBbi:00000450 jm 2010-03-14T10:22:41Z image FBbi:00000451 Fluorescein (FITC) FBbi:00000451 jm 2010-03-14T10:22:41Z image FBbi:00000452 Rhodamine FBbi:00000452 fluorophore with ex/em 589/615 jm 2010-03-14T10:22:41Z image FBbi:00000453 TexasRed FBbi:00000453 fluorophore derivative of rhodamine with ex/em 547/572 jm 2010-03-14T10:22:41Z image FBbi:00000454 Tetramethyl rhodamine (TRITC) FBbi:00000454 jm 2010-03-14T10:25:58Z image FBbi:00000455 fluorescent label FBbi:00000455 jm 2010-03-14T10:25:58Z image FBbi:00000456 enzyme label FBbi:00000456 jm 2010-03-14T10:25:58Z image FBbi:00000457 electron dense label FBbi:00000457 jm 2010-03-14T10:25:58Z image FBbi:00000458 biotin FBbi:00000458 jm 2010-03-14T10:28:34Z image FBbi:00000459 affinity for specific proteins FBbi:00000459 jm 2010-03-14T10:28:34Z image FBbi:00000460 non-specific protein affinity FBbi:00000460 jm 2010-03-17T02:09:45Z image FBbi:00000461 AzuriteFP FBbi:00000461 jm 2010-03-17T02:09:45Z image FBbi:00000462 SiriusFP FBbi:00000462 jm 2010-03-14T10:32:01Z image FBbi:00000463 non-immunological protein probe FBbi:00000463 jm 2010-03-14T10:36:52Z image FBbi:00000464 alpha-bungarotoxin FBbi:00000464 jm 2010-03-14T10:36:52Z image FBbi:00000465 botulinum toxin FBbi:00000465 jm 2010-03-14T10:37:23Z image FBbi:00000466 tetrodotoxin FBbi:00000466 jm 2010-03-14T10:37:23Z image FBbi:00000467 batrachatoxin FBbi:00000467 jm 2010-03-17T02:10:21Z image FBbi:00000468 CeruleanFP FBbi:00000468 jm 2010-03-17T02:10:21Z image FBbi:00000469 CyPet FBbi:00000469 jm 2010-03-17T02:10:21Z image FBbi:00000470 SCFP FBbi:00000470 jm 2010-03-17T02:11:07Z image FBbi:00000471 EmeraldFP FBbi:00000471 jm 2010-03-17T02:11:07Z image FBbi:00000472 SuperfolderFP FBbi:00000472 jm 2010-03-17T02:11:07Z image FBbi:00000473 T-SapphireFP FBbi:00000473 jm 2010-03-17T02:14:30Z image FBbi:00000474 CitrineFP FBbi:00000474 jm 2010-03-17T02:14:30Z image FBbi:00000475 SYFP FBbi:00000475 jm 2010-03-17T02:14:30Z image FBbi:00000476 TopazFP FBbi:00000476 jm 2010-03-17T02:14:30Z image FBbi:00000478 yPet FBbi:00000478 jm 2010-03-17T02:16:24Z image FBbi:00000479 Blue fluorescent proteins from Anthozoa FBbi:00000479 jm 2010-03-17T02:16:24Z image FBbi:00000480 Cyan fluorescent proteins from Anthozoa FBbi:00000480 jm 2010-03-17T02:16:24Z image FBbi:00000481 Green fluorescent proteins from Anthozoa FBbi:00000481 jm 2010-03-17T02:16:24Z image FBbi:00000482 Orange fluorescent proteins from Anthozoa FBbi:00000482 jm 2010-03-17T02:16:24Z image FBbi:00000484 Far-red fluorescent proteins from Anthozoa FBbi:00000484 jm 2010-03-17T02:16:24Z image FBbi:00000485 Yellow fluorescent proteins from Anthozoa FBbi:00000485 jm 2010-03-17T02:16:38Z image FBbi:00000486 mTagBFP FBbi:00000486 jm 2010-03-17T02:17:42Z image FBbi:00000487 AmCyanFP FBbi:00000487 jm 2010-03-17T02:17:42Z image FBbi:00000488 mCyFP FBbi:00000488 jm 2010-03-17T02:17:42Z image FBbi:00000489 mTFP1 FBbi:00000489 jm 2010-03-17T02:17:42Z image FBbi:00000490 TagCFP FBbi:00000490 jm 2010-03-17T02:19:04Z image FBbi:00000491 AQ143 FBbi:00000491 jm 2010-03-17T02:19:04Z image FBbi:00000492 HcRed-tandemFP FBbi:00000492 jm 2010-03-17T02:19:04Z image FBbi:00000493 KatushkaFP FBbi:00000493 jm 2010-03-17T02:19:04Z image FBbi:00000494 mKateFP FBbi:00000494 jm 2010-03-17T02:19:04Z image FBbi:00000496 mPlumFP FBbi:00000496 jm 2010-03-17T02:19:04Z image FBbi:00000497 tdKatuskaFP FBbi:00000497 jm 2010-03-17T02:19:04Z image FBbi:00000498 tdRFP639 FBbi:00000498 jm 2010-03-17T02:20:00Z image FBbi:00000499 AceFP FBbi:00000499 jm 2010-03-17T02:20:00Z image FBbi:00000500 Azami GreenFP FBbi:00000500 jm 2010-03-17T02:20:00Z image FBbi:00000501 CopGFP FBbi:00000501 jm 2010-03-17T02:20:00Z image FBbi:00000502 mWasabiFP FBbi:00000502 jm 2010-03-17T02:20:00Z image FBbi:00000503 TagGFP FBbi:00000503 jm 2010-03-17T02:20:00Z image FBbi:00000504 TagGFP2 FBbi:00000504 jm 2010-03-17T02:20:00Z image FBbi:00000505 ZsGreenFP FBbi:00000505 jm 2010-03-17T02:22:53Z image FBbi:00000506 DsRed-ExpressFP FBbi:00000506 jm 2010-03-17T02:22:53Z image FBbi:00000507 DsRed-Express2FP FBbi:00000507 jm 2010-03-17T02:22:53Z image FBbi:00000508 DsRed-MaxFP FBbi:00000508 jm 2010-03-17T02:22:53Z image FBbi:00000509 DsRed-monomerFP FBbi:00000509 jm 2010-03-17T02:22:53Z image FBbi:00000510 DsRed2FP FBbi:00000510 jm 2010-03-17T02:22:53Z image FBbi:00000511 dTomatoFP FBbi:00000511 jm 2010-03-17T02:22:53Z image FBbi:00000512 Kusabira OrangeFP FBbi:00000512 jm 2010-03-17T02:22:53Z image FBbi:00000513 Kusabira OrangeFP2 FBbi:00000513 jm 2010-03-17T02:22:53Z image FBbi:00000514 mOrangeFP FBbi:00000514 jm 2010-03-17T02:22:53Z image FBbi:00000515 mOrange2FP FBbi:00000515 jm 2010-03-17T02:22:53Z image FBbi:00000516 TagRFP FBbi:00000516 jm 2010-03-17T02:22:53Z image FBbi:00000517 TagRFP-T FBbi:00000517 jm 2010-03-17T02:22:53Z image FBbi:00000519 turboRFP FBbi:00000519 jm 2010-03-17T02:24:26Z image FBbi:00000520 AsRed2FP FBbi:00000520 jm 2010-03-17T02:24:26Z image FBbi:00000521 eqFP611 FBbi:00000521 jm 2010-03-17T02:24:26Z image FBbi:00000522 HcRed1FP FBbi:00000522 jm 2010-03-17T02:24:26Z image FBbi:00000523 JRedFP FBbi:00000523 jm 2010-03-17T02:24:26Z image FBbi:00000524 mAppleFP FBbi:00000524 jm 2010-03-17T02:24:26Z image FBbi:00000526 mRasberryFP FBbi:00000526 jm 2010-03-17T02:24:26Z image FBbi:00000527 mRFP1 FBbi:00000527 jm 2010-03-17T02:24:26Z image FBbi:00000528 mRubyFP FBbi:00000528 jm 2010-03-17T02:24:26Z image FBbi:00000529 mStrawberryFP FBbi:00000529 jm 2010-03-17T02:24:26Z image FBbi:00000530 tdRFP611 FBbi:00000530 jm 2010-03-17T02:25:15Z image FBbi:00000531 PhiYFP FBbi:00000531 jm 2010-03-17T02:25:15Z image FBbi:00000532 TagYFP FBbi:00000532 jm 2010-03-17T02:25:15Z image FBbi:00000533 TurboYFP FBbi:00000533 jm 2010-03-17T02:25:15Z image FBbi:00000534 ZsYellowFP FBbi:00000534 jm 2010-03-17T02:27:50Z image FBbi:00000535 fluorescent protein timer FBbi:00000535 jm 2010-03-17T02:27:50Z image FBbi:00000536 photoactivatable fluorescent protein FBbi:00000536 jm 2010-03-17T02:27:50Z image FBbi:00000537 photoconvertible fluorescent protein FBbi:00000537 jm 2010-03-17T02:27:50Z image FBbi:00000538 photoconvertible/photoswitchable fluorescent protein FBbi:00000538 jm 2010-03-17T02:27:50Z image FBbi:00000539 photoswitchable fluorescent protein FBbi:00000539 jm 2010-03-17T02:29:47Z image FBbi:00000540 DsRed-ES FP FBbi:00000540 jm 2010-03-17T02:29:47Z image FBbi:00000541 Fast-FT FBbi:00000541 jm 2010-03-17T02:29:47Z image FBbi:00000542 Medium-FT FBbi:00000542 jm 2010-03-17T02:29:47Z image FBbi:00000543 Slow-FT FBbi:00000543 jm 2010-03-17T02:31:26Z image FBbi:00000544 PA-GFP FBbi:00000544 jm 2010-03-17T02:31:26Z image FBbi:00000545 PA-CFP FBbi:00000545 jm 2010-03-17T02:31:26Z image FBbi:00000546 PA-mCherry1FP FBbi:00000546 jm 2010-03-17T02:31:26Z image FBbi:00000547 PA-mRFP FBbi:00000547 jm 2010-03-17T02:31:26Z image FBbi:00000548 Phamret FBbi:00000548 jm 2010-03-17T02:32:35Z image FBbi:00000549 Dendra2FP FBbi:00000549 jm 2010-03-17T02:32:35Z image FBbi:00000550 dEOSFP FBbi:00000550 jm 2010-03-17T02:32:35Z image FBbi:00000551 KaedeFP FBbi:00000551 jm 2010-03-17T02:32:35Z image FBbi:00000552 mEOS2FP FBbi:00000552 jm 2010-03-17T02:32:35Z image FBbi:00000553 mKikGR FBbi:00000553 jm 2010-03-17T02:32:35Z image FBbi:00000554 wtEOSFP FBbi:00000554 jm 2010-03-17T02:32:35Z image FBbi:00000555 wtKIikGR FBbi:00000555 jm 2010-03-17T02:32:44Z image FBbi:00000556 IrisFP FBbi:00000556 jm 2010-03-17T02:34:12Z image FBbi:00000557 bsDronpa FBbi:00000557 jm 2010-03-17T02:34:12Z image FBbi:00000558 Dronpa FBbi:00000558 jm 2010-03-17T02:34:12Z image FBbi:00000559 Dronpa-3 FBbi:00000559 jm 2010-03-17T02:34:12Z image FBbi:00000560 E2GFP FBbi:00000560 jm 2010-03-17T02:34:12Z image FBbi:00000561 KFP1 FBbi:00000561 jm 2010-03-17T02:34:12Z image FBbi:00000562 mTFP0.7 FBbi:00000562 jm 2010-03-17T02:34:12Z image FBbi:00000563 PadronFP FBbi:00000563 jm 2010-03-17T02:34:12Z image FBbi:00000564 rsCherryFP FBbi:00000564 jm 2010-03-17T02:34:12Z image FBbi:00000565 rsCherryRevFP FBbi:00000565 jm 2010-03-17T02:34:12Z image FBbi:00000566 rsFastLimeFP FBbi:00000566 jm 2010-04-27T10:29:56Z image FBbi:00000567 optically-dense stain FBbi:00000567 jm 2010-04-27T10:29:56Z image FBbi:00000568 electron-dense stain FBbi:00000568 jm 2010-04-27T10:38:31Z image FBbi:00000569 uranyl salt FBbi:00000569 jm 2010-04-27T10:38:31Z image FBbi:00000570 lead salt FBbi:00000570 jm 2010-04-27T10:38:31Z image FBbi:00000571 osmium tetroxide FBbi:00000571 jm 2010-04-27T10:38:31Z image FBbi:00000572 potassium permanganate FBbi:00000572 jm 2010-04-27T10:39:43Z image FBbi:00000573 uranium compound FBbi:00000573 jm 2010-04-27T10:39:43Z image FBbi:00000574 molybdenum compound FBbi:00000574 jm 2010-04-27T10:39:43Z image FBbi:00000575 tungsten compound FBbi:00000575 jm 2010-04-27T10:39:43Z image FBbi:00000576 aurothioglucose FBbi:00000576 jm 2010-04-28T06:06:52Z image FBbi:00000577 other negative stain FBbi:00000577 jm 2010-04-28T06:08:02Z image FBbi:00000578 other radioisotope FBbi:00000578 A fragment of a cell, subcellular organelle, or macromolecular complex. jm 2010-04-28T06:08:42Z image FBbi:00000579 isolated subcellular component FBbi:00000579 electrons generated by inelastic scattering of other radiation, the primary radiation. jm 2010-05-04T12:25:14Z image FBbi:00000580 secondary electron generation FBbi:00000580 specimen from which water has been removed by a process that avoids liquid-gas and solid-gas phase transitions. jm 2010-05-04T12:31:12Z image FBbi:00000581 critical_point dried specimen FBbi:00000581 data as acquired, with no alterations that change the pixel values. jm 2010-05-04T12:42:17Z image FBbi:00000582 unprocessed raw data FBbi:00000582 specimen from which water has been removed by evaporation under vacuum at a temperature below freezing. jm 2010-05-04T12:49:31Z image FBbi:00000583 lyophilized specimen FBbi:00000583 fluorophore derivative of rhodamine with ex/em 580/605 jm 2010-05-04T09:02:54Z image FBbi:00000584 X-Rhodamine FBbi:00000584 A method of reconstructing 3D structure by combining serial sectioning with scanning EM. jm 2010-09-02T05:10:33Z image FBbi:00000585 serial block face SEM (SBFSEM) FBbi:00000585 A method of reconstructing 3D structure by combining serial sectioning with scanning EM. PMID:15514700 jm 2010-09-03T08:42:47Z image FBbi:00000586 elastic scattering of electrons FBbi:00000586 jm 2010-09-03T08:42:47Z image FBbi:00000587 elastic scattering of photons FBbi:00000587 jm 2010-09-03T08:43:42Z image FBbi:00000588 inelastic scattering of electrons FBbi:00000588 jm 2010-09-03T08:43:42Z image FBbi:00000589 inelastic scattering of photons (Raman scattering) FBbi:00000589 jm 2010-09-03T09:55:12Z image FBbi:00000591 differences in chemical composition FBbi:00000591 jm 2010-09-03T09:55:12Z image FBbi:00000592 distribution of epitope FBbi:00000592 jm 2010-09-03T09:55:12Z image FBbi:00000593 form birefringence FBbi:00000593 jm 2010-09-03T09:55:12Z image FBbi:00000594 intrinsic birefringence FBbi:00000594 jm 2010-09-03T09:55:12Z image FBbi:00000595 stress-induced birefringence FBbi:00000595 jm 2010-09-03T09:55:12Z image FBbi:00000596 distribution of a specific nucleic acid sequence FBbi:00000596 jm 2010-09-03T09:55:12Z image FBbi:00000597 distribution of a specific protein FBbi:00000597 jm 2010-09-03T09:55:12Z image FBbi:00000598 differences in adsorption or binding of stain FBbi:00000598 jm 2010-09-03T09:55:12Z image FBbi:00000599 boundaries between regions with different refractive index FBbi:00000599 jm 2010-09-03T09:55:12Z image FBbi:00000600 differences in amount of elastic light scattering FBbi:00000600 jm 2010-09-04T11:57:06Z image FBbi:00000601 differences in deposition of metal shadow FBbi:00000601 jm 2010-09-04T12:55:54Z image FBbi:00000602 differences in intrinsic optical density FBbi:00000602 jm 2010-09-04T01:28:20Z image FBbi:00000603 fluorescence polarization microscopy FBbi:00000603 jm 2010-09-04T01:31:54Z image FBbi:00000604 compartmentalization of stain or label FBbi:00000604 jm 2010-09-04T01:35:37Z image FBbi:00000605 differences in fluorescence lifetime FBbi:00000605 jm 2010-09-04T01:36:45Z image FBbi:00000606 differences in orientation of fluorophore FBbi:00000606 jm 2010-09-04T01:51:14Z image FBbi:00000607 intrinsic mass distribution FBbi:00000607 jm 2010-09-04T02:05:02Z image FBbi:00000608 X-ray fluorescence FBbi:00000608 jm 2010-09-04T11:49:25Z image FBbi:00000609 heat fixed tissue FBbi:00000609 jm 2010-09-04T11:56:02Z image FBbi:00000610 copper salt FBbi:00000610 jm 2010-09-28T04:35:54Z image FBbi:00000611 dispersed cells in vitro FBbi:00000611 jm 2011-05-23T09:33:44Z image FBbi:00000612 fluorescent protein derived from Arabidopsis FBbi:00000612 jm 2011-05-23T09:49:58Z image FBbi:00000613 vidicon tube camera FBbi:00000613 jm 2011-05-23T09:55:54Z image FBbi:00000614 phototropin 2 FBbi:00000614 jm 2011-05-23T09:57:01Z image FBbi:00000615 miniSOG FBbi:00000615 jm 2011-05-23T10:09:41Z image FTIR frustrated total internal reflection FBbi:00000616 evanescent wave scattering FBbi:00000616 jm 2011-05-23T10:10:58Z image total internal reflection fluorescence TIRF FBbi:00000617 evanescent wave microscopy FBbi:00000617 jm 2011-05-23T10:34:07Z image FBbi:00000618 ground state depletion scanning (GSD) FBbi:00000618 jm 2011-05-23T10:43:15Z image FBbi:00000619 nearfield illumination FBbi:00000619 jm 2011-05-23T10:44:03Z image FBbi:00000620 nearfield illumination FBbi:00000620 jm 2011-05-23T10:51:16Z image FBbi:00000621 freeze-substituted tissue FBbi:00000621 jm 2011-05-23T10:53:45Z image FBbi:00000622 high-voltage electron microscopy (HVEM) FBbi:00000622 jm 2011-05-23T10:53:45Z image FBbi:00000623 intermediate voltage electron microacopy (IVEM) FBbi:00000623 An imaging technique that uses high energy electromagnetic radiation, typically X-rays, as a source of illumination. image FBbi:00001000 radiography FBbi:00001000 An imaging technique that uses high energy electromagnetic radiation, typically X-rays, as a source of illumination. http://en.wikipedia.org/w/index.php?title=Radiography&oldid=606628211 Radiography using X-rays X-radiography image X-ray FBbi:00001001 X-ray radiography FBbi:00001001 MeSH:D014057 http://en.wikipedia.org/wiki/X-ray_computed_tomography CAT scan CT scan X-ray CT image computed axial tomography FBbi:00001002 X-ray computed tomography FBbi:00001002 Tomography using X-ray illumination. image FBbi:00001003 X-ray tomography FBbi:00001003 An imaging technique that creates virtual sections through the use of any kind of penetrating wave. image FBbi:00001004 tomography FBbi:00001004 Tomography in which virtual sections are taken from multiple angles and the results are processed via tomographic reconstruction software to produce 2 or 3D images. image FBbi:00001005 computed tomography FBbi:00001005 image FBbi:00001006 x-ray/gamma ray illumination FBbi:00001006 image FBbi:00001007 gamma ray illumination FBbi:00001007 image FBbi:00001012 fixation method FBbi:00001012 image FBbi_root:00000000 method involved in biological imaging FBbi_root:00000000 An intracellular protein kinase cascade containing at least a MAP kinase (MAPK). It starts with the activation of a MAP3K, and the consecutive activation of a MPK2K and a MAPK. The cascade can also contain an additional tier: the upstream MAP4K. The kinases in each tier phosphorylate and activate the kinase in the downstream tier to transmit a signal within a cell. https://github.com/geneontology/go-ontology/issues/26806 GO:0007255 Reactome:R-HSA-169893 Reactome:R-HSA-5673001 Wikipedia:MAPK_cascade Wikipedia:Mitogen-activated_protein_kinase MAP kinase cascade MAP kinase kinase kinase cascade MAPK signal transduction MAPKKK cascade mitogen-activated protein kinase cascade ERK/MAPK cascade MAPKKK cascade during sporulation biological_process MAPK signaling MAPK signalling GO:0000165 MAPK cascades lie downstream of many cell surface receptors and cooperate in transmitting various extracellular signals to the nucleus. One way by which the specificity of each cascade is regulated is through the existence of several distinct components in each tier of the different cascades. The cascades are typically named according to the component in the MAPK tier. MAPK cascade GO:0000165 A chromosome found in the mitochondrion of a eukaryotic cell. NIF_Subcellular:sao1186327184 mitochondrial DNA mtDNA cellular_component mitochondrial genome GO:0000262 mitochondrial chromosome GO:0000262 The division of a mitochondrion within a cell to form two or more separate mitochondrial compartments. mitochondrial division biological_process mitochondrial proliferation GO:0000266 mitochondrial fission GO:0000266 The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. GO:0044244 polysaccharide breakdown polysaccharide catabolism polysaccharide degradation multicellular organismal polysaccharide catabolic process biological_process GO:0000272 polysaccharide catabolic process GO:0000272 Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GO:0007067 Reactome:R-HSA-69278 Wikipedia:Mitosis biological_process mitosis GO:0000278 Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. mitotic cell cycle GO:0000278 A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules. https://github.com/geneontology/go-ontology/issues/21126 https://github.com/geneontology/go-ontology/issues/23605 GO:0000777 GO:0000778 GO:0005699 GO:0031617 Wikipedia:Kinetochore condensed chromosome kinetochore condensed nuclear chromosome kinetochore NMS complex cellular_component GO:0000776 Note that the kinetochore overlaps the centromeric DNA, but centromeric DNA is not part of the kinetochore. kinetochore GO:0000776 A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures. GO:0000787 GO:0000788 GO:0005718 Wikipedia:Nucleosome cytoplasmic nucleosome nuclear nucleosome cellular_component GO:0000786 nucleosome GO:0000786 The developmental process in which the size or shape of a cell is generated and organized. GO:0007148 GO:0045790 GO:0045791 cellular morphogenesis biological_process GO:0000902 cell morphogenesis GO:0000902 Cell migration that is accomplished by extension and retraction of a pseudopodium. ameboid cell migration amoeboid cell migration amoeboidal cell migration biological_process GO:0001667 Note that this term refers to a mode of migration rather than to any particular cell type. ameboidal-type cell migration GO:0001667 A multicellular organismal process by which exposure to an activating factor such as a cellular or soluble ligand results in a change in the morphology or behavior of a cell. https://github.com/geneontology/go-ontology/issues/24416 biological_process GO:0001775 cell activation GO:0001775 The change in form (cell shape and size) that occurs during the differentiation of an endothelial cell. biological_process GO:0001886 endothelial cell morphogenesis GO:0001886 A homeostatic process involved in the maintenance of an internal steady state within a defined tissue of an organism, including control of cellular proliferation and death and control of metabolic function. tissue maintenance biological_process GO:0001894 tissue homeostasis GO:0001894 The pronucleus originating from the spermatozoa that was involved in fertilization. cellular_component GO:0001940 male pronucleus GO:0001940 The process whose specific outcome is the progression of the hair follicle over time, from its formation to the mature structure. A hair follicle is a tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open. GO:0001943 biological_process GO:0001942 hair follicle development GO:0001942 A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring. puberty biological_process reproductive developmental process GO:0003006 developmental process involved in reproduction GO:0003006 A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective. organ system process biological_process GO:0003008 system process GO:0003008 A circulatory process that occurs at the level of the vasculature. vasculature process biological_process GO:0003018 vascular process in circulatory system GO:0003018 The series of events by which an endogenous stimulus is received by a cilium on a cell and converted to a molecular signal contributing to left/right asymmetry. tb 2009-09-22T02:45:48Z biological_process GO:0003127 detection of nodal flow GO:0003127 The change in form that occurs when an epithelial cell progresses from its initial formation to its mature state. dph 2009-12-09T07:21:06Z biological_process GO:0003382 epithelial cell morphogenesis GO:0003382 The progression of the retinal pigment epithelium over time, from its initial formation to the mature structure. The retinal pigment epithelium is the melanin-containing layer of cells between the retina and the choroid that absorbs scattered and reflected light and removes waste products produced by the photoreceptor cells. dph 2009-12-21T02:04:27Z biological_process RPE development GO:0003406 retinal pigment epithelium development GO:0003406 Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires the presence of AMP. Reactome:R-HSA-1592244 Reactome:R-HSA-163691 Reactome:R-HSA-200423 Reactome:R-HSA-380927 Reactome:R-HSA-447074 Reactome:R-HSA-5673768 Reactome:R-HSA-6805470 5'-AMP-activated protein kinase activity protein kinase A activity SNF1A/AMP-activated protein kinase activity molecular_function AMPK activity GO:0004679 AMP-activated protein kinase activity GO:0004679 A laminin complex composed of alpha2, beta1 and gamma1 polypeptide chains. laminin-211 complex cellular_component GO:0005607 laminin-2 complex GO:0005607 GO:0005634 A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. Wikipedia:Chromosome interphase chromosome prophase chromosome cellular_component chromatid GO:0005694 Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. chromosome GO:0005694 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. https://github.com/geneontology/go-ontology/issues/23023 Wikipedia:Cytoplasm cellular_component GO:0005737 cytoplasm GO:0005737 The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation. GO:0031980 NIF_Subcellular:sao1804523077 Wikipedia:Mitochondrial_matrix mitochondrial lumen mitochondrial stroma cellular_component GO:0005759 mitochondrial matrix GO:0005759 A small lytic vacuole that has cell cycle-independent morphology found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions. NIF_Subcellular:sao585356902 Wikipedia:Lysosome cellular_component GO:0005764 lysosome GO:0005764 A vacuole to which materials ingested by endocytosis are delivered. NIF_Subcellular:sao1720343330 Wikipedia:Endosome cellular_component GO:0005768 endosome GO:0005768 A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism. GO:0019818 peroxisome vesicle NIF_Subcellular:sao499555322 Wikipedia:Peroxisome cellular_component peroxisomal GO:0005777 peroxisome GO:0005777 A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle. Wikipedia:Centrosome cellular_component GO:0005813 centrosome GO:0005813 An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides. Wikipedia:Microtubule_organizing_center MTOC microtubule organising centre cellular_component GO:0005815 microtubule organizing center GO:0005815 The microtubule organizing center in fungi; functionally homologous to the animal cell centrosome. Wikipedia:Spindle_pole_body SPB cellular_component GO:0005816 spindle pole body GO:0005816 The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart. Wikipedia:Spindle_apparatus cellular_component GO:0005819 spindle GO:0005819 Any of the spindle microtubules that attach to the kinetochores of chromosomes by their plus ends, and maneuver the chromosomes during mitotic or meiotic chromosome segregation. pole-to-kinetochore microtubule cellular_component GO:0005828 kinetochore microtubule GO:0005828 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. GO:0033279 NIF_Subcellular:sao1429207766 Wikipedia:Ribosome free ribosome membrane bound ribosome cellular_component ribosomal RNA GO:0005840 ribosome GO:0005840 A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. Wikipedia:Cytoskeleton cellular_component GO:0005856 cytoskeleton GO:0005856 Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. NIF_Subcellular:sao1846835077 Wikipedia:Microtubule microtubuli microtubulus neurotubule cellular_component GO:0005874 microtubule GO:0005874 A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane. FMA:63850 NIF_Subcellular:sao1588493326 Wikipedia:Actin microfilament cellular_component GO:0005884 actin filament GO:0005884 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0005887 GO:0005904 juxtamembrane NIF_Subcellular:sao1663586795 Wikipedia:Cell_membrane cell membrane cellular membrane cytoplasmic membrane plasmalemma bacterial inner membrane inner endospore membrane integral component of plasma membrane integral to plasma membrane plasma membrane lipid bilayer cellular_component GO:0005886 plasma membrane GO:0005886 A cell junction that forms a connection between two or more cells of an organism; excludes direct cytoplasmic intercellular bridges, such as ring canals in insects. https://github.com/geneontology/go-ontology/issues/22122 cell-cell contact region cell-cell contact zone NIF_Subcellular:sao1922892319 intercellular junction cellular_component GO:0005911 cell-cell junction GO:0005911 A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. GO:0072372 FMA:67181 NIF_Subcellular:sao787716553 Wikipedia:Cilium eukaryotic flagellum microtubule-based flagellum primary cilium cellular_component flagellum GO:0005929 Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. Also, 'cilium' may be used when axonemal structure and/or motility are unknown, or when axonemal structure is unusual. For all other cases, please refer to children of 'cilium'. Finally, note that any role of ciliary proteins in sensory events should be captured by annotating to relevant biological process terms. cilium GO:0005929 An enzyme complex, composed of regulatory and catalytic subunits, that catalyzes protein phosphorylation. Inactive forms of the enzyme have two regulatory chains and two catalytic chains; activation by cAMP produces two active catalytic monomers and a regulatory dimer. 3',5' cAMP-dependent protein kinase complex 3',5'-cAMP-dependent protein kinase complex adenosine 3',5'-cyclophosphate-dependent protein kinase complex cyclic AMP-dependent protein kinase complex cellular_component PKA GO:0005952 cAMP-dependent protein kinase complex GO:0005952 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. https://github.com/geneontology/go-ontology/issues/22880 jl 2012-10-23T15:40:34Z GO:0044261 GO:0044723 Reactome:R-HSA-71387 Wikipedia:Carbohydrate_metabolism carbohydrate metabolism biological_process GO:0005975 carbohydrate metabolic process GO:0005975 The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. GO:0044263 polysaccharide metabolism glycan metabolic process glycan metabolism multicellular organismal polysaccharide metabolic process biological_process GO:0005976 polysaccharide metabolic process GO:0005976 The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages. Reactome:R-HSA-8982491 glycogen metabolism biological_process GO:0005977 glycogen metabolic process GO:0005977 The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues. https://github.com/geneontology/go-ontology/issues/27107 https://github.com/geneontology/go-ontology/issues/28527 Reactome:R-HSA-70221 glycogen breakdown glycogen catabolism glycogen degradation glycogenolysis biological_process GO:0005980 glycogen catabolic process GO:0005980 A dynamic process of chromatin reorganization resulting in changes to chromatin structure. These changes allow DNA metabolic processes such as transcriptional regulation, DNA recombination, DNA repair, and DNA replication. https://github.com/geneontology/go-ontology/issues/21732 https://github.com/geneontology/go-ontology/issues/21748 GO:0043044 chromatin modeling chromatin modelling chromatin remodelling ATP-dependent chromatin remodeling ATP-dependent chromatin remodelling biological_process GO:0006338 chromatin remodeling GO:0006338 The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein. https://github.com/geneontology/go-ontology/issues/20292 jl 2012-12-13T16:25:32Z GO:0015457 GO:0015460 GO:0044765 Reactome:R-HSA-382551 biological_process single-organism transport GO:0006810 Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. transport GO:0006810 The directed movement of zinc (Zn II) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. zinc II ion transport zinc transport biological_process GO:0006829 zinc ion transport GO:0006829 The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. GO:0032779 biological_process copper-induced intracellular protein transport GO:0006886 intracellular protein transport GO:0006886 The cellular catabolic process in which cells digest cellular materials, such as organelles and other macromolecular constituents, or non-self materials such as intracellular pathogens. Autophagy serves to provide essential nutrients under conditions of cellular stress; or can remodel intracellular structures during cell differentiation. https://github.com/geneontology/go-ontology/issues/25541 GO:0016238 Reactome:R-HSA-9612973 Wikipedia:Autophagy_(cellular) biological_process GO:0006914 autophagy GO:0006914 The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis). Wikipedia:Chemotaxis taxis in response to chemical stimulus biological_process GO:0006935 chemotaxis GO:0006935 A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Reactome:R-HSA-445355 Wikipedia:Muscle_contraction biological_process GO:0006936 muscle contraction GO:0006936 A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length. visceral muscle contraction biological_process GO:0006939 smooth muscle contraction GO:0006939 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). https://github.com/geneontology/go-ontology/issues/26810 biological_process response to abiotic stress response to biotic stress GO:0006950 response to stress GO:0006950 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. https://github.com/geneontology/go-ontology/issues/27189 jl 2013-12-19T15:25:51Z GO:1902589 Reactome:R-HSA-1852241 organelle organisation single organism organelle organization biological_process organelle organization and biogenesis single-organism organelle organization GO:0006996 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. organelle organization GO:0006996 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components. Reactome:R-HSA-1592230 mitochondria organization mitochondrial biogenesis mitochondrial organization mitochondrion biogenesis mitochondrion organisation biological_process mitochondrion morphogenesis mitochondrion organization and biogenesis GO:0007005 mitochondrion organization GO:0007005 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the cytoplasm. The cytoplasm is all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. cytoplasm organisation biological_process cytoplasm organization and biogenesis GO:0007028 cytoplasm organization GO:0007028 The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. Reactome:R-HSA-1640170 Wikipedia:Cell_cycle cell-division cycle biological_process GO:0007049 cell cycle GO:0007049 The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. Wikipedia:Chromosome_segregation chromosome division biological_process chromosome transmission GO:0007059 chromosome segregation GO:0007059 The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other. Reactome:R-HSA-2468052 cohesion-mediated DNA tethering biological_process GO:0007062 sister chromatid cohesion GO:0007062 The directed movement of the nucleus to a specific location within a cell. GO:0040023 establishment of position of nucleus nuclear movement nuclear positioning nucleus migration nucleus positioning positioning of nucleus biological_process establishment of cell nucleus localization establishment of localization of nucleus establishment of nucleus localisation establishment of nucleus localization GO:0007097 nuclear migration GO:0007097 The first meiotic nuclear division in which homologous chromosomes are paired and segregated from each other, producing two haploid daughter nuclei. Wikipedia:Meiosis#Meiosis_I meiosis I nuclear division biological_process GO:0007127 meiosis I GO:0007127 The attachment of a plasma membrane adhesion molecule in one cell to an identical molecule in an adjacent cell. biological_process GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules GO:0007156 The attachment of a neuron to another cell via adhesion molecules. neuron adhesion neuronal cell adhesion biological_process GO:0007158 neuron cell-cell adhesion GO:0007158 The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. GO:0023014 GO:0023015 GO:0023016 GO:0023033 GO:0023045 Reactome:R-HSA-212718 Wikipedia:Signal_transduction signaling cascade signalling cascade biological_process signaling pathway signalling pathway GO:0007165 Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not. signal transduction GO:0007165 The series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription. Reactome:R-HSA-177929 EGF receptor signaling pathway EGF receptor signalling pathway EGFR signaling pathway ERBB1 signaling pathway epidermal growth factor receptor signalling pathway receptor tyrosine-protein kinase erbB-1 signaling pathway biological_process GO:0007173 epidermal growth factor receptor signaling pathway GO:0007173 The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). https://github.com/geneontology/go-ontology/issues/21234 biological_process GO:0007275 Note that this term was 'developmental process'. multicellular organism development GO:0007275 The process in which the egg becomes metabolically active, initiates protein and DNA synthesis and undergoes structural changes to its cortex and/or cytoplasm. Wikipedia:Egg_activation biological_process GO:0007343 egg activation GO:0007343 The establishment of an organism's body plan or part of an organism with respect to the left and right halves. The pattern can either be symmetric, such that the halves are mirror images, or asymmetric where the pattern deviates from this symmetry. determination of left/right asymmetry biological_process GO:0007368 determination of left/right symmetry GO:0007368 Formation of a ventral indentation (furrow) from the blastoderm epithelium, which is internalized to form a tube in the interior of the embryo, marking the start of gastrulation. biological_process GO:0007370 ventral furrow formation GO:0007370 Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate. biological_process pattern biosynthesis pattern formation GO:0007389 pattern specification process GO:0007389 The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state. Reactome:R-HSA-9675108 biological_process pan-neural process GO:0007399 nervous system development GO:0007399 The aggregation, arrangement and bonding together of a set of components to form a synapse. This process ends when the synapse is mature (functional). Wikipedia:Synaptogenesis synapse biogenesis synaptogenesis biological_process GO:0007416 synapse assembly GO:0007416 The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.). biological_process GO:0007420 brain development GO:0007420 The orderly movement of epithelial cells during development of an open tracheal system. An example of this is found in Drosophila melanogaster. tracheal cell migration biological_process tracheal epithelial cell migration GO:0007427 epithelial cell migration, open tracheal system GO:0007427 The process whose specific outcome is the progression of the salivary gland over time, from its formation to the mature structure. Salivary glands include any of the saliva-secreting exocrine glands of the oral cavity. biological_process GO:0007431 salivary gland development GO:0007431 A biological process in which an animal physically develops after birth or hatching, involving a conspicuous and relatively abrupt change in the animal's form or structure. Examples include the change from tadpole to frog, and the change from larva to adult. An example of this is found in Drosophila melanogaster. GO:0046698 GO:0046699 Wikipedia:Metamorphosis biological_process GO:0007552 metamorphosis GO:0007552 Any process that modulates the frequency, rate or extent of the regulated release of ecdysteroid from a cell. biological_process GO:0007555 regulation of ecdysteroid secretion GO:0007555 The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. jl 2012-09-20T14:06:08Z GO:0023032 GO:0044708 GO:0044709 Wikipedia:Behavior behavioral response to stimulus behaviour behavioural response to stimulus biological_process single-organism behavior GO:0007610 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. 2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). behavior GO:0007610 Any biological process in an organism that recurs with a regularity of approximately 24 hours. GO:0050895 Reactome:R-HSA-400253 Wikipedia:Circadian_rhythm circadian process biological_process circadian response response to circadian rhythm GO:0007623 circadian rhythm GO:0007623 The orderly movement of mesodermal cells from one site to another. mesoderm cell migration biological_process GO:0008078 mesodermal cell migration GO:0008078 A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation. https://github.com/geneontology/go-ontology/issues/26424 https://github.com/geneontology/go-ontology/issues/28932 jl 2012-10-17T15:46:40Z GO:0044236 GO:0044710 Reactome:R-HSA-1430728 Wikipedia:Metabolism metabolism biological_process GO:0008152 Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. metabolic process GO:0008152 The production of light by certain enzyme-catalyzed reactions in cells. Wikipedia:Bioluminescence biological_process GO:0008218 bioluminescence GO:0008218 A protein complex that contains one or more cysteine-type endopeptidases (also called caspases), which give the complex a peptidase activity with specificity for the hydrolysis of aspartyl bonds. These complexes may be involved e.g. in apoptotic or inflammation processes. cysteine-type endopeptidase complex cellular_component GO:0008303 Note that this term was reinstated from obsolete. caspase complex GO:0008303 The process in which the structures of a photoreceptor cell are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a photoreceptor cell, a sensory cell that reacts to the presence of light. An example of this is found in Drosophila melanogaster. biological_process photoreceptor development GO:0008594 photoreceptor cell morphogenesis GO:0008594 Modulation of the activity of the enzyme cAMP-dependent protein kinase. 3',5' cAMP-dependent protein kinase regulator activity 3',5'-cAMP-dependent protein kinase regulator activity adenosine 3',5'-cyclophosphate-dependent protein kinase regulator activity cyclic AMP-dependent protein kinase regulator activity cAMP-dependent protein kinase, intrinsic regulator activity molecular_function GO:0008603 cAMP-dependent protein kinase regulator activity GO:0008603 Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by heterochromatin formation leading to a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex. https://github.com/geneontology/go-ontology/issues/25955 chromosome inactivation Wikipedia:X-inactivation X chromosome inactivation biological_process Barr body formation GO:0009048 dosage compensation by inactivation of X chromosome GO:0009048 A cellular process consisting of the biochemical pathways by which a living organism breaks down substances. This includes the breakdown of carbon compounds with the liberation of energy for use by the cell or organism. https://github.com/geneontology/go-ontology/issues/28921 https://github.com/geneontology/go-ontology/issues/28932 https://github.com/geneontology/go-ontology/issues/29627 jl 2012-10-17T15:52:35Z GO:0044243 GO:0044712 Wikipedia:Catabolism breakdown of chemical breakdown of molecule breakdown of substance catabolism cellular breakdown cellular catabolism cellular degradation degradation biological_process GO:0009056 catabolic process GO:0009056 The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GO:0043285 GO:0044266 biopolymer catabolic process macromolecule breakdown macromolecule catabolism macromolecule degradation multicellular organismal macromolecule catabolic process biological_process cellular macromolecule catabolic process cellular macromolecule catabolism cellular macromolecule degradation GO:0009057 macromolecule catabolic process GO:0009057 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. https://github.com/geneontology/go-ontology/issues/28932 jl 2012-10-17T15:52:18Z GO:0044274 GO:0044711 formation Wikipedia:Anabolism anabolism biosynthesis synthesis multicellular organismal biosynthetic process biological_process single-organism biosynthetic process GO:0009058 biosynthetic process GO:0009058 The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/15249 https://github.com/geneontology/go-ontology/issues/25418 https://github.com/geneontology/go-ontology/issues/27189 GO:0043284 biopolymer biosynthetic process macromolecule anabolism macromolecule biosynthesis macromolecule formation macromolecule synthesis biological_process GO:0009059 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. macromolecule biosynthetic process GO:0009059 The chemical reactions and pathways resulting in the breakdown of glucans, polysaccharides consisting only of glucose residues. glucan breakdown glucan catabolism glucan degradation biological_process GO:0009251 glucan catabolic process GO:0009251 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a xenobiotic, a compound foreign to the organism exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical. https://github.com/geneontology/go-ontology/issues/19460 GO:0017035 GO:0017104 GO:0042493 biological_process drug resistance drug susceptibility/resistance response to drug GO:0009410 response to xenobiotic stimulus GO:0009410 The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). https://github.com/geneontology/go-ontology/issues/20176 Wikipedia:Fertilisation syngamy biological_process GO:0009566 fertilization GO:0009566 The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form. embryogenesis and morphogenesis Wikipedia:Morphogenesis anatomical structure organization morphogenesis biological_process GO:0009653 anatomical structure morphogenesis GO:0009653 The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure. histogenesis and organogenesis Wikipedia:Histogenesis histogenesis biological_process GO:0009888 tissue development GO:0009888 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. regulation of anabolism regulation of biosynthesis regulation of formation regulation of synthesis biological_process GO:0009889 regulation of biosynthetic process GO:0009889 Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances. down regulation of biosynthetic process down-regulation of biosynthetic process downregulation of biosynthetic process negative regulation of anabolism negative regulation of biosynthesis negative regulation of formation negative regulation of synthesis inhibition of biosynthetic process biological_process GO:0009890 negative regulation of biosynthetic process GO:0009890 Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044252 down regulation of metabolic process down-regulation of metabolic process downregulation of metabolic process negative regulation of metabolism negative regulation of organismal metabolism inhibition of metabolic process inhibition of organismal metabolic process negative regulation of multicellular organismal metabolic process biological_process GO:0009892 negative regulation of metabolic process GO:0009892 Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances. regulation of breakdown regulation of catabolism regulation of degradation biological_process GO:0009894 regulation of catabolic process GO:0009894 Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. down regulation of catabolic process down-regulation of catabolic process downregulation of catabolic process negative regulation of breakdown negative regulation of catabolism negative regulation of degradation inhibition of catabolic process biological_process GO:0009895 negative regulation of catabolic process GO:0009895 Any process that modulates the frequency, rate or extent of signal transduction. GO:0035466 biological_process regulation of signaling pathway regulation of signalling pathway GO:0009966 regulation of signal transduction GO:0009966 The external part of the cell wall and/or plasma membrane. GO:0009928 GO:0009929 cell associated cell bound cellular_component GO:0009986 Note that this term is intended to annotate gene products that are attached (integrated or loosely bound) to the plasma membrane or cell wall. cell surface GO:0009986 Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. jl 2012-12-11T16:56:55Z GO:0008151 GO:0044763 GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance biological_process single-organism cellular process GO:0009987 This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. cellular process GO:0009987 The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes. https://github.com/geneontology/go-ontology/issues/22557 https://github.com/geneontology/go-ontology/issues/25419 Wikipedia:Gene_expression biological_process GO:0010467 gene expression GO:0010467 Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). https://github.com/geneontology/go-ontology/issues/22557 Reactome:R-HSA-163767 Reactome:R-HSA-9752946 Wikipedia:Regulation_of_gene_expression regulation of protein expression biological_process gene regulation regulation of gene product expression GO:0010468 This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availability of mRNA or circRNA for translation and thereby regulates the rate of production of the encoded protein via translation. regulation of gene expression GO:0010468 Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010556 regulation of macromolecule biosynthetic process GO:0010556 Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010558 negative regulation of macromolecule biosynthetic process GO:0010558 Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010605 negative regulation of macromolecule metabolic process GO:0010605 Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). https://github.com/geneontology/go-ontology/issues/22557 biological_process gene silencing GO:0010629 This term covers any process that negatively regulates the rate of production of a mature gene product, and so includes processes that negatively regulate that rate by reducing the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that reduces the level, stability or availability of mRNA or circRNA for translation and thereby reduces the rate of production of the encoded protein via translation. negative regulation of gene expression GO:0010629 Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. biological_process GO:0010646 regulation of cell communication GO:0010646 A tissue homeostatic process required for the maintenance of epithelial structure. biological_process GO:0010669 epithelial structure maintenance GO:0010669 The movement of organelles or other particles from one location in the cell to another along microtubules, driven by motor activity. tb 2009-05-27T10:56:08Z microtubule-based transport establishment of localization by movement along microtubule movement along microtubule biological_process GO:0010970 transport along microtubule GO:0010970 An electron dense network of proteins within and adjacent to the postsynaptic membrane of an asymmetric, neuron-neuron synapse. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components. pr 2013-07-02T09:44:28Z GO:0097481 GO:0097483 NIF_Subcellular:sao1196688972 Wikipedia:Postsynaptic_density neuronal postsynaptic density post synaptic density post-synaptic density postsynaptic density of dendrite cellular_component GO:0014069 postsynaptic density GO:0014069 A process in which force is generated within oscillatory skeletal muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Oscillatory muscle contraction occurs in insect wing muscles and is characterized by asynchrony between action potential and contraction and by stretch activation. biological_process GO:0014703 oscillatory muscle contraction GO:0014703 A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the artery. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The artery is a vessel carrying blood away from the heart. biological_process GO:0014824 artery smooth muscle contraction GO:0014824 A process, occurring in the vascular tissue, whereby actin/myosin complex activity generates force through ATP hydrolysis resulting in a change in smooth muscle geometry. This process is always coupled to chemo-mechanical energy conversion. vascular smooth muscle contraction biological_process GO:0014829 vascular associated smooth muscle contraction GO:0014829 A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the arteriole. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The arteriole is the smallest division of the artery located between the muscular arteries and the capillaries. biological_process GO:0014830 arteriole smooth muscle contraction GO:0014830 The process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotube differentiation starts with myoblast fusion and the appearance of specific cell markers (this is the cell development step). Then individual myotubes can fuse to form bigger myotubes and start to contract. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. biological_process GO:0014902 myotube differentiation GO:0014902 The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0015831 enzyme transport biological_process GO:0015031 protein transport GO:0015031 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 2014-03-06T11:37:54Z GO:0016021 GO:0098589 GO:0098805 Wikipedia:Biological_membrane Wikipedia:Transmembrane_protein integral component of membrane integral to membrane membrane region region of membrane whole membrane cellular_component transmembrane GO:0016020 membrane GO:0016020 A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GO:0044235 GO:0071842 cell organisation cellular component organisation at cellular level cellular component organisation in other organism cellular component organization at cellular level cellular component organization in other organism biological_process cell organization and biogenesis GO:0016043 cellular component organization GO:0016043 The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. GO:0048591 cellular growth growth of cell biological_process cell expansion metabolic process resulting in cell growth metabolism resulting in cell growth non-developmental cell growth non-developmental growth of a unicellular organism GO:0016049 cell growth GO:0016049 The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. jl 2012-10-23T16:34:39Z GO:0006095 GO:0044276 GO:0044724 carbohydrate breakdown carbohydrate catabolism carbohydrate degradation catabolic carbohydrate metabolic process catabolic carbohydrate metabolism multicellular organismal carbohydrate catabolic process biological_process single-organism carbohydrate catabolic process GO:0016052 carbohydrate catabolic process GO:0016052 The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. https://github.com/geneontology/go-ontology/issues/24787 Wikipedia:Cell_migration biological_process GO:0016477 cell migration GO:0016477 The chemical reactions and pathways involving naphthalenesulfonate, sulfonated derivatives of naphthalene. GO:0018932 UM-BBD_pathwayID:nphs naphthalenesulfonate metabolism naphthalenesulphonate metabolic process naphthalenesulphonate metabolism biological_process GO:0018984 naphthalenesulfonate metabolic process GO:0018984 A process by which a viral gene is converted into a mature gene product or products (proteins or RNA). This includes viral transcription, processing to produce a mature RNA product, and viral translation. viral genome expression biological_process GO:0019080 viral gene expression GO:0019080 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044246 Reactome:R-HSA-1989781 regulation of metabolism regulation of multicellular organismal metabolic process regulation of organismal metabolic process biological_process GO:0019222 regulation of metabolic process GO:0019222 Any intracellular signal transduction in which the signal is passed on within the cell via calcium ions. Wikipedia:Calcium_signaling calcium ion signaling calcium signaling calcium signalling calcium-mediated signalling biological_process GO:0019722 calcium-mediated signaling GO:0019722 A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. antibody cellular_component GO:0019814 Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. immunoglobulin complex GO:0019814 An intracellular signaling cassette that starts with production of cyclic AMP (cAMP), and ends with activation of downstream effectors that further transmit the signal within the cell. 3',5' cAMP-mediated signaling 3',5' cAMP-mediated signalling 3',5'-cAMP-mediated signaling 3',5'-cAMP-mediated signalling adenosine 3',5'-cyclophosphate-mediated signaling adenosine 3',5'-cyclophosphate-mediated signalling cAMP signaling cAMP signalling cAMP-mediated signal transduction cAMP-mediated signalling cyclic AMP-mediated signaling cyclic AMP-mediated signalling biological_process GO:0019933 cAMP-mediated signaling GO:0019933 That part of the plasma membrane found in the ciliary pocket (also called flagellar pocket). cilial pocket membrane cilium pocket membrane flagellar pocket membrane cellular_component GO:0020018 Note that cilia and eukaryotic flagella are deemed to be equivalent. In this case community usage is mostly 'flagellar', but the primary term name reflects the cilium parentage. ciliary pocket membrane GO:0020018 Generation of cells within the nervous system. Wikipedia:Neurogenesis nervous system cell generation biological_process neural cell differentiation GO:0022008 neurogenesis GO:0022008 The movement of the nucleus of the ventricular zone cell between the apical and the basal zone surfaces. Mitosis occurs when the nucleus is near the apical surface, that is, the lumen of the ventricle. biological_process GO:0022027 interkinetic nuclear migration GO:0022027 The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. biological_process GO:0022402 cell cycle process GO:0022402 A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. https://github.com/geneontology/go-ontology/issues/27054 jl 2012-09-19T15:56:06Z GO:0044702 Wikipedia:Reproduction biological_process single organism reproductive process GO:0022414 reproductive process GO:0022414 The aggregation, arrangement and bonding together of a cellular component. GO:0071844 cell structure assembly cellular component assembly at cellular level biological_process GO:0022607 cellular component assembly GO:0022607 Any process that modulates the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z biological_process regulation of signaling process regulation of signalling process GO:0023051 regulation of signaling GO:0023051 The specification and formation of anisotropic intracellular organization or cell growth patterns. GO:0000283 GO:0030468 cell polarization bud site selection/establishment of cell polarity biological_process GO:0030010 establishment of cell polarity GO:0030010 The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism. Wikipedia:Myofibril cellular_component GO:0030016 myofibril GO:0030016 Assembly of actin filaments by the addition of actin monomers to a filament. actin polymerization biological_process actin polymerizing activity GO:0030041 actin filament polymerization GO:0030041 A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella. Wikipedia:Cell_junction cellular_component GO:0030054 cell junction GO:0030054 Any process that modulates the frequency, rate or extent of endocytosis. biological_process GO:0030100 regulation of endocytosis GO:0030100 The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. https://github.com/geneontology/go-ontology/issues/24390 Wikipedia:Cellular_differentiation biological_process GO:0030154 cell differentiation GO:0030154 The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax. biological_process GO:0030324 lung development GO:0030324 The controlled breakdown of any cell membrane in the context of a normal process such as autophagy. membrane breakdown membrane catabolism membrane degradation biological_process GO:0030397 membrane disassembly GO:0030397 The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter. NIF_Subcellular:sao1770195789 Wikipedia:Axon cellular_component GO:0030424 axon GO:0030424 A neuron projection that has a short, tapering, morphology. Dendrites receive and integrate signals from other neurons or from sensory stimuli, and conduct nerve impulses towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body. NIF_Subcellular:sao1211023249 Wikipedia:Dendrite cellular_component GO:0030425 dendrite GO:0030425 A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. NIF_Subcellular:sao830981606 cellular_component intracellular membrane GO:0031090 organelle membrane GO:0031090 A cilium which may have a variable arrangement of axonemal microtubules and also contains molecular motors. It may beat with a whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface, such as on epithelial cells that line the lumenal ducts of various tissues; or they may display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface to affect asymmetric body plan organization. Motile cilia can be found in single as well as multiple copies per cell. GO:0009434 GO:0031512 motile cilia cellular_component microtubule-based flagellum motile primary cilia motile primary cilium motile secondary cilium nodal cilium GO:0031514 motile cilium GO:0031514 A protein complex that possesses nucleotide-dependent protein kinase activity. The nucleotide can be AMP (in S. pombe and human) or ADP (in S. cerevisiae). 5'-AMP-activated protein kinase complex ADP-activated protein kinase complex AMP-activated protein kinase complex SNF1/AMPK protein kinase complex Snf1 kinase complex Snf1 serine/threonine protein kinase complex cellular_component AMPK complex GO:0031588 nucleotide-activated protein kinase complex GO:0031588 The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential. NIF_Subcellular:sao1124888485 Wikipedia:Neuromuscular_junction cellular_component NMJ motor endplate GO:0031594 In vertebrates, the term 'neuromuscular junction' is limited to synapses targeting skeletal muscle fibers - all of which are cholinergic and excitatory. Both inhibitory and excitatory neuromuscular junctions exist in invertebrates, utilizing a range of neurotransmitters including glutamate, GABA and 5-HT. neuromuscular junction GO:0031594 Any homeostatic process in which an organism releases excess heat to the environment, thereby lowering its internal temperature. biological_process GO:0031653 heat dissipation GO:0031653 Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. NIF_Subcellular:sao1687101204 cellular_component GO:0031965 nuclear membrane GO:0031965 Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope. NIF_Subcellular:sao1045389829 cellular_component GO:0031966 mitochondrial membrane GO:0031966 The outer, i.e. cytoplasm-facing in a cellular organelle, lipid bilayer of an organelle envelope. cellular_component GO:0031968 organelle outer membrane GO:0031968 Any process that modulates the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0032368 regulation of lipid transport GO:0032368 The portion of the photoreceptor cell cilium linking the photoreceptor inner and outer segments. It's considered to be equivalent to the ciliary transition zone. cellular_component photoreceptor cilium GO:0032391 photoreceptor connecting cilium GO:0032391 Any biological process, occurring at the level of a multicellular organism, pertinent to its function. https://github.com/geneontology/go-ontology/issues/27189 jl 2012-09-19T16:07:47Z GO:0044707 GO:0050874 organismal physiological process biological_process single-multicellular organism process GO:0032501 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. multicellular organismal process GO:0032501 A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. jl 2012-12-19T12:21:31Z GO:0044767 development biological_process single-organism developmental process GO:0032502 developmental process GO:0032502 The directed movement of a protein from one location to another within a lipid bilayer. protein translocation within membrane receptor translocation within membrane receptor transport within lipid bilayer biological_process GO:0032594 protein transport within lipid bilayer GO:0032594 The process whose specific outcome is the progression of the lacrimal gland over time, from its formation to the mature structure. The lacrimal gland produces secretions that lubricate and protect the cornea of the eye. biological_process GO:0032808 lacrimal gland development GO:0032808 Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location. https://github.com/geneontology/go-ontology/issues/26424 regulation of localisation biological_process GO:0032879 regulation of localization GO:0032879 A change in the morphology or behavior of a keratinocyte resulting from exposure to an activating factor such as a cellular or soluble ligand. Upon activation, keratinocytes become migratory and hyperproliferative, and produce growth factors and cytokines. biological_process GO:0032980 keratinocyte activation GO:0032980 A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. GO:0043234 macromolecular complex macromolecule complex protein containing complex protein complex protein-protein complex cellular_component GO:0032991 A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. protein-containing complex GO:0032991 A macromolecular complex containing separate protein and lipid molecules. Separate in this context means not covalently bound to each other. cellular_component GO:0032994 Macromolecular complexes in which the lipid component is all covalently bound to protein are not considered protein-lipid complexes. protein-lipid complex GO:0032994 The chemical reactions and pathways leading to the formation of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next. tetrapyrrole anabolism tetrapyrrole biosynthesis tetrapyrrole formation tetrapyrrole synthesis biological_process GO:0033014 tetrapyrrole biosynthetic process GO:0033014 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipid stimulus. biological_process GO:0033993 response to lipid GO:0033993 A cellular process that results in the aggregation, arrangement and bonding together of a set of components to form a cell junction. Reactome:R-HSA-446728 biological_process GO:0034329 cell junction assembly GO:0034329 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell junction. A cell junction is a specialized region of connection between two cells or between a cell and the extracellular matrix. cell junction assembly and maintenance cell junction organisation biological_process cell junction biogenesis GO:0034330 cell junction organization GO:0034330 The directed movement of the male and female pronuclei towards each other prior to their fusion. biological_process GO:0035046 pronuclear migration GO:0035046 The increase in size or mass of an organ. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that function together as to perform a specific function. biological_process GO:0035265 organ growth GO:0035265 The regionalization process that divides an organism or part of an organism into a series of semi-repetitive parts, or segments, often arranged along a longitudinal axis. Wikipedia:Segmentation_(biology) biological_process GO:0035282 segmentation GO:0035282 The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. bf 2010-05-14T01:14:37Z GO:0007242 GO:0007243 GO:0023013 GO:0023034 intracellular signal transduction pathway signal transmission via intracellular cascade biological_process intracellular signaling cascade intracellular signaling pathway GO:0035556 intracellular signal transduction GO:0035556 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lack of contact with other members of the same species. bf 2011-06-22T09:39:57Z response to social isolation biological_process GO:0035900 response to isolation stress GO:0035900 A membrane-tethered, short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum) that is similar in structure to a centriole and derives from it. The cilium basal body is the site of assembly and remodeling of the cilium and serves as a nucleation site for axoneme growth. As well as anchoring the cilium, it is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport. bf 2011-12-15T10:40:20Z GO:0005932 basal body NIF_Subcellular:sao11978067 cilial basal body cilium basal body kinetosome microtubule basal body cellular_component GO:0036064 In most eukaryotic cells, 'ciliary basal body' (GO:0036064) and 'centriole' (GO:0005814) represent a common entity that cycles through its function in cell division, then ciliogenesis, then cell division again. However, these structures are modified extensively as they transition into each other, and may contain different proteins, specific to each component. ciliary basal body GO:0036064 The trafficking of synaptic vesicles from the pre-synaptic membrane so the vesicle can dock and prime for another round of exocytosis and neurotransmitter release. Recycling occurs after synaptic vesicle exocytosis, and is necessary to replenish presynaptic vesicle pools, sustain transmitter release and preserve the structural integrity of the presynaptic membrane. Recycling can occur following transient fusion with the presynaptic membrane (kiss and run), or via endocytosis of presynaptic membrane. bf 2014-06-26T11:03:08Z kiss-and-run synaptic vesicle recycling kiss-and-stay synaptic vesicle recycling biological_process GO:0036465 synaptic vesicle recycling GO:0036465 The series of molecular signals initiated by binding of a ligand to a member of the ERBB family of receptor tyrosine kinases on the surface of a cell, and ending with the regulation of a downstream cellular process, e.g. transcription. bf 2012-03-30T09:23:01Z EGF receptor family signaling pathway ERBB signalling pathway ErbB signaling biological_process EGFR family signaling pathway GO:0038127 ERBB signaling pathway GO:0038127 The series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor ERBB2 on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription. ERBB2 receptors are themselves unable to bind to ligands, but act as a signal-amplifying tyrosine kinase within a heterodimeric pair. bf 2012-03-30T10:05:12Z Reactome:R-HSA-1227986 ERBB2 signalling pathway HER2 signaling pathway NEU signaling receptor tyrosine-protein kinase erbB-2 signaling pathway biological_process GO:0038128 ERBB2 signaling pathway GO:0038128 The series of molecular signals initiated by binding of a ligand to an epidermal growth factor receptor (EGFR/ERBB1) on the surface of a cell, followed by transmission of the signal by a heterodimeric complex of ERBB2 and EGFR. ERBB2, which does not bind any known ligand, is activated through formation of a heterodimer with another ligand-activated ERBB family member such as EGFR. bf 2012-03-30T11:16:28Z EGFR-HER2 signaling pathway ERBB2-EGFR signalling pathway biological_process GO:0038134 ERBB2-EGFR signaling pathway GO:0038134 The increase in size or mass of an entire organism, a part of an organism or a cell. GO:0048590 biological_process growth pattern non-developmental growth GO:0040007 See also the biological process term 'cell growth ; GO:0016049'. growth GO:0040007 Self-propelled movement of a cell or organism from one location to another. biological_process GO:0040011 locomotion GO:0040011 A process that modulates the frequency, rate or extent of gene expression through chromatin remodeling either by modifying higher order chromatin fiber structure, nucleosomal histones, or cytosine methylation of DNA. Once established, this regulation may be maintained over many cell divisions. It can also be heritable in the absence of the instigating signal. https://github.com/geneontology/go-ontology/issues/22201 https://github.com/geneontology/go-ontology/issues/24794 Reactome:R-HSA-212165 Reactome:R-HSA-8986944 regulation of gene expression, epigenetic biological_process GO:0040029 epigenetic regulation of gene expression GO:0040029 The behavior of an organism in response to an odor. behavioral response to scent behavioral response to smell behavioural response to odour behavioural response to scent behavioural response to smell olfactory behaviour biological_process GO:0042048 olfactory behavior GO:0042048 The series of events that restore integrity to a damaged tissue, following an injury. Wikipedia:Wound_healing biological_process GO:0042060 wound healing GO:0042060 The process that results in the generation of glial cells. This includes the production of glial progenitors and their differentiation into mature glia. glial cell generation biological_process GO:0042063 gliogenesis GO:0042063 A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. Wikipedia:T_cell_receptor T lymphocyte receptor complex T-cell receptor complex T-lymphocyte receptor complex TCR complex cellular_component TCR GO:0042101 T cell receptor complex GO:0042101 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. https://github.com/geneontology/go-ontology/issues/23112 kmv 2014-08-21T15:05:45Z GO:1903362 GO:2000598 regulation of cellular protein breakdown regulation of cellular protein catabolic process regulation of cellular protein catabolism regulation of cellular protein degradation regulation of protein breakdown regulation of protein catabolism regulation of protein degradation regulation of cyclin breakdown regulation of cyclin catabolic process regulation of cyclin catabolism regulation of cyclin degradation regulation of degradation of cyclin biological_process GO:0042176 regulation of protein catabolic process GO:0042176 Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process. https://github.com/geneontology/go-ontology/issues/23112 GO:1903363 GO:2000599 down regulation of cellular protein breakdown down regulation of cellular protein catabolic process down regulation of cellular protein catabolism down regulation of cellular protein degradation down regulation of protein catabolic process down-regulation of cellular protein breakdown down-regulation of cellular protein catabolic process down-regulation of cellular protein catabolism down-regulation of cellular protein degradation down-regulation of protein catabolic process downregulation of cellular protein breakdown downregulation of cellular protein catabolic process downregulation of cellular protein catabolism downregulation of cellular protein degradation downregulation of protein catabolic process negative regulation of cellular protein breakdown negative regulation of cellular protein catabolic process negative regulation of cellular protein catabolism negative regulation of cellular protein degradation negative regulation of protein breakdown negative regulation of protein catabolism negative regulation of protein degradation inhibition of cellular protein breakdown inhibition of cellular protein catabolic process inhibition of cellular protein catabolism inhibition of cellular protein degradation inhibition of protein catabolic process biological_process GO:0042177 negative regulation of protein catabolic process GO:0042177 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. response to chemical stimulus response to chemical substance biological_process GO:0042221 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to chemical GO:0042221 Development of a photoreceptor, a sensory cell in the eye that reacts to the presence of light. They usually contain a pigment that undergoes a chemical change when light is absorbed, thus stimulating a nerve. biological_process GO:0042462 eye photoreceptor cell development GO:0042462 The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s). A tooth is any hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food. GO:0042477 Wikipedia:Odontogenesis odontogeny odontosis tooth morphogenesis odontogenesis of calcareous or chitinous tooth biological_process tooth development GO:0042476 odontogenesis GO:0042476 Any biological process involved in the maintenance of an internal steady state. GO:0032844 GO:0032845 GO:0032846 homeostasis activation of homeostatic process inhibition of homeostatic process biological_process negative regulation of homeostatic process positive regulation of homeostatic process regulation of homeostatic process GO:0042592 homeostatic process GO:0042592 The cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair; one of the collection or mass of filaments growing from the skin of an animal, and forming a covering for a part of the head or for any part or the whole of the body. biological_process GO:0042633 hair cycle GO:0042633 The part of the circadian sleep/wake cycle where the organism is not asleep. biological_process GO:0042746 circadian sleep/wake cycle, wakefulness GO:0042746 A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. NIF_Subcellular:sao867568886 neuron process neuron protrusion neuronal cell projection neurite cellular_component nerve fiber GO:0043005 neuron projection GO:0043005 The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/26424 GO:0034960 GO:0043283 GO:0044259 biopolymer metabolic process macromolecule metabolism organismal macromolecule metabolism multicellular organismal macromolecule metabolic process biological_process GO:0043170 macromolecule metabolic process GO:0043170 A small, membranous protrusion from a dendrite that forms a postsynaptic compartment, typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable:they can be thin, stubby, mushroom, or branched, with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity. NIF_Subcellular:sao1799103720 Wikipedia:Dendritic_spine dendrite spine branched dendritic spine mushroom dendritic spine sessile dendritic spine stubby dendritic spine thin dendritic spine cellular_component GO:0043197 dendritic spine GO:0043197 Cylindric portion of the dendrite, directly stemming from the perikaryon, and carrying the dendritic spines. NIF_Subcellular:sao2034472720 cellular_component trunk GO:0043198 dendritic shaft GO:0043198 Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. NIF_Subcellular:sao1539965131 Wikipedia:Organelle cellular_component GO:0043226 organelle GO:0043226 Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. https://github.com/geneontology/go-ontology/issues/28153 NIF_Subcellular:sao414196390 membrane-enclosed organelle cellular_component GO:0043227 membrane-bounded organelle GO:0043227 Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. https://github.com/geneontology/go-ontology/issues/28153 cellular_component GO:0043229 intracellular organelle GO:0043229 Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. intracellular membrane-enclosed organelle cellular_component GO:0043231 intracellular membrane-bounded organelle GO:0043231 Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. https://github.com/geneontology/go-ontology/issues/29106 intracellular non-membrane-bounded organelle intracellular non-membrane-enclosed organelle cellular_component GO:0043232 intracellular membraneless organelle GO:0043232 Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle. https://github.com/geneontology/go-ontology/issues/27281 contractile fibre cellular_component GO:0043292 contractile muscle fiber GO:0043292 A functional unit located near the cell apex at the points of contact between epithelial cells, which in vertebrates is composed of the tight junction, the zonula adherens, and desmosomes and in some invertebrates, such as Drosophila, is composed of the subapical complex (SAC), the zonula adherens and the septate junction. Functions in the regulation of cell polarity, tissue integrity and intercellular adhesion and permeability. apical cell junction complex apical junction cellular_component GO:0043296 apical junction complex GO:0043296 Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. https://github.com/geneontology/go-ontology/issues/22580 mah 2010-09-08T10:01:42Z GO:0034600 GO:0034621 GO:0071822 protein complex subunit organisation protein complex subunit organization biological_process cellular macromolecular complex organization cellular macromolecular complex subunit organisation cellular macromolecular complex subunit organization macromolecular complex organization macromolecular complex subunit organisation macromolecular complex subunit organization protein-containing complex subunit organization GO:0043933 protein-containing complex organization GO:0043933 The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues. glucan metabolism biological_process GO:0044042 glucan metabolic process GO:0044042 The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections. jl 2010-02-05T10:37:16Z FBbt:00005107 FMA:67301 Wikipedia:Cell_body cell soma cellular_component GO:0044297 Note that 'cell body' and 'cell soma' are not used in the literature for cells that lack projections, nor for some cells (e.g. yeast with mating projections) that do have projections. cell body GO:0044297 A small membranous protrusion, often ending in a bulbous head and attached to the neuron by a narrow stalk or neck. jl 2010-02-05T04:25:10Z spine NIF_Subcellular:sao1145756102 cellular_component GO:0044309 neuron spine GO:0044309 A type of intermediate filament, typically made up of one or more of the proteins vimentin, desmin, glial fibrillary acidic protein (GFAP), and peripherin. Unlike the keratins, the type III proteins can form both homo- and heteropolymeric IF filaments. desmin glial fibrillary acidic protein peripherin type III intermediate filament associated protein vimentin cellular_component GO:0045098 type III intermediate filament GO:0045098 The directed movement of a protein to a specific location. establishment of protein localisation protein positioning protein recruitment biological_process GO:0045184 establishment of protein localization GO:0045184 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ether stimulus. biological_process GO:0045472 response to ether GO:0045472 An epigenetic process that silences gene expression at specific genomic regions through chromatin remodeling either by modifying higher order chromatin fiber structure, nucleosomal histones, or the cytosine DNA methylation. https://github.com/geneontology/go-ontology/issues/22201 Reactome:R-HSA-212300 Reactome:R-HSA-5250941 down regulation of gene expression, epigenetic down-regulation of gene expression, epigenetic downregulation of gene expression, epigenetic inhibition of gene expression, epigenetic biological_process gene silencing GO:0045814 negative regulation of gene expression, epigenetic GO:0045814 Any process that modulates the frequency, rate or extent of the regulated release of a hormone from a cell. biological_process GO:0046883 regulation of hormone secretion GO:0046883 The directed movement of substances within a cell. jl 2013-12-18T14:04:50Z GO:1902582 biological_process single organism intracellular transport single-organism intracellular transport GO:0046907 intracellular transport GO:0046907 The creation of two or more organelles by division of one organelle. biological_process GO:0048285 organelle fission GO:0048285 Any process that establishes the spatial arrangement of mitochondria between and within cells. https://github.com/geneontology/go-ontology/issues/28919 distribution of mitochondria mitochondrial distribution biological_process positioning of mitochondria GO:0048311 mitochondrion distribution GO:0048311 The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place. https://github.com/geneontology/go-ontology/issues/24390 biological_process terminal differentiation GO:0048468 cell development GO:0048468 The specific behavior of an organism that recurs with a regularity of approximately 24 hours. circadian rhythm behavior biological_process GO:0048512 circadian behavior GO:0048512 Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. https://github.com/geneontology/go-ontology/issues/25943 Wikipedia:Organogenesis development of an organ organogenesis biological_process GO:0048513 animal organ development GO:0048513 Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051242 positive regulation of cellular physiological process up regulation of cellular process up-regulation of cellular process upregulation of cellular process activation of cellular process stimulation of cellular process biological_process GO:0048522 positive regulation of cellular process GO:0048522 Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051243 down regulation of cellular process down-regulation of cellular process downregulation of cellular process negative regulation of cellular physiological process inhibition of cellular process biological_process GO:0048523 negative regulation of cellular process GO:0048523 The process whose specific outcome is the progression of lymph nodes over time, from their formation to the mature structure. A lymph node is a round, oval, or bean shaped structure localized in clusters along the lymphatic vessels, with a distinct internal structure including specialized vasculature and B- and T-zones for the activation of lymphocytes. lymph gland development biological_process GO:0048535 lymph node development GO:0048535 The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. formation of an anatomical structure involved in morphogenesis biological_process GO:0048646 Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense. anatomical structure formation involved in morphogenesis GO:0048646 The process in which the structures of a neuron are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a neuron. neuron morphogenesis involved in differentiation biological_process GO:0048667 cell morphogenesis involved in neuron differentiation GO:0048667 The process whose specific outcome is the progression of a gland over time, from its formation to the mature structure. A gland is an organ specialised for secretion. biological_process GO:0048732 gland development GO:0048732 The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. https://github.com/geneontology/go-ontology/issues/26424 development of an anatomical structure biological_process GO:0048856 anatomical structure development GO:0048856 A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. biological_process GO:0048869 cellular developmental process GO:0048869 Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. https://github.com/geneontology/go-ontology/issues/19809 cell locomotion movement of a cell biological_process cell movement GO:0048870 cell motility GO:0048870 Any process involved in the maintenance of an internal steady state at the level of the multicellular organism. biological_process GO:0048871 multicellular organismal-level homeostasis GO:0048871 Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0050791 regulation of physiological process biological_process GO:0050789 regulation of biological process GO:0050789 Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051244 regulation of cellular physiological process biological_process GO:0050794 regulation of cellular process GO:0050794 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell). synapse organisation biological_process synapse development synapse morphogenesis synapse organization and biogenesis GO:0050808 synapse organization GO:0050808 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GO:0051869 physiological response to stimulus biological_process GO:0050896 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stimulus GO:0050896 Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0051049 regulation of transport GO:0051049 The cell cycle process in which the controlled breakdown of the nuclear membranes during meiotic cell division occurs. biological_process meiotic nuclear envelope breakdown meiotic nuclear envelope catabolism meiotic nuclear envelope degradation meiotic nuclear envelope disassembly GO:0051078 meiotic nuclear membrane disassembly GO:0051078 The controlled breakdown of the nuclear membranes during the first division of meiosis. biological_process meiosis I nuclear envelope breakdown meiosis I nuclear envelope catabolism meiosis I nuclear envelope degradation meiosis I nuclear envelope disassembly GO:0051079 meiosis I nuclear membrane disassembly GO:0051079 The controlled breakdown of the nuclear membranes, for example during cellular division. biological_process nuclear envelope breakdown nuclear envelope catabolism nuclear envelope degradation nuclear envelope disassembly GO:0051081 nuclear membrane disassembly GO:0051081 Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. regulation of cellular component organisation biological_process regulation of cell organisation regulation of cell organization regulation of cellular component organization and biogenesis GO:0051128 regulation of cellular component organization GO:0051128 Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. positive regulation of cell organisation up regulation of cell organization up-regulation of cell organization upregulation of cell organization activation of cell organization stimulation of cell organization biological_process positive regulation of cellular component organization and biogenesis GO:0051130 positive regulation of cellular component organization GO:0051130 Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. https://github.com/geneontology/go-ontology/issues/27052 jl 2013-12-18T13:51:04Z GO:1902578 establishment and maintenance of localization establishment and maintenance of position localisation establishment and maintenance of cellular component location establishment and maintenance of substance location establishment and maintenance of substrate location biological_process single organism localization single-organism localization GO:0051179 localization GO:0051179 Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. https://github.com/geneontology/go-ontology/issues/24200 establishment of localisation biological_process GO:0051234 establishment of localization GO:0051234 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein. https://github.com/geneontology/go-ontology/issues/23112 GO:0032268 regulation of protein metabolism biological_process regulation of cellular protein metabolic process regulation of cellular protein metabolism GO:0051246 regulation of protein metabolic process GO:0051246 Any process that stops, prevents, or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein. https://github.com/geneontology/go-ontology/issues/23112 GO:0032269 down regulation of cellular protein metabolic process down regulation of protein metabolic process down-regulation of cellular protein metabolic process down-regulation of protein metabolic process downregulation of cellular protein metabolic process downregulation of protein metabolic process negative regulation of cellular protein metabolic process negative regulation of cellular protein metabolism negative regulation of protein metabolism inhibition of cellular protein metabolic process inhibition of protein metabolic process biological_process GO:0051248 negative regulation of protein metabolic process GO:0051248 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. Wikipedia:Cell_division biological_process GO:0051301 Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division. cell division GO:0051301 Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions. https://github.com/geneontology/go-ontology/issues/24599 GO:0007126 Wikipedia:Meiosis biological_process meiosis GO:0051321 Note that this term should not be confused with 'GO:0140013 ; meiotic nuclear division'. 'GO:0051321 ; meiotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140013 meiotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. meiotic cell cycle GO:0051321 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a calcium ion stimulus. response to Ca2+ ion biological_process GO:0051592 response to calcium ion GO:0051592 Any process in which an organelle is transported to, and/or maintained in, a specific location. https://github.com/geneontology/go-ontology/issues/19809 establishment and maintenance of organelle localization organelle localisation biological_process GO:0051640 organelle localization GO:0051640 A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane. https://github.com/geneontology/go-ontology/issues/27189 jl 2013-12-18T14:04:32Z GO:1902580 cellular localisation establishment and maintenance of cellular localization establishment and maintenance of localization in cell or cell membrane single organism cellular localization intracellular localization localization within cell biological_process single-organism cellular localization GO:0051641 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular localization GO:0051641 Any process in which the nucleus is transported to, and/or maintained in, a specific location within the cell. cell nucleus localization establishment and maintenance of nucleus localization localization of nucleus nucleus localisation biological_process GO:0051647 nucleus localization GO:0051647 Any process, occurring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. establishment of localisation in cell establishment of intracellular localization establishment of localization within cell positioning within cell biological_process establishment of cellular localization GO:0051649 establishment of localization in cell GO:0051649 The directed movement of an organelle to a specific location. establishment of organelle localisation biological_process GO:0051656 establishment of organelle localization GO:0051656 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism. GO:0009613 GO:0042828 biological_process GO:0051707 response to other organism GO:0051707 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. Reactome:R-HSA-8953897 biological_process GO:0051716 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular response to stimulus GO:0051716 Any process that modulates the rate or extent of progression through the cell cycle. GO:0000074 GO:0007050 GO:0071156 GO:0071157 GO:0071158 GO:0071850 Reactome:R-HSA-156711 Reactome:R-HSA-380972 cell cycle modulation cell cycle regulation control of cell cycle progression modulation of cell cycle progression regulation of cell cycle progression regulation of progression through cell cycle arrest of mitotic cell cycle progression cell cycle arrest mitotic cell cycle arrest negative regulation of cell cycle arrest positive regulation of cell cycle arrest regulation of cell cycle arrest biological_process cell cycle regulator tumor suppressor GO:0051726 regulation of cell cycle GO:0051726 Any process that activates, maintains or increases the frequency, rate or extent of synaptic structural plasticity. up regulation of synapse structural plasticity up-regulation of synapse structural plasticity upregulation of synapse structural plasticity activation of synapse structural plasticity stimulation of synapse structural plasticity biological_process GO:0051835 positive regulation of synapse structural plasticity GO:0051835 The process in which the potential difference across the mitochondrial membrane is reduced from its steady state level. mitochondria depolarization mitochondrial depolarisation mitochondrial membrane depolarization mitochondrion depolarization biological_process GO:0051882 mitochondrial depolarization GO:0051882 The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. GO:0002073 retina development in camera-style eye biological_process retinal development GO:0060041 retina development in camera-type eye GO:0060041 The portion of the plasma membrane surrounding a cilium. GO:0020017 cilial membrane cilium membrane flagellar membrane flagellum membrane cellular_component GO:0060170 Note that cilia and eukaryotic flagella are deemed to be equivalent. ciliary membrane GO:0060170 The process in which a relatively unspecialized cell acquires the specialized features of a retinal rod cell. biological_process GO:0060221 retinal rod cell differentiation GO:0060221 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0060255 regulation of macromolecule metabolic process GO:0060255 The process of creating a trabecula in an organ. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue. trabeculation biological_process trabecula biogenesis GO:0060343 trabecula formation GO:0060343 The process whose specific outcome is the progression of an epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure. biological_process GO:0060429 epithelium development GO:0060429 The increase in size or mass of a lung. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax. biological_process GO:0060437 lung growth GO:0060437 The process whose specific outcome is the progression of a trachea over time, from its formation to the mature structure. The trachea is the portion of the airway that attaches to the bronchi as it branches. biological_process GO:0060438 trachea development GO:0060438 Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell. dph 2009-05-18T02:29:43Z biological_process GO:0060627 regulation of vesicle-mediated transport GO:0060627 The developmental process pertaining to the initial formation of a submandibular salivary gland. This process begins with a thickening of the epithelium next to the tongue and ends when a bud linked to the oral surface is formed. dph 2009-06-01T08:07:16Z biological_process GO:0060661 submandibular salivary gland formation GO:0060661 The process in which a venous blood vessel endothelial cell acquires specialized features of a lymphatic vessel endothelial cell, a thin flattened cell that lines the inside surfaces of lymph vessels. dph 2009-08-11T03:45:20Z biological_process GO:0060836 lymphatic endothelial cell differentiation GO:0060836 The process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission. dph 2010-01-20T09:06:33Z biological_process GO:0060996 dendritic spine development GO:0060996 A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. jl 2010-02-08T02:43:11Z GO:0016044 GO:0044802 Reactome:R-HSA-199991 cellular membrane organisation cellular membrane organization membrane organisation biological_process membrane organization and biogenesis single-organism membrane organization GO:0061024 membrane organization GO:0061024 The progression of a somite from its initial formation to the mature structure. Somites are mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo. dph 2010-03-02T12:05:13Z biological_process GO:0061053 somite development GO:0061053 The progression of the sclerotome over time, from its initial formation to the mature structure. The sclerotome is the portion of the somite that will give rise to a vertebra. dph 2010-03-02T12:12:40Z biological_process GO:0061056 sclerotome development GO:0061056 The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex. https://github.com/geneontology/go-ontology/issues/22580 GO:0006461 GO:0034622 GO:0043623 cellular protein complex assembly biological_process cellular macromolecule complex assembly cellular protein-containing complex assembly chaperone activity macromolecular complex assembly macromolecule complex assembly protein complex assembly protein complex formation GO:0065003 protein-containing complex assembly GO:0065003 The aggregation, arrangement and bonding together of proteins and lipids to form a protein-lipid complex. biological_process GO:0065005 protein-lipid complex assembly GO:0065005 Any process that modulates a measurable attribute of any biological process, quality or function. regulation biological_process GO:0065007 biological regulation GO:0065007 Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc. regulation of biological attribute regulation of biological characteristic biological_process GO:0065008 regulation of biological quality GO:0065008 The process whose specific outcome is the progression of the Harderian gland over time, from its formation to the mature structure. The Harderian gland is an anterior orbital structure usually associated with the nictitating membrane, and produces and secretes a variety of substances to the eye, depending upon the species. biological_process GO:0070384 Note that the Harderian gland is found in all terrestrial vertebrate groups, including amphibia, reptiles, birds, and mammals. However, it appears to be absent in certain mammals such as bats, cows, horses, and higher primates. Though largely absent in the adult human, it is present in the fetal and neonatal stages. Harderian gland development GO:0070384 A protein complex that contains the epidermal growth factor receptor (EGFR) and Grb2, and is involved in linking EGFR activation to the p21-Ras pathway. Grb2-Egfr complex, EGF stimulated cellular_component GO:0070436 Grb2-EGFR complex GO:0070436 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fatty acid stimulus. biological_process GO:0070542 response to fatty acid GO:0070542 The cell cycle process in which the sister chromatids of a replicated chromosome are joined along the length of the centromeric region of the chromosome. mah 2009-04-28T04:31:00Z sister chromatid cohesion at centromere biological_process GO:0070601 centromeric sister chromatid cohesion GO:0070601 Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. mah 2009-06-16T04:08:29Z cellular macromolecule localisation biological_process GO:0070727 cellular macromolecule localization GO:0070727 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. mah 2009-08-27T04:41:45Z biological_process GO:0070887 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular response to chemical stimulus GO:0070887 The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. mah 2009-09-15T03:00:51Z biological_process GO:0070925 organelle assembly GO:0070925 The establishment, maintenance and elaboration of the left/right axis. The left/right axis is defined by a line that runs orthogonal to both the anterior/posterior and dorsal/ventral axes. Each side is defined from the viewpoint of the organism rather of the observer (as per anatomical axes). mah 2009-10-29T01:43:34Z left-right axis specification biological_process left/right axis determination GO:0070986 left/right axis specification GO:0070986 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ether stimulus. mah 2009-12-11T03:03:22Z biological_process GO:0071362 cellular response to ether GO:0071362 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipid stimulus. mah 2009-12-11T04:37:10Z biological_process GO:0071396 cellular response to lipid GO:0071396 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fatty acid stimulus. mah 2009-12-11T04:39:56Z biological_process GO:0071398 cellular response to fatty acid GO:0071398 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a temperature stimulus. mah 2009-12-18T02:56:45Z cellular response to thermal stimulus biological_process GO:0071502 cellular response to temperature stimulus GO:0071502 The process in which calcium salts, mainly carbonated hydroxyapatite, are deposited into the initial acellular cementum. mah 2010-01-07T04:18:54Z biological_process cementum formation GO:0071529 cementum mineralization GO:0071529 The process whose specific outcome is the progression of the filament over time, from its formation to the mature structure. Filament is the stalk of a stamen. dhl 2009-04-22T03:12:03Z filament development biological_process GO:0080086 stamen filament development GO:0080086 A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. pr 2011-11-23T09:45:24Z Reactome:R-HSA-75153 execution phase of apoptotic process apoptosis biological_process GO:0097194 execution phase of apoptosis GO:0097194 A protein complex that contains G protein-coupled receptors. pr 2014-09-10T09:14:30Z G-protein coupled receptor complex cellular_component GO:0097648 G protein-coupled receptor complex GO:0097648 Any vesicle that is part of the intracellular region. pr 2016-03-29T17:39:45Z cellular_component GO:0097708 intracellular vesicle GO:0097708 A cilium which may have a variable array of axonemal microtubules but does not contain molecular motors. pr 2016-09-29T14:02:11Z GO:0031513 immotile cilium nonmotile cilium cellular_component immotile primary cilium nonmotile primary cilia nonmotile primary cilium sensory cilium GO:0097730 non-motile cilium GO:0097730 A specialised 9+0 non-motile cilium found in photoreceptor cells. A ciliary transition zone called 'photoreceptor connecting cilium' links the photoreceptor outer segment to the inner segment. pr 2016-09-30T10:50:11Z photoreceptor cilium cellular_component GO:0097733 photoreceptor cell cilium GO:0097733 Any process that modulates the diameter of blood vessels. https://github.com/geneontology/go-ontology/issues/12253 pr 2016-11-24T15:45:05Z GO:0042312 GO:0050880 blood vessel diameter homeostasis regulation of blood vessel diameter biological_process regulation of blood vessel size regulation of vasodilatation regulation of vasodilation GO:0097746 blood vessel diameter maintenance GO:0097746 Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism. https://github.com/geneontology/go-ontology/issues/22173 dos 2013-11-11T12:59:11Z GO:0009814 defence response incompatible interaction defence response to pathogen, incompatible interaction defense response, incompatible interaction resistance response to pathogen biological_process GO:0098542 defense response to other organism GO:0098542 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a virus. dos 2014-01-24T14:54:08Z biological_process GO:0098586 cellular response to virus GO:0098586 The lipid bilayer that forms the outer-most layer of an organelle. dos 2014-02-26T13:41:31Z cellular_component GO:0098588 Examples include the outer membranes of double membrane bound organelles such as mitochondria as well as the bounding membranes of single-membrane bound organelles such as lysosomes. bounding membrane of organelle GO:0098588 The attachment of one cell to another cell via adhesion molecules. dos 2014-04-16T13:40:03Z GO:0016337 biological_process single organismal cell-cell adhesion GO:0098609 cell-cell adhesion GO:0098609 The process whose specific outcome is the progression of the skin epidermis over time, from its formation to the mature structure. biological_process GO:0098773 skin epidermis development GO:0098773 Any protein complex that is part of a membrane. cellular_component GO:0098796 membrane protein complex GO:0098796 Any protein complex that is part of the plasma membrane. cellular_component GO:0098797 plasma membrane protein complex GO:0098797 Any protein complex that is part of the plasma membrane and which functions as a signaling receptor. cellular_component GO:0098802 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. plasma membrane signaling receptor complex GO:0098802 The directed movement of organelles or molecules along microtubules in axons. Wikipedia:Axoplasmic_transport axon cargo transport axoplasmic transport biological_process GO:0098930 axonal transport GO:0098930 A defense response of that serves to clear host cells of foreign DNA and RNA. It has three distinct stage: acquisition of foreign DNA by integration into CRISPR loci in the host chromosome, CRISPR RNA (crRNA) biogenesis, and target interference. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeat, which describes the nature of the loci. https://github.com/geneontology/go-ontology/issues/10994 biological_process GO:0099048 CRISPR-cas system GO:0099048 A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber. cellular_component GO:0099080 supramolecular complex GO:0099080 A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure. GO:0043205 cellular_component fibril GO:0099512 supramolecular fiber GO:0099512 A component of the cytoskeleton consisting of a homo or heteropolymeric fiber constructed from an indeterminate number of protein subunits. cellular_component GO:0099513 polymeric cytoskeletal fiber GO:0099513 A type of synapse occurring between an axon and a dendritic spine. hjd 2017-07-05T19:20:48Z dendritic spine synapse cellular_component GO:0106033 spine synapse GO:0106033 A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses. https://github.com/geneontology/go-ontology/issues/24200 https://github.com/geneontology/go-ontology/issues/26424 https://github.com/geneontology/go-ontology/issues/28978 kmv 2019-08-12T18:01:37Z cellular anatomical entity cellular_component GO:0110165 cellular anatomical structure GO:0110165 A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13193 krc 2017-03-21T17:26:07Z cellular_component GO:0120025 plasma membrane bounded cell projection GO:0120025 One of the two nuclear divisions that occur as part of the meiotic cell cycle. https://github.com/geneontology/go-ontology/issues/19910 pg 2017-03-23T09:40:00Z meiosis biological_process GO:0140013 meiotic nuclear division GO:0140013 A protein-containing complex located intracellularly. https://github.com/geneontology/go-ontology/issues/19952 pg 2020-10-28T14:40:16Z cellular_component GO:0140535 intracellular protein-containing complex GO:0140535 The chemical reactions or pathway resulting in the formation of phycocyanobilin, which involves the oxidative cleavage of heme by a heme oxygenase (HO) to form biliverdin IX alpha. Biliverdin IX alpha is subsequently converted to phycocyanobilin by a ferredoxin-dependent oxidoreductase (PCYA). https://github.com/geneontology/go-ontology/issues/20941 pg 2021-02-24T10:02:19Z phycocyanobilin biosynthesis biological_process GO:0140609 phycocyanobilin biosynthetic process GO:0140609 An intracellular signaling module that is part of larger signaling pathways that can be initiated either intracellularly or by cell surface receptors. Intracellular signaling cassettes are discrete signaling units that are often shared by multiple signaling pathways. https://github.com/geneontology/go-ontology/issues/26557 pg 2023-12-04T14:13:20Z intracellular signaling cascade intracellular signaling module biological_process GO:0141124 intracellular signaling cassette GO:0141124 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oxygen-containing compound stimulus. https://github.com/geneontology/go-ontology/issues/27194 pr 2012-12-13T15:11:37Z response to oxygen molecular entity biological_process GO:1901700 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to oxygen-containing compound GO:1901700 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oxygen-containing compound stimulus. pr 2012-12-13T15:11:42Z cellular response to oxygen molecular entity biological_process GO:1901701 cellular response to oxygen-containing compound GO:1901701 A protein complex which is capable of catalytic activity. https://github.com/geneontology/go-ontology/issues/19980 bhm 2013-11-13T16:18:47Z enzyme complex cellular_component GO:1902494 catalytic complex GO:1902494 A protein complex which is capable of protein kinase activity. bhm 2014-04-17T13:52:40Z cellular_component GO:1902911 An example of this is PKM2 in human (P14618) in PMID:24606918 (inferred from direct assay). protein kinase complex GO:1902911 A process that is part of the meiotic cell cycle. jl 2014-05-22T14:22:28Z biological_process GO:1903046 meiotic cell cycle process GO:1903046 Any process that modulates the frequency, rate or extent of secretion by cell. pm 2014-10-08T13:24:59Z regulation of cellular secretion biological_process GO:1903530 regulation of secretion by cell GO:1903530 Any process that modulates the frequency, rate or extent of G protein-coupled receptor internalization. pga 2015-03-10T17:10:45Z regulation of G-protein-coupled receptor internalization biological_process GO:1904020 regulation of G protein-coupled receptor internalization GO:1904020 Any process that modulates the frequency, rate or extent of protein catabolic process in the vacuole. rl 2015-06-12T09:10:36Z biological_process regulation of vacuolar protein breakdown regulation of vacuolar protein catabolic process regulation of vacuolar protein catabolism regulation of vacuolar protein degradation GO:1904350 regulation of protein catabolic process in the vacuole GO:1904350 Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process in the vacuole. rl 2015-06-12T09:10:42Z down regulation of protein catabolic process in the vacuole down-regulation of protein catabolic process in the vacuole downregulation of protein catabolic process in the vacuole inhibition of protein catabolic process in the vacuole biological_process down regulation of vacuolar protein breakdown down regulation of vacuolar protein catabolic process down regulation of vacuolar protein catabolism down regulation of vacuolar protein degradation down-regulation of vacuolar protein breakdown down-regulation of vacuolar protein catabolic process down-regulation of vacuolar protein catabolism down-regulation of vacuolar protein degradation downregulation of vacuolar protein breakdown downregulation of vacuolar protein catabolic process downregulation of vacuolar protein catabolism downregulation of vacuolar protein degradation inhibition of vacuolar protein breakdown inhibition of vacuolar protein catabolic process inhibition of vacuolar protein catabolism inhibition of vacuolar protein degradation negative regulation of vacuolar protein breakdown negative regulation of vacuolar protein catabolic process negative regulation of vacuolar protein catabolism negative regulation of vacuolar protein degradation GO:1904351 negative regulation of protein catabolic process in the vacuole GO:1904351 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ionomycin stimulus. sl 2015-08-31T14:39:18Z biological_process GO:1904636 response to ionomycin GO:1904636 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ionomycin stimulus. sl 2015-08-31T14:39:25Z biological_process GO:1904637 cellular response to ionomycin GO:1904637 Any process that stops, prevents or reduces the frequency, rate or extent of lysosomal protein catabolic process. bf 2016-04-26T12:10:10Z down regulation of cellular protein breakdown in lysosome down regulation of cellular protein catabolic process in lysosome down regulation of cellular protein catabolism in lysosome down regulation of cellular protein degradation in lysosome down regulation of lysosomal protein catabolic process down regulation of lysosomal protein catabolism down regulation of lysosomal protein degradation down-regulation of cellular protein breakdown in lysosome down-regulation of cellular protein catabolic process in lysosome down-regulation of cellular protein catabolism in lysosome down-regulation of cellular protein degradation in lysosome down-regulation of lysosomal protein catabolic process down-regulation of lysosomal protein catabolism down-regulation of lysosomal protein degradation downregulation of cellular protein breakdown in lysosome downregulation of cellular protein catabolic process in lysosome downregulation of cellular protein catabolism in lysosome downregulation of cellular protein degradation in lysosome downregulation of lysosomal protein catabolic process downregulation of lysosomal protein catabolism downregulation of lysosomal protein degradation negative regulation of cellular protein breakdown in lysosome negative regulation of cellular protein catabolic process in lysosome negative regulation of cellular protein catabolism in lysosome negative regulation of cellular protein degradation in lysosome negative regulation of lysosomal protein catabolism negative regulation of lysosomal protein degradation inhibition of cellular protein breakdown in lysosome inhibition of cellular protein catabolic process in lysosome inhibition of cellular protein catabolism in lysosome inhibition of cellular protein degradation in lysosome inhibition of lysosomal protein catabolic process inhibition of lysosomal protein catabolism inhibition of lysosomal protein degradation biological_process down regulation of lysosomal proteolysis down regulation of proteolysis within lysosome down-regulation of lysosomal proteolysis down-regulation of proteolysis within lysosome downregulation of lysosomal proteolysis downregulation of proteolysis within lysosome inhibition of lysosomal proteolysis inhibition of proteolysis within lysosome negative regulation of lysosomal proteolysis negative regulation of proteolysis within lysosome GO:1905166 negative regulation of lysosomal protein catabolic process GO:1905166 The aggregation, arrangement and bonding together of a set of components to form a spine apparatus. bf 2016-08-09T10:12:29Z spine apparatus formation dense material assembly dense material formation biological_process GO:1905355 spine apparatus assembly GO:1905355 A circulatory process that occurs at the level of the lymphatic vasculature. sl 2013-09-10T22:26:40Z biological_process GO:1990183 lymphatic vascular process in circulatory system GO:1990183 Any process that modulates the frequency, rate or extent of steroid hormone secretion. bf 2011-07-26T08:38:46Z biological_process GO:2000831 regulation of steroid hormone secretion GO:2000831 IAO:0000003 measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label IAO:0000006 narrative object Examples of narrative objects are reports, journal articles, and patents submission. A narrative object is an information content entity that is a set of propositions. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions person:Chris Stoeckert OBI_0000013 group:OBI narrative object IAO:0000009 datum label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. datum label IAO:0000013 journal article Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. A report that is published in a journal. PERSON: Alan Ruttenberg PERSON: Chris Stoeckert OBI_0000159 group:OBI journal article IAO:0000017 model number A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers Person: Alan Ruttenberg model number IAO:0000027 data item Data items include counts of things, analyte concentrations, and statistical summaries. An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item IAO:0000028 symbol a serial number such as "12324X" a stop sign a written proper name such as "OBI" An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. 20091104, MC: this needs work and will most probably change 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). PERSON: James A. Overton PERSON: Jonathan Rees based on Oxford English Dictionary symbol IAO:0000029 numeral A symbol that denotes a number. PERSON: Jonathan Rees numeral IAO:0000030 information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 information content entity IAO:0000031 integer numeral A numeral that denotes an integer PERSON: Jonathan Rees integer numeral IAO:0000032 10 feet. 3 ml. A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. PERSON: Alan Ruttenberg PERSON: Melanie Courtot scalar measurement datum IAO:0000033 An information content entity whose concretizations indicate to their bearer how to realize them in a process. 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity IAO:0000088 report Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record). 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted. 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Melanie Courtot GROUP: OBI OBI_0000099 report IAO:0000096 source code module The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script. A source code module is a directive information entity that specifies, using a programming language, some algorithm. person:Alan Ruttenberg person:Chris Stoeckert OBI_0000039 group:OBI source code module IAO:0000098 data format specification A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file" PERSON: Alan Ruttenberg PlanAndPlannedProcess Branch OBI branch derived OBI_0000187 data format specification IAO:0000100 data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set IAO:0000101 image An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. person:Alan Ruttenberg person:Allyson person:Chris Stoeckert OBI_0000030 group:OBI image IAO:0000109 measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum IAO:0000129 version number A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version GROUP: IAO version number IAO:0000131 serial number A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-) GROUP: IAO serial number IAO:0000132 lot number A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots. GROUP: IAO batch number lot number IAO:0000300 textual entity Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. PERSON: Lawrence Hunter text textual entity IAO:0000302 author identification L. Hunter A textual entity intended to identify a particular author PERSON: Lawrence Hunter author identification IAO:0000303 institutional identification University of Colorado Denver School of Medicine A textual entity intended to identify a particular institution PERSON: Lawrence Hunter institutional identification IAO:0000306 table | T F --+----- T | T F F | F F A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions PERSON: Lawrence Hunter table IAO:0000307 table of abbreviations IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology A table where the constituent texts are abbreviations and their expansions PERSON: Lawrence Hunter table of abbreviations IAO:0000308 figure Any picture, diagram or table An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. PERSON: Lawrence Hunter figure IAO:0000310 document A journal article, patent application, laboratory notebook, or a book A collection of information content entities intended to be understood together as a whole PERSON: Lawrence Hunter document IAO:0000311 publication journal article, newspaper story, book, etc. A document that is the output of a publishing process. PERSON: Chris Stoeckert PERSON: Jie Zheng PERSON: Lawrence Hunter published document Revisit the term in Octorber 2020. Improve the defintion. publication IAO:0000312 publication about an investigation Most scientific journal articles A publication that is about an investigation PERSON: Lawrence Hunter scientific publication publication about an investigation IAO:0000313 patent US Patent 6,449,603 A document that has been accepted by a patent authority PERSON: Lawrence Hunter patent IAO:0000327 table of contents A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred). PERSON: Lawrence Hunter table of contents IAO:0000328 table of figures A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred). PERSON: Lawrence Hunter table of figures 1 IAO:0000400 A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 Alan Ruttenberg AR notes: We need to discuss whether it should include site. cartesian spatial coordinate datum http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 1 IAO:0000401 A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region Alan Ruttenberg one dimensional cartesian spatial coordinate datum 1 1 IAO:0000402 A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region Alan Ruttenberg two dimensional cartesian spatial coordinate datum 1 1 1 IAO:0000403 A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region Alan Ruttenberg three dimensional cartesian spatial coordinate datum 1 IAO:0000408 length measurement datum A scalar measurement datum that is the result of measurement of length quality Alan Ruttenberg length measurement datum 1 IAO:0000414 mass measurement datum A scalar measurement datum that is the result of measurement of mass quality 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg mass measurement datum 1 IAO:0000416 time measurement datum A scalar measurement datum that is the result of measuring a temporal interval 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg time measurement datum IAO:0000422 A textual entity that is used as directive to deliver something to a person, or organization 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59 postal address IAO:0000429 email address Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583 Person:Alan Ruttenberg Person:Chris Stoeckart email address IAO:0000442 author role A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name. PERSON: Alan Ruttenberg PERSON: Melanie Courtot author role IAO:0000445 A document that is in preparation for submission to be published. PERSON: Jie Zheng EFO_0001795 in preparation VEuPathDB document in preparation for publication IAO:0000577 The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID symbol Original proposal from Bjoern, discussions at IAO calls centrally registered identifier symbol IAO:0000578 The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID Original proposal from Bjoern, discussions at IAO calls centrally registered identifier IAO:0000579 PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles. A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process. Justin Whorton PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID registry Original proposal from Bjoern, discussions at IAO calls https://github.com/information-artifact-ontology/IAO/issues/237 centrally registered identifier registry IAO:0000582 time stamped measurement datum IAO:0000584 pmid:20604925 - time-lapse live cell microscopy A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time. Alan Ruttenberg experimental time series time sampled measurement data set IAO:0000590 written name "Bill Clinton" "The Eiffel Tower" "United States of America" A textual entity that denotes a particular in reality. PERSON: Bill Hogan https://github.com/information-artifact-ontology/IAO/issues/114 The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name. written name IAO:0000608 author information textual entity From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD. A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. PERSON: Bill Baumgartner author information textual entity IAO:0000610 author summary textual entity From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX. A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). PERSON: Bill Baumgartner Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). author summary textual entity IAO:0000624 funding souce declaration textual entity From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication. A textual entity documenting the source of funding that supported some study. PERSON: Bill Baumgartner funding source declaration textual entity IAO:0000629 keyword textual entity From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): Exon orthology; alternative splicing; exon duplication; intron-exon structure. A textual entity listing keywords indicating the major theme(s) of a document. PERSON: Bill Baumgartner keyword textual entity IAO:0000646 An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail. Mathias Brochhausen postal code IAO:0000648 A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes. Mathias Brochhausen ZIP code zone improvement plan code IAO:0000708 A centrally registered identifier that is issued by ORCID (https://orcid.org/) and used to persistantly identify oneself as a human researcher or contributor. "You can connect your iD with your professional information — affiliations, grants, publications, peer review, and more. You can use your iD to share your information with other systems, ensuring you get recognition for all your contributions, saving you time and hassle, and reducing the risk of errors." [https://orcid.org/] This class was originally defined in Apollo_SV (http://purl.obolibrary.org/obo/APOLLO_SV_00000496) but due to it being more in scope of IAO, it was decided to add it to IAO and deprecate its Apollo_SV equivalent. (2022-10-25) http://orcid.org/0000-0002-1595-3213 ORCID ID ORCiD Open Researcher and Contributor ID Open Researcher and Contributor Identifier https://orcid.org/ https://github.com/information-artifact-ontology/IAO/issues/259 ORCID identifier IAO:0020000 identifier An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. Justin Whorton Mathias Brochhausen proper name https://github.com/information-artifact-ontology/IAO/issues/237 Mathias Brochhausen Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB) identifier IAO:0020015 An identifier referring to an individual entity that is ascribed personhood by the user of the identifier. Justin Whorton Mathias Brochhausen http://en.wikipedia.org/wiki/Personal_name https://github.com/information-artifact-ontology/IAO/issues/237 Personal names "today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names." (http://en.wikipedia.org/wiki/Personal_name) Personal names to not include names of fictional characters, e.g. Sherlock Holmes. Sep 29, 2016: The comment that including the wikipedia definition of personal name is not to be interpreted in a way that restricts this class to only contain strings of letters. A numerical or alphanumerical identifier that denotes a human is being is a personal name, too. (MB) personal name IAO:0020016 A personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name Justin Whorton Mathias Brochhausen first name http://en.wikipedia.org/wiki/Given_name https://github.com/information-artifact-ontology/IAO/issues/237 given name IAO:0020017 An identifier that is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children. Justin Whorton Mathias Brochhausen last name surname http://en.wikipedia.org/wiki/Family_name https://github.com/information-artifact-ontology/IAO/issues/237 family name IAO:0020020 An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things. Alan Ruttenberg Justin Whorton Mathias Brochhausen code map code system codeset coding system controlled vocabulary https://github.com/information-artifact-ontology/IAO/issues/237 Alan Ruttenberg Clint Dowland Matt Diller Sarah Bost William R. Hogan Code sets might include non-entities/things (e.g. missing thumbs). Does not imply absence vs. presence of any taxonomy. Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities. Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. When there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean). For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs). For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets. Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain. The information content entities do not denote each other. code set NCBITaxon:10116 Rattus norvegicus Norway rat brown rat rat rats Rattus norvegicus NCBITaxon:10141 Cavia porcellus domestic guinea pig guinea pig Cavia porcellus NCBITaxon:10239 Viruses Viruses NCBITaxon:10245 Vaccinia virus vaccinia virus VV Vaccinia virus NCBITaxon:102793 H5N1 subtype Avian influenza virus H5N1 H5N1 H5N1 subtype NCBITaxon:10376 human gammaherpesvirus 4 Epstein Barr virus Epstein-Barr virus Epstein-Barr virus EBV Human herpesvirus 4 Human herpesvirus 4 (Epstein-Barr virus) Human herpesvirus type 4 human gammaherpesvirus 4 NCBITaxon:10906 Bluetongue virus 10 Bluetongue virus (SEROTYPE 10) Bluetongue virus type 10 Bluetongue virus 10 NCBITaxon:11036 Venezuelan equine encephalitis virus Venezuelan equine encephalitis VEE Venezuelan equine encephalitis virus VEE Venezuelan equine encephalomyelitis virus Venezuelan equine encephalitis virus NCBITaxon:11082 West Nile virus West Nile virus NCBITaxon:11250 human respiratory syncytial virus Human orthopneumovirus human RSV human respiratory syncytial virus NCBITaxon:11676 Human immunodeficiency virus 1 human immunodeficiency virus 1 HIV-1 human immunodeficiency virus HIV-1 human immunodeficiency virus type 1 HIV 1 human immunodeficiency virus type 1 HIV1 human immunodeficiency virus type 1, HIV-1 human immunodeficiency virus type I HIV-1 human immunodeficiency virus type-1 HIV-1 human immunodeficiency virus-1 HIV-1 Human immunodeficiency virus 1 NCBITaxon:1236 Gammaproteobacteria Gammaproteobacteria NCBITaxon:1239 Bacillota low G+C Gram-positive bacteria low GC Gram+ Bacillota NCBITaxon:1245 Leuconostoc mesenteroides Leuconostoc mesenteroides NCBITaxon:1280 Staphylococcus aureus Staphylococcus aureus NCBITaxon:1351 Enterococcus faecalis Enterococcus faecalis NCBITaxon:1385 Bacillales Bacillales NCBITaxon:1392 Bacillus anthracis anthrax anthrax bacterium Bacillus anthracis NCBITaxon:1422 Geobacillus stearothermophilus Geobacillus stearothermophilus NCBITaxon:1437183 Mesangiospermae Mesangiospermae NCBITaxon:1491 Clostridium botulinum Clostridium botulinum NCBITaxon:1773 Mycobacterium tuberculosis Mycobacterium tuberculosis NCBITaxon:1783272 Bacillati Terrabacteria group Bacillati NCBITaxon:186826 Lactobacillales Lactobacillales NCBITaxon:2 Bacteria eubacteria Bacteria NCBITaxon:208964 Pseudomonas aeruginosa PAO1 Pseudomonas sp. PAO1 Pseudomonas aeruginosa PAO1 NCBITaxon:210 Helicobacter pylori Helicobacter pylori NCBITaxon:2157 Archaea Archaea NCBITaxon:2497569 Negarnaviricota Negative-strand RNA viruses Negarnaviricota NCBITaxon:2559587 Riboviria RNA viruses RNA viruses and viroids Riboviria NCBITaxon:2732396 Orthornavirae Orthornavirae NCBITaxon:2732406 Kitrinoviricota Tombus-Noda-like virus sp. Kitrinoviricota NCBITaxon:2759 Eukaryota eucaryotes eukaryotes Eukaryota NCBITaxon:3379134 Pseudomonadati Pseudomonadati NCBITaxon:3702 Arabidopsis thaliana mouse-ear cress thale cress thale-cress Arabidopsis thaliana NCBITaxon:373153 Streptococcus pneumoniae D39 Streptococcus pneumoniae str. D39 Streptococcus pneumoniae strain D39 Streptococcus pneumoniae D39 NCBITaxon:38568 Leishmania <subgenus> Leishmania Leishmania <subgenus> NCBITaxon:39107 Murinae Murinae NCBITaxon:39947 Oryza sativa Japonica Group Japanese rice Japonica rice Oryza sativa Japonica Group NCBITaxon:40674 mammals Mammalia NCBITaxon:469 Acinetobacter Acinetobacter NCBITaxon:4751 Fungi NCBITaxon:4932 Saccharomyces cerevisiae Saccharomyces cerevisiae 'var. diastaticus' baker's yeast brewer's yeast Saccharomyces cerevisiae NCBITaxon:543 Enterobacteriaceae Enterobacteriaceae NCBITaxon:562 Escherichia coli E. coli Escherichia/Shigella coli Escherichia coli NCBITaxon:5654 Trypanosomatidae Trypanosomatidae NCBITaxon:5664 Leishmania major Leishmania major NCBITaxon:5665 Leishmania mexicana Leishmania mexicana NCBITaxon:5690 Trypanosoma Trypanosoma NCBITaxon:5691 Trypanosoma brucei Trypanosoma brucei NCBITaxon:5693 Trypanosoma cruzi Trypanosoma cruzi NCBITaxon:573 Klebsiella pneumoniae Klebsiella pneumoniae NCBITaxon:5833 Plasmodium falciparum malaria parasite P. falciparum Plasmodium falciparum NCBITaxon:59201 Salmonella enterica subsp. enterica Salmonella enterica subsp. enterica NCBITaxon:629 Yersinia <enterobacteria> Yersinia Yersinia <enterobacteria> NCBITaxon:630 Yersinia enterocolitica Yersinia enterocolitica NCBITaxon:633 Yersinia pseudotuberculosis Yersinia pseudotuberculosis NCBITaxon:669 Vibrio harveyi Vibrio harveyi NCBITaxon:7742 vertebrates Vertebrata <vertebrates> NCBITaxon:7955 Danio rerio leopard danio zebra danio zebra fish zebrafish Danio rerio NCBITaxon:8292 Amphibia NCBITaxon:8355 Xenopus laevis African clawed frog clawed frog common platanna platanna Xenopus laevis NCBITaxon:90370 Salmonella enterica subsp. enterica serovar Typhi Salmonella enterica subsp. enterica serovar Typhi NCBITaxon:90371 Salmonella enterica subsp. enterica serovar Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium NCBITaxon:91061 Bacilli Bacilli NCBITaxon:91347 Enterobacterales Enterobacterales NCBITaxon:9541 Macaca fascicularis crab eating macaque crab-eating macaque cynomolgus macaque cynomolgus monkey cynomolgus monkeys long-tailed macaque Macaca fascicularis NCBITaxon:9913 Bos taurus bovine cow dairy cow domestic cattle domestic cow ox Bos taurus NCBITaxon:9989 Rodentia rodent Rodentia OBI:0000011 planned process A process that realizes a plan which is the concretization of a plan specification. planned process OBI:0000020 contract research organization role a worker role of carrying out the study according to the protocol document or study plan delivered by the PI, under the control of the study director. This role cannot make decisions about the study execution Person: Jennifer Fostel contract research organization contract research organization role OBI:0000066 study a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). investigation OBI:0000086 reagent role OBI:0000091 detector reagent role a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus. 19feb2009. not clear we need this term. originally if came from microarrays -- the probes on the array are termed detectors in some instances One that detects, especially a mechanical, electrical, or chemical device that automatically identifies and records or registers a stimulus, such as an environmental change in pressure or temperature, an electric signal, or radiation from a radioactive material. http://www.answers.com/topic/detector 19feb2009 detector reagent role 1 1 1 1 1 OBI:0000245 organization PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization OBI:0000272 protocol OBI:0000671 sample from organism a material obtained from an organism in order to be a representative of the whole 5/29: This is a helper class for now we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about. sample from organism OBI:0000740 specimen role OBI:0000963 categorical label The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. Bjoern Peters Bjoern Peters categorical label OBI:0000968 device A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. device OBI:0001687 OBI:0001866 secondary cultured cell A cultured cell that has been passaged or derives from a cell that has been passaged in culture. The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. Person: Matthew Brush PERSON: Matthew Brush A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture. secondary cultured cell OBI:0001942 grant agency An organization that provides funding support for projects such as investigations. PERSON: Jie Zheng, Chris Stoeckert funding organization NIAID GSCID-BRC metadata working group NIAID GSCID-BRC grant agency 'funding organization' http://vivoweb.org/ontology/core#FundingOrganization OBI:0002744 molecular label A molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay JZ (3-30-20): discussed on the OBI call. Since the REO was never actually registered, we decided to adopt the term into OBI and replaced OBI:0002744 by newly assigned ID: OBI:0002744. Group: OBI molecular tracer OBI developer call, 3-12-12 https://github.com/obi-ontology/obi/issues/1135 molecular label OBI:0100051 specimen OBI:0100065 synthetic peptide the synthesized peptide SIINFEKL which also occurs in hen-egg lysozyme a synthetic peptide is an material entity which is artificially engineered and results from the synthesis of a chain of amino acids which may also be found in natural protein and be identical in sequence to a protein fragment changed from synthetic polypeptide to peptide, to get rid of the restriction of having more than 10 amino acids (required by Chebi). Bjoern Peters IEDB PRS:22-02-2008: a chebi entity which has output role in a synthesis protocol application original term: protein fragment split into synthetic polypeptide and fragment derived from protein DS: Is this synthetic an oxymoron to the biomaterial? synthetic peptide PATO:0000033 concentration of PATO:0000122 length A 1-D extent quality which is equal to the distance between two points. length PATO:0000125 mass A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. mass Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales. Mammary glands develop by similar mechanisms, and there is an argument for including them here (e.g. http://www.ncbi.nlm.nih.gov/pubmed/20484386), but these structures do not fit the current definition (lactiferous glands are part of the integumentary system in FMA). Note the FMA class is a subdivision of epidermis, which may be too restrictive for our purposes here. CALOHA:TS-0051 FMA:71012 SCTID:276160000 skin appendage epidermal appendage uberon epidermal growth UBERON:0000021 cutaneous appendage UBERON:0000021 Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts) tubular galen:Tube anatomical tube duct uberon UBERON:0000025 tube UBERON:0000025 Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:305751 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:D000825 SCTID:362889002 TAO:0000037 TGMA:0001823 VHOG:0001759 XAO:0003000 ZFA:0000037 http://dbpedia.org/ontology/AnatomicalStructure biological structure connected biological structure uberon UBERON:0000061 anatomical structure UBERON:0000061 Anatomical structure that performs a specific function or group of functions [WP]. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 BIRNLEX:4 CARO:0020004 EFO:0000634 EMAPA:35949 ENVO:01000162 FMA:67498 MA:0003001 NCIT:C13018 SCTID:272625005 UMLS:C0178784 WBbt:0003760 Wikipedia:Organ_(anatomy) uberon anatomical unit body organ element UBERON:0000062 organ UBERON:0000062 A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. FMA:86140 uberon organ region with fixed fiat boundary organ segment segment of organ UBERON:0000063 organ subunit UBERON:0000063 A multicellular structure that is a part of an organ. currently defined in a very broad sense, may be replaced by more specific classes in the future AAO:0011124 BIRNLEX:16 EFO:0000635 FMA:82472 SCTID:113343008 SCTID:91717005 cardinal organ part uberon regional part of organ UBERON:0000064 organ part UBERON:0000064 Stage succeeding embryo, including mature structure. In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) BilaDO:0000003 OGES:000010 OGES:000014 OGES:000024 WBls:0000022 WBls:0000093 WBls:0000103 oboInOwl:SsalDv_0000038 postembryonic stage post-hatching stage uberon postembryonic UBERON:0000092 post-embryonic stage https://github.com/obophenotype/uberon/issues/344 UBERON:0000092 UBERON:0000107 cleavage stage An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. consider adding a preceding stage 'morula stage' as part of cleavage BILS:0000108 BilaDO:0000007 EFO:0001282 HsapDv:0000006 MmusDv:0000007 OGES:000003 OGES:000016 OGES:000021 WBls:0000005 Wikipedia:Blastula XAO:1000003 ZFS:0000045 oboInOwl:GgalDv_0000091 oboInOwl:OariDv_0000025 oboInOwl:RnorDv_0000054 oboInOwl:SsalDv_0000012 oboInOwl:SscrDv_0000089 uberon UBERON:0000108 blastula stage UBERON:0000108 http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. BILS:0000109 BilaDO:0000008 EFO:0001296 FBdv:00005317 HsapDv:0000010 MmusDv:0000013 OGES:000004 OGES:000019 WBls:0000010 XAO:1000005 ZFS:0000047 oboInOwl:GgalDv_0000092 oboInOwl:OariDv_0000026 oboInOwl:RnorDv_0000005 oboInOwl:SsalDv_0000016 oboInOwl:SscrDv_0000090 uberon blastocystis trilaminaris stage trilaminar blastocyst stage trilaminar blastoderm stage trilaminar disk stage trilaminar germ stage trilaminar stage UBERON:0000109 gastrula stage UBERON:0000109 Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos. BILS:0000110 BilaDO:0000009 HsapDv:0000012 MmusDv:0000017 XAO:1000006 oboInOwl:GgalDv_0000093 oboInOwl:OariDv_0000027 oboInOwl:RnorDv_0000007 oboInOwl:SscrDv_0000091 uberon UBERON:0000110 neurula stage https://github.com/obophenotype/developmental-stage-ontologies/issues/84 https://github.com/obophenotype/uberon/issues/343 UBERON:0000110 A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class) EMAPA:37946 FMA:12224 segment of tracheobronchial tree respiratory conducting tube segment of tracheobronchial tree tracheobronchial tree segment uberon airway UBERON:0000117 respiratory tube UBERON:0000117 Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. 2009-04-08T04:38:19Z CARO:0000081 uberon blood or blood analog circulating fluid UBERON:0000179 haemolymphatic fluid UBERON:0000179 A mesodermal signaling center of the hair follicle consisting of closely packed specialized mesenchymal fibroblasts. Framed by the enlarged bulb matrix in anagen. consider adding grouping class for TAO:0001995 ! papilla In humans, at the surface of the skin in hands and feet, they appear as epidermal or papillary ridges (colloquially known as fingerprints) Blood vessels in the dermal papillae nourish all hair follicles and bring nutrients and oxygen to the lower layers of epidermal cells. ncit has 'hair papilla' as part of hypodermis BTO:0001858 CALOHA:TS-0431 EMAPA:36484 FMA:70737 NCIT:C32710 NCIT:C83189 SCTID:320101005 UMLS:C0221931 Wikipedia:Dermal_papillae dermal papillae follicular papilla uberon dermal papilla cell hair follicle dermal papilla hair papilla papilla corii papilla dermatis papilla dermis papilla of corium papillae dermis skin papilla UBERON:0000412 dermal papilla UBERON:0000412 http://upload.wikimedia.org/wikipedia/commons/3/34/Skin.jpg Anatomical entity that has mass. AAO:0010264 AEO:0000006 BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 VHOG:0001721 uberon UBERON:0000465 material anatomical entity UBERON:0000465 Anatomical structure that is an individual member of a species and consists of more than one cell. TODO - split body and mc organism? body continues after death stage organismal organism AAO:0010026 AEO:0000191 BILA:0000012 BIRNLEX:18 BSA:0000038 BTO:0000042 CARO:0000012 EFO:0002906 EHDAA2:0003103 EHDAA2:0003191 EHDAA:1 EMAPA:25765 EV:0100016 FBbt:00000001 FMA:256135 HAO:0000012 NCIT:C13041 SCTID:243928005 TADS:0000001 TAO:0001094 TGMA:0001832 VHOG:0000671 WBbt:0007833 Wikipedia:Multi-cellular_organism XAO:0003004 ZFA:0001094 galen:Organism ncithesaurus:Whole_Organism multi-cellular organism uberon Koerper body whole body whole organism UBERON:0000468 multicellular organism UBERON:0000468 Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. changed label and definition to reflect CARO2 AAO:0000607 AAO:0010054 AEO:0000043 BILA:0000043 BIRNLEX:19 CALOHA:TS-2090 CARO:0000043 EHDAA2:0003043 EMAPA:35868 FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 MESH:D014024 NCIT:C12801 TAO:0001477 TGMA:0001844 UMLS:C0040300 VHOG:0001757 WBbt:0005729 XAO:0003040 ZFA:0001477 galen:Tissue portion of tissue tissue portion simple tissue uberon UBERON:0000479 tissue UBERON:0000479 Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] epithelial AAO:0000144 AAO:0010055 AEO:0000066 BILA:0000066 BTO:0000416 CALOHA:TS-0288 CARO:0000066 EHDAA2:0003066 EMAPA:32738 FBbt:00007005 FMA:9639 GAID:402 HAO:0000066 MA:0003060 MESH:D004848 NCIT:C12710 SCTID:31610004 TAO:0001486 UMLS:C0014609 VHOG:0000387 Wikipedia:Epithelium XAO:0003045 ZFA:0001486 epithelial tissue portion of epithelium uberon UBERON:0000483 Editor note: surface epithelium may contain non-epithelial cells, such as melanocytes, lymphocytes and dendritic cells, within the sheet of epithelial cells. Do we consider these part of the epithelium, or located-in it? epithelium UBERON:0000483 https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. embryonic Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo AAO:0011035 AEO:0000169 BILA:0000056 BSA:0000039 BTO:0000379 CALOHA:TS-0229 EFO:0001367 EHDAA2:0000002 EHDAA2_RETIRED:0003236 EHDAA:38 EMAPA:16039 FBbt:00000052 FMA:69068 GAID:963 IDOMAL:0000646 MAT:0000226 MESH:D004622 MIAA:0000019 NCIT:C28147 OGEM:000001 SCTID:57991002 UMLS:C0013935 VHOG:0001766 Wikipedia:Embryo XAO:0000113 ZFA:0000103 http://neurolex.org/wiki/Category:Embryonic_organism embryonic organism uberon developing organism developmental tissue UBERON:0000922 embryo https://github.com/obophenotype/uberon/issues/503 UBERON:0000922 https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. requires review for applicability to invertebrate structures, e.g. synganglion Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO) (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] AAO:0010478 ABA:Brain BAMS:Br BAMS:Brain BILA:0000135 BIRNLEX:796 BTO:0000142 CALOHA:TS-0095 DHBA:10155 EFO:0000302 EHDAA2:0000183 EHDAA:2641 EHDAA:6485 EMAPA:16894 EV:0100164 FBbt:00005095 FMA:50801 GAID:571 HBA:4005 MA:0000168 MAT:0000098 MBA:8 MBA:997 MESH:D001921 MIAA:0000098 NCIT:C12439 PBA:3999 SCTID:258335003 TAO:0000008 UMLS:C0006104 UMLS:C1269537 VHOG:0000157 Wikipedia:Brain XAO:0000010 ZFA:0000008 galen:Brain neuronames:21 uberon encephalon suprasegmental levels of nervous system suprasegmental structures synganglion the brain UBERON:0000955 brain UBERON:0000955 https://cdn.humanatlas.io/digital-objects/ref-organ/brain-female/v1.4/assets/3d-allen-f-brain.glb https://cdn.humanatlas.io/digital-objects/ref-organ/brain-male/v1.4/assets/3d-allen-m-brain.glb The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex. We follow NIFSTD in defining cerebral cortex and including both neocortex and hippocampal formation (DG+hippocampus). The cerebral cortex is a structure within the brain that plays a key role in memory, attention, perceptual awareness, thought, language, and consciousness. It constitutes the outermost layer of the cerebrum. In preserved brains, it has a grey color, hence the name 'grey matter'. Grey matter is formed by neurons and their unmyelinated fibers, whereas the white matter below the grey matter of the cortex is formed predominantly by myelinated axons interconnecting different regions of the central nervous system. The human cerebral cortex is 2-4 mm (0.08-0.16 inches) thick. The surface of the cerebral cortex is folded in large mammals, such that more than two-thirds of the cortical surface is buried in the grooves, called 'sulci. ' The phylogenetically most recent part of the cerebral cortex, the neocortex, also called isocortex, is differentiated into six horizontal layers; the more ancient part of the cerebral cortex, the hippocampus (also called archicortex), has at most three cellular layers, and is divided into subfields. Relative variations in thickness or cell type (among other parameters) allow us to distinguish between different neocortical architectonic fields. The geometry of at least some of these fields seems to be related to the anatomy of the cortical folds, and, for example, layers in the upper part of the cortical ridges seem to be more clearly differentiated than in its deeper parts. [WP,unvetted][Wikipedia:Cerebral_cortex]. Migration of neurons from the basal or striatal portions of the anterior part of the neural tube occurs to varying degrees in different vertebrate classes, but a true cerebral cortex is generally acknowledged to have made its first appearance in reptiles. The definition can be unambiguous, since 'cortex' simply implies the existence of a surface neuronal layer with an overlying 'zonal lamina' or 'molecular' layer containing dendrites and axons, which is separated from the underlying basal 'matrix' by white matter. Although reptilian cerebral cortex does indeed fulfill these conditions in certain locations, the separation from striatal structures is often indistinct, so that it may even be argued that some primitive dipnoans possess a pallium or cortex. Nevertheless, an extensive laminated layer separated by underlying white matter is well represented only in reptiles and mammals.[well established][VHOG] hagfishes have independently evolved a highly laminated cerebral cortex, comparable in many ways to the cerebral cortex of mammals [http://icb.oxfordjournals.org/content/42/4/743] BAMS:C BAMS:CTX BAMS:Cerebral_cortex BAMS:Cx BIRNLEX:1494 BM:Tel-Cx BTO:0000233 CALOHA:TS-0091 DHBA:10159 EFO:0000328 EHDAA2:0000234 EHDAA:5464 EMAPA:17544 EV:0100166 FMA:61830 GAID:629 HBA:4008 MA:0000185 MAT:0000108 MBA:688 MESH:D002540 MIAA:0000108 NCIT:C12443 PBA:128011354 SCTID:362880003 UMLS:C0007776 VHOG:0000722 Wikipedia:Cerebral_cortex neuronames:39 cortex of cerebral hemisphere uberon brain cortex cortex cerebralis cortex cerebri cortical plate (CTXpl) cortical plate (areas) pallium of the brain UBERON:0000956 cerebral cortex UBERON:0000956 http://upload.wikimedia.org/wikipedia/commons/7/7b/Cerebral_Cortex_location.jpg http://upload.wikimedia.org/wikipedia/commons/9/9a/Brainmaps-macaque-hippocampus.jpg A cuticular covering that is composed primarily of chitin. The main structural component of arthropod cuticle is a polysaccharide, chitin, composed of N-acetylglucosamine units, together with proteins and lipids[WP]. exoskeleton EFO:0000944 FBbt:00004970 HAO:0000240 MAT:0000150 MIAA:0000150 Wikipedia:Arthropod_exoskeleton cuticle uberon arthropod cuticle arthropod exoskeleton insect cuticle UBERON:0001001 EDITOR_NOTE TODO - split from exoskeleton? Also: See above sf item to see if this belongs in GO chitin-based cuticle UBERON:0001001 The outer epithelial layer of the skin that is superficial to the dermis. A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO] The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO] relationship loss: subclass external integument structures (AAO:0000961)[AAO] (...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG] epidermal Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes). epidermis skin AAO:0000143 BTO:0000404 CALOHA:TS-0283 EFO:0000954 EMAPA:17528 EV:0100153 FMA:70596 GAID:932 MA:0000153 MAT:0000154 MESH:D004817 MIAA:0000154 NCIT:C12708 SCTID:361694003 TAO:0000105 UMLS:C0014520 VHOG:0000077 Wikipedia:Epidermis_(skin) XAO:0000028 ZFA:0000105 vertebrate epidermis uberon UBERON:0001003 skin epidermis UBERON:0001003 The tiny hair-like projections that protrude from the inside of the small intestine that contain blood vessels that capture digested nutrients that are absorbed through the intestinal wall; the villi increase the absorptive surface area of the small intestine by approximately 30-fold. in mammals, villi are (largely?) absent from the large intestine, so we treat this as equivalent to small intestinal villus. small/large subdivision may not make sense for all species for which this is present (see ZFA). Note that VHOG quotes ISBN:978-0030223693 as suggesting there are some villi in the large intestine The entire digestive tract is lined by well developed villi, which are longest in the intestinal bulb and decrease progressively in size towards the caudal end of the intestine. No crypts are present, but, the regions between the villi, the intervillus pockets, have a crypt-like function. Cells are produced in the intervillus pockets and shed from the villus tips. Crosnier et al. 2005[TAO] the BTO class refers to a generic villous UBERON:0007607 BTO:0003121 EMAPA:35784 FMA:15072 MA:0001563 NCIT:C33874 SCTID:23230007 TAO:0005125 UMLS:C1519988 Wikipedia:Intestinal_villus ZFA:0005125 enteric villi enteric villous enteric villus intestinal villi villi intestinales villus villus intestinalis (intestinum tenue) uberon intestinal villus layer small intestine villus villi intestinales UBERON:0001213 intestinal villus UBERON:0001213 http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg A holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts.[MP]. sebaceous glands are also found in glabrous areas of eyelids, nose, penis, labia minora and nipples, and do not always secrete into hair follices. This causes some confusion in classification. In addition some structures, such as preputial glands are sometimes called 'modified' sebaceous glands, implying a non-subclass relationship. we follow MP and MA in keeping this class generic and creating a distinct subclass for sebaceuous glands of the skin. The FMA class may be better placed under this subclass. Any of the numerous holocrine glands in the dermis that empty into a hair follicle and produce and secrete sebum. [TFD][VHOG] Sebaceous glands are also limited to mammals.[well established][VHOG] BTO:0001980 CALOHA:TS-2384 EMAPA:35754 EV:0100161 FMA:59160 GAID:900 MA:0002565 MESH:D012627 NCIT:C33519 SCTID:361697005 UMLS:C0036505 VHOG:0001468 Wikipedia:Sebaceous_gland uberon glandula sebacea glandula sebaceae sebaceous follicle UBERON:0001821 sebaceous gland UBERON:0001821 http://upload.wikimedia.org/wikipedia/commons/4/49/HairFollicle.png The most anterior region of the brain including both the telencephalon and diencephalon. Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO] The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO] relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO] In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG] prosencephalic FB AAO:0010147 BAMS:FB BAMS:Forebrain BIRNLEX:1509 BTO:0000478 CALOHA:TS-0380 DHBA:10156 DMBA:15566 EFO:0000909 EHDAA2:0000556 EHDAA:3470 EMAPA:16895 FMA:61992 MA:0000170 MAT:0000105 MESH:D016548 MIAA:0000105 NCIT:C40185 SCTID:362291003 TAO:0000109 UMLS:C0085140 VHOG:0000383 Wikipedia:Forebrain XAO:0000011 ZFA:0000109 neuronames:27 uberon prosencephalon UBERON:0001890 forebrain UBERON:0001890 http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg A vessel through which blood circulates in the body. consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] Any of the vessels through which blood circulates in the body.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] annelids have blood vessels, but this class is not applicable to annelids. FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX vascular element AAO:0011004 AEO:0000207 BTO:0001102 CALOHA:TS-0080 EFO:0000817 EHDAA2:0003252 EHDAA:240 EMAPA:32743 EMAPA:35993 FMA:50722 FMA:63183 GAID:169 MA:0000060 MAT:0000393 MESH:D001808 NCIT:C12679 NLXANAT:090901 SCTID:361097006 TAO:0002137 UMLS:C0005847 VHOG:0001250 Wikipedia:Blood_vessel XAO:0001011 ZFA:0005314 region of vascular tree organ vascular tree organ region uberon vas sanguineum UBERON:0001981 blood vessel UBERON:0001981 http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg The tubular intestinal glands found in the mucosal membranes. In histology, an intestinal crypt, also crypt of LieberkC<hn and intestinal gland, is a gland found in the epithelial lining of the small intestine and colon. The crypts secrete various enzymes, including sucrase and maltase, along with endopeptidases and exopeptidases. Also new epithelium is formed here, keeping in mind that the epithelium at this site is frequently worn away by the passing food. Loss of proliferation control in the crypts is thought to lead to colorectal cancer. The basal portion of the Crypt contains multipotent stem cells. At each mitosis one daughter remains a stem cell while the other differentiates and migrates up the side of the crypt and eventually the villus. Goblet cells are among the cells produced in this fashion[Wikipedia:Intestinal_crypt]. Most fish lack intestinal glands that extend into the mucosa, Gadidae (Jacobshagen 1937) and Macrouridae (Geisterdoerfer 1973( have glands at the base of surface folds throughout intestine - these have been called crypts, but cell types are the same as for surface epithelium. Crypts have been described in salamander midguts (Reeder 1964) some reptiles (Luppa 1977) and some birds (Ziswiler and Farner 1972). Reptile crypts are less developed than birds and mammals, with epithelium similar to the surface. Avian crypts vary from those with absorprive and goblet cells to those that have cells with basophilic granules intestinal gland EMAPA:35266 FMA:63621 MA:0001535 NCIT:C32411 SCTID:118652008 UMLS:C1621887 Wikipedia:Intestinal_crypt Lieberkuhn crypt Lieberkuhn gland Lieberkuhn's gland Lieberkuhn's glands Lieberkühn crypt crypt of Lieberkuhn crypt of Lieberkühn crypts of Lieberkühn follicles of Lieberkühn intestinal crypt intestinal crypts uberon intestinal gland of Lieberkuhn UBERON:0001983 crypt of Lieberkuhn UBERON:0001983 http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg The deepest layer of the epidermis, which is composed of dividing stem cells and anchoring cells. replaces damaged cells on outside of body consisting of non-keratinized, viable cells, in contrast to the outer (upper) layer of epidermis made up of keratinized, anucleated, non-viable cells Malpighian layer rete Malphighii rete Malpighii stratum Malpighi stratum basale stratum germinosum AAO:0010598 BTO:0000438 EMAPA:32779 FMA:67540 MA:0000803 NCIT:C33466 NCIT:C33623 SCTID:419481005 TAO:0001180 UMLS:C0221925 Wikipedia:Stratum_germinativum XAO:0000041 ZFA:0001180 basal cell layer of epidermis basal epidermal layer epidermal basal stratum epidermis stratum basale stratum basalis of epidermis stratum germinativum stratum germinosum of epidermis uberon basal cell layer of skin basal layer of epidermis epidermis basal layer epidermis sensorial layer epidermis stratum germinativum UBERON:0002025 stratum basale of epidermis UBERON:0002025 The layer of polyhedral cells in the epidermis found between the stratum granulosum and stratum basale; shrinkage and adhesion of these cells gives a spiny or prickly appearance. Has cells that produce and secrete bipolar lipids which prevent evaporation, helping to 'water-proof' the skin. Keratinization begins in the stratum spinosum. [Wikipedia:Stratum_spinosum] Malpighian layer stratum Malpighii BTO:0000435 EMAPA:32785 FMA:67542 MA:0000807 NCIT:C12850 SCTID:420086000 UMLS:C0221924 Wikipedia:Stratum_spinosum epidermis stratum spinosum prickle cell layer of epidermis squamous cell layer of epidermis stratum spinosum uberon epidermis prickle cell layer prickle cell layer UBERON:0002026 stratum spinosum of epidermis UBERON:0002026 The outer layer of the epidermis, consisting of several layers of flat keratinized non-nucleated cells. The keratinized outermost layer of the epidermis, which is periodically shed.[AAO] some oral epitehlium also has cornified layer / stratum corneum horny layer keratinized squame layer stratum corneum AAO:0010597 BTO:0000344 CALOHA:TS-0981 EMAPA:32787 FMA:67545 MA:0000804 NCIT:C33625 SCTID:361695002 UMLS:C0221921 Wikipedia:Stratum_corneum cornified layer epidermis stratum corneum horny layer of epidermis keratinized squame layer of epidermis uberon stratum corneum epidermidis UBERON:0002027 stratum corneum of epidermis UBERON:0002027 http://upload.wikimedia.org/wikipedia/commons/2/20/Skinlayers.png https://upload.wikimedia.org/wikipedia/commons/e/e4/Epidermal_layers.png Respiration organ that develops as an outpocketing of the esophagus. Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO] Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG] pulmonary respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi AAO:0000275 AAO:0010567 BTO:0000763 CALOHA:TS-0568 EFO:0000934 EHDAA2:0001042 EHDAA:1554 EHDAA:2205 EMAPA:16728 EV:0100042 FMA:7195 GAID:345 MA:0000415 MAT:0000135 MESH:D008168 MIAA:0000135 NCIT:C12468 SCTID:181216001 UMLS:C0024109 Wikipedia:Lung XAO:0000119 galen:Lung pulmo uberon UBERON:0002048 Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP] lung https://github.com/obophenotype/uberon/issues/701 UBERON:0002048 https://cdn.humanatlas.io/digital-objects/ref-organ/lung-female/v1.4/assets/3d-vh-f-lung.glb https://cdn.humanatlas.io/digital-objects/ref-organ/lung-male/v1.4/assets/3d-vh-m-lung.glb Anatomical structure that is part of an embryo. Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] in FMA embryo is_a embryonic structure AAO:0000138 BILA:0000034 BTO:0000174 CALOHA:TS-2110 EFO:0000461 FBbt:00004208 FMA:69067 GAID:407 MESH:D004628 NCIT:C13229 RETIRED_EHDAA2:0003169 SCTID:667009 TAO:0001105 UMLS:C0013948 VSAO:0000178 XAO:0003042 ZFA:0001105 developing embryonic structure embryonic anatomical structure uberon developing structure embryonale Struktur embryonic structures UBERON:0002050 embryonic structure UBERON:0002050 The layer of flattened cells containing basophilic granules of keratohyalin and lying just above the stratum spinosum (spiny layer) of the epidermis. BTO:0000361 EMAPA:32786 FMA:70344 MA:0000805 NCIT:C33627 SCTID:418563001 UMLS:C0221923 Wikipedia:Stratum_granulosum epidermis stratum granulosum granular layer of epidermis stratum granulosum uberon epidermis granular layer UBERON:0002069 stratum granulosum of epidermis UBERON:0002069 A tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open[GO]. The earliest reliable record of hair is found in a fossil of the Paleocene period, in which the structure of hair cuticles is preserved. Its appearance suggests that the complicated structure of the hair follicle, closely similar to that of present-day mammals, had already appeared at this time.[well established][VHOG] BTO:0000554 CALOHA:TS-0432 EFO:0002464 EMAPA:18771 EMAPA:29741 EV:0100156 FMA:70660 GAID:934 MA:0000154 MESH:D018859 NCIT:C13317 SCTID:280830006 UMLS:C0221971 VHOG:0001268 Wikipedia:Hair_follicle uberon folliculus pili UBERON:0002073 Development notes:Formation largely takes place during fetal and perinatal skin development. However, after skin wounding de novo hair follicle formation may also occur in adult mouse and rabbit skin[DOI:10.1016/j.cub.2008.12.005]. hair follicle UBERON:0002073 https://upload.wikimedia.org/wikipedia/commons/4/4d/Hair_follicle-en.svg The main part of the hair which is composed of trichocytes and is divided into the cortex and medulla. TODO - add distinct subclasses for coat hair vs vibrissa hair TODO - check definition of trichocyte in CL BTO:0004672 EMAPA:36498 FMA:70728 MA:0000159 NCIT:C33543 SCTID:361359004 UMLS:C0221961 shaft of hair uberon scapus pili UBERON:0002074 hair shaft UBERON:0002074 The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one). The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] duodenal In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum. In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz. AAO:0010402 BTO:0000365 CALOHA:TS-0214 EFO:0000851 EMAPA:18852 EV:0100073 FMA:7206 GAID:284 MA:0000338 MAT:0000044 MESH:D004386 MIAA:0000044 NCIT:C12263 SCTID:181247007 UMLS:C0013303 VHOG:0000052 Wikipedia:Duodenum XAO:0000236 galen:Duodenum uberon proximal intestine upper intestine UBERON:0002114 duodenum UBERON:0002114 http://upload.wikimedia.org/wikipedia/commons/b/b3/Tractus_intestinalis_duodenum.svg https://cdn.humanatlas.io/digital-objects/ref-organ/small-intestine-female/v1.2/assets/3d-vh-f-small-intestine.glb https://cdn.humanatlas.io/digital-objects/ref-organ/small-intestine-male/v1.2/assets/3d-vh-m-small-intestine.glb A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas. Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses AEO:0000097 BTO:0000765 CALOHA:TS-2012 EHDAA2:0003097 EMAPA:35327 FMA:9596 GAID:34 MA:0002564 MESH:D005088 NCIT:C12712 SCTID:115976003 UMLS:C0015282 Wikipedia:Exocrine_gland ducted gland glandula exocrina uberon UBERON:0002365 exocrine gland UBERON:0002365 Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine. A duct that carries bile from the liver to the intestine. Any of the excretory ducts in the liver that convey bile between the liver and the intestine. [TFD][VHOG] (...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG] we place the ZFA class here as this fits its textual definition and child nodes. We may recommend a label change for ZFA AAO:0011019 BTO:0000122 CALOHA:TS-0075 EMAPA:35171 EV:0100091 FMA:9706 GAID:280 MA:0000354 MESH:D001652 NCIT:C12376 SCTID:276157007 TAO:0001100 UMLS:C0005400 VHOG:0000212 Wikipedia:Bile_duct XAO:0000134 ZFA:0001100 uberon bile tube biliary duct gall duct hepatic duct UBERON:0002394 bile duct UBERON:0002394 http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png A gland that is part of a skin of body [Automatically generated definition]. check FMA, use plural for now as general class not there EMAPA:35774 FMA:71878 MA:0000146 SCTID:110485007 glandulae cutis uberon set of skin glands skin glands skin glands set UBERON:0002419 skin gland UBERON:0002419 An organ that functions as a secretory or excretory organ. glandular AAO:0000212 AEO:0000096 BTO:0000522 EFO:0000797 EHDAA2:0003096 EHDAA:2161 EMAPA:18425 FBbt:00100317 FMA:7146 FMA:86294 HAO:0000375 MA:0003038 MAT:0000021 MIAA:0000021 NCIT:C13319 SCTID:134358001 UMLS:C1285092 Wikipedia:Gland WikipediaCategory:Glands galen:Gland glandular organ uberon Druese glandula UBERON:0002530 gland UBERON:0002530 http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png The rapidly proliferating mass of cells at the caudal extremity of the embryo; remnant of the primitive node. See notes from https://github.com/obophenotype/uberon/wiki/The-neural-crest Rapidly proliferating mass of cells at the caudal extremity of the embryo. Its formation is reflected in a caudal carving of the posterior portion of the archenteric canal at NF stage 22. With its further outgrowth, the postanal gut primordium becomes stretched. Its lumen is in broad communication with the hindgut at NF stage 25.[AAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (5) a larva or embryo with a postanal tail.[well established][VHOG] AAO:0011104 BTO:0001445 EFO:0002748 EHDAA2:0001976 EHDAA:1595 EMAPA:16580 MAT:0000070 MIAA:0000070 TAO:0000077 VHOG:0000201 XAO:0000107 ZFA:0000077 tail bud tailbud uberon end bud tail bud mesenchyme UBERON:0002533 post-anal tail bud UBERON:0002533 Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia. BIRNLEX:1167 FMA:55676 NCIT:C13031 SCTID:384763002 UMLS:C0445620 anatomical structure of brain biological structure of brain brain anatomical structure brain biological structure brain part neuraxis segment neuroanatomical region segment of brain uberon UBERON:0002616 regional part of brain UBERON:0002616 Proliferative region that is part of the ventricular system. Proliferative zone in the region of the neural tube adjacent to the lumen. There are two primary regions that are thought to give rise to neurons that make up the cerebellum. The first region is the ventricular zone (the roof of the fourth ventricle). This area produces Purkinje cells and deep cerebellar nuclear neurons[BTO:0003654]. in BTO this is restricted to the 4th ventricle - however this class also represents the early ventricular zone as well as its post-natal remnants. The MA class is named 'ventricular zone of brain' and is presumably restricted to the post-natal zone; DHBA class is forebrain; PBA class is neocortex; TAO/ZFA is neocortex AAO:0011112 BTO:0003654 DHBA:10542 EFO:0003624 EMAPA:32679 MA:0000819 PBA:294022030 TAO:0001083 VHOG:0001224 XAO:0000021 ZFA:0001083 VZ brain ventricular zone ventricular zone of brain uberon ventricular zones UBERON:0003053 ventricular zone UBERON:0003053 Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. consider obsoleting. See issue/1305 Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA] AAO:0010337 AEO_RETIRED:0000010 EHDAA2_RETIRED:0003010 TAO:0000292 VSAO:0000001 Wikipedia:Surface_structure XAO:0003028 ZFA:0000292 galen:SurfaceRegion anatomical surface feature uberon surface feature surface region surface structures UBERON:0003102 surface structure UBERON:0003102 Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme. the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] mesenchymal AAO:0010427 AEO:0000145 BTO:0001393 CALOHA:TS-0620 EHDAA2:0003145 EV:0100007 NCIT:C13301 TAO:0000393 UMLS:C0162415 VHOG:0000170 Wikipedia:Mesenchyme XAO:0003046 ZFA:0000393 mesenchymal tissue mesenchyme tissue portion of mesenchymal tissue portion of mesenchyme tissue uberon mesenchyma UBERON:0003104 mesenchyme UBERON:0003104 http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. An elongated tube which carries air to and from the lungs.[AAO] The respiratory tube between the larynx and the bronchi. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] In primitive fishes and most tetrapods, the lungs of adults are usually paired. They lie ventral to the digestive tract and are connected to the outside environment through the trachea.[well established][VHOG] tracheal In birds, the trachea runs from the pharynx to the syrinx, from which the primary bronchi diverge. Swans have an unusually elongated trachea, part of which is coiled beneath the sternum; this may act as a resonator to amplify sound. In some birds, the cartilagenous rings are complete, and may even be ossified. In amphibians, the trachea is normally extremely short, and leads directly into the lungs, without clear primary bronchi. A longer trachea is, however found in some long-necked salamanders, and in caecilians. While there are irregular cartilagenous nodules on the amphibian trachea, these do not form the rings found in amniotes. The only vertebrate to have lungs, but no trachea, is Polypterus, in which the lungs arise directly from the pharynx. in mouse 15-18 C-rings, 15-20 in human. AAO:0010140 BTO:0001388 CALOHA:TS-1060 EFO:0000935 EHDAA2:0002066 EHDAA:3078 EMAPA:16853 EV:0100040 FMA:7394 GAID:361 MA:0000441 MAT:0000137 MESH:D014132 MIAA:0000137 NCIT:C12428 SCTID:181213009 UMLS:C0040578 VHOG:0000371 Wikipedia:Vertebrate_trachea XAO:0000118 cartilaginous trachea vertebrate trachea windpipe uberon tracheal tubule UBERON:0003126 trachea UBERON:0003126 http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg https://cdn.humanatlas.io/digital-objects/ref-organ/trachea-female/v1.1/assets/3d-vh-f-trachea.glb https://cdn.humanatlas.io/digital-objects/ref-organ/trachea-male/v1.1/assets/3d-vh-m-trachea.glb An organism at the pupal stage. A life cycle stage of holometabolous insects in which the organism is a pupa and starts with the larval-pupal apolysis and ends with pupal-adult apolysis. pupal BTO:0001143 EFO:0002684 FBbt:00002953 HAO:0000886 MESH:D011679 Wikipedia:Pupa aurelia chrysalides chrysalis uberon pupae UBERON:0003143 pupa UBERON:0003143 A gland that is part of a integumental system [Automatically generated definition]. EHDAA2:0000837 EMAPA:17758 MA:0000144 VHOG:0000654 integumental gland integumental system gland integumentary gland uberon UBERON:0003297 gland of integumental system UBERON:0003297 A gland that is part of a digestive tract [Automatically generated definition]. EMAPA:18815 MA:0003202 digestive tract gland gland of digestive tract gland of lower gastrointestinal tract gut gland lower gastrointestinal tract gland uberon UBERON:0003408 gland of digestive tract UBERON:0003408 An insect gland dorsal to the insect gut, with a function analogous to that of the vertebrate liver. It is a storage organ for fats, glycogen and protein and is a major site of intermediary metabolism. this term should be ceded to the arthropod anatomy ontology A fatty tissue especially of nearly mature insect larvae that serves as a food reserve[BTO]. BTO:0000442 EFO:0000810 FBbt:00005066 GAID:1213 MESH:D005216 MIAA:0000096 TADS:0000321 TGMA:0001856 fat body uberon fat body sensu invertebrata UBERON:0003917 arthropod fat body UBERON:0003917 Any tube, opening or passage that connects two distinct anatomical spaces. FMA has both conduit and conduit space. In EHDAA2 this is a surface feature AEO:0000080 EHDAA2:0003080 FMA:242873 SCTID:346902003 Wikipedia:Foramen foramen foramina uberon opening ostia ostium UBERON:0004111 anatomical conduit UBERON:0004111 An anatomical structure that develops (entirely or partially) from the endoderm. Grouping term for query purposes uberon UBERON:0004119 endoderm-derived structure UBERON:0004119 An anatomical structure that develops (entirely or partially) from the ectoderm. Grouping term for query purposes ectodermal deriviative uberon UBERON:0004121 ectoderm-derived structure UBERON:0004121 A part of a wall of an organ that forms a layer. FMA:82485 uberon UBERON:0004923 organ component layer UBERON:0004923 An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]. consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates. in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures AEO:0000218 uberon epithelial placode UBERON:0005085 ectodermal placode UBERON:0005085 A bud-like thickening in the epidermis consisting of elongated keratinocytes, which at the distal end are in touch with numerous aggregated specialized dermal fibroblasts, the dermal condensate. An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud[GO]. EMAPA:36479 hair placode vibrissa placode uberon hair gem hair germ hair peg UBERON:0005086 hair follicle placode UBERON:0005086 A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.' AAO:0011000 CARO:0001000 FBbt:00007060 FMA:83115 multi-cell-component structure multi-cell-part structure uberon cell part cluster UBERON:0005162 multi cell part structure UBERON:0005162 AEO:0000125 CALOHA:TS-2122 EHDAA2:0003125 FBbt:00007006 FMA:292313 MIAA:0000019 uberon developing structure developmental structure developmental tissue UBERON:0005423 developing anatomical structure UBERON:0005423 The area located in the bottom of the permanent portion of a resting (telogen) hair follicle where the cells of the external root sheath of the hair follicle are contiguous with the basal layer of the epidermis; this portion of the follicle is involved in the generation of a new hair at the onset of the hair growth cycle (anagen) and contains the hair follicle stem cells. add cell type to CL Convex protrusion of the outer root sheath in the most distal permanent portion of the hair follicle, just below the sebaceous gland and at the insertion site of the muscle arrector pili. Contains the hair follicle stem cells. BTO:0004904 EMAPA:37876 FMA:70735 bulge of hair follicle bulge uberon UBERON:0005975 hair follicle bulge UBERON:0005975 Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers. add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis. the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678] EMAPA:37883 Wikipedia:Skin_appendage body hair or bristle uberon adnexae cutis skin adnexa skin adnexal structure skin appendage UBERON:0006003 integumentary adnexa UBERON:0006003 Organism at the cleavage stage. BILA:0000058 uberon UBERON:0007010 cleaving embryo UBERON:0007010 An embryonic structure that will either develop into a post-anal tail or recede into a vestigial remnant of the tail. By the fourth week a clear tail is seen in the human embryo. It recedes after a few weeks and these tissues form what is commonly known as the tailbone (coccyx). EMAPA:16748 FMA:85540 embryo tail tail of embryo uberon embryonic tail UBERON:0007144 embryonic post-anal tail UBERON:0007144 The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]. this grouping class exists primarily to align with GO - see GO:0008544. BSA:0000073 BTO:0000313 FBbt:00004993 HAO:0000298 TADS:0000109 WBbt:0005733 Wikipedia:Epidermis_(zoology) epidermis epidermis (sensu Metazoa) outer epidermal layer outer epithelial layer uberon hypoderm hypodermis UBERON:0007376 outer epithelium UBERON:0007376 An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 multicellular structure uberon UBERON:0010000 multicellular anatomical structure UBERON:0010000 Epithelium composed of cells that develops from the ectoderm[FMA,modified]. FMA:69064 ectoderm-derived epithelium uberon UBERON:0010371 ecto-epithelium UBERON:0010371 A multi cell part structure that is part of a central nervous system. FMA:83143 cell part cluster of neuraxis neuraxis layer uberon UBERON:0011215 central nervous system cell part cluster UBERON:0011215 An ectodermal placode that gives rise to any of the cutaneous appendages that protrude from the skin epidermis (heair, feathers, epidermal scales). cutaneous appendage follicle placode skin follicle placode uberon UBERON:0011817 skin appendage placode UBERON:0011817 FMA:70945 uberon UBERON:0011901 The hair matrix surrounds the top and sides of the dermal papilla. The hair matrix cells give rise to 6 different types of cells that make up the different layers of the hair shaft and the inner root sheath. hair matrix UBERON:0011901 Anatomical projection that is part of the integumentl system. skin projection uberon UBERON:0013703 integumentary projection UBERON:0013703 An organ component layer that is part of a integumental system. SCTID:314820002 layer of skin skin layer uberon UBERON:0013754 integumentary system layer UBERON:0013754 SZ EMAPA:32704 MA:0003188 uberon cerebral cortex subventricular zone UBERON:0014940 cerebral cortex subventricular zone UBERON:0014940 An exocrine gland that is part of a integumental system. integumental exocrine gland integumental system exocrine gland uberon UBERON:0019319 exocrine gland of integumental system UBERON:0019319 Column of keratinocytes growing into the dermis during embryonic hair follicle development. The concave proximal end starts to encase the dermal condensate, the future dermal papilla. uberon UBERON:0035611 hair peg UBERON:0035611 An organ subunit in the skin that gives rise to cutaneous appendage. follicle cutaneous appendage follicle skin follicle uberon UBERON:0036150 skin appendage follicle UBERON:0036150 Elastoidin fin ray that is slender, sometimes branched distally and present in the embryonic fin fold. Actinotrichia are translucent and exhibit birefringence. This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon ZFA:0000089 ZFA:0005435 actinotrichia uberon UBERON:2000089 Actinotrichia are required for lepidotrichium development. They are occasionally retained in adult fishes. Further taxon comments from Witten & Huysseune (2007): 'Actinotrichia are found in the embryonic fin fold, along the outer edge of the fin in Actinopterygii, and in the adipose fin in teleosts (Starck 1979; Géraudie and Meunier 1982; Becerra et al. 1983). Only in polypterids has their presence been reported in the joints between adjacent lepidotrichial elements (Géraudie 1988). In the sarcopterygian lineage, actinotrichia are present in coelacanths (Géraudie and Meunier 1980) and in young dipnoans (Arratia et al. 2001).' actinotrichium UBERON:2000089 FBbt:00004983 larval cuticle uberon UBERON:6004983 insect embryonic/larval cuticle UBERON:6004983 The third stage of instar larva stage. third instar larva uberon UBERON:8000002 third instar larva stage UBERON:8000002 UO:0000000 unit UO:0000001 length unit length unit UO:0000002 mass unit mass unit UO:0000005 temperature unit temperature unit UO:0000006 substance unit substance unit UO:0000010 second UO:0000028 microsecond UO:0000031 minute UO:0000032 hour UO:0000033 day UO:0000034 UO:0000036 UO:0000052 mass desnsity unit UO:0000061 unit of molarity UO:0000063 millimolar UO:0000095 volume unit volume unit UO:0000105 frequency unit frequency unit UO:0000109 pressure unit pressure unit UO:0000182 density unit UO:0000186 "A unit which is a standard measure of physical quantity consisting of only a numerical number without any units." [Wikipedia:Wikipedia] dimensionless unit UO:0000189 count "A dimensionless unit which denotes a simple count of things." [MGED:MGED] count unit UO:0000239 spatial resolution unit UO:0000241 UO:0000270 volumetric flow rate unit volumetric flow rate unit UO:0000280 rate unit rate unit UO:1000010 second based unit UO:1000031 minute based unit UO:1000032 hour based unit UO:1000033 day based unit UO:1000034 week based unit UO:1000036 year based unit UO:1000062 molar based unit dcterms:LicenseDocument LicenseDocument SSBD_OME-NGFF-ZARR_information SSBD OME-NGFF-ZARR information SSBD_OME_Metadata SSBD OME Metadata 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 SSBD_Project SSBD project SSBD study 1 1 1 SSBD_X_dimension_data example: ('has measurement unit label' some 'micron pixel') and ('has measurement value' some xsd:float) ('has measurement unit label' some 'micron pixel') and ('has X cordinte value' some xsd:float) SSBD X dimension data 1 1 1 SSBD_Y_dimension_data example: ('has measurement unit label' some 'micron pixel') and ('has measurement value' some xsd:float) ('has measurement unit label' some 'micron pixel') and ('has X cordinte value' some xsd:float) SSBD Y dimension data 1 1 1 SSBD_Z_dimension_data example: ('has measurement unit label' some 'micron pixel') and ('has measurement value' some xsd:float) ('has measurement unit label' some 'micron pixel') and ('has X cordinte value' some xsd:float) SSBD Z dimension data 1 SSBD_biosample_information SSBD biosample information SSBD_biosample_mouse for OWL reasoning SSBD biosample mouse 1 1 1 1 1 1 1 1 1 SSBD_dataset SSBD dataset an item that refers to a collection of data from a data source. 1 1 1 1 1 1 SSBD_dimension_data example: ('has measurement unit label' some 'micron pixel') and ('has measurement value' some xsd:float) ('has measurement unit label' some 'micron pixel') and ('has X cordinte value' some xsd:float) SSBD dimension data SSBD_genetic_information SSBD genetic information 1 1 1 1 1 1 1 SSBD_imaging_instruments SSBD imaging instruments SSBD_imaging_method_information SSBD imaging method information 1 1 1 1 1 1 SSBD_paper_information A description about the SSBD project. SSBD paper information Any article information in SSBD. 1 1 1 1 1 1 1 1 SSBD_person SSBD person A person who provides information about the SSBD project (i.e., knowledge association) SSBD_reagent_concentration_datum SSBD reagent concentration datum SSBD_reagent_fold_dilution_datum SSBD reagent fold dilution datum SSBD_reagent_information SSBD reagent information 1 1 1 1 SSBD_time_scale_data SSBD time scale data concentration_measurement_datum concentration measurement datum detector detector device_body device body device_dichroic device dichroic device_filter_set device filter set device_module device module device_objective device objective experimental_variable experimental variable 1 laboratory An organization that performs assays, processes specimens, analyses data and conducts planned processes relevant to the life sciences. laboratory light_source light source pixel_measurement_datum pixel measurement datum ssbd-biosample-test_class141-Fig1a ssbd-biosample-test_class141-Fig1a ssbd-biosample-test_class_human-Fig1a ssbd-biosample-test_class_human-Fig1a owl:Thing vocab:AdministrativeEntity administrative entity 1 vocab:Agent agent group person, group, organization or project that provides a piece of information (i.e. a knowledge association) zic1 Actb Arc Bmal1 BubR1 crx Smc3 CtsB CtsL ErbB2 Gnaq Hes1 Ifngr1 Lamp1 Lamp2 Nrl Ascl1 daf-16 Foxc1 Mist1 pkc-3 pat-4 gei-4 par-2 tufm-1 daf-2 C34C12.8 sel-8 rnr-2 ccdc-55 mcm-5 dcn-1 snfc-5 rnp-4 mel-28 pal-1 rpb-8 rpb-2 gars-1 gop-2 gop-3 ucr-1 par-3 him-10 ddx-23 nmt-1 rps-3 mel-32 dlc-1 R13F6.1 cyk-1 pars-1 ykt-6 let-754 mdt-30 pbs-6 knl-1 sas-4 eif-3.D cls-2 glp-1 rnr-1 T26G10.1 emb-30 baf-1 hcp-3 tlk-1 chc-1 cts-1 pie-1 ani-1 cpf-2 klp-19 lis-1 taf-9 lit-1 mdh-1 fog-2 Odf2 him-5 K06H7.1 tbx-33 Prox1 Ptger1 Flna Ptgfr Ptgs1 Ptgs2 Ret Sfrp2 Sfrp1 Sox10 Sox2 Sox9 Xist Tbxa2r Tbxas1 Trb2 Thy1 Zo1 Tsix Wnt3a Wnt5a Wnt5b Zp3 Prc1 kbp-1 pcf-11 sid4 Cut11 mev-1 Troy Fstl4 Lrig3 spe-42 rho CycA Rab11a bnl Lamp1 Egfl6 Sfrp5 Pex3 Rec8 Rac1 Hec1 Knl1 Hes7 hmx1 Cdc42 ttribution-NonCommercial 4.0 International CC BY-NC 4.0 Attribution-ShareAlike 4.0 International CC BY-SA 4.0 Hamamatsu Photonics ORCA C4742-95 Laboratory for Developmental Dynamics Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research Leica DMRE https://ror.org/01sjwvz98 RIKEN RIKEN https://ror.org/023rffy11 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan RIKEN Center for Biosystems Dynamics Research RIKEN Center for Biosystems Dynamics Research RIKEN Information R&D and Strategy Headquarters Life Science Data Sharing Unit Life Science Data Sharing Unit, RIKEN Information R&D and Strategy Headquarters ssbd-biosample-141-Fig1a_FIB-SEM_somatosensory ssbd-biosample-141-Fig2a_FIB-SEM_spine_synapse ssbd-biosample-141-Fig2b_FIB-SEM_spine_synapse ssbd-biosample-141-Fig2c_FIB-SEM_spine_synapse ssbd-biosample-141-Fig2d_FIB-SEM_spine_synapse ssbd-biosample-141-Fig2e_FIB-SEM_shaft_synapse ssbd-biosample-141-Fig2f_FIB-SEM_shaft_synapse ssbd-biosample-141-Fig2g_FIB-SEM_shaft_synapse ssbd-biosample-141-Fig2h_FIB-SEM_shaft_synapse ssbd-biosample-141-Fig3a_FIB-SEM_synapse ssbd-biosample-141-Fig3b_FIB-SEM_synapse ssbd-biosample-141-Fig3c_FIB-SEM_synapse ssbd-biosample-141-Fig3d_FIB-SEM_synapse ssbd-biosample-141-Fig3i_FIB-SEM_synapse ssbd-biosample-141-Fig3j_FIB-SEM_synapse ssbd-biosample-141-Fig3k_FIB-SEM_synapse ssbd-biosample-141-Fig3l_FIB-SEM_synapse HeLa cell ssbd-biosample-163-Fig2A_STED_mitochondria HeLa cell ssbd-biosample-163-Fig2B_STED_mitochondria_after HeLa cell ssbd-biosample-163-Fig2B_STED_mitochondria_before HeLa cell ssbd-biosample-163-Fig3_STED_mitochondria_inner_outer HeLa cell ssbd-biosample-163-Fig4A_STED_mitochondial_DMEM HeLa cell ssbd-biosample-163-Fig4A_STED_mitochondial_HBSS12h HeLa cell ssbd-biosample-163-Fig4A_STED_mitochondial_HBSS3h HeLa cell ssbd-biosample-163-Fig4C_STED_cristae_HeLa ssbd-biosample-163-Fig5AC_Mitochondrial_MitoPB HeLa cell ssbd-biosample-163-Fig5B_Mitochondrial_MitoPB wild-type C57BL/6N mice ssbd-biosample-170-Airyscan_hook_BM ssbd-biosample-199-Fig2_BrainSliceRGB MDCK cells ssbd-biosample-199-Fig3_MDCKpostconfl MDCK cells ssbd-biosample-199-Fig3_MDCKpreconfl HeLa cells ssbd-biosample-199-Fig4_HeLaYC360_10fps HeLa cells ssbd-biosample-199-Fig4_HeLaYC360_5spf D. discoideum expressing Flamindo2 ssbd-biosample-199-Fig5-6_Flamindo2 D. discoideum expressing RFP ssbd-biosample-199-Fig5-6_RFP dsRNA of rpl-23 was injected into the adult, and the embryo was removed. dsRNA of par-2 was injected into the adult, and the embryo was removed. ssbd-biosample-2-RNAi_F58B6.3_080401_01 ssbd-biosample-2-wt_N2_030303_01 R26-pCAG-nuc-3x mKate2 knockin mouse ssbd-biosample-48-Fig3A_R26-pCAG-nuc-3xmKate2 R26-H2B-mCherry mouse ssbd-biosample-48-Fig3C_H2B-mCherry R26-H2B-EGFP mouse ssbd-biosample-48-Fig3D_H2B-EGFP Thy1-YFP-H transgenic mouse ssbd-biosample-48-Fig3E_Thy1-YFP-H R26-H2B-EGFP mouse ssbd-biosample-48-Fig4B_Series055 R26-H2B-EGFP mouse ssbd-biosample-48-Fig4B_Series072 R26-H2B-EGFP mouse ssbd-biosample-48-Fig4C_CryDKO-CT12 R26-H2B-EGFP mouse ssbd-biosample-48-Fig4C_CryDKO-CT18 R26-H2B-EGFP mouse ssbd-biosample-48-Fig4C_CryDKO-CT24 R26-H2B-EGFP mouse ssbd-biosample-48-Fig4C_CryDKO-CT30 R26-H2B-EGFP mouse ssbd-biosample-48-Fig4C_WT-CT12 R26-H2B-EGFP mouse ssbd-biosample-48-Fig4C_WT-CT18 R26-H2B-EGFP mouse ssbd-biosample-48-Fig4C_WT-CT24 R26-H2B-EGFP mouse ssbd-biosample-48-Fig4C_WT-CT30 A newborn infant marmoset ssbd-biosample-48-Fig5_1310045_21-46-25 Arc-dVenus transgenic mouse ssbd-biosample-48-Fig6_131118_10-09-33 Arc-dVenus transgenic mouse ssbd-biosample-48-Fig6_131118_10-50-37 Arc-dVenus transgenic mouse ssbd-biosample-48-Fig6_131118_12-51-39 Arc-dVenus transgenic mouse ssbd-biosample-48-Fig6_131118_13-39-52 Arc-dVenus transgenic mouse ssbd-biosample-48-Fig6_131118_20-29-52 Arc-dVenus transgenic mouse ssbd-biosample-48-Fig6_131118_20-58-17 Arc-dVenus transgenic mouse ssbd-biosample-48-Fig6_131118_22-31-24 Arc-dVenus transgenic mouse ssbd-biosample-48-Fig6_131119_08-22-10 Arc-dVenus transgenic mouse ssbd-biosample-48-Fig6_131119_09-13-05 Arc-dVenus transgenic mouse ssbd-biosample-48-Fig6_131119_09-46-00 Arc-dVenus transgenic mouse ssbd-biosample-48-Fig6_131119_11-38-20 Arc-dVenus transgenic mouse ssbd-biosample-48-Fig6_131119_12-13-00 B6.B6D2-Tg(Fucci)504Bsi mouse ssbd-biosample-98-fig2ab_trajectory_epithelialcell ssbd-biosample-test_instance141-Fig1a ssbd-biosample-test_instance169-Fig1a Single FIB-SEM image of the somatosensory cortex in wild-type (C57BL/6J) mice Figure 1a tif Fig1a_FIB-SEM_somatosensory ssbd-dataset-141-Fig1a_FIB-SEM_somatosensory FIB-SEM image of spine synapse profiles in wild-type (C57BL/6J) mice Figure 2a tif Fig2a_FIB-SEM_spine_synapse ssbd-dataset-141-Fig2a_FIB-SEM_spine_synapse FIB-SEM image of spine synapse profiles in wild-type (C57BL/6J) mice Figure 2b tif Fig2b_FIB-SEM_spine_synapse ssbd-dataset-141-Fig2b_FIB-SEM_spine_synapse FIB-SEM image of spine synapse profiles in wild-type (C57BL/6J) mice Figure 2c tif Fig2c_FIB-SEM_spine_synapse ssbd-dataset-141-Fig2c_FIB-SEM_spine_synapse FIB-SEM image of spine synapse profiles in wild-type (C57BL/6J) mice Figure 2d tif Fig2d_FIB-SEM_spine_synapse ssbd-dataset-141-Fig2d_FIB-SEM_spine_synapse FIB-SEM image of shaft synapse profiles in wild-type (C57BL/6J) mice Figure 2e tif Fig2e_FIB-SEM_shaft_synapse ssbd-dataset-141-Fig2e_FIB-SEM_shaft_synapse FIB-SEM image of shaft synapse profiles in wild-type (C57BL/6J) mice Figure 2f tif Fig2f_FIB-SEM_shaft_synapse ssbd-dataset-141-Fig2f_FIB-SEM_shaft_synapse FIB-SEM image of shaft synapse profiles in wild-type (C57BL/6J) mice Figure 2g tif Fig2g_FIB-SEM_shaft_synapse ssbd-dataset-141-Fig2g_FIB-SEM_shaft_synapse FIB-SEM image of shaft synapse profiles in wild-type (C57BL/6J) mice Figure 2h tif Fig2h_FIB-SEM_shaft_synapse ssbd-dataset-141-Fig2h_FIB-SEM_shaft_synapse Single FIB-SEM images of spine synapse in wild-type (C57BL/6J) mice Figure 3a tif Fig3a_FIB-SEM_synapse ssbd-dataset-141-Fig3a_FIB-SEM_synapse Single FIB-SEM images of shaft synapses in wild-type (C57BL/6J) mice Figure 3b tif Fig3b_FIB-SEM_synapse ssbd-dataset-141-Fig3b_FIB-SEM_synapse Single FIB-SEM images of spine synapse in spectrum disorder (ASD) model mice with human 15q11-13 chromosomal duplication (15q dup mice) Figure 3c tif Fig3c_FIB-SEM_synapse ssbd-dataset-141-Fig3c_FIB-SEM_synapse Single FIB-SEM images of shaft synapses in spectrum disorder (ASD) model mice with human 15q11-13 chromosomal duplication (15q dup mice) Figure 3d tif Fig3d_FIB-SEM_synapse ssbd-dataset-141-Fig3d_FIB-SEM_synapse Single FIB-SEM images of spine synapse in wild-type (C57BL/6J) mice Figure 3i tif Fig3i_FIB-SEM_synapse ssbd-dataset-141-Fig3i_FIB-SEM_synapse Single FIB-SEM images of shaft synapses in wild-type (C57BL/6J) mice Figure 3j tif Fig3j_FIB-SEM_synapse ssbd-dataset-141-Fig3j_FIB-SEM_synapse Single FIB-SEM images of spine synapse in spectrum disorder (ASD) model mice with human 15q11-13 chromosomal duplication (15q dup mice) Figure 3k tif Fig3k_FIB-SEM_synapse ssbd-dataset-141-Fig3k_FIB-SEM_synapse Single FIB-SEM images of shaft synapses in spectrum disorder (ASD) model mice with human 15q11-13 chromosomal duplication (15q dup mice) Figure 3l tif Fig3l_FIB-SEM_synapse ssbd-dataset-141-Fig3l_FIB-SEM_synapse STED imaging of mitochondria of living HeLa cells Figure 2A Fig2A_STED_mitochondria ssbd-dataset-163-Fig2A_STED_mitochondria STED images of mitochondria after deconvolution Figure 2B Fig2B_STED_mitochondria_after ssbd-dataset-163-Fig2B_STED_mitochondria_after STED images of mitochondria before deconvolution. Figure 2B Fig2B_STED_mitochondria_before ssbd-dataset-163-Fig2B_STED_mitochondria_before STED images of mitochondria inner and outer membrane labeled with two-color. Figure 3 Fig3_STED_mitochondria_inner_outer ssbd-dataset-163-Fig3_STED_mitochondria_inner_outer Deconvoluted STED images of the mitochondrial inner membrane cultured in DMEM as control Figure 4A Fig4A_STED_mitochondial_DMEM ssbd-dataset-163-Fig4A_STED_mitochondial_DMEM Deconvoluted STED images of the mitochondrial inner membrane cultured in HBSS with nutrition starvation for 12h Figure 4A Fig4A_STED_mitochondial_HBSS12h ssbd-dataset-163-Fig4A_STED_mitochondial_HBSS12h Deconvoluted STED images of the mitochondrial inner membrane cultured in HBSS with nutrition starvation for 3h Figure 4A Fig4A_STED_mitochondial_HBSS3h ssbd-dataset-163-Fig4A_STED_mitochondial_HBSS3h STED image of cristae in HeLa cells pretreated with 10 μM mitochondrial DNA replication inhibitor (ddC) for 5 d Figure 4C Fig4C_STED_cristae_HeLa ssbd-dataset-163-Fig4C_STED_cristae_HeLa Time-lapse STED imaging of mitochondrial dynamics in MitoPB Yellow-labeled cells Figure 5AC Fig5AC_Mitochondrial_MitoPB ssbd-dataset-163-Fig5AC_Mitochondrial_MitoPB Time-lapse STED imaging of mitochondrial dynamics in MitoPB Yellow-labeled cells Figure 5B Fig5B_Mitochondrial_MitoPB ssbd-dataset-163-Fig5B_Mitochondrial_MitoPB High-resolution three-dimensional images of the hook basement membrane in mouse dorsal skin. Figure 7 czi Airyscan_hook_BM ssbd-dataset-170-Airyscan_hook_BM AMATERAS imaging of mouse brain slice. Figure 2 Fig2_BrainSliceRGB ssbd-dataset-199-Fig2_BrainSliceRGB AMATERAS nucleus image of MDCK cells in the post-confluent state. Figure 3 Fig3_MDCKpostconfl ssbd-dataset-199-Fig3_MDCKpostconfl AMATERAS nucleus image of MDCK cells in the pre-confluent state. Figure 3 Fig3_MDCKpreconfl ssbd-dataset-199-Fig3_MDCKpreconfl Fluoresence imaging of FRET-based calcium ion imaging in HeLa cells. Figure 4 Fig4_HeLaYC360_10fps ssbd-dataset-199-Fig4_HeLaYC360_10fps Fluoresence imaging of FRET-based calcium ion imaging in HeLa cells. Figure 4 Fig4_HeLaYC360_5spf ssbd-dataset-199-Fig4_HeLaYC360_5spf Fluoresence imaging of D. discoideum expressing Flamindo2 on a centimeter scale. Figure 5 Fig5-6_Flamindo2 ssbd-dataset-199-Fig5-6_Flamindo2 Fluoresence imaging of D. discoideum expressing RFP on a centimeter scale. Figure 5 Fig5-6_RFP ssbd-dataset-199-Fig5-6_RFP 3D time-lapse microscopy images about nuclear division dynamics in B0336.10(RNAi) embryo (rpl-23(RNAi)) embryo) Figure 2a ipm RNAi_B0336.10_040518_01 ssbd-dataset-2-RNAi_B0336.10_040518_01 3D time-lapse microscopy images about nuclear division dynamics in F58B6.3(RNAi) embryo (par-2(RNAi)) embryo) Figure 2a ipm RNAi_F58B6.3_080401_01 ssbd-dataset-2-RNAi_F58B6.3_080401_01 3D time-lapse microscopy images about nuclear division dynamics in wild-type embryo Figure 2a ipm wt_N2_030303_01 ssbd-dataset-2-wt_N2_030303_01 Light-sheet fluorescence microscopy (LSFM) images of R26-pCAG-nuc-3 x mKate2 mouse brain Figure 3A Fig3A_R26-pCAG-nuc-3xmKate2 ssbd-dataset-48-Fig3A_R26-pCAG-nuc-3xmKate2 Light-sheet fluorescence microscopy (LSFM) images of R26-H2B-mCherry mouse brain Figure 3C Fig3C_H2B-mCherry ssbd-dataset-48-Fig3C_H2B-mCherry Light-sheet fluorescence microscopy (LSFM) images of R26-H2B-EGFP mouse brain Figure 3D Fig3D_H2B-EGFP ssbd-dataset-48-Fig3D_H2B-EGFP Light-sheet fluorescence microscopy (LSFM) images of Thy1-YFP-H transgenic mouse brain Figure 3E Fig3E_Thy1-YFP-H ssbd-dataset-48-Fig3E_Thy1-YFP-H Immunohistochemistry (3D-IHC) images of suprachiasmatic nucleus (SCN) and paraventricular nucleus (PVM) regions of R26-H2B-EGFP mouse Figure 4B Fig4B_Series055 ssbd-dataset-48-Fig4B_Series055 Immunohistochemistry (3D-IHC) images of suprachiasmatic nucleus (SCN) and paraventricular nucleus (PVM) regions of R26-H2B-EGFP mouse Figure 4B Fig4B_Series072 ssbd-dataset-48-Fig4B_Series072 Immunohistochemistry (3D-IHC) images of suprachiasmatic nucleus (SCN) and paraventricular nucleus (PVM) regions of R26-H2B-EGFP mouse Figure 4C Fig4C_CryDKO-CT12 ssbd-dataset-48-Fig4C_CryDKO-CT12 Immunohistochemistry (3D-IHC) images of suprachiasmatic nucleus (SCN) and paraventricular nucleus (PVM) regions of R26-H2B-EGFP mouse Figure 4C Fig4C_CryDKO-CT18 ssbd-dataset-48-Fig4C_CryDKO-CT18 Immunohistochemistry (3D-IHC) images of suprachiasmatic nucleus (SCN) and paraventricular nucleus (PVM) regions of R26-H2B-EGFP mouse Figure 4C Fig4C_CryDKO-CT24 ssbd-dataset-48-Fig4C_CryDKO-CT24 Immunohistochemistry (3D-IHC) images of suprachiasmatic nucleus (SCN) and paraventricular nucleus (PVM) regions of R26-H2B-EGFP mouse Figure 4C Fig4C_CryDKO-CT30 ssbd-dataset-48-Fig4C_CryDKO-CT30 Immunohistochemistry (3D-IHC) images of suprachiasmatic nucleus (SCN) and paraventricular nucleus (PVM) regions of R26-H2B-EGFP mouse Figure 4C Fig4C_WT-CT12 ssbd-dataset-48-Fig4C_WT-CT12 Immunohistochemistry (3D-IHC) images of suprachiasmatic nucleus (SCN) and paraventricular nucleus (PVM) regions of R26-H2B-EGFP mouse Figure 4C Fig4C_WT-CT18 ssbd-dataset-48-Fig4C_WT-CT18 Immunohistochemistry (3D-IHC) images of suprachiasmatic nucleus (SCN) and paraventricular nucleus (PVM) regions of R26-H2B-EGFP mouse Figure 4C Fig4C_WT-CT24 ssbd-dataset-48-Fig4C_WT-CT24 Immunohistochemistry (3D-IHC) images of suprachiasmatic nucleus (SCN) and paraventricular nucleus (PVM) regions of R26-H2B-EGFP mouse Figure 4C Fig4C_WT-CT30 ssbd-dataset-48-Fig4C_WT-CT30 Light-sheet fluorescence microscopy (LSFM) images of CUBIC treatment and SYTO 16 nuclear staining of the marmoset hemisphere Figure 5 Fig5_1310045_21-46-25 ssbd-dataset-48-Fig5_1310045_21-46-25 Light-sheet fluorescence microscopy (LSFM) images of Arc-dVenus transgenic mouse brain Figure 6 Fig6_131118_10-09-33 ssbd-dataset-48-Fig6_131118_10-09-33 Light-sheet fluorescence microscopy (LSFM) images of Arc-dVenus transgenic mouse brain Figure 6 Fig6_131118_10-50-37 ssbd-dataset-48-Fig6_131118_10-50-37 Light-sheet fluorescence microscopy (LSFM) images of Arc-dVenus transgenic mouse brain Figure 6 Fig6_131118_12-51-39 ssbd-dataset-48-Fig6_131118_12-51-39 Light-sheet fluorescence microscopy (LSFM) images of Arc-dVenus transgenic mouse brain Figure 6 Fig6_131118_13-39-52 ssbd-dataset-48-Fig6_131118_13-39-52 Light-sheet fluorescence microscopy (LSFM) images of Arc-dVenus transgenic mouse brain Figure 6 Fig6_131118_20-29-52 ssbd-dataset-48-Fig6_131118_20-29-52 Light-sheet fluorescence microscopy (LSFM) images of Arc-dVenus transgenic mouse brain Figure 6 Fig6_131118_20-58-17 ssbd-dataset-48-Fig6_131118_20-58-17 Light-sheet fluorescence microscopy (LSFM) images of Arc-dVenus transgenic mouse brain Figure 6 Fig6_131118_22-31-24 ssbd-dataset-48-Fig6_131118_22-31-24 Light-sheet fluorescence microscopy (LSFM) images of Arc-dVenus transgenic mouse brain Figure 6 Fig6_131119_08-22-10 ssbd-dataset-48-Fig6_131119_08-22-10 Light-sheet fluorescence microscopy (LSFM) images of Arc-dVenus transgenic mouse brain Figure 6 Fig6_131119_09-13-05 ssbd-dataset-48-Fig6_131119_09-13-05 Light-sheet fluorescence microscopy (LSFM) images of Arc-dVenus transgenic mouse brain Figure 6 Fig6_131119_09-46-00 ssbd-dataset-48-Fig6_131119_09-46-00 Light-sheet fluorescence microscopy (LSFM) images of Arc-dVenus transgenic mouse brain Figure 6 Fig6_131119_11-38-20 ssbd-dataset-48-Fig6_131119_11-38-20 Light-sheet fluorescence microscopy (LSFM) images of Arc-dVenus transgenic mouse brain Figure 6 Fig6_131119_12-13-00 ssbd-dataset-48-Fig6_131119_12-13-00 Time-lapse images of tracking the epithelial cells during tooth morphogenesis Figure 2AB ims fig2ab_trajectory_epithelialcell ssbd-dataset-98-fig2ab_trajectory_epithelialcell ssbd-dataset-test_instance169-Fig1a ssbd-dataset-test_instance169-Fig1a 1 channel 2048x1536x1x1x1 5.58 nanometer 5.58 nanometer ssbd-dimension-141-Fig1a_FIB-SEM_somatosensory 1 channel 2048x1538x1x1x1 5.58 nanometer 5.58 nanometer ssbd-dimension-141-Fig2a_FIB-SEM_spine_synapse 1 channel 2048x1538x1x1x1 5.58 nanometer 5.58 nanometer ssbd-dimension-141-Fig2b_FIB-SEM_spine_synapse 1 channel 2048x1538x1x1x1 5.58 nanometer 5.58 nanometer ssbd-dimension-141-Fig2c_FIB-SEM_spine_synapse 1 channel 2048x1538x1x1x1 5.58 nanometer 5.58 nanometer ssbd-dimension-141-Fig2d_FIB-SEM_spine_synapse 1 channel 2048x1538x1x1x1 5.58 nanometer 5.58 nanometer ssbd-dimension-141-Fig2e_FIB-SEM_shaft_synapse 1 channel 2048x1538x1x1x1 5.58 nanometer 5.58 nanometer ssbd-dimension-141-Fig2f_FIB-SEM_shaft_synapse 1 channel 2048x1538x1x1x1 5.58 nanometer 5.58 nanometer ssbd-dimension-141-Fig2g_FIB-SEM_shaft_synapse 1 channel 2048x1538x1x1x1 5.58 nanometer 5.58 nanometer ssbd-dimension-141-Fig2h_FIB-SEM_shaft_synapse 1 channel 2048x1538x1x1x1 5.58 nanometer 5.58 nanometer ssbd-dimension-141-Fig3a_FIB-SEM_synapse 1 channel 2048x1538x1x1x1 5.58 nanometer 5.58 nanometer ssbd-dimension-141-Fig3b_FIB-SEM_synapse 1 channel 2048x1538x1x1x1 5.58 nanometer 5.58 nanometer ssbd-dimension-141-Fig3c_FIB-SEM_synapse 1 channel 2048x1538x1x1x1 5.58 nanometer 5.58 nanometer ssbd-dimension-141-Fig3d_FIB-SEM_synapse 1 channel 2048x1538x1x1x1 5.58 nanometer 5.58 nanometer ssbd-dimension-141-Fig3i_FIB-SEM_synapse 1 channel 2048x1538x1x1x1 5.58 nanometer 5.58 nanometer ssbd-dimension-141-Fig3j_FIB-SEM_synapse 1 channel 2048x1538x1x1x1 5.58 nanometer 5.58 nanometer ssbd-dimension-141-Fig3k_FIB-SEM_synapse 1 channel 2048x1538x1x1x1 5.58 nanometer 5.58 nanometer ssbd-dimension-141-Fig3l_FIB-SEM_synapse 1 channel 960x960x1x1x1 0.0227272 micrometer 0.0227272 micrometer ssbd-dimension-163-Fig2A_STED_mitochondria 1 channel 960x960x1x1x1 0.0142045 micrometer 0.0142045 micrometer ssbd-dimension-163-Fig2B_STED_mitochondria_after 1 channel 960x960x1x1x1 0.0142045 micrometer 0.0142045 micrometer ssbd-dimension-163-Fig2B_STED_mitochondria_before 2 channel 960x960x1x1x1 0.0122189 micrometer 0.0122189 micrometer ssbd-dimension-163-Fig3_STED_mitochondria_inner_outer 1 channel 960x960x1x1x1 0.0142045 micrometer 0.0142045 micrometer ssbd-dimension-163-Fig4A_STED_mitochondial_DMEM 1 channel 960x960x1x1x1 0.0142045 micrometer 0.0142045 micrometer ssbd-dimension-163-Fig4A_STED_mitochondial_HBSS12h 1 channel 960x960x1x1x1 0.0142045 micrometer 0.0142045 micrometer ssbd-dimension-163-Fig4A_STED_mitochondial_HBSS3h 1 channel 960x960x1x1x1 0.01623337 micrometer 0.0162337 micrometer ssbd-dimension-163-Fig4C_STED_cristae_HeLa 1 channel 1024x256x1x1x361 1.31 seconds 0.0227272 micrometer 0.0227272 micrometer ssbd-dimension-163-Fig5AC_Mitochondrial_MitoPB 1 channel 1024x256x1x1x400 1.31 seconds 0.0227272 micrometer 0.0227272 micrometer ssbd-dimension-163-Fig5B_Mitochondrial_MitoPB 3 channels 844x844x58x3x1 0.0408118 micrometer 0.0408118 micrometer 0.1804551 micrometer ssbd-dimension-170-Airyscan_hook_BM 3 channels 13264x9180x1x3x1 1.1 micrometer 1.1 micrometer ssbd-dimension-199-Fig2_BrainSliceRGB 1 channel 13264x9180x1x1x1 1.1 micrometer 1.1 micrometer ssbd-dimension-199-Fig3_MDCKpostconfl 1 channel 13264x9180x1x1x1 1.1 micrometer 1.1 micrometer ssbd-dimension-199-Fig3_MDCKpreconfl 1 channel 13264x9180x1x1x200 0.106 seconds 1.1 micrometer 1.1 micrometer ssbd-dimension-199-Fig4_HeLaYC360_10fps 1 channel 13264x9180x1x1x200 5 seconds 1.1 micrometer 1.1 micrometer ssbd-dimension-199-Fig4_HeLaYC360_5spf 1 channel 13264x9180x1x1x1922 30 seconds 1.1 micrometer 1.1 micrometer ssbd-dimension-199-Fig5-6_Flamindo2 1 channel 13264x9180x1x1x1922 30 seconds 1.1 micrometer 1.1 micrometer ssbd-dimension-199-Fig5-6_RFP 1 channel 600x600x66x1x180 40 seconds 0.105 micrometer 0.105 micrometer 0.5 micrometer ssbd-dimension-2-RNAi_B0336.10_040518_01 1 channel 600x600x66x1x180 40 seconds 0.105 micrometer 0.105 micrometer 0.5 micrometer ssbd-dimension-2-RNAi_F58B6.3_080401_01 1 channel 600x600x66x1x180 40 seconds 0.105 micrometer 0.105 micrometer 0.5 micrometer ssbd-dimension-2-wt_N2_030303_01 1 channel 2560x2160x520x1x1 5.16 micrometer 5.16 micrometer 10 micrometer ssbd-dimension-48-Fig3A_R26-pCAG-nuc-3xmKate2 1 channel 2560x2160x709x1x1 5.16 micrometer 5.16 micrometer 10 micrometer ssbd-dimension-48-Fig3C_H2B-mCherry 1 channel 2560x2160x665x1x1 5.16 micrometer 5.16 micrometer 10 micrometer ssbd-dimension-48-Fig3D_H2B-EGFP 1 channel 2560x2160x696x1x1 5.16 micrometer 5.16 micrometer 10 micrometer ssbd-dimension-48-Fig3E_Thy1-YFP-H 3 channels 512x512x173x3x1 2.026 micrometer 2.026 micrometer 4.989 micrometer ssbd-dimension-48-Fig4B_Series055 3 channels 512x512x67x3x1 2.209 micrometer 2.209 micrometer 4.989 micrometer ssbd-dimension-48-Fig4B_Series072 3 channels 512x512x144x3x1 2.26 micrometer 2.26 micrometer 1.98 micrometer ssbd-dimension-48-Fig4C_CryDKO-CT12 3 channels 512x512x144x3x1 2.26 micrometer 2.26 micrometer 1.98 micrometer ssbd-dimension-48-Fig4C_CryDKO-CT18 3 channels 512x512x151x3x1 2.26 micrometer 2.26 micrometer 1.98 micrometer ssbd-dimension-48-Fig4C_CryDKO-CT24 3 channels 512x512x145x3x1 2.26 micrometer 2.26 micrometer 1.98 micrometer ssbd-dimension-48-Fig4C_CryDKO-CT30 3 channels 512x512x144x3x1 2.26 micrometer 2.26 micrometer 1.98 micrometer ssbd-dimension-48-Fig4C_WT-CT12 3 channels 512x512x144x3x1 2.26 micrometer 2.26 micrometer 1.98 micrometer ssbd-dimension-48-Fig4C_WT-CT18 3 channels 512x512x144x3x1 2.26 micrometer 2.26 micrometer 1.98 micrometer ssbd-dimension-48-Fig4C_WT-CT24 3 channels 512x512x144x3x1 2.26 micrometer 2.26 micrometer 1.98 micrometer ssbd-dimension-48-Fig4C_WT-CT30 1 channel 2560x2160x200x1x1 5.16 micrometer 5.16 micrometer 10 micrometer ssbd-dimension-48-Fig5_1310045_21-46-25 1 channel 2560x2160x200x1x1 5.16 micrometer 5.16 micrometer 10 micrometer ssbd-dimension-48-Fig6_131118_10-09-33 1 channel 2560x2160x200x1x1 5.16 micrometer 5.16 micrometer 10 micrometer ssbd-dimension-48-Fig6_131118_10-50-37 1 channel 2560x2160x200x1x1 5.16 micrometer 5.16 micrometer 10 micrometer ssbd-dimension-48-Fig6_131118_12-51-39 1 channel 2560x2160x200x1x1 5.16 micrometer 5.16 micrometer 10 micrometer ssbd-dimension-48-Fig6_131118_13-39-52 1 channel 2560x2160x200x1x1 5.16 micrometer 5.16 micrometer 10 micrometer ssbd-dimension-48-Fig6_131118_20-29-52 1 channel 2560x2160x200x1x1 5.16 micrometer 5.16 micrometer 10 micrometer ssbd-dimension-48-Fig6_131118_20-58-17 1 channel 2560x2160x200x1x1 5.16 micrometer 5.16 micrometer 10 micrometer ssbd-dimension-48-Fig6_131118_22-31-24 1 channel 2560x2160x200x1x1 5.16 micrometer 5.16 micrometer 10 micrometer ssbd-dimension-48-Fig6_131119_08-22-10 1 channel 2560x2160x200x1x1 5.16 micrometer 5.16 micrometer 10 micrometer ssbd-dimension-48-Fig6_131119_09-13-05 1 channel 2560x2160x200x1x1 5.16 micrometer 5.16 micrometer 10 micrometer ssbd-dimension-48-Fig6_131119_09-46-00 1 channel 2560x2160x200x1x1 5.16 micrometer 5.16 micrometer 10 micrometer ssbd-dimension-48-Fig6_131119_11-38-20 1 channel 2560x2160x200x1x1 5.16 micrometer 5.16 micrometer 10 micrometer ssbd-dimension-48-Fig6_131119_12-13-00 3 channels 862x855x43x3x271 30 minutes 0.554 micrometer 0.554 micrometer ssbd-dimension-98-fig2ab_trajectory_epithelialcell ssbd-genetic-199-Fig2_BrainSliceRGB Yellow Cameleon 3.60 ssbd-genetic-199-Fig4_HeLaYC360_10fps Yellow Cameleon 3.60 ssbd-genetic-199-Fig4_HeLaYC360_5spf Flamindo2 ssbd-genetic-199-Fig5-6_Flamindo2 ssbd-genetic-199-Fig5-6_RFP rpl-23 RNAi experiment http://edamontology.org/topic_3523 ssbd-genetic-2-RNAi_B0336.10_040518_01 par-2 RNAi experiment http://edamontology.org/topic_3523 ssbd-genetic-2-RNAi_F58B6.3_080401_01 http://purl.obolibrary.org/obo/FBbi_00000495 ssbd-genetic-48-Fig3A_R26-pCAG-nuc-3xmKate2 H2B http://purl.obolibrary.org/obo/FBbi_00000525 ssbd-genetic-48-Fig3C_H2B-mCherry H2B http://purl.obolibrary.org/obo/FBbi_00000082 ssbd-genetic-48-Fig3D_H2B-EGFP Thy1 http://purl.obolibrary.org/obo/FBbi_00000439 ssbd-genetic-48-Fig3E_Thy1-YFP-H H2B http://purl.obolibrary.org/obo/FBbi_00000082 ssbd-genetic-48-Fig4B_Series055 H2B http://purl.obolibrary.org/obo/FBbi_00000082 ssbd-genetic-48-Fig4B_Series072 Cry1 Cry2 gene knock out http://purl.obolibrary.org/obo/OBI_0001148 H2B http://purl.obolibrary.org/obo/FBbi_00000082 ssbd-genetic-48-Fig4C_CryDKO-CT12 Cry1 Cry2 gene knock out http://purl.obolibrary.org/obo/OBI_0001148 H2B http://purl.obolibrary.org/obo/FBbi_00000082 ssbd-genetic-48-Fig4C_CryDKO-CT18 Cry1 Cry2 gene knock out http://purl.obolibrary.org/obo/OBI_0001148 H2B http://purl.obolibrary.org/obo/FBbi_00000082 ssbd-genetic-48-Fig4C_CryDKO-CT24 Cry1 Cry2 gene knock out http://purl.obolibrary.org/obo/OBI_0001148 H2B http://purl.obolibrary.org/obo/FBbi_00000082 ssbd-genetic-48-Fig4C_CryDKO-CT30 H2B http://purl.obolibrary.org/obo/FBbi_00000082 ssbd-genetic-48-Fig4C_WT-CT12 H2B http://purl.obolibrary.org/obo/FBbi_00000082 ssbd-genetic-48-Fig4C_WT-CT18 H2B http://purl.obolibrary.org/obo/FBbi_00000082 ssbd-genetic-48-Fig4C_WT-CT24 H2B http://purl.obolibrary.org/obo/FBbi_00000082 ssbd-genetic-48-Fig4C_WT-CT30 ssbd-genetic-48-Fig5_1310045_21-46-25 Arc http://purl.obolibrary.org/obo/FBbi_00000477 ssbd-genetic-48-Fig6_131118_10-09-33 Arc http://purl.obolibrary.org/obo/FBbi_00000477 ssbd-genetic-48-Fig6_131118_10-50-37 Arc http://purl.obolibrary.org/obo/FBbi_00000477 ssbd-genetic-48-Fig6_131118_12-51-39 Arc http://purl.obolibrary.org/obo/FBbi_00000477 ssbd-genetic-48-Fig6_131118_13-39-52 Arc http://purl.obolibrary.org/obo/FBbi_00000477 ssbd-genetic-48-Fig6_131118_20-29-52 Arc http://purl.obolibrary.org/obo/FBbi_00000477 ssbd-genetic-48-Fig6_131118_20-58-17 Arc http://purl.obolibrary.org/obo/FBbi_00000477 ssbd-genetic-48-Fig6_131118_22-31-24 Arc http://purl.obolibrary.org/obo/FBbi_00000477 ssbd-genetic-48-Fig6_131119_08-22-10 Arc http://purl.obolibrary.org/obo/FBbi_00000477 ssbd-genetic-48-Fig6_131119_09-13-05 Arc http://purl.obolibrary.org/obo/FBbi_00000477 ssbd-genetic-48-Fig6_131119_09-46-00 Arc http://purl.obolibrary.org/obo/FBbi_00000477 ssbd-genetic-48-Fig6_131119_11-38-20 Arc http://purl.obolibrary.org/obo/FBbi_00000477 ssbd-genetic-48-Fig6_131119_12-13-00 Fucci ssbd-genetic-98-fig2ab_trajectory_epithelialcell ZEISS CrossBeam 540 ssbd-imaging-method-141-Fig1a_FIB-SEM_somatosensory ZEISS CrossBeam 540 ssbd-imaging-method-141-Fig2a_FIB-SEM_spine_synapse ZEISS CrossBeam 540 ssbd-imaging-method-141-Fig2b_FIB-SEM_spine_synapse ZEISS CrossBeam 540 ssbd-imaging-method-141-Fig2c_FIB-SEM_spine_synapse ZEISS CrossBeam 540 ssbd-imaging-method-141-Fig2d_FIB-SEM_spine_synapse ZEISS CrossBeam 540 ssbd-imaging-method-141-Fig2e_FIB-SEM_shaft_synapse ZEISS CrossBeam 540 ssbd-imaging-method-141-Fig2f_FIB-SEM_shaft_synapse ZEISS CrossBeam 540 ssbd-imaging-method-141-Fig2g_FIB-SEM_shaft_synapse ZEISS CrossBeam 540 ssbd-imaging-method-141-Fig2h_FIB-SEM_shaft_synapse ZEISS CrossBeam 540 ssbd-imaging-method-141-Fig3a_FIB-SEM_synapse ZEISS CrossBeam 540 ssbd-imaging-method-141-Fig3b_FIB-SEM_synapse ZEISS CrossBeam 540 ssbd-imaging-method-141-Fig3c_FIB-SEM_synapse ZEISS CrossBeam 540 ssbd-imaging-method-141-Fig3d_FIB-SEM_synapse ZEISS CrossBeam 540 ssbd-imaging-method-141-Fig3i_FIB-SEM_synapse ZEISS CrossBeam 540 ssbd-imaging-method-141-Fig3j_FIB-SEM_synapse ZEISS CrossBeam 540 ssbd-imaging-method-141-Fig3k_FIB-SEM_synapse ZEISS CrossBeam 540 ssbd-imaging-method-141-Fig3l_FIB-SEM_synapse Leica TCS SP8 STED 3x Leica HyD Time-Lapse Imaging ssbd-imaging-method-163-Fig2A_STED_mitochondria Leica TCS SP8 STED 3x Leica HyD Time-Lapse Imaging ssbd-imaging-method-163-Fig2B_STED_mitochondria_after Leica TCS SP8 STED 3x Leica HyD Time-Lapse Imaging ssbd-imaging-method-163-Fig2B_STED_mitochondria_before Leica TCS SP8 STED 3x Leica HyD Time-Lapse Imaging ssbd-imaging-method-163-Fig3_STED_mitochondria_inner_outer Leica TCS SP8 STED 3x Leica HyD Time-Lapse Imaging ssbd-imaging-method-163-Fig4A_STED_mitochondial_DMEM Leica TCS SP8 STED 3x Leica HyD Time-Lapse Imaging ssbd-imaging-method-163-Fig4A_STED_mitochondial_HBSS12h Leica TCS SP8 STED 3x Leica HyD Time-Lapse Imaging ssbd-imaging-method-163-Fig4A_STED_mitochondial_HBSS3h Leica TCS SP8 STED 3x Leica HyD Time-Lapse Imaging ssbd-imaging-method-163-Fig4C_STED_cristae_HeLa Leica TCS SP8 STED 3x Leica HyD Time-Lapse Imaging ssbd-imaging-method-163-Fig5AC_Mitochondrial_MitoPB Leica TCS SP8 STED 3x Leica HyD Time-Lapse Imaging ssbd-imaging-method-163-Fig5B_Mitochondrial_MitoPB Zeiss LSM880 Zeiss AiryScan ssbd-imaging-method-170-Airyscan_hook_BM ssbd-imaging-method-199-Fig2_BrainSliceRGB ssbd-imaging-method-199-Fig3_MDCKpostconfl ssbd-imaging-method-199-Fig3_MDCKpreconfl ssbd-imaging-method-199-Fig4_HeLaYC360_10fps ssbd-imaging-method-199-Fig4_HeLaYC360_5spf ssbd-imaging-method-199-Fig5-6_Flamindo2 ssbd-imaging-method-199-Fig5-6_RFP Leica DMRE Hamamatsu ORCA CCD Leica HCX PL APO 100x/1,40 ssbd-imaging-method-2-RNAi_B0336.10_040518_01 Leica DMRE Hamamatsu ORCA CCD Leica HCX PL APO 100x/1,40 ssbd-imaging-method-2-RNAi_F58B6.3_080401_01 Leica DMRE Hamamatsu ORCA CCD Leica HCX PL APO 100x/1,40 ssbd-imaging-method-2-wt_N2_030303_01 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-imaging-method-48-Fig3A_R26-pCAG-nuc-3xmKate2 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-imaging-method-48-Fig3C_H2B-mCherry Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-imaging-method-48-Fig3D_H2B-EGFP Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-imaging-method-48-Fig3E_Thy1-YFP-H Leica DMI6000B Leica HCX PL APO CS 10x/0.40 DRY ssbd-imaging-method-48-Fig4B_Series055 Leica DMI6000B Leica HCX PL APO CS 10x/0.40 DRY ssbd-imaging-method-48-Fig4B_Series072 Leica DMI6000B Leica HCX PL APO CS 10x/0.40 DRY ssbd-imaging-method-48-Fig4C_CryDKO-CT12 Leica DMI6000B Leica HCX PL APO CS 10x/0.40 DRY ssbd-imaging-method-48-Fig4C_CryDKO-CT18 Leica DMI6000B Leica HCX PL APO CS 10x/0.40 DRY ssbd-imaging-method-48-Fig4C_CryDKO-CT24 Leica DMI6000B Leica HCX PL APO CS 10x/0.40 DRY ssbd-imaging-method-48-Fig4C_CryDKO-CT30 Leica DMI6000B Leica HCX PL APO CS 10x/0.40 DRY ssbd-imaging-method-48-Fig4C_WT-CT12 Leica DMI6000B Leica HCX PL APO CS 10x/0.40 DRY ssbd-imaging-method-48-Fig4C_WT-CT18 Leica DMI6000B Leica HCX PL APO CS 10x/0.40 DRY ssbd-imaging-method-48-Fig4C_WT-CT24 Leica DMI6000B Leica HCX PL APO CS 10x/0.40 DRY ssbd-imaging-method-48-Fig4C_WT-CT30 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-imaging-method-48-Fig5_1310045_21-46-25 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-imaging-method-48-Fig6_131118_10-09-33 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-imaging-method-48-Fig6_131118_10-50-37 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-imaging-method-48-Fig6_131118_12-51-39 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-imaging-method-48-Fig6_131118_13-39-52 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-imaging-method-48-Fig6_131118_20-29-52 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-imaging-method-48-Fig6_131118_20-58-17 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-imaging-method-48-Fig6_131118_22-31-24 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-imaging-method-48-Fig6_131119_08-22-10 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-imaging-method-48-Fig6_131119_09-13-05 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-imaging-method-48-Fig6_131119_09-46-00 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-imaging-method-48-Fig6_131119_11-38-20 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-imaging-method-48-Fig6_131119_12-13-00 Zeiss LSM780 ssbd-imaging-method-98-fig2ab_trajectory_epithelialcell ZEISS CrossBeam 540 ssbd-instrument-141-Fig1a_FIB-SEM_somatosensory ZEISS CrossBeam 540 ssbd-instrument-141-Fig2a_FIB-SEM_spine_synapse ZEISS CrossBeam 540 ssbd-instrument-141-Fig2b_FIB-SEM_spine_synapse ZEISS CrossBeam 540 ssbd-instrument-141-Fig2c_FIB-SEM_spine_synapse ZEISS CrossBeam 540 ssbd-instrument-141-Fig2d_FIB-SEM_spine_synapse ZEISS CrossBeam 540 ssbd-instrument-141-Fig2e_FIB-SEM_shaft_synapse ZEISS CrossBeam 540 ssbd-instrument-141-Fig2f_FIB-SEM_shaft_synapse ZEISS CrossBeam 540 ssbd-instrument-141-Fig2g_FIB-SEM_shaft_synapse ZEISS CrossBeam 540 ssbd-instrument-141-Fig2h_FIB-SEM_shaft_synapse ZEISS CrossBeam 540 ssbd-instrument-141-Fig3a_FIB-SEM_synapse ZEISS CrossBeam 540 ssbd-instrument-141-Fig3b_FIB-SEM_synapse ZEISS CrossBeam 540 ssbd-instrument-141-Fig3c_FIB-SEM_synapse ZEISS CrossBeam 540 ssbd-instrument-141-Fig3d_FIB-SEM_synapse ZEISS CrossBeam 540 ssbd-instrument-141-Fig3i_FIB-SEM_synapse ZEISS CrossBeam 540 ssbd-instrument-141-Fig3j_FIB-SEM_synapse ZEISS CrossBeam 540 ssbd-instrument-141-Fig3k_FIB-SEM_synapse ZEISS CrossBeam 540 ssbd-instrument-141-Fig3l_FIB-SEM_synapse Leica TCS SP8 STED 3x Leica HyD ssbd-instrument-163-Fig2A_STED_mitochondria Leica TCS SP8 STED 3x Leica HyD ssbd-instrument-163-Fig2B_STED_mitochondria_after Leica TCS SP8 STED 3x Leica HyD ssbd-instrument-163-Fig2B_STED_mitochondria_before Leica TCS SP8 STED 3x Leica HyD ssbd-instrument-163-Fig3_STED_mitochondria_inner_outer Leica TCS SP8 STED 3x Leica HyD ssbd-instrument-163-Fig4A_STED_mitochondial_DMEM Leica TCS SP8 STED 3x Leica HyD ssbd-instrument-163-Fig4A_STED_mitochondial_HBSS12h Leica TCS SP8 STED 3x Leica HyD ssbd-instrument-163-Fig4A_STED_mitochondial_HBSS3h Leica TCS SP8 STED 3x Leica HyD ssbd-instrument-163-Fig4C_STED_cristae_HeLa Leica TCS SP8 STED 3x Leica HyD ssbd-instrument-163-Fig5AC_Mitochondrial_MitoPB Leica TCS SP8 STED 3x Leica HyD ssbd-instrument-163-Fig5B_Mitochondrial_MitoPB Zeiss LSM880 Zeiss AiryScan ssbd-instrument-170-Airyscan_hook_BM ssbd-instrument-199-Fig2_BrainSliceRGB ssbd-instrument-199-Fig3_MDCKpostconfl ssbd-instrument-199-Fig3_MDCKpreconfl ssbd-instrument-199-Fig4_HeLaYC360_10fps ssbd-instrument-199-Fig4_HeLaYC360_5spf ssbd-instrument-199-Fig5-6_Flamindo2 ssbd-instrument-199-Fig5-6_RFP Leica DMRE Hamamatsu ORCA CCD Leica HCX PL APO 100x/1,40 ssbd-instrument-2-RNAi_B0336.10_040518_01 Leica DMRE Hamamatsu ORCA CCD Leica HCX PL APO 100x/1,40 ssbd-instrument-2-RNAi_F58B6.3_080401_01 Leica DMRE Hamamatsu ORCA CCD Leica HCX PL APO 100x/1,40 ssbd-instrument-2-wt_N2_030303_01 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-instrument-48-Fig3A_R26-pCAG-nuc-3xmKate2 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-instrument-48-Fig3C_H2B-mCherry Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-instrument-48-Fig3D_H2B-EGFP Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-instrument-48-Fig3E_Thy1-YFP-H Leica DMI6000B Leica HCX PL APO CS 10x/0.40 DRY ssbd-instrument-48-Fig4B_Series055 Leica DMI6000B Leica HCX PL APO CS 10x/0.40 DRY ssbd-instrument-48-Fig4B_Series072 Leica DMI6000B Leica HCX PL APO CS 10x/0.40 DRY ssbd-instrument-48-Fig4C_CryDKO-CT12 Leica DMI6000B Leica HCX PL APO CS 10x/0.40 DRY ssbd-instrument-48-Fig4C_CryDKO-CT18 Leica DMI6000B Leica HCX PL APO CS 10x/0.40 DRY ssbd-instrument-48-Fig4C_CryDKO-CT24 Leica DMI6000B Leica HCX PL APO CS 10x/0.40 DRY ssbd-instrument-48-Fig4C_CryDKO-CT30 Leica DMI6000B Leica HCX PL APO CS 10x/0.40 DRY ssbd-instrument-48-Fig4C_WT-CT12 Leica DMI6000B Leica HCX PL APO CS 10x/0.40 DRY ssbd-instrument-48-Fig4C_WT-CT18 Leica DMI6000B Leica HCX PL APO CS 10x/0.40 DRY ssbd-instrument-48-Fig4C_WT-CT24 Leica DMI6000B Leica HCX PL APO CS 10x/0.40 DRY ssbd-instrument-48-Fig4C_WT-CT30 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-instrument-48-Fig5_1310045_21-46-25 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-instrument-48-Fig6_131118_10-09-33 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-instrument-48-Fig6_131118_10-50-37 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-instrument-48-Fig6_131118_12-51-39 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-instrument-48-Fig6_131118_13-39-52 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-instrument-48-Fig6_131118_20-29-52 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-instrument-48-Fig6_131118_20-58-17 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-instrument-48-Fig6_131118_22-31-24 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-instrument-48-Fig6_131119_08-22-10 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-instrument-48-Fig6_131119_09-13-05 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-instrument-48-Fig6_131119_09-46-00 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-instrument-48-Fig6_131119_11-38-20 Olympus-Evident MVX-ZB10 Andor Neo 5.5 CL Coherent Sapphire488LP-100/Sapphire5588LP-50 LaVision light sheet illumination unit Olympus-Evident MVPLAPO0.63X ssbd-instrument-48-Fig6_131119_12-13-00 Zeiss LSM780 ssbd-instrument-98-fig2ab_trajectory_epithelialcell XY https://ssbd.riken.jp/100118-dcacbb41/zarr/v0.4/Fig3a_FIB-SEM_synapse.zarr 1 1 2048 1538 1 https://ssbd.riken.jp/omero/webclient/?show=image-126113 https://ssbd.riken.jp/mmiranda/vizarr/?source=https://ssbd.riken.jp/100118-dcacbb41/zarr/v0.4/Fig3a_FIB-SEM_synapse.zarr ssbd-ome-ngff-141-Fig3a_FIB-SEM_synapse XYT 1 361 1024 256 1 ssbd-ome-ngff-163-Fig5AC_Mitochondrial_MitoPB XYC https://ssbd.riken.jp/100118-dcacbb41/zarr/v0.4/Fig2_BrainSliceRGB.zarr 3 1 13264 9180 1 https://ssbd.riken.jp/omero/webclient/?show=image-1089960 https://ssbd.riken.jp/mmiranda/vizarr/?source=https://ssbd.riken.jp/100118-dcacbb41/zarr/v0.4/Fig2_BrainSliceRGB.zarr ssbd-ome-ngff-199-Fig2_BrainSliceRGB XYT 1 200 13264 9180 1 ssbd-ome-ngff-199-Fig4_HeLaYC360_5spf XYT 1 1922 13264 9180 1 ssbd-ome-ngff-199-Fig5-6_Flamindo2 XYZT 1 180 600 600 66 ssbd-ome-ngff-2-wt_N2_030303_01 XYZ 1 1 2560 2160 520 ssbd-ome-ngff-48-Fig3A_R26-pCAG-nuc-3xmKate2 XYZ 1 1 2560 2160 709 ssbd-ome-ngff-48-Fig3C_H2B-mCherry XYZ 1 1 2560 2160 665 ssbd-ome-ngff-48-Fig3D_H2B-EGFP XYZ 1 1 2560 2160 696 ssbd-ome-ngff-48-Fig3E_Thy1-YFP-H XYZCT 2 271 862 855 43 ssbd-ome-ngff-98-fig2ab_trajectory_epithelialcell 30371805 https://doi.org/10.1093/jmicro/dfy128 Yuka Sato, Shigeo Okabe (2019) Nano-scale analysis of synapse morphology in an autism mouse model with 15q11-13 copy number variation using focused ion beam milling and scanning electron microscopy., Microscopy (Oxford, England), Volume 68, Number 2, pp. 122-132 https://academic.oup.com/jmicro/article/68/2/122/5146312 ssbd-paper-141-30371805 31337683 https://doi.org/10.1073/pnas.1905924116 Chenguang Wang, Masayasu Taki, Yoshikatsu Sato, Yasushi Tamura, Hideyuki Yaginuma, Yasushi Okada, Shigehiro Yamaguchi (2019) A photostable fluorescent marker for the superresolution live imaging of the dynamic structure of the mitochondrial cristae., Proceedings of the National Academy of Sciences of the United States of America, Volume 116, Number 32, pp. 15817-15822 https://www.pnas.org/doi/full/10.1073/pnas.1905924116 ssbd-paper-163-31337683 33972551 https://doi.org/10.1038/s41467-021-22881-y Ko Tsutsui, Hiroki Machida, Asako Nakagawa, Kyungmin Ahn, Ritsuko Morita, Kiyotoshi Sekiguchi, Jeffrey H Miner, Hironobu Fujiwara (2021) Mapping the molecular and structural specialization of the skin basement membrane for inter-tissue interactions., Nature communications, Volume 12, Number 1, pp. 2577 https://www.nature.com/articles/s41467-021-22881-y ssbd-paper-170-33972551 34400683 https://doi.org/10.1038/s41598-021-95930-7 Ichimura, T., Kakizuka, T., Horikawa, K. et al. Exploring rare cellular activity in more than one million cells by a transscale scope. Sci Rep 11, 16539 (2021). https://www.nature.com/articles/s41598-021-95930-7 ssbd-paper-199-34400683 23172286 https://doi.org/10.1093/nar/gks1107 Kyoda, K. et al. “WDDD: Worm Developmental Dynamics Database.” Nucleic acids research vol. 41,Database issue (2013): D732-7. doi:10.1093/nar/gks1107 PMC3531189 ssbd-paper-2-23172286 24746791 https://doi.org/10.1016/j.cell.2014.03.042 Etsuo A Susaki, Kazuki Tainaka, Dimitri Perrin, Fumiaki Kishino, Takehiro Tawara, Tomonobu M Watanabe, Chihiro Yokoyama, Hirotaka Onoe, Megumi Eguchi, Shun Yamaguchi, Takaya Abe, Hiroshi Kiyonari, Yoshihiro Shimizu, Atsushi Miyawaki, Hideo Yokota, Hiroki R Ueda (2014) Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis., Cell, Volume 157, Number 3, pp. 726-39 https://www.sciencedirect.com/science/article/pii/S0092867414004188 ssbd-paper-48-24746791 27588418 https://doi.org/10.1371/journal.pone.0161336 Ritsuko Morita, Miho Kihira, Yousuke Nakatsu, Yohei Nomoto, Miho Ogawa, Kazumasa Ohashi, Kensaku Mizuno, Tetsuhiko Tachikawa, Yukitaka Ishimoto, Yoshihiro Morishita, Takashi Tsuji (2016) Coordination of Cellular Dynamics Contributes to Tooth Epithelium Deformations., PloS one, Volume 11, Number 9, pp. e0161336 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0161336 ssbd-paper-98-27588418 Department of Cellular Neurobiology Okabe Shigeo 0000-0003-1216-8890 Universitoy of Tokyo Contact ssbd-person-141-3 Institute of Transformative Bio-Molecules taki@itbm.nagoya-u.ac.jp Masayasu Taki 0000-0003-2185-4593 Nagoya University Contact ssbd-person-163-6 Laboratory for Cell Polarity Regulation y.okada@riken.jp Okada Yasushi 0000-0003-2601-3689 RIKEN BDR Contact ssbd-person-163-7 Institute of Transformative Bio-Molecules yamaguchi@chem.nagoya-u.ac.jp Yamaguchi Shigehiro 0000-0003-0072-8969 Nagoya University Contact ssbd-person-163-8 Laboratory for Tissue Microenvironment hironobu.fujiwara@riken.jp Fujiwara Hironobu RIKEN BDR Contact ssbd-person-170-4 SANKEN (The Institute of Scientific and Industrial Research) ng1@sanken.osaka-u.ac.jp Nagai Takeharu Osaka University Contact ssbd-person-199-2 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan Laboratory for Developmental Dynamics sonami@riken.jp Onami Shuichi 0000-0002-8255-1724 RIKEN BDR Contact https://so.riken.jp ssbd-person-2-9 Laboratory for Synthetic Biology uedah-tky@umin.ac.jp Ueda Hiroki R 0000-0001-8342-9176 RIKEN QBiC Contact ssbd-person-48-1 Laboratory for Organ Regeneration Tsuji Takashi RIKEN BDR Contact ssbd-person-98-5 FIB-SEM images of spine synapses morphology in spectrum disorder (ASD) model mice with human 15q11-13 chromosomal duplication (15q dup mice) FIB-SEM images of spine synapses morphology in spectrum disorder (ASD) model mice with human 15q11-13 chromosomal duplication (15q dup mice) 141-Sato-CellMorphology Image datasets https://ssbd.riken.jp/database/project/141/ 2019-11-20 ssbd-project-141 Time-lapse STED imaging of mitochondrial dynamics in MitoPB Yellow-labeled cells Time-lapse STED imaging of mitochondrial dynamics in MitoPB Yellow-labeled cells 163-Wang-MitochondrialDyn Image datasets https://ssbd.riken.jp/database/project/163/ 2022-11-23 ssbd-project-163 High-resolution three-dimensional images of the hook basement membrane in mouse dorsal skin. High-resolution three-dimensional images of the hook basement membrane in mouse dorsal skin. 170-Tsutsui-HookBM Image datasets https://ssbd.riken.jp/database/project/170/ 2022-03-31 ssbd-project-170 Imaging data of centimeter-scale dynamics of multicellular systems observed with sub-cellular resolution. Imaging data of centimeter-scale dynamics of multicellular systems observed with sub-cellular resolution. 199-Ichimura-MulticellularDyn Image datasets https://ssbd.riken.jp/database/project/199/ 2021-09-23 ssbd-project-199 Worm developmental dynamics database project This project provides a collection of quantitative nuclear division dynamics data from wild-type and RNAi-treated embryos. 2013-09-02 2-Kyoda-WormEmbryoRNAi Image datasets and Quantitative datasets https://ssbd.riken.jp/database/project/2-Kyoda-WormEmbryoRNAi/ 2013-09-02 2013-09-02 2020-02-03 ssbd-project-2 Development of a whole-brain clearning and imaging method Thie project performed comprehensive chemical screening to develop a whole-brain clearing and imaging method, termed CUBIC 48-Susaki-MouseBrainCUBIC Image datasets https://ssbd.riken.jp/database/project/48/ 2017-10-03 2018-11-15 ssbd-project-48 BDML quantitative informations and time-lapse confocal images of the epithelial tissue deformation in tooth development BDML quantitative informations and time-lapse confocal images of the epithelial tissue deformation in tooth development 98-Morita-ToothEpiCellDyn Image datasets and Quantitative datasets https://ssbd.riken.jp/database/project/98/ 2019-11-20 ssbd-project-98 ssbd-reagent-141-nan 500 MitoPB Yellow ssbd-reagent-163-Fig2A_STED_mitochondria 500 MitoPB Yellow ssbd-reagent-163-Fig2B_STED_mitochondria_after 500 MitoPB Yellow ssbd-reagent-163-Fig2B_STED_mitochondria_before 500 MitoPB Yellow ssbd-reagent-163-Fig3A_STED_mitochondial_DMEM 500 100 MitoPB Yellow TOMM20-TMR ssbd-reagent-163-Fig3_STED_mitochondria_inner_outer Dulbecco's modified Eagle medium http://purl.obolibrary.org/obo/OBI_0000918 ssbd-reagent-163-Fig4A_STED_mitochondial_DMEM 500 10 MitoPB Yellow Hanks’ balanced salt solution ssbd-reagent-163-Fig4A_STED_mitochondial_HBSS12h 500 10 MitoPB Yellow Hanks’ balanced salt solution http://purl.obolibrary.org/obo/CHMO_0002438 ssbd-reagent-163-Fig4A_STED_mitochondial_HBSS3h 500 10 MitoPB Yellow zalcitabine http://purl.obolibrary.org/obo/CHEBI_10101 ssbd-reagent-163-Fig4C_STED_cristae_HeLa 500 MitoPB Yellow ssbd-reagent-163-Fig5AC_Mitochondrial_MitoPB 500 MitoPB Yellow ssbd-reagent-163-Fig5B_Mitochondrial_MitoPB 4',6-diamidino-2-phenylindole (DAPI) http://purl.obolibrary.org/obo/FBbi_00000056 ssbd-reagent-170-Airyscan_hook_BM 1 Hoechst 33342 http://purl.obolibrary.org/obo/FBbi_00000052 ssbd-reagent-199-Fig2_BrainSliceRGB 5 NucleoSeeing ssbd-reagent-199-Fig3_MDCKpostconfl 5 NucleoSeeing ssbd-reagent-199-Fig3_MDCKpreconfl ssbd-reagent-2-nan 300.0 100.0 rabbit anti-VIP goat anti-Copeptin ssbd-reagent-48-Fig4B_Series055 300.0 100.0 rabbit anti-VIP goat anti-Copeptin ssbd-reagent-48-Fig4B_Series072 300.0 100.0 rabbit anti-VIP goat anti-Copeptin ssbd-reagent-48-Fig4C_CryDKO-CT12 300.0 100.0 rabbit anti-VIP goat anti-Copeptin ssbd-reagent-48-Fig4C_CryDKO-CT18 300.0 100.0 rabbit anti-VIP goat anti-Copeptin ssbd-reagent-48-Fig4C_CryDKO-CT24 300.0 100.0 rabbit anti-VIP goat anti-Copeptin ssbd-reagent-48-Fig4C_CryDKO-CT30 300.0 100.0 rabbit anti-VIP goat anti-Copeptin ssbd-reagent-48-Fig4C_WT-CT12 300.0 100.0 rabbit anti-VIP goat anti-Copeptin ssbd-reagent-48-Fig4C_WT-CT18 300.0 100.0 rabbit anti-VIP goat anti-Copeptin ssbd-reagent-48-Fig4C_WT-CT24 100.0 300.0 rabbit anti-VIP goat anti-Copeptin ssbd-reagent-48-Fig4C_WT-CT30 0.25-2.0 SYTO 16 ssbd-reagent-48-Fig5_1310045_21-46-25 ssbd-reagent-98-nan https://large.riken.jp/distribution/reporter-mouse.html CDB0238K https://large.riken.jp/distribution/reporter-mouse.html CDB0239K Leica HCX PL Apo 100x/1.40 O Attribution 4.0 International CC BY 4.0 https://doi.org/10.1073/pnas.0511111103 https://pubmed.ncbi.nlm.nih.gov/16477039/ B6.Cg-Tg(Fucci)504Bsi, Fucci S/2G/M-Green#504, B6;B6D2-Tg(Fucci)504Bsi B6.Cg-Tg(FucciS/G2/M)#504Bsi C57BL/6J B6.Cg-Tg(Thy1-YFP)HJrs/J 2025-05-08 has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part BFO:0000051 external has_part has part CLO:0003684 LCL-1512 an immortal human uterine cervix-derived epithelial cell line that was derived from cervical adenocarcinoma cancer cells taken on February 8, 1951 from Henrietta Lacks, a patient who died of her cancer on October 4, 1951. HeLa WEB: http://en.wikipedia.org/wiki/HeLa WEB: http://www.atcc.org/products/all/CCL-2.aspx WEB: https://www.ncbi.nlm.nih.gov/pubmed/12001993 HeLa cell ATCC: CCL-2 CHEMBL: CHEMBL3308376 EFO: EFO_0001185 HyperCLDB: cl1601 MeSH: D006367 RRID:CVCL_0030 CLO:0007646 A model mammalian cell line cell that was genereated from the initial isolation in 1958 of epithelial cells from the kidney tubule of an adult Cocker Spaniel dog by Stewart H. Madin and Norman B. Darby, Jr.. MDCK Madin-Darby canine kidney cell https://en.wikipedia.org/wiki/Madin-Darby_canine_kidney_cells MDCK cell HyperCLDB: cl5078 CL:0000000 cell PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CALOHA:TS-2035 FBbt:00007002 FMA:68646 GO:0005623 KUPO:0000002 MESH:D002477 VHOG:0001533 WBbt:0004017 XAO:0003012 ZFA:0009000 cell The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell cell type EFO_URI: http://www.ebi.ac.uk/efo/EFO_0000324 CL:0000732 amoeboid cell CL:0001034 A cell that is maintained or propagated in a controlled artificial environment for use in an investigation. haendel 2012-01-12T09:58:38Z cell 'In vitro', translating literally to 'in glass', typically refers to a controlled, often sterile, laboratory setting where cells or other specimens are placed by some agent for the purpose of studying or manipulating them as part of some research investigation. 'In vitro' is intended to contrast with 'native',which refers to cells or other biological entities that are found in a natural setting. It describes unicellular organisms removed from a natural environement and multicellular organism cells removed from an organism, or cells derived in culture from such displaced cells. cell in vitro image FBbi:00000001 sample preparation method FBbi:00000001 image FBbi:00000031 visualization method FBbi:00000031 image FBbi:00000079 genetically encoded tag FBbi:00000079 image GFP FBbi:00000082 EGFP FBbi:00000082 image FBbi:00000222 imaging method FBbi:00000222 FBbi:00000245 differential interference contrast microscopy image FBbi:00000246 fluorescence microscopy FBbi:00000246 image FBbi:00000251 confocal microscopy FBbi:00000251 sources and methods for illumination jm 2010-03-09T10:38:14Z image FBbi:00000268 illumination method FBbi:00000268 media and devices employed for recording the alterations in the illumination that result from its interaction with the sample jm 2010-03-09T10:38:14Z image FBbi:00000269 detection method FBbi:00000269 The physical property of the specimen that leads to the modifications of the illumination that are recorded in the image. jm 2010-03-09T10:38:14Z image FBbi:00000270 imaged parameter FBbi:00000270 jm 2010-03-09T10:38:14Z image FBbi:00000271 contrast-enhancing method FBbi:00000271 jm 2010-03-09T11:33:49Z image FBbi:00000294 charge coupled device (CCD) FBbi:00000294 jm 2010-03-09T11:33:49Z image FBbi:00000295 photomultiplier tube (PMT) FBbi:00000295 jm 2010-03-09T11:33:49Z image FBbi:00000304 complementary metal oxide semiconductor (CMOS) FBbi:00000304 methods for increasing the resolution beyond the classical Abbe diffraction limit jm 2010-03-09T03:12:34Z image FBbi:00000321 resolution-enhancing method FBbi:00000321 a birefringent optical element typically used to split polarized illumination into two sets of parallel but displaced rays jm 2010-03-09T03:20:14Z image FBbi:00000326 Wollaston prism FBbi:00000326 jm 2010-03-09T03:24:02Z image FBbi:00000334 stimulated emission depletion (STED) FBbi:00000334 illumination in the form of a thin sheet of light directed perpendicular to the optic axis jm 2010-03-11T10:06:20Z image FBbi:00000364 light-sheet illumination FBbi:00000364 Fluorescence (or Forster) resonance energy transfer; a method of estimating the distance between two fluorophores by measuring the extent of non-radiative energy transfer between the two. Experimentally, this involves selective excitation of one while observing emission from the other. jm 2010-03-11T10:09:33Z image FBbi:00000367 FRET FBbi:00000367 jm 2010-03-17T02:01:22Z image FBbi:00000439 Yellow fluorescent protein from Aequorea FBbi:00000439 jm 2010-03-17T02:14:30Z image FBbi:00000477 VenusFP FBbi:00000477 jm 2010-03-17T02:16:24Z image FBbi:00000483 Red fluorescent proteins from Anthozoa FBbi:00000483 jm 2010-03-17T02:19:04Z image FBbi:00000495 mKate2FP FBbi:00000495 jm 2010-03-17T02:22:53Z image FBbi:00000518 tdTomatoFP FBbi:00000518 jm 2010-03-17T02:24:26Z image FBbi:00000525 mCherryFP FBbi:00000525 The source of the variation in the imaged parameter across the field of view. jm 2010-09-03T08:53:13Z image FBbi:00000590 source of contrast FBbi:00000590 A method of reconstructing 3D structure by combining focussed ion beam milling to remove sucessive layers from a sample block with scanning EM to image the exposed surface between each milling step. FIB-SEM image FBbi:00050000 focussed ion beam scanning electron microscopy (FIB-SEM) FBbi:00050000 A method of reconstructing 3D structure by combining focussed ion beam milling to remove sucessive layers from a sample block with scanning EM to image the exposed surface between each milling step. PMID:22119321 A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. GO:0005554 molecular function molecular_function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. molecular_function GO:0003674 A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). https://github.com/geneontology/go-ontology/issues/17729 GO:0008372 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component cellular_component subcellular entity GO:0005575 Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. cellular_component GO:0005575 A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers. https://github.com/geneontology/go-ontology/issues/29267 GO:0005605 GO:0008003 Wikipedia:Basement_membrane cellular_component basal lamina basement lamina lamina densa GO:0005604 Note that this term has no relationship to 'membrane ; GO:0016020' because the basement membrane is not a lipid bilayer. basement membrane GO:0005604 A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. NIF_Subcellular:sao1860313010 Wikipedia:Mitochondrion mitochondria cellular_component GO:0005739 Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.) mitochondrion GO:0005739 The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope. NIF_Subcellular:sao1289741256 Wikipedia:Outer_mitochondrial_membrane mitochondrion outer membrane outer mitochondrial membrane outer mitochondrion membrane cellular_component GO:0005741 mitochondrial outer membrane GO:0005741 The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae. NIF_Subcellular:sao1371347282 Wikipedia:Inner_mitochondrial_membrane inner mitochondrial membrane inner mitochondrion membrane mitochondrion inner membrane cellular_component GO:0005743 mitochondrial inner membrane GO:0005743 Merging of two or more mitochondria within a cell to form a single compartment. https://github.com/geneontology/go-ontology/issues/23133 vw 2015-01-21T06:58:18Z GO:1990613 mitochondrion fusion biological_process mitochondrial membrane fusion GO:0008053 mitochondrial fusion GO:0008053 A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. https://github.com/geneontology/go-ontology/issues/24968 jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological_process GO:0008150 GO:0009790 Any of the inward folds of the mitochondrial inner membrane. Their number, extent, and shape differ in mitochondria from different tissues and organisms. They appear to be devices for increasing the surface area of the mitochondrial inner membrane, where the enzymes of electron transport and oxidative phosphorylation are found. Their shape can vary with the respiratory state of the mitochondria. cristae NIF_Subcellular:sao333328131 mitochondrial cristae cellular_component GO:0030061 See also the cellular component term 'mitochondrial inner membrane ; GO:0005743'. mitochondrial crista GO:0030061 has measurement unit label is about This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. is_about is a (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes. From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input. This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. Alan Ruttenberg is quality measurement of NCBITaxon:10090 Mus musculus house mouse mouse Mus musculus Mus musculus NCBITaxon:44689 Dictyostelium discoideum NCBITaxon:6239 Caenorhabditis elegans NCBITaxon:9483 Callithrix jacchus NCBITaxon:9606 Homo sapiens human Homo sapiens NCBITaxon:9615 Canis lupus familiaris dog dogs Canis lupus familiaris OBI:0000747 material sample blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general. A material entity that has the material sample role OBI: workshop sample population sample material sample is member of organization OBI:0001879 reagent A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output. 2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For examples, see editor note on OBI:device. PERSON:Matthew Brush PERSON:Matthew Brush (copied from ReO) Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). reagent OBI:0003030 oligonucleotide primer set OBI:0100026 organism animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism organism OGG:0000000002 A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule. A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule. Physical and functional unit of heredity, which carries information from one generation to the next. In molecular terms, it is the entire DNA sequence including exons, introns, and noncoding transcription-control regions necessary for production of a functional protein or RNA. Physical and functional unit of heredity, which carries information from one generation to the next. In molecular terms, it is the entire DNA sequence including exons, introns, and noncoding transcription-control regions necessary for production of a functional protein or RNA. gene A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule. http://www.ncbi.nlm.nih.gov/books/NBK21640/ Physical and functional unit of heredity, which carries information from one generation to the next. In molecular terms, it is the entire DNA sequence including exons, introns, and noncoding transcription-control regions necessary for production of a functional protein or RNA. ISBN:9780716737063 PR:000000001 protein antithrombin III is a protein An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. protein inheres in this fragility inheres in this vase this fragility is a characteristic of this vase this red color inheres in this apple this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of inheres in has role this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role has role SO:0001027 genetype UBERON:0000104 life cycle A spatiotemporal region encompassing some part of the life cycle of an organism. this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here the WBls class 'all stages' belongs here as it is the superclass of other WBls stages we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage BILS:0000105 EFO:0000399 FBdv:00007012 FMA:24120 HsapDv:0000000 MESH:D008018 MmusDv:0000000 PdumDv:0000090 WBls:0000002 XAO:1000000 ZFS:0000000 ZFS:0100000 ncithesaurus:Developmental_Stage oboInOwl:AcarDv_0000000 oboInOwl:BtauDv_0000000 oboInOwl:CfamDv_0000000 oboInOwl:CporDv_0000000 oboInOwl:DpseDv_0000000 oboInOwl:DsimDv_0000000 oboInOwl:EcabDv_0000000 oboInOwl:FcatDv_0000000 oboInOwl:GgalDv_0000000 oboInOwl:GgorDv_0000000 oboInOwl:MdomDv_0000000 oboInOwl:MmulDv_0000000 oboInOwl:OanaDv_0000000 oboInOwl:OariDv_0000000 oboInOwl:OcunDv_0000000 oboInOwl:PpanDv_0000000 oboInOwl:PtroDv_0000000 oboInOwl:RnorDv_0000000 oboInOwl:SsalDv_0000000 oboInOwl:SscrDv_0000000 developmental stage stage uberon UBERON:0000105 life cycle stage UBERON:0000105 Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. AAO:0010841 AEO:0000000 BFO:0000004 BILA:0000000 BIRNLEX:6 CARO:0000000 EHDAA2:0002229 FBbt:10000000 FMA:62955 HAO:0000000 MA:0000001 NCIT:C12219 TAO:0100000 TGMA:0001822 UMLS:C1515976 WBbt:0000100 XAO:0000000 ZFA:0100000 uberon UBERON:0001062 anatomical entity UBERON:0001062 UBERON:0007232 2 cell stage UBERON:0007233 4 cell stage UBERON:0007236 8 cell stage UO:0000003 time unit time unit UO:0000051 concentration unit concentration unit UO:0000064 micromolar UO:0000065 nanomolar UO:0000236 image resolution unit UO:0000274 microgram per milliliter UO:0000322 "A unit that is the ratio of concentration of two solutions of interest, typically with one solution derived from the other by the addition of solvent." [UO:PC] fold dilution fold dilution strain strain en Yuki Yamagata SSBD Ontology Emi Fujisawa Fangfang Wang Haruna Yamamoto Hiroya Itoga Koji Kyoda Miguel Miranda-Miranda Shuichi Onami Yasue Nakano Yukako Tohsato Yuki Yamagata The SSBD Ontology is an ontology of SSBD (https://ssbd.riken.jp). SSBD is a platform for sharing and reusing bioimaging data. SSBD:database is an added-value database for bioimages and biological dynamics data. It provides a rich set of open resources for analyzing microscopy images and qunatitative data of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Microscopy images and quantitative biological data are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations. image 2025-05-08 gene_detection_method gene detection method gene_detection_signal gene detection signal