An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies. Biological Spatial Ontology * BSPO:$sequence(7,0,999999999)$ spatial CTENO is an ontology describing the anatomy and developmet of ctenophores. based on FBql 2023-05-27 definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 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 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.obofoundry.org/obo/obi> editor note 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 has ontology root term 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 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 synonym typically used in the context of human anatomy synonym typically used in the context of vertebrate anatomy acronym anamorph blast name common name equivalent name genbank acronym genbank anamorph genbank common name genbank synonym in-part misnomer misspelling scientific name synonym teleomorph namespace-id-rule synonym_type_property database_cross_reference An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 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 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. 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 has_scope has_synonym_type shorthand http://www.w3.org/2000/01/rdf-schema#seeAlso spatial seeAlso true seeAlso see also 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/ 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 spatial part_of part_of part of part of http://www.obofoundry.org/ro/#OBO_REL:part_of preceded by 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 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. precedes BSPO:0000095 spatial anatomical_relation anatomical_relation anatomical relation true x proximal to y iff x is closer to the point of attachment with the body than y. BSPO:0000100 NCIT:C25236 spatial proximal_to proximal_to The elbow is proximal to the hand, but distal to the shoulder. proximal to x proximal to y iff x is closer to the point of attachment with the body than y. BSPO:cjm RO:0002221 BSPO:0000101 spatial obsolete_surrounds obsolete_surrounds obsolete surrounds true x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000102 spatial ventral_to ventral_to ventral to x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:cjm BSPO:0000103 spatial vicinity_of vicinity_of vicinity of On the same side as. For example, the left arm is ipsilateral to the left leg. BSPO:0000105 spatial ipsilateral_to ipsilateral_to ipsilateral to On the same side as. For example, the left arm is ipsilateral to the left leg. BSPO:cjm On the opposite side from. For example, the left arm is contralateral to the right arm (and the right leg). BSPO:0000106 spatial contralateral_to contralateral_to contralateral to On the opposite side from. For example, the left arm is contralateral to the right arm (and the right leg). BSPO:cjm Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:0000108 spatial superficial_to superficial_to superficial to Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:cjm RO:0002219 BSPO:0000109 spatial obsolete_surrounded_by obsolete_surrounded_by obsolete surrounded_by true Closer to the right side of the organism. Example: The dorsal fin is right of the left pectoral fin, but is left of the right eye. On the type level: X left of Y <=> every instance x of X is right of some instance y of Y, and there exists some organism o such that x part of o and y part of o. BSPO:0000111 spatial right_of right_of right of Closer to the right side of the organism. Example: The dorsal fin is right of the left pectoral fin, but is left of the right eye. On the type level: X left of Y <=> every instance x of X is right of some instance y of Y, and there exists some organism o such that x part of o and y part of o. BSPO:cjm X lateral to y if x is further from the midsagittal plane than y. Jennifer Girón 2021-04-21T01:01:01Z lateral to Jennifer Girón 2021-04-21T01:01:01Z X medial to y if x is closer to the midsagittal plane than y. medial to X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion. BSPO:0000120 NCIT:C25229 spatial in_left_side_of in_left_side_of in left side of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion. BSPO:PATO_mtg_2009 X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion. BSPO:0000121 NCIT:C25228 spatial in_right_side_of in_right_side_of in right side of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion. BSPO:PATO_mtg_2009 X posterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the posterior portion. BSPO:0000122 spatial in_posterior_side_of in_posterior_side_of in posterior side of X posterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the posterior portion. BSPO:PATO_mtg_2009 X anterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the anterior portion. BSPO:0000123 spatial in_anterior_side_of in_anterior_side_of in anterior side of X anterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the anterior portion. BSPO:PATO_mtg_2009 x in proximal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the proximal portion. BSPO:0000124 spatial in_proximal_side_of in_proximal_side_of in proximal side of x in proximal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the proximal portion. BSPO:PATO_mtg_2009 x in distal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the distal portion. BSPO:0000125 spatial in_distal_side_of in_distal_side_of in distal side of x in distal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the distal portion. BSPO:PATO_mtg_2009 X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure BSPO:0000126 spatial in_lateral_side_of in_lateral_side_of in lateral side of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure UBERON:cjm X superficial part of Y <=> if Y is subdivided into two superficial and deep portions, X is part of the superficial portion. BSPO:0001100 spatial in_superficial_part_of in_superficial_part_of in superficial part of X superficial part of Y <=> if Y is subdivided into two superficial and deep portions, X is part of the superficial portion. BSPO:cjm X superficial part of Y <=> if Y is subdivided into two superficial and deep portions, X is part of the deep portion. BSPO:0001101 spatial in_deep_part_of in_deep_part_of in deep part of X superficial part of Y <=> if Y is subdivided into two superficial and deep portions, X is part of the deep portion. BSPO:cjm X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y BSPO:0001106 spatial proximalmost_part_of proximalmost_part_of proximalmost part of X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y https://orcid.org/0000-0002-6601-2165 x immediately deep to y iff x deep_to y and x is contiguous with y. BSPO:0001107 spatial immediately_deep_to immediately_deep_to immediately deep to x immediately deep to y iff x deep_to y and x is contiguous with y. BSPO:curators X distalmost part of Y <=> X is in distal side of Y and X is adjacent to the distal boundary of Y BSPO:0001108 spatial distalmost_part_of distalmost_part_of distalmost part of X distalmost part of Y <=> X is in distal side of Y and X is adjacent to the distal boundary of Y https://orcid.org/0000-0002-6601-2165 BSPO:0001113 spatial preaxialmost_part_of preaxialmost_part_of preaxialmost part of x preaxial to y iff x is further along the preaxial-postaxial axis than y, towards the postaxial side. BSPO:0001114 spatial posterior to (developmentally) postaxial_to postaxial_to postaxial to x preaxial to y iff x is further along the preaxial-postaxial axis than y, towards the postaxial side. http://medical-dictionary.thefreedictionary.com/postaxial posterior to (developmentally) MA:th BSPO:0001115 spatial postaxialmost_part_of postaxialmost_part_of postaxialmost part of X intersects median plane of iff X crosses the midine plane of Y. BSPO:0005001 spatial intersects_midsagittal_plane_of intersects_midsagittal_plane_of intersects midsagittal plane of A relation between an axis and a part of an organism, in which the part defines the initial point of the axis. BSPO:0015004 spatial has_end_point has_end_point Axes can be defined in a given species by subtyping the relevant axis type and stating a end and end point has end point A relation between an axis and a part of an organism, in which the part defines the initial point of the axis. BSPO:cjm x immediately anterior to y iff x anterior to y and x is contiguous with y. BSPO:0015009 spatial immediately_anterior_to immediately_anterior_to immediately anterior to x immediately anterior to y iff x anterior to y and x is contiguous with y. BSPO:curators x immediately distal to y iff x distal to y and x is contiguous with y. BSPO:0015010 spatial immediately_distal_to immediately_distal_to immediately distal to x immediately distal to y iff x distal to y and x is contiguous with y. BSPO:curators x immediately dorsal to y iff x dorsal to y and x is contiguous with y. BSPO:0015011 spatial immediately_dorsal_to immediately_dorsal_to immediately dorsal to x immediately dorsal to y iff x dorsal to y and x is contiguous with y. BSPO:curators x immediately posterior to y iff x posterior_to y and x is contiguous with y. BSPO:0015012 spatial immediately_posterior_to immediately_posterior_to immediately posterior to x immediately posterior to y iff x posterior_to y and x is contiguous with y. BSPO:curators x immediately proximal to y iff x proximal to y and x is contiguous with y. BSPO:0015013 spatial immediately_proximal_to immediately_proximal_to immediately proximal to x immediately proximal to y iff x proximal to y and x is contiguous with y. BSPO:curators x immediately superficial to y iff x superficial to y and x is contiguous with y. BSPO:0015014 spatial immediately_superficial_to immediately_superficial_to immediately superficial to x immediately superficial to y iff x superficial to y and x is contiguous with y. BSPO:curators x immediately ventral to y iff x ventral to y and x is contiguous with y. BSPO:0015015 spatial immediately_ventral_to immediately_ventral_to immediately ventral to x immediately ventral to y iff x ventral to y and x is contiguous with y. BSPO:curators x immediately left of y iff x left_of y and x is contiguous with y. BSPO:0015016 spatial immediately_left_of immediately_left_of immediately left of x immediately left of y iff x left_of y and x is contiguous with y. BSPO:curators x immediately right of y iff x right of y and x is contiguous with y. BSPO:0015017 spatial immediately_right_of immediately_right_of immediately right of x immediately right of y iff x right of y and x is contiguous with y. BSPO:curators X dorsal side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the dorsal portion. BSPO:0015101 spatial in_dorsal_side_of in_dorsal_side_of in dorsal side of X dorsal side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the dorsal portion. BSPO:cjm X ventral side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the ventral portion. BSPO:0015102 spatial in_ventral_side_of in_ventral_side_of in ventral side of X ventral side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the ventral portion. BSPO:cjm nearer to the oral opening of the organism, on the oral-aboral axis. BSPO:0015201 spatial oral_to oral_to oral to nearer to the oral opening of the organism, on the oral-aboral axis. BSPO:cjm nearer to the aboral opening of the organism, on the oral-aboral axis. BSPO:0015202 spatial aboral_to aboral_to aboral to nearer to the aboral opening of the organism, on the oral-aboral axis. BSPO:cjm X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides. This was migrated from http://purl.obolibrary.org/obo/uberon/core#in_central_side_of in Uberon. in central side of X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides. BSPO:cjm A relation between an axis and a part of an organism, in which the part defines the initial point of the axis. This relationship was originally called http://purl.obolibrary.org/obo/#_has_start_point, but was renamed because of the non-standard IRI syntax. :has_start_point spatial has_start_point has_start_point Axes can be defined in a given species by subtyping the relevant axis type and stating a start and end point. has start point A relation between an axis and a part of an organism, in which the part defines the initial point of the axis. BSPO:cjm x dorsalmost_part_of y iff x part_of y and there is no z which is part_of y and is more dorsal than x but not part_of x; x is adjacent to the dorsal boundary of y BSPO:0030003 spatial dorsalmost_part_of dorsalmost_part_of dorsalmost part of x dorsalmost_part_of y iff x part_of y and there is no z which is part_of y and is more dorsal than x but not part_of x; x is adjacent to the dorsal boundary of y https://orcid.org/0000-0003-2699-3066 x anteriormost_part_of y iff x part_of y and there is no z which is part_of y and is more anterior than x but not part_of x; x is adjacent to the anterior boundary of y BSPO:0030004 spatial anteriormost_part_of anteriormost_part_of anteriormost part of x anteriormost_part_of y iff x part_of y and there is no z which is part_of y and is more anterior than x but not part_of x; x is adjacent to the anterior boundary of y https://orcid.org/0000-0003-2699-3066 x lateralmost_part_of y iff x part_of y and there is no z which is part_of y and is more lateral than x but not part_of x; x is adjacent to the lateral boundary of y BSPO:0030005 spatial lateralmost_part_of lateralmost_part_of lateralmost part of x lateralmost_part_of y iff x part_of y and there is no z which is part_of y and is more lateral than x but not part_of x; x is adjacent to the lateral boundary of y https://orcid.org/0000-0003-2699-3066 X medial side of Y <=> if Y is subdivided into two medial and lateral portions, X is part of the medial portion. BSPO:0030006 spatial in_medial_side_of in_medial_side_of in medial side of X medial side of Y <=> if Y is subdivided into two medial and lateral portions, X is part of the medial portion. https://orcid.org/0000-0003-2699-3066 x medialmost_part_of y iff x part_of y and there is no z which is part_of y and is more medial than x but not part_of x; x is adjacent to the medial boundary of y BSPO:0030007 spatial medialmost_part_of medialmost_part_of medialmost part of x medialmost_part_of y iff x part_of y and there is no z which is part_of y and is more medial than x but not part_of x; x is adjacent to the medial boundary of y https://orcid.org/0000-0003-2699-3066 x preaxial to y iff x is further along the preaxial-postaxial axis than y, towards the front. BSPO:1000000 spatial anterior to (developmentally) lateral (radial) to medial (tibial) to preaxial_to preaxial_to preaxial to x preaxial to y iff x is further along the preaxial-postaxial axis than y, towards the front. http://medical-dictionary.thefreedictionary.com/preaxial anterior to (developmentally) MA:th inheres in this fragility is a characteristic of this vase 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. 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 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 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 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 has quality 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 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 inverse of 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 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. dos 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, 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. dos 2017-05-24T09:49:21Z has component process dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes true A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern 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. has component RO:0002202 develops_from develops from develops_from p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. negatively regulates (process to process) negatively regulates p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. positively regulates (process to process) positively regulates true 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 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. consumes has input RO:0002258 developmentally_preceded_by developmentally preceded by A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. causally upstream of, negative effect 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 inheres in part of characteristic of part of true A mereological relationship or a topological relationship Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships RO:0002323 mereotopologically_related_to mereotopologically related to RO:0002324 developmentally_related_to developmentally related to a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 functionally_related_to functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. false part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p actively involved in enables part of involved in inverse of enables enabled by inverse of regulates regulated by (processual) regulated by inverse of negatively regulates negatively regulated by inverse of positively regulates positively regulated by inverse of has input input of inverse of upstream of causally downstream of immediately causally downstream of p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. indirectly activates indirectly positively regulates p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. indirectly inhibits indirectly negatively regulates relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002410 causally_related_to causally related to relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. https://en.wikipedia.org/wiki/Causality p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. causally upstream of p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. immediately causally upstream of p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 influences (processual) affects causally upstream of or within inverse of causally upstream of or within causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union involved in or reguates involved in or involved in regulation of A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. molecularly controls directly regulates activity of The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. directly inhibits molecularly decreases activity of directly negatively regulates activity of The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. directly activates molecularly increases activity of directly positively regulates activity of This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) is kinase activity A relationship between a material entity and a process where the material entity has some causal role that influences the process RO:0002500 causal_agent_in causal agent in causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes depends on The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities causally influenced by (entity-centric) causally influenced by interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ molecular interaction relation helper property The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). causally influences (entity-centric) causally influences p directly regulates q iff p is immediately causally upstream of q and p regulates q. directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002595 causal_relation_between_material_entity_and_a_process causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent RO:0002609 related_via_dependence_to related via dependence to p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) directly positively regulates p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) directly negatively regulates Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. 2018-01-25T23:20:13Z enables subfunction 2018-01-26T23:49:30Z acts upstream of or within, positive effect 2018-01-26T23:49:51Z acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive 2018-01-26T23:53:14Z acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative 2018-01-26T23:53:22Z acts upstream of, negative effect 2018-03-13T23:55:05Z causally upstream of or within, negative effect 2018-03-13T23:55:19Z causally upstream of or within, positive effect The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. regulates activity of p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. pg 2022-09-26T06:07:17Z indirectly causally upstream of p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. pg 2022-09-26T06:08:01Z indirectly regulates A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z utilizes device utilizes material A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. regulates characteristic A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. positively regulates characteristic A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. negatively regulates characteristic BFO:0000002 An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. continuant BFO:0000003 An entity that has temporal parts and that happens, unfolds or develops through time. occurrent BFO:0000004 A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant BFO:0000015 An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process BFO:0000016 disposition BFO:0000017 A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. realizable entity BFO:0000019 quality BFO:0000020 A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. specifically dependent continuant BFO:0000023 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. role BFO:0000031 BFO:0000034 function BFO:0000040 An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. material entity BFO:0000141 immaterial entity BSPO:0000000 The side of an organism that is left of the sagittal plane. left spatial BSPO:0000000 left side BSPO:0000000 The side of an organism that is left of the sagittal plane. BSPO:cjm BSPO:0000001 upper spatial BSPO:0000001 Consider merging with superior side. upper side BSPO:0000001 BSPO:0000002 lower spatial BSPO:0000002 Consider merging with inferior side. lower side BSPO:0000002 BSPO:00000021 BSPO:0000021 spatial BSPO:00000021 was made obsolete because the ID had too many digits deep-superficial gradient (obsolete) true BSPO:00000021 BSPO:0000003 deep spatial BSPO:0000003 deep side BSPO:0000003 BSPO:0000004 superficial spatial BSPO:0000004 superficial side BSPO:0000004 BSPO:0000005 A 2D surface of an anatomical continuant. FMA:24137 surface spatial BSPO:0000005 to be merged into CARO anatomical surface BSPO:0000005 A 2D surface of an anatomical continuant. BSPO:cjm BSPO:0000006 Fiat anatomical region extending a short distance from the boundary of an object inwards. edge margin spatial BSPO:0000006 anatomical margin BSPO:0000006 Fiat anatomical region extending a short distance from the boundary of an object inwards. BSPO:cjm BSPO:0000007 The side of an organism that is right of the sagittal plane. right spatial BSPO:0000007 right side BSPO:0000007 The side of an organism that is right of the sagittal plane. BSPO:cjm BSPO:wd BSPO:0000008 Sagittal plane that divides a bilateral body into unequal left and right parts. parasagittal section spatial BSPO:0000008 parasagittal plane BSPO:0000008 Sagittal plane that divides a bilateral body into unequal left and right parts. BSPO:mah BSPO:0000009 Sagittal plane that divides bilateral body into equal left and right parts. FMA:74563 median sagittal plane midline plane midsagittal section spatial median plane BSPO:0000009 only in bilaterally symmetrical organisms midsagittal plane BSPO:0000009 Sagittal plane that divides bilateral body into equal left and right parts. BSPO:mah median sagittal plane FMA:74563 BSPO:0000010 A straight line through space, intersecting an anatomical entity. http://upload.wikimedia.org/wikipedia/commons/3/34/Anatomical_Directions_and_Axes.JPG spatial BSPO:0000010 Axis directions are defined in terms of axes. anatomical axis BSPO:0000010 A straight line through space, intersecting an anatomical entity. BSPO:cjm BSPO:0000011 An anatomical axis determined by gravity. spatial superior-inferior axis BSPO:0000011 upper-lower axis BSPO:0000011 An anatomical axis determined by gravity. BSPO:cjm BSPO:0000012 An axis that extends from an internal position to a more external position in the body or body part. spatial BSPO:0000012 Muscles are frequently categorized as 'deep', 'intermediate', and 'superficial'. deep-superficial axis BSPO:0000012 An axis that extends from an internal position to a more external position in the body or body part. BSPO:PM BSPO:0000013 An axis that extends through an organism from head end to opposite end of body or tail. A-P axis AP axis anteroposterior axis cephalocaudal axis craniocaudal axis rostral/caudal rostrocaudal axis spatial longitudinal axis BSPO:0000013 In sponges, AP is used to indicate the direction of movement [in larval stage] (as it is in other metazoans that move, e.g., the basal bilaterians). [PM] anterior-posterior axis BSPO:0000013 An axis that extends through an organism from head end to opposite end of body or tail. BSPO:cjm cephalocaudal axis http://en.wikipedia.org/wiki/Anatomical_terms_of_location craniocaudal axis rostral/caudal rostrocaudal axis BSPO:0000014 An axis that extends through an organism or organism part from the part of the organism or organism part attached to a substrate (basal) to the furthest from the attachment (apical). Note that the apical-basal axis is often used for organismal parts where there is attachment via a basal lamina or other structure. apical/basal spatial longitudinal axis BSPO:0000014 apical-basal axis relative to substrate BSPO:0000014 An axis that extends through an organism or organism part from the part of the organism or organism part attached to a substrate (basal) to the furthest from the attachment (apical). Note that the apical-basal axis is often used for organismal parts where there is attachment via a basal lamina or other structure. BSPO:mah BSPO:0000015 An axis that extends from the point of attachment of a structure (proximal) to the point furthest away from the plane of attachment (distal). proximal/distal proximodistal spatial BSPO:0000015 In some communities, proximal and distal are used when specifying the position of parts of elements that are contained within the body, such as gill arches or vertebral spines. In these cases, use of the classes medial-lateral axis or medial-external axis are more appropriate. proximal-distal axis BSPO:0000015 An axis that extends from the point of attachment of a structure (proximal) to the point furthest away from the plane of attachment (distal). BSPO:curators http://en.wikipedia.org/wiki/Anatomical_terms_of_location BSPO:0000016 An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body. D-V axis DV axis dorsoventral axis anterior-posterior axis spatial BSPO:0000016 dorsal-ventral axis BSPO:0000016 An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body. BSPO:curators anterior-posterior axis BSPO:0000017 An axis that bisects an organism from left to right sides of body, through a sagittal plane. L-R axis LR axis R-L axis RL axis dextro-sinister axis left to right axis right to left axis right-left axis spatial BSPO:0000017 left-right axis BSPO:0000017 An axis that bisects an organism from left to right sides of body, through a sagittal plane. BSPO:cjm BSPO:0000018 Anatomical plane that divides body into anterior and posterior parts. FMA:12247 axial plane axial section transverse section spatial cross-section BSPO:0000018 transverse plane BSPO:0000018 Anatomical plane that divides body into anterior and posterior parts. BSPO:mah BSPO:0000019 Anatomical plane that divides bilateral body into dorsal and ventral parts. FMA:52810 frontal plane horizontal anatomical plane horizontal section spatial coronal section frontal section BSPO:0000019 horizontal plane BSPO:0000019 Anatomical plane that divides bilateral body into dorsal and ventral parts. BSPO:mah horizontal anatomical plane FMA:52810 BSPO:0000020 Anatomical gradient that is distributed along the upper-lower axis. spatial BSPO:0000020 upper-lower gradient BSPO:0000020 Anatomical gradient that is distributed along the upper-lower axis. BSPO:wd BSPO:0000021 Anatomical gradient that is distributed along the deep-superficial axis. spatial BSPO:0000021 deep-superficial gradient BSPO:0000021 Anatomical gradient that is distributed along the deep-superficial axis. BSPO:wd BSPO:0000022 The side that is higher relative to the substrate. superior spatial cranial BSPO:0000022 superior side BSPO:0000022 The side that is higher relative to the substrate. BSPO:curators BSPO:0000023 Anatomical gradient that is distributed along the apical-basal axis. spatial BSPO:0000023 apical-basal gradient BSPO:0000023 Anatomical gradient that is distributed along the apical-basal axis. BSPO:wd BSPO:0000024 Anatomical gradient that is distributed along the proximal-distal axis. spatial BSPO:0000024 proximal-distal gradient BSPO:0000024 Anatomical gradient that is distributed along the proximal-distal axis. BSPO:wd BSPO:0000025 The side that is lower relative to the substrate. inferior spatial caudal BSPO:0000025 inferior side BSPO:0000025 The side that is lower relative to the substrate. BSPO:curators BSPO:0000026 Anatomical region that overlaps the anterior and dorsal regions of a body or body part. Melissa Haendel 2009-06-15T01:01:38Z anterodorsal region spatial BSPO:0000026 antero-dorsal region BSPO:0000026 Anatomical region that overlaps the anterior and dorsal regions of a body or body part. BSPO:wd BSPO:0000027 Anatomical region that overlaps the anterior and ventral regions of a body or body part. Melissa Haendel 2009-06-15T01:04:59Z anteroventral region spatial BSPO:0000027 antero-ventral region BSPO:0000027 Anatomical region that overlaps the anterior and ventral regions of a body or body part. BSPO:wd BSPO:0000028 Anatomical region that overlaps the posterior and lateral regions of the body or body part. Melissa Haendel 2009-06-15T01:06:01Z posterolateral region spatial BSPO:0000028 postero-lateral region BSPO:0000028 Anatomical region that overlaps the posterior and lateral regions of the body or body part. BSPO:wd BSPO:0000029 Anatomical region that overlaps the anterior and lateral regions of a body or body part. Melissa Haendel 2009-06-15T01:07:18Z anterolateral region spatial BSPO:0000029 antero-lateral region BSPO:0000029 Anatomical region that overlaps the anterior and lateral regions of a body or body part. BSPO:wd BSPO:0000030 Anatomical region that overlaps the posterior and dorsal regions of the body or body part. Melissa Haendel 2009-06-15T01:08:13Z posterodorsal region spatial BSPO:0000030 postero-dorsal region BSPO:0000030 Anatomical region that overlaps the posterior and dorsal regions of the body or body part. BSPO:wd BSPO:0000031 spatial BSPO:0000031 upper region BSPO:0000031 BSPO:0000032 spatial BSPO:0000032 lower region BSPO:0000032 BSPO:0000033 Anatomical region located deep within an organism or structure. spatial BSPO:0000033 deep region BSPO:0000033 Anatomical region located deep within an organism or structure. BSPO:wd BSPO:0000034 Anatomical region superficially located on the body or body part. spatial BSPO:0000034 superficial region BSPO:0000034 Anatomical region superficially located on the body or body part. BSPO:wd BSPO:0000035 Anatomical region that overlaps the posterior and ventral regions of a body or body part. Melissa Haendel 2009-06-15T01:08:38Z posteroventral region spatial BSPO:0000035 postero-ventral region BSPO:0000035 Anatomical region that overlaps the posterior and ventral regions of a body or body part. BSPO:wd BSPO:0000036 Melissa Haendel 2009-06-16T08:49:03Z anterior-most anteriormost spatial BSPO:0000036 anterior-most region BSPO:0000036 BSPO:0000037 Melissa Haendel 2009-06-16T08:49:50Z posterior-most posteriormost spatial BSPO:0000037 posterior-most region BSPO:0000037 BSPO:0000038 Melissa Haendel 2009-06-16T08:50:26Z dorsal-most dorsalmost spatial BSPO:0000038 dorsal-most region BSPO:0000038 BSPO:0000039 Melissa Haendel 2009-06-16T08:51:07Z ventral-most ventralmost spatial BSPO:0000039 ventral-most region BSPO:0000039 BSPO:0000040 spatial BSPO:0000040 upper/lower compartment boundary BSPO:0000040 BSPO:0000041 spatial BSPO:0000041 deep/superficial compartment boundary BSPO:0000041 BSPO:0000042 Anatomical margin that is located on the antero-medial region of the body or body part. Melissa Haendel 2009-09-10T08:49:57Z anteromedial margin spatial BSPO:0000042 antero-medial margin BSPO:0000042 Anatomical margin that is located on the antero-medial region of the body or body part. BSPO:wd BSPO:0000043 spatial BSPO:0000043 apical/basal compartment boundary BSPO:0000043 BSPO:0000044 spatial BSPO:0000044 proximal/distal compartment boundary BSPO:0000044 BSPO:0000045 Anatomical margin that is located on the antero-lateral region of the body or body part. Melissa Haendel 2009-09-10T08:50:37Z anterolateral margin spatial BSPO:0000045 antero-lateral margin BSPO:0000045 Anatomical margin that is located on the antero-lateral region of the body or body part. BSPO:wd BSPO:0000046 Anatomical margin that is located on the postero-medial region of the body or body part. Melissa Haendel 2009-09-10T08:51:07Z posteromedial margin spatial BSPO:0000046 postero-medial margin BSPO:0000046 Anatomical margin that is located on the postero-medial region of the body or body part. BSPO:wd BSPO:0000047 Anatomical margin that is located on the postero-lateral region of the body or body part. Melissa Haendel 2009-09-10T08:51:42Z posterolateral margin spatial BSPO:0000047 postero-lateral margin BSPO:0000047 Anatomical margin that is located on the postero-lateral region of the body or body part. BSPO:wd BSPO:0000048 Anatomical margin that is located on the dorso-medial region of the body or body part. Melissa Haendel 2009-09-10T08:52:04Z dorso-medial margin spatial BSPO:0000048 dorso-medial margin BSPO:0000048 Anatomical margin that is located on the dorso-medial region of the body or body part. BSPO:wd BSPO:0000049 Anatomical margin that is located on the ventro-medial region of the body or body part. Melissa Haendel 2009-09-10T08:52:48Z ventromedial margin spatial BSPO:0000049 ventro-medial margin BSPO:0000049 Anatomical margin that is located on the ventro-medial region of the body or body part. BSPO:wd BSPO:0000050 Anatomical region that overlaps the anterior and medial regions of the body or body part. Melissa Haendel 2009-09-10T08:55:32Z anteromedial region spatial BSPO:0000050 antero-medial region BSPO:0000050 Anatomical region that overlaps the anterior and medial regions of the body or body part. BSPO:wd BSPO:0000051 Material anatomical entity defined by change in the value of some quantity per unit of distance across some spatial axis. FBql:00005254 spatial BSPO:0000051 anatomical gradient BSPO:0000051 Material anatomical entity defined by change in the value of some quantity per unit of distance across some spatial axis. BSPO:cjm BSPO:0000052 Anatomical gradient that is distributed along the anterior-posterior axis. FBcv:0000142 FBql:00005256 spatial BSPO:0000052 anterior-posterior gradient BSPO:0000052 Anatomical gradient that is distributed along the anterior-posterior axis. BSPO:wd BSPO:0000053 Anatomical gradient that is distributed along the dorsal-ventral axis. FBcv:0000143 FBql:00005255 spatial BSPO:0000053 dorsal-ventral gradient BSPO:0000053 Anatomical gradient that is distributed along the dorsal-ventral axis. BSPO:wd BSPO:0000054 An anatomical region bounded by a plane perpendicular to an axis through the middle. FBql:00005841 spatial BSPO:0000054 anatomical side BSPO:0000054 An anatomical region bounded by a plane perpendicular to an axis through the middle. BSPO:cjm BSPO:0000055 An anatomical region that is the entire part of an anatomical structure anterior to a transverse plane and bounded on one side by the same transverse plane. FBcv:0000053 FBql:00005848 anterior rostral spatial BSPO:0000055 anterior side BSPO:0000055 An anatomical region that is the entire part of an anatomical structure anterior to a transverse plane and bounded on one side by the same transverse plane. BSPO:RW BSPO:0000056 An anatomical region that is the entire part of an anatomical structure posterior to a transverse plane and bounded on one side by the same transverse plane. FBcv:0000065 FBql:00005849 posterior caudal spatial BSPO:0000056 posterior side BSPO:0000056 An anatomical region that is the entire part of an anatomical structure posterior to a transverse plane and bounded on one side by the same transverse plane. BSPO:RW BSPO:wd caudal BSPO:0000057 Anatomical side that is located on the apical end of an organism or structure. FBcv:0000054 FBql:00005854 apical spatial BSPO:0000057 apical side BSPO:0000057 Anatomical side that is located on the apical end of an organism or structure. BSPO:wd BSPO:0000058 Anatomical side that is located on the basal end of an organism or structure. FBcv:0000055 FBql:00005855 basal spatial BSPO:0000058 The part of the organism attached to a substrate. Axis of symmetry. basal side BSPO:0000058 Anatomical side that is located on the basal end of an organism or structure. BSPO:wd BSPO:0000059 Anatomical side that is centrally located on an organism or structure. FBcv:0000056 FBql:00015851 central spatial BSPO:0000059 central is not an axis direction central side BSPO:0000059 Anatomical side that is centrally located on an organism or structure. BSPO:wd BSPO:0000060 On the opposite side. FBcv:0000057 FBql:00005851 contralateral spatial BSPO:0000060 inherited from flybase cv. not clear how this would be used. Suggest we obsolete, and use the corresponding relation. contralateral side BSPO:0000060 On the opposite side. BSPO:cjm BSPO:0000061 FBcv:0000066 FBql:00005852 proximal spatial BSPO:0000061 proximal side BSPO:0000061 BSPO:0000062 Anatomical side that is distally located on an organism or structure. FBcv:0000058 FBql:00005853 distal spatial BSPO:0000062 distal side BSPO:0000062 Anatomical side that is distally located on an organism or structure. BSPO:wd BSPO:0000063 An anatomical region that is the entire part of an anatomical structure dorsal to a horizontal plane and bounded on one side by the same transverse plane. FBcv:0000059 FBql:00005842 dorsal spatial BSPO:0000063 dorsal side BSPO:0000063 An anatomical region that is the entire part of an anatomical structure dorsal to a horizontal plane and bounded on one side by the same transverse plane. BSPO:wd BSPO:0000064 Anatomical region that overlaps the posterior and medial regions of the body or body part. Melissa Haendel 2009-09-10T08:56:39Z posteromedial region spatial BSPO:0000064 postero-medial region BSPO:0000064 Anatomical region that overlaps the posterior and medial regions of the body or body part. BSPO:wd BSPO:0000065 On the same side FBcv:0000062 FBql:00005850 ipsilateral spatial BSPO:0000065 inherited from flybase cv. not clear how this would be used. Suggest we obsolete, and use the corresponding relation. ipsilateral side BSPO:0000065 On the same side BSPO:cjm BSPO:0000066 FBcv:0000063 FBql:00005844 lateral spatial BSPO:0000066 lateral side BSPO:0000066 BSPO:0000067 FBcv:0000064 FBql:00005847 medial spatial BSPO:0000067 a point in the centre of the organism (where the left-right axis intersects the midsagittal plane) medial side BSPO:0000067 BSPO:0000068 An anatomical region that is the entire part of an anatomical structure ventral to a horizontal plane and bounded on one side by the same horizontal plane. FBcv:0000070 FBql:00005843 ventral spatial BSPO:0000068 ventral side BSPO:0000068 An anatomical region that is the entire part of an anatomical structure ventral to a horizontal plane and bounded on one side by the same horizontal plane. BSPO:RW BSPO:wd BSPO:0000069 Anatomical region that overlaps the dorsal and medial regions of the body or body part. Melissa Haendel 2009-09-10T08:57:22Z dorsomedial region spatial BSPO:0000069 dorso-medial region BSPO:0000069 Anatomical region that overlaps the dorsal and medial regions of the body or body part. BSPO:wd BSPO:0000070 A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. FBql:00005841 spatial BSPO:0000070 to be merged into CARO anatomical region BSPO:0000070 A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. BSPO:cjm BSPO:0000071 Anatomical region anteriorly located on the body or body part. FBql:00005848 spatial BSPO:0000071 anterior region BSPO:0000071 Anatomical region anteriorly located on the body or body part. BSPO:wd BSPO:0000072 Anatomical region posteriorly located on the body or body part. FBql:00005849 spatial BSPO:0000072 posterior region BSPO:0000072 Anatomical region posteriorly located on the body or body part. BSPO:wd BSPO:0000073 Anatomical region located on the apical end on the body or body part. FBql:00005854 spatial BSPO:0000073 apical region BSPO:0000073 Anatomical region located on the apical end on the body or body part. BSPO:wd BSPO:0000074 Anatomical region located basally on the body or body part. FBql:00005855 spatial BSPO:0000074 basal region BSPO:0000074 Anatomical region located basally on the body or body part. BSPO:wd BSPO:0000075 Anatomical region centrally located on the body or body part. FBql:00015851 spatial BSPO:0000075 central region BSPO:0000075 Anatomical region centrally located on the body or body part. BSPO:wd BSPO:0000076 FBql:00005851 spatial BSPO:0000076 inherited from flybase cv. not clear how this would be used contralateral region BSPO:0000076 BSPO:0000077 Anatomical region proximally located on the body or body part. FBql:00005852 spatial BSPO:0000077 proximal region BSPO:0000077 Anatomical region proximally located on the body or body part. BSPO:wd BSPO:0000078 Anatomical region distally located on the body or body part. FBql:00005853 spatial BSPO:0000078 distal region BSPO:0000078 Anatomical region distally located on the body or body part. BSPO:wd BSPO:0000079 Anatomical region dorsally located on the body or body part. FBql:00005842 spatial BSPO:0000079 dorsal region BSPO:0000079 Anatomical region dorsally located on the body or body part. BSPO:wd BSPO:0000080 Anatomical region that overlaps the dorsal and lateral regions of a body or body part. FBql:00005845 dorsolateral region spatial BSPO:0000080 dorso-lateral region BSPO:0000080 Anatomical region that overlaps the dorsal and lateral regions of a body or body part. BSPO:wd BSPO:0000081 FBql:00005850 spatial BSPO:0000081 ipsilateral region BSPO:0000081 BSPO:0000082 Anatomical region laterally located on the body or body part. FBql:00005844 spatial BSPO:0000082 lateral region BSPO:0000082 Anatomical region laterally located on the body or body part. BSPO:wd BSPO:0000083 Anatomical region medially located on the body or body part. FBql:00005847 spatial BSPO:0000083 medial region BSPO:0000083 Anatomical region medially located on the body or body part. BSPO:wd BSPO:0000084 Anatomical region ventrally located on the body or body part. FBql:00005843 spatial BSPO:0000084 ventral region BSPO:0000084 Anatomical region ventrally located on the body or body part. BSPO:wd BSPO:0000085 Anatomical region that overlaps the ventral and lateral regions of a body or body part. FBql:00005846 ventrolateral region spatial BSPO:0000085 This is an example of a composition of two axis positions. ventro-lateral region BSPO:0000085 Anatomical region that overlaps the ventral and lateral regions of a body or body part. BSPO:wd BSPO:0000086 FBql:00005873 FMA:9647 spatial BSPO:0000086 to be merged into CARO anatomical compartment BSPO:0000086 BSPO:0000087 FBcv:0000031 FBql:00005874 spatial BSPO:0000087 anterior compartment BSPO:0000087 BSPO:0000088 FBcv:0000032 FBql:00005878 spatial BSPO:0000088 compartment boundary BSPO:0000088 BSPO:0000089 FBcv:0000035 FBql:00005876 spatial BSPO:0000089 dorsal compartment BSPO:0000089 BSPO:0000090 FBcv:0000036 FBql:00005875 spatial BSPO:0000090 posterior compartment BSPO:0000090 BSPO:0000091 FBcv:0000037 FBql:00005877 spatial BSPO:0000091 ventral compartment BSPO:0000091 BSPO:0000092 FBql:00005881 spatial BSPO:0000092 to be merged into CARO anatomical compartment boundary BSPO:0000092 BSPO:0000093 FBcv:0000033 FBql:00005880 spatial BSPO:0000093 anterior/posterior compartment boundary BSPO:0000093 BSPO:0000094 FBcv:0000034 FBql:00005879 spatial BSPO:0000094 dorsal/ventral compartment boundary BSPO:0000094 BSPO:0000112 The region corresponding to the ventral region of the entity, towards the midline. Melissa Haendel 2009-09-10T08:57:54Z medioventral region ventromedial region spatial BSPO:0000112 ventro-medial region BSPO:0000112 The region corresponding to the ventral region of the entity, towards the midline. BSPO:wd BSPO:0000127 Anatomical region peripherally located on the body or body part. spatial BSPO:0000127 peripheral region BSPO:0000127 Anatomical region peripherally located on the body or body part. BSPO:wd BSPO:0000128 spatial BSPO:0000128 axial region BSPO:0000128 BSPO:0000129 spatial BSPO:0000129 peripheral side BSPO:0000129 BSPO:0000130 spatial BSPO:0000130 axial side BSPO:0000130 BSPO:0000195 An anatomical axis that extends from the side of the anatomical entity that is closer to an axis (adaxial) to the side that is further from the same axis (abaxial). wasila.dahdul 2013-07-02T11:20:29Z AA axis spatial dorsal-ventral axis BSPO:0000195 adaxial-abaxial axis BSPO:0000195 An anatomical axis that extends from the side of the anatomical entity that is closer to an axis (adaxial) to the side that is further from the same axis (abaxial). BSPO:RW BSPO:0000196 An anatomical axis that extends from the center of the body outwards or externally. wasila.dahdul 2013-07-02T11:21:42Z spatial proximal-distal axis BSPO:0000196 The medial-external axis could apply to a sphere-shaped body. medial-external axis BSPO:0000196 An anatomical axis that extends from the center of the body outwards or externally. BSPO:curators BSPO:0000197 An anatomical axis that is perpendicular to an apical/basal axis or proximal/distal axis and extends from the center of an axis (shoot axis or root in the case of plants) to any point on the exterior of the axis. wasila.dahdul 2013-07-02T11:23:31Z M-R axis MR axis spatial BSPO:0000197 In plants, lateral growth (http://purl.obolibrary.org/obo/GO_0080190) run is along the medial/radial axis (from medial to radial) [RW]. Also applies to radially symmetrical animals such as sea urchins, cnidarians [PM] or applies to more-or-less cylindrical body parts in animals, like limbs. medial-radial axis BSPO:0000197 An anatomical axis that is perpendicular to an apical/basal axis or proximal/distal axis and extends from the center of an axis (shoot axis or root in the case of plants) to any point on the exterior of the axis. BSPO:curators BSPO:0000198 An axis that extends from the oral opening to the furthest point in an organism that is directly opposite. wasila.dahdul 2013-07-02T11:29:33Z spatial BSPO:0000198 oral-aboral axis BSPO:0000198 An axis that extends from the oral opening to the furthest point in an organism that is directly opposite. BSPO:PM BSPO:0000199 An axis that extends from the animal end of an egg or early embryo to the opposite, vegetal end. In animals with yolk-bearing eggs, the vegetal end is the yolk bearing pole. (pertains to animals only - both vertebrate and invertebrate embryos). wasila.dahdul 2013-07-02T11:30:13Z A-V axis AV axis animal/vegetal axis spatial BSPO:0000199 animal-vegetal axis BSPO:0000199 An axis that extends from the animal end of an egg or early embryo to the opposite, vegetal end. In animals with yolk-bearing eggs, the vegetal end is the yolk bearing pole. (pertains to animals only - both vertebrate and invertebrate embryos). BSPO:PM BSPO:0000200 An axis of a plant structure that is determined by the direction of apical growth, either by an apical meristem or an apical cell. Apical is toward the direction of apical growth: toward the tip of a growing shoot axis, root, thallus, or non-vascular leaf. Basal is away from the direction of apical growth: toward the root-shoot junction in the case of the primary root or stem, toward the primary root or stem for higher order roots or branches, toward the point of attachment for non-vascular leaves, and toward the original point of growth (as determined in the embryo) for thalli. spatial BSPO:0000200 Plant structures that do not grow from an apical meristem, such as vascular leaves or petals, should be described using the proximal-distal axis. The proximal-distal axis may also be used for branches or lateral roots, and, in those cases, is concordant with the apical-basal axis. apical-basal axis relative to direction of growth BSPO:0000200 An axis of a plant structure that is determined by the direction of apical growth, either by an apical meristem or an apical cell. Apical is toward the direction of apical growth: toward the tip of a growing shoot axis, root, thallus, or non-vascular leaf. Basal is away from the direction of apical growth: toward the root-shoot junction in the case of the primary root or stem, toward the primary root or stem for higher order roots or branches, toward the point of attachment for non-vascular leaves, and toward the original point of growth (as determined in the embryo) for thalli. BSPO:RW BSPO:0000201 Anatomical plane that is perpendicular to a radial plane. wasila.dahdul 2014-01-22T15:34:31Z spatial BSPO:0000201 Need to add logical definitions. tangential plane BSPO:0000201 Anatomical plane that is perpendicular to a radial plane. BSPO:wd BSPO:0000202 Anatomical plane that follows the two dimensions specified by an apical-basal axis relative to direction of growth and a medial-lateral axis. wasila.dahdul 2014-01-22T15:34:02Z spatial BSPO:0000202 Need to add logical definitions. radial plane BSPO:0000202 Anatomical plane that follows the two dimensions specified by an apical-basal axis relative to direction of growth and a medial-lateral axis. BSPO:wd BSPO:0000371 Anatomical surface that is located on the anterior side of the body or body part. FBql:00005848 spatial BSPO:0000371 anterior surface BSPO:0000371 Anatomical surface that is located on the anterior side of the body or body part. BSPO:wd BSPO:0000372 Anatomical surface that is located on the posterior side of the body or body part. FBql:00005849 spatial BSPO:0000372 posterior surface BSPO:0000372 Anatomical surface that is located on the posterior side of the body or body part. BSPO:wd BSPO:0000373 Anatomical surface that is located on the apical side of the body or body part. FBql:00005854 spatial BSPO:0000373 apical surface BSPO:0000373 Anatomical surface that is located on the apical side of the body or body part. BSPO:wd BSPO:0000374 Anatomical surface that is located on the basal side of the body or body part. FBql:00005855 spatial BSPO:0000374 basal surface BSPO:0000374 Anatomical surface that is located on the basal side of the body or body part. BSPO:wd BSPO:0000376 FBql:00005851 spatial BSPO:0000376 contralateral surface BSPO:0000376 BSPO:0000377 Anatomical surface that is located on the proximal side of the body or body part. FBql:00005852 spatial BSPO:0000377 proximal surface BSPO:0000377 Anatomical surface that is located on the proximal side of the body or body part. BSPO:wd BSPO:0000378 Anatomical surface that is located on the distal side of the body or body part. FBql:00005853 spatial BSPO:0000378 distal surface BSPO:0000378 Anatomical surface that is located on the distal side of the body or body part. BSPO:wd BSPO:0000379 Anatomical surface that located on the dorsal side of the body or body part. FBql:00005842 spatial BSPO:0000379 dorsal surface BSPO:0000379 Anatomical surface that located on the dorsal side of the body or body part. BSPO:wd BSPO:0000381 Anatomical surface that is located on the same side of an organism or structure. FBql:00005850 spatial BSPO:0000381 ipsilateral surface BSPO:0000381 Anatomical surface that is located on the same side of an organism or structure. BSPO:wd BSPO:0000382 Anatomical surface that located on the lateral side of the body or body part. FBql:00005844 spatial BSPO:0000382 lateral surface BSPO:0000382 Anatomical surface that located on the lateral side of the body or body part. BSPO:wd BSPO:0000383 Anatomical surface that located on the medial side of the body or body part. FBql:00005847 spatial BSPO:0000383 medial surface BSPO:0000383 Anatomical surface that located on the medial side of the body or body part. BSPO:wd BSPO:0000384 Anatomical surface that is located on the ventral side of the body or body part. FBql:00005843 spatial BSPO:0000384 ventral surface BSPO:0000384 Anatomical surface that is located on the ventral side of the body or body part. BSPO:wd BSPO:0000400 A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions. FMA:242982 anatomical cross-section anatomical section plane section spatial cross-section BSPO:0000400 These anatomical sections are applicable to most bilaterally symmetrical animals, but bipedal animals such as humans have more complex usage of these terms. For example, in post-embryonic humans a coronal plane is vertical and a transverse plane is horizontal, but for embryos and quadrupeds a coronal plane is horizontal and a transverse plane is vertical. anatomical plane BSPO:0000400 A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions. BSPO:cjm BSPO:0000417 Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size. FMA:11361 left/right plane median plane sagittal section spatial BSPO:0000417 sagittal plane BSPO:0000417 Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size. BSPO:DOS BSPO:cjm BSPO:mah BSPO:0000671 Anatomical margin that is located on the anterior side of a body or body part. spatial BSPO:0000671 anterior margin BSPO:0000671 Anatomical margin that is located on the anterior side of a body or body part. BSPO:wd BSPO:0000672 Anatomical margin that is located on the posterior side of the body or body part. spatial BSPO:0000672 posterior margin BSPO:0000672 Anatomical margin that is located on the posterior side of the body or body part. BSPO:wd BSPO:0000673 Anatomical margin that is located on the apical side of the body or body part. spatial BSPO:0000673 apical margin BSPO:0000673 Anatomical margin that is located on the apical side of the body or body part. BSPO:wd BSPO:0000674 Anatomical margin that is located on the basal side of the body or body part. spatial BSPO:0000674 basal margin BSPO:0000674 Anatomical margin that is located on the basal side of the body or body part. BSPO:wd BSPO:0000677 Anatomical margin that is located on the proximal region of the body or body part. spatial BSPO:0000677 proximal margin BSPO:0000677 Anatomical margin that is located on the proximal region of the body or body part. BSPO:wd BSPO:0000678 Anatomical margin that is located on the distal side of the body or body part. spatial BSPO:0000678 distal margin BSPO:0000678 Anatomical margin that is located on the distal side of the body or body part. BSPO:wd BSPO:0000679 Anatomical margin that is located on the dorsal side of body or body part. spatial BSPO:0000679 dorsal margin BSPO:0000679 Anatomical margin that is located on the dorsal side of body or body part. BSPO:wd BSPO:0000680 Anatomical margin that is located on the dorso-lateral region of the body or body part. dorsolateral margin spatial BSPO:0000680 dorso-lateral margin BSPO:0000680 Anatomical margin that is located on the dorso-lateral region of the body or body part. BSPO:wd BSPO:0000682 Anatomical margin that is located on the lateral side of the body or body part. spatial BSPO:0000682 lateral margin BSPO:0000682 Anatomical margin that is located on the lateral side of the body or body part. BSPO:wd BSPO:0000683 Anatomical margin that is located on the medial side of the body or body part. spatial BSPO:0000683 medial margin BSPO:0000683 Anatomical margin that is located on the medial side of the body or body part. BSPO:wd BSPO:0000684 Anatomical margin that is located on the ventral side of the body or body part. spatial BSPO:0000684 ventral margin BSPO:0000684 Anatomical margin that is located on the ventral side of the body or body part. BSPO:wd BSPO:0000685 Anatomical margin that is located on the ventro-lateral region of the body or body part. ventrolateral margin spatial BSPO:0000685 This is an example of a composition of two axis positions ventro-lateral margin BSPO:0000685 Anatomical margin that is located on the ventro-lateral region of the body or body part. BSPO:wd BSPO:0000686 Anatomical margin that is located on the antero-dorso region of the body or body part. anterodorsal margin spatial BSPO:0000686 antero-dorsal margin BSPO:0000686 Anatomical margin that is located on the antero-dorso region of the body or body part. BSPO:wd BSPO:0000687 Anatomical margin that is located on the postero-dorsal region of the body or body part. posterodorsal margin spatial BSPO:0000687 postero-dorsal margin BSPO:0000687 Anatomical margin that is located on the postero-dorsal region of the body or body part. BSPO:wd BSPO:0000688 Anatomical margin that is located on the antero-ventral region of the body or body part. anteroventral margin spatial BSPO:0000688 antero-ventral margin BSPO:0000688 Anatomical margin that is located on the antero-ventral region of the body or body part. BSPO:wd BSPO:0000689 Anatomical margin that is located on the postero-ventral region of the body or body part. posteroventral margin spatial BSPO:0000689 postero-ventral margin BSPO:0000689 Anatomical margin that is located on the postero-ventral region of the body or body part. BSPO:wd BSPO:0001001 An axis that extends from the center of organism to one or other side. http://upload.wikimedia.org/wikipedia/commons/3/34/Anatomical_Directions_and_Axes.JPG M-L axis ML axis medio-lateral axis mediolateral axis spatial proximal-distal axis BSPO:0001001 Properly, the ML axis is a half axis; practically, its usage is less clumsy and less linguistically biased than "left-right". The terms may still be used relatively to describe locations along the LR axis. The gills are medial to the operculum, but lateral to the heart. medial-lateral axis BSPO:0001001 An axis that extends from the center of organism to one or other side. BSPO:cjm CARO:0000000 A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. 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. spatial CARO:0000000 Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure. anatomical entity CARO:0000000 A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. CAROC:Brownsville2014 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. CARO:MAH CARO:0000003 Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. spatial CARO:0000003 Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development. anatomical structure connected anatomical structure CARO:0000003 Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CC:DOS CARO:0000006 An anatomical entity that has mass. spatial CARO:0000006 material anatomical entity CARO:0000006 An anatomical entity that has mass. CC:DOS CARO:0000007 An anatomical entity that has no mass. Anatomical entity that has no mass. spatial CARO:0000007 immaterial anatomical entity CARO:0000007 An anatomical entity that has no mass. CC:DOS CARO:0000008 A one dimensional, immaterial anatomical entity. spatial CARO:0000008 anatomical line CARO:0000008 A one dimensional, immaterial anatomical entity. CC:DOS CARO:0000010 A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. spatial CARO:0000010 anatomical boundary CARO:0000010 A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. CC:DOS CHEBI:23367 molecular entity CHEBI:24431 chemical entity CHEBI:33579 main group molecular entity CHEBI:33582 carbon group molecular entity CHEBI:33675 p-block molecular entity CHEBI:33694 biomacromolecule CHEBI:33695 information biomacromolecule CHEBI:33839 macromolecule CHEBI:36080 protein CHEBI:36357 polyatomic entity CHEBI:50860 organic molecular entity CL:0000000 cell CL:0000003 native cell CL:0000006 neuronal receptor cell CL:0000007 early embryonic cell CL:0000031 neuroblast CL:0000034 stem cell CL:0000047 neuronal stem cell CL:0000048 multi fate stem cell CL:0000055 non-terminally differentiated cell CL:0000056 myoblast CL:0000064 ciliated cell CL:0000066 epithelial cell CL:0000067 ciliated epithelial cell CL:0000075 columnar/cuboidal epithelial cell CL:0000098 sensory epithelial cell CL:0000101 sensory neuron CL:0000133 neurectodermal cell CL:0000134 mesenchymal stem cell CL:0000183 contractile cell CL:0000187 muscle cell CL:0000197 receptor cell CL:0000199 mechanoreceptor cell CL:0000210 photoreceptor cell CL:0000211 electrically active cell CL:0000219 motile cell CL:0000221 ectodermal cell CL:0000222 mesodermal cell CL:0000225 anucleate cell CL:0000255 eukaryotic cell CL:0000353 blastoderm cell CL:0000393 electrically responsive cell CL:0000404 electrically signaling cell CL:0000526 afferent neuron CL:0000540 neuron CL:0000548 animal cell CL:0000680 muscle precursor cell CL:0000710 neurecto-epithelial cell CL:0002077 ecto-epithelial cell CL:0002078 meso-epithelial cell CL:0002242 nucleate cell CL:0002319 neural cell CL:0002320 connective tissue cell CL:0002321 embryonic cell CL:0002371 somatic cell CL:0011115 precursor cell CL:2000029 central nervous system neuron CTENO:0000001 A collection of cilia attached to basal cushions and made up of polster cells. A characteristic feature of ctenophores lost in Platyctenida ctene comb plate The move- ment of the ctene plates are controlled by the apical organ, a sensory structure containing a statocyst located at the aboral pole (Tamm, 1982, for review) ctene plate CTENO:0000002 outer epidermis CTENO:0000003 gastrodermis https://en.wikipedia.org/wiki/Gastrodermis CTENO:0000004 A thick jelly-like layer between the epidermis and gastrodermis. The mesoglea is mostly acellular and composed of extracellular matrix, but it also has some muscle and mesenchymal cells. mesoglea https://en.wikipedia.org/wiki/Mesoglea CTENO:0000005 comb plate cilium CTENO:0000006 sensory cell cilium CTENO:0000007 tentacle sheath cilium CTENO:0000008 polar field cilium CTENO:0000009 auricular cilium CTENO:0000010 pharyngeal cilium CTENO:0000011 good groove cilium CTENO:0000012 balancer cilium CTENO:0000013 The statocyst is protected by a transparent dome made of long, immobile cilia. dome cilium CTENO:0000014 aboral groove cilium CTENO:0000015 mesogleal extracellular matrix extracellular matrix of mesoglea CTENO:0000016 polster cell 0 CTENO:0000017 aboral organ apical organ apical sense organ CTENO:0000018 absent in beroids Most ctenophores also bear two muscular tentacles which are used for prey capture, and ultrastruc- tural studies have shown that these structures are distinct from cnidarian tentacles (Hernandez-Nicaise, 1991) tentacle CTENO:0000019 Light-producing cell present in nearly all ctenophores photocyte CTENO:0000020 A specialized adhesive cell found in ctenophores colloblast https://en.wikipedia.org/wiki/Colloblast CTENO:0000021 A conspicuous lobed structure used for feeding, characteristic of the Lobata ("sea walnuts") oral lobe CTENO:0000022 Pleurobrachia species maintain cydippid forms as adults, but the others become radically different: M. leidyi greatly reduce their tentacles and form large oral lobes; B. ovata lack tentacles and form large oral lips that they use to engulf or nip at other ctenophores; and platyctenes become compressed in the oral-aboral direction and adopt a sessile or creeping lifestyle, crawling around the substratum rather than locomoting by beating their ctene rows. adult ctenophore Pleurobrachia species maintain cydippid forms as adults, but the others become radically different: M. leidyi greatly reduce their tentacles and form large oral lobes; B. ovata lack tentacles and form large oral lips that they use to engulf or nip at other ctenophores; and platyctenes become compressed in the oral-aboral direction and adopt a sessile or creeping lifestyle, crawling around the substratum rather than locomoting by beating their ctene rows. doi:10.1101/pdb.emo106 CTENO:0000023 A ctenophore larva cydippid larva CTENO:0000024 cydippid stage CTENO:0000025 ctenophore adult stage CTENO:0000026 A canal that is associated with a testis and an ovary meridional canal A canal that is associated with a testis and an ovary doi:10.1101/pdb.emo106 CTENO:0000027 In Bolinopsis microptera each oocyte is associated with as many as 100 nurse cells. connected to the oocyte by cytoplasmic bridges that transport cytoplasm and yolk to the oocyte (Dunlap Pianka 1974) nurse cell CTENO:0000028 ectoplasm CTENO:0000029 endoplasm CTENO:0000030 subcortical plasm CTENO:0000031 periodic acid Schiff positive yolk particles CTENO:0000032 gonadopore CTENO:0000033 anal pore CTENO:0000034 ctenophore anal canal CTENO:0000035 To be ceded to cnidarian anatomy ontology epitheliomuscular cell CTENO:0000036 Ribbon-shaped smooth muscle that resides between the glandular epithelial cells and the basal lamina parietal muscle CTENO:0000037 giant smooth muscle CTENO:0000038 mesogleal muscle CTENO:0000039 longitudinal mesogleal muscle CTENO:0000040 circumferential mesogleal muscle CTENO:0000041 radial mesogleal muscle CTENO:0000042 Within the tentacles themselves are mesogleal muscles that are constantly being produced from cells at the base of the tentacle. We need to distinguish between muscles that are part of the tentacle proper and the mesogleal component (see mesogleal muscles) tentacular muscle CTENO:0000043 A muscle that connects the two tentacle apparatuses trans-tentacular muscle CTENO:0000044 tentilla CTENO:0000045 The only description of striated muscle is in the tentilla of Euplokamis (Chun 1880) striated muscle of tentilla CTENO:0000046 cross the basal lamina and run through the mesoglea mesogleal nerve fiber CTENO:0000047 subepidermal nerve net https://en.wikipedia.org/wiki/Nerve_net CTENO:0000048 subgastrodermal nerve gastrodermal nerve CTENO:0000049 mesoglea of tentacle CTENO:0000050 characterized by a single thin ciliary projection tastborsten cell CTENO:0000051 hoplocyst possess one or several short pointed pegs taststiften cell CTENO:0000052 nerve network cell CTENO:0000053 nerve fiber of mesoglea of tentacle CTENO:0000054 oral pole CTENO:0000055 Genes: MlIslet apical organ floor CTENO:0000056 A mineralized cell generated and constantly replaced in the floor of the apical organ. They are supported on top of the balancing cilia that make up the gravity-sensing statocyst of the apical organ. control the posture of the animal lithocyte CTENO:0000057 balancer cell CTENO:0000058 covered by a dome of nonmotile cilia apical organ statolith CTENO:0000059 tentacular nerve CTENO:0000060 epithelial papilla CTENO:0000061 mnemiopsin emits light in the presence of calcium ions (Ward and Seliger 1974). photoprotein CTENO:0000062 One of of four nearly identical quadrants organized along the oral-aboral axis. Each of the four quadrants is derived largely from one cell of the four-cell-stage embryo. At the eight-cell stage each quadrant contains a single E ("end") and M ("middle") blastomere. Subsequently, micromeres are formed first at the aboral pole and later at the oral pole. Two orthogonal planes run along the oral–aboral axis which define four quadrants (Fig. quadrant One of of four nearly identical quadrants organized along the oral-aboral axis. Each of the four quadrants is derived largely from one cell of the four-cell-stage embryo. At the eight-cell stage each quadrant contains a single E ("end") and M ("middle") blastomere. Subsequently, micromeres are formed first at the aboral pole and later at the oral pole. PMID:10525332 CTENO:0000063 ctenophore blastomere CTENO:0000064 E macromere, 8 cell stage CTENO:0000065 M blastomere CTENO:0000066 micromere CTENO:0000067 2M macromere CTENO:0000068 3E macromere CTENO:0000069 circumpharyngeal muscle cell CTENO:0000070 EM macromere, 4 cell stage CTENO:0000071 EM-slash blastomere CTENO:0000072 EM-backslash blastomere CTENO:0000073 M-slash blastomere CTENO:0000074 M-blackslash blastomere CTENO:0000075 macromere CTENO:0000076 1M macromere, 16 cell stage CTENO:0000078 2E macromere, 32 cell stage CTENO:0000079 3M macromere CTENO:0000081 M macromere, 8 cell stage CTENO:0000082 macromere, 8 cell stage CTENO:0000083 M-backslash macromere CTENO:0000084 M-slash macromere CTENO:0000085 macromere, 16 cell stage CTENO:0000086 1E macromere, 16 cell stage CTENO:0000087 32 cell stage refers to time of birth. 2M cells persist macromere, 32 cell stage and above CTENO:0000088 2M cells persist macromere, 60 cell stage CTENO:0000090 1M-backslash macromere, 16 cell stage CTENO:0000091 1M-slash macromere, 16 cell stage CTENO:0000092 2M-slash macromere CTENO:0000093 2M-backslash macromere CTENO:0000094 3M-slash macromere, 60 cell stage CTENO:0000095 3M-backslash macromere, 30 cell stage CTENO:0000096 micromere, 16 cell stage CTENO:0000097 micromere, 32 cell stage CTENO:0000098 micromere, 60 cell stage CTENO:0000099 e1 micromere CTENO:0000100 m1 micromere CTENO:0000101 m2 micromere CTENO:0000102 m11 micromere CTENO:0000103 m12 micromere CTENO:0000104 e2 micromere CTENO:0000105 e11 and m11 lie closest to sagittal plane e11 micromere CTENO:0000106 e12 micromere CTENO:0000107 m21 micromere CTENO:0000108 m22 micromere CTENO:0000109 m121 micromere CTENO:0000110 m122 micromere CTENO:0000111 e3 micromere CTENO:0000112 e22 micromere CTENO:0000113 e21 micromere CTENO:0000114 m111 micromere CTENO:0000115 m112 micromere CTENO:0000116 ctenophore 16 cell stage CTENO:0000117 ctenophore 32 cell stage CTENO:0000118 ctenophore 60 cell stage CTENO:0000119 micromere, formed during gastulation CTENO:0000120 tentacle epithelium CTENO:0000121 tentacle sheath CTENO:0000122 An ectodermal structure which connects the mouth to the endodermal component of the gut, deep inside the animal ctenophore pharynx CTENO:0000123 tentacle sheath cell CTENO:0000124 longitudinal mesogleal muscle cell CTENO:0000125 radial mesogleal muscle cell CTENO:0000126 A multipolar mesenchymal cell found in the stellate mesenchyme. May be phagocytic. absent in derivatives of 2M? macromeres. stellate mesenchymal cell CTENO:0000127 tentacle muscle cell CTENO:0000128 longitudinal pharyngeal muscle cell CTENO:0000130 trans-tentacular muscle cell CTENO:0000131 apical organ ctene row muscle CTENO:0000132 E-lineage cell CTENO:0000133 M-lineage cell CTENO:0000134 reserve lithocyte lithocyte progenitor CTENO:0000135 esophageal plane sagittal plane plane of first cleavage (Freeman 1977) adesophageal plane CTENO:0000136 The plane of second cleavage includes the tentacular axis tentacular axis CTENO:0000137 A row that is composed of individual ctene plates, which are arranged in longitudinal rows parallel to the oral–aboral axis comb row ctene row CTENO:0000138 a balance sensor consisting of a statolith, a solid particle supported on four bundles of cilia, called "balancers", that sense its orientation apical organ statocyst CTENO:0000139 A groove that runs along the surface of the animal to each of the eight ctene rows ciliated furrow ciliated groove CTENO:0000140 tentacular plane CTENO:0000141 slash quadrant CTENO:0000142 backslash quadrant CTENO:0000143 tentacle bulb CTENO:0000145 an ectodermal structure emanating from the apical organ along the esophageal axis. polar field CTENO:0000146 polar field cell CTENO:0000147 esophague-tentacle muscle cell CTENO:0000148 anal canal cell CTENO:0000149 tentacle-apical organ muscle cell CTENO:0000150 oral side of organism CTENO:0000151 aboral part of organism CTENO:0000152 tentacle apparatus CTENO:0000153 endodermal canal CTENO:0000154 mixed E and M lineage structure CTENO:0000155 pharyngeal muscle CTENO:0000156 Genes: MlLhx1/5 ctenophore blastopore GO:0001649 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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. molecular function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use 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 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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. GOC:pdt GO:0005575 cellular_component GO:0005576 extracellular region GO:0005622 intracellular GO:0005623 cell GO:0005634 GO:0005737 cytoplasm GO:0005902 GO:0005929 cilium GO:0008150 A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. 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. jl 2012-09-19T15:05:24Z Wikipedia:Biological_process biological process physiological 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 use 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 A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. 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. GOC:pdt true Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. Reactome:R-HSA-6788855 Reactome:R-HSA-6788867 phosphokinase activity GO:0016301 Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. kinase activity GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. ISBN:0198506732 Reactome:R-HSA-6788855 FN3KRP phosphorylates PsiAm, RibAm Reactome:R-HSA-6788867 FN3K phosphorylates ketosamines GO:0016477 GO:0017145 GO:0019226 GO:0030154 GO:0030182 GO:0030855 GO:0031012 extracellular matrix GO:0032838 cell projection cytoplasm GO:0040011 locomotion GO:0042613 GO:0042995 cell projection GO:0043226 organelle GO:0043230 extracellular organelle GO:0044420 extracellular matrix component GO:0044421 extracellular region part GO:0044422 organelle part GO:0044424 intracellular part GO:0044441 ciliary part GO:0044444 cytoplasmic part GO:0044463 cell projection part GO:0044464 cell part GO:0045444 GO:0048870 GO:0050906 GO:0050962 GO:0050974 GO:0055007 GO:0060591 GO:0099568 cytoplasmic region IAO:0000027 data item data item IAO:0000030 information content entity information content entity IAO:0000078 curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification IAO:0000102 data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part IAO:0000225 obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification IAO:0000409 denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type NCBITaxon:10197 comb jellies sea walnuts Coelenterata coelenterates ctenophores NCBITaxon:10197 Ctenophora NCBITaxon:10197 comb jellies sea walnuts Coelenterata coelenterates ctenophores NCBITaxon:10199 NCBITaxon:10199 Beroe NCBITaxon:10199 NCBITaxon:10200 NCBITaxon:10200 Beroe mitrata NCBITaxon:10200 NCBITaxon:10201 NCBITaxon:10201 Beroe ovata NCBITaxon:10201 NCBITaxon:127144 NCBITaxon:127144 Lampocteis NCBITaxon:127144 NCBITaxon:127145 NCBITaxon:127145 Lampocteis cruentiventer NCBITaxon:127145 NCBITaxon:12996 NCBITaxon:12996 Cestum NCBITaxon:12996 NCBITaxon:12997 Cestus veneris NCBITaxon:12997 Cestum veneris NCBITaxon:12997 Cestus veneris NCBITaxon:131567 biota NCBITaxon:131567 cellular organisms NCBITaxon:131567 biota NCBITaxon:140453 NCBITaxon:140453 Beroe forskalii NCBITaxon:140453 NCBITaxon:140454 NCBITaxon:140454 Beroe gracilis NCBITaxon:140454 NCBITaxon:140455 NCBITaxon:140455 Bolinopsis infundibulum NCBITaxon:140455 NCBITaxon:140456 NCBITaxon:140456 Hormiphora plumosa NCBITaxon:140456 NCBITaxon:140457 NCBITaxon:140457 Pleurobrachia pileus NCBITaxon:140457 NCBITaxon:140460 NCBITaxon:140460 Mertensiidae NCBITaxon:140460 NCBITaxon:140461 NCBITaxon:140461 Charistephane NCBITaxon:140461 NCBITaxon:140462 NCBITaxon:140462 Charistephane fugiens NCBITaxon:140462 NCBITaxon:140463 NCBITaxon:140463 Callianira NCBITaxon:140463 NCBITaxon:140464 NCBITaxon:140464 Callianira cristata NCBITaxon:140464 NCBITaxon:140465 NCBITaxon:140465 Haeckeliidae NCBITaxon:140465 NCBITaxon:140466 NCBITaxon:140466 Aulacoctena NCBITaxon:140466 NCBITaxon:140467 NCBITaxon:140467 Aulacoctena acuminata NCBITaxon:140467 NCBITaxon:140468 NCBITaxon:140468 Haeckelia NCBITaxon:140468 NCBITaxon:140469 NCBITaxon:140469 Haeckelia beehleri NCBITaxon:140469 NCBITaxon:140470 NCBITaxon:140470 Haeckelia rubra NCBITaxon:140470 NCBITaxon:140471 NCBITaxon:140471 Platyctenida NCBITaxon:140471 NCBITaxon:140472 NCBITaxon:140472 Coeloplanidae NCBITaxon:140472 NCBITaxon:140473 NCBITaxon:140473 Coeloplana NCBITaxon:140473 NCBITaxon:140474 Coeloplana banwarthii NCBITaxon:140474 Coeloplana bannwarthii NCBITaxon:140474 Coeloplana banwarthii NCBITaxon:140475 NCBITaxon:140475 Leucotheidae NCBITaxon:140475 NCBITaxon:140476 NCBITaxon:140476 Leucothea NCBITaxon:140476 NCBITaxon:140477 NCBITaxon:140477 Leucothea pulchra NCBITaxon:140477 NCBITaxon:140478 NCBITaxon:140478 Ocyropsidae NCBITaxon:140478 NCBITaxon:140479 NCBITaxon:140479 Ocyropsis NCBITaxon:140479 NCBITaxon:140480 NCBITaxon:140480 Ocyropsis crystallina NCBITaxon:140480 NCBITaxon:140481 NCBITaxon:140481 Ocyropsis crystallina crystallina NCBITaxon:140481 NCBITaxon:140482 NCBITaxon:140482 Ocyropsis crystallina guttata NCBITaxon:140482 NCBITaxon:140483 NCBITaxon:140483 Ocyropsis maculata NCBITaxon:140483 NCBITaxon:140484 NCBITaxon:140484 Thalassocalycida NCBITaxon:140484 NCBITaxon:140485 NCBITaxon:140485 Thalassocalycidae NCBITaxon:140485 NCBITaxon:140486 NCBITaxon:140486 Thalassocalyce NCBITaxon:140486 NCBITaxon:140487 NCBITaxon:140487 Thalassocalyce inconstans NCBITaxon:140487 NCBITaxon:140488 NCBITaxon:140488 Vallicula NCBITaxon:140488 NCBITaxon:140489 Vallicula multiformia NCBITaxon:140489 Vallicula multiformis NCBITaxon:140489 Vallicula multiformia NCBITaxon:140490 NCBITaxon:140490 Velamen NCBITaxon:140490 NCBITaxon:140491 NCBITaxon:140491 Velamen parallelum NCBITaxon:140491 NCBITaxon:140492 NCBITaxon:140492 Typhlocoela NCBITaxon:140492 NCBITaxon:140493 NCBITaxon:140493 Cyclocoela NCBITaxon:140493 NCBITaxon:140495 NCBITaxon:140495 Mertensia NCBITaxon:140495 NCBITaxon:140496 NCBITaxon:140496 Mertensia ovum NCBITaxon:140496 NCBITaxon:140497 Undescribed mertensiid A Undescribed pleurobrachiid A NCBITaxon:140497 Undescribed mertensiid sp. 1 NCBITaxon:140497 Undescribed mertensiid A Undescribed pleurobrachiid A NCBITaxon:140498 Undescribed mertensiid B (At) NCBITaxon:140498 Undescribed mertensiid sp. 2 NCBITaxon:140498 Undescribed mertensiid B (At) NCBITaxon:140499 Undescribed mertensiid C (RTC) NCBITaxon:140499 Undescribed mertensiid sp. 3 NCBITaxon:140499 Undescribed mertensiid C (RTC) NCBITaxon:140500 NCBITaxon:140500 unclassified Lobata NCBITaxon:140500 NCBITaxon:140501 Undescribed sp E (Ll) NCBITaxon:140501 Undescribed Lobata sp. 4 NCBITaxon:140501 Undescribed sp E (Ll) NCBITaxon:148608 NCBITaxon:148608 Lampoctenidae NCBITaxon:148608 NCBITaxon:158797 NCBITaxon:158797 Mnemiopsis sp. RFW-2001 NCBITaxon:158797 NCBITaxon:168726 NCBITaxon:168726 Coeloplana agniae NCBITaxon:168726 NCBITaxon:220132 NCBITaxon:220132 Beroe sp. SL-2003 NCBITaxon:220132 NCBITaxon:2759 eucaryotes eukaryotes Eucarya Eucaryotae Eukarya Eukaryotae NCBITaxon:2759 Eukaryota NCBITaxon:2759 eucaryotes eukaryotes Eucarya Eucaryotae Eukarya Eukaryotae NCBITaxon:27919 NCBITaxon:27919 Cestida NCBITaxon:27919 NCBITaxon:27920 NCBITaxon:27920 Cestidae NCBITaxon:27920 NCBITaxon:27921 Labata NCBITaxon:27921 Lobata NCBITaxon:27921 Labata NCBITaxon:27922 NCBITaxon:27922 Mnemiopsis NCBITaxon:27922 NCBITaxon:27923 NCBITaxon:27923 Mnemiopsis leidyi NCBITaxon:27923 NCBITaxon:31167 NCBITaxon:31167 Beroe cucumis NCBITaxon:31167 NCBITaxon:320166 NCBITaxon:320166 Beroe abyssicola NCBITaxon:320166 NCBITaxon:33154 Opisthokonta opisthokonts NCBITaxon:33154 Fungi/Metazoa group NCBITaxon:33154 Opisthokonta opisthokonts NCBITaxon:33208 metazoans multicellular animals Animalia animals NCBITaxon:33208 Metazoa NCBITaxon:33208 metazoans multicellular animals Animalia animals NCBITaxon:34498 NCBITaxon:34498 Pleurobrachia NCBITaxon:34498 NCBITaxon:34499 Pleurobranchia bachei NCBITaxon:34499 Pleurobrachia bachei NCBITaxon:34499 Pleurobranchia bachei NCBITaxon:354105 NCBITaxon:354105 Coeloplana willeyi NCBITaxon:354105 NCBITaxon:37538 NCBITaxon:37538 Beroida NCBITaxon:37538 NCBITaxon:37539 NCBITaxon:37539 Beroidae NCBITaxon:37539 NCBITaxon:488512 NCBITaxon:488512 unclassified Mertensiidae NCBITaxon:488512 NCBITaxon:499920 NCBITaxon:499920 Cestum sp. SC-2008 NCBITaxon:499920 NCBITaxon:499921 NCBITaxon:499921 Beroe sp. KUR20 NCBITaxon:499921 NCBITaxon:499922 NCBITaxon:499922 Beroe sp. KUR21 NCBITaxon:499922 NCBITaxon:499923 NCBITaxon:499923 Thalassocalyce sp. KUR22 NCBITaxon:499923 NCBITaxon:499924 NCBITaxon:499924 Thalassocalyce sp. KUR23 NCBITaxon:499924 NCBITaxon:500090 NCBITaxon:500090 unclassified Cydippida NCBITaxon:500090 NCBITaxon:500091 NCBITaxon:500091 Cydippida sp. KUR30 NCBITaxon:500091 NCBITaxon:50341 NCBITaxon:50341 Cydippida NCBITaxon:50341 NCBITaxon:51105 NCBITaxon:51105 Bolinopsidae NCBITaxon:51105 NCBITaxon:51106 NCBITaxon:51106 Bolinopsis NCBITaxon:51106 NCBITaxon:51107 NCBITaxon:51107 Bolinopsis sp. NCBITaxon:51107 NCBITaxon:541220 NCBITaxon:541220 Ctenellidae NCBITaxon:541220 NCBITaxon:624130 NCBITaxon:624130 Ctenophora environmental sample NCBITaxon:624130 NCBITaxon:86008 NCBITaxon:86008 Pleurobrachiidae NCBITaxon:86008 NCBITaxon:86009 NCBITaxon:86009 Hormiphora NCBITaxon:86009 NCBITaxon:86010 NCBITaxon:86010 Hormiphora sp. NCBITaxon:86010 A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATO:0000001 quality PATO:0000001 A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATOC:GVG PATO:0001402 PATO:0001405 PATO:0002505 PR:000001003 PR:000001006 PR:000001345 PR:000001800 PR:000001843 UBERON:0000000 processual entity UBERON:0000009 submucosa UBERON:0000010 peripheral nervous system UBERON:0000020 sense organ UBERON:0000025 tube UBERON:0000026 appendage UBERON:0000059 large intestine UBERON:0000060 anatomical wall UBERON:0000061 anatomical structure UBERON:0000062 organ UBERON:0000064 organ part UBERON:0000066 fully formed stage UBERON:0000067 embryo stage part UBERON:0000068 embryo stage UBERON:0000069 larval stage UBERON:0000076 external ectoderm UBERON:0000092 post-embryonic stage UBERON:0000100 blastopore UBERON:0000104 life cycle UBERON:0000105 life cycle stage UBERON:0000107 cleavage stage UBERON:0000109 gastrula stage UBERON:0000122 neuron projection bundle UBERON:0000159 anal canal UBERON:0000160 intestine UBERON:0000161 orifice UBERON:0000307 blastula UBERON:0000328 gut wall UBERON:0000344 mucosa UBERON:0000383 musculature of body UBERON:0000465 material anatomical entity UBERON:0000467 anatomical system UBERON:0000468 multicellular organism UBERON:0000475 organism subdivision UBERON:0000476 acellular anatomical structure UBERON:0000477 anatomical cluster UBERON:0000479 tissue UBERON:0000483 epithelium UBERON:0000485 simple columnar epithelium UBERON:0000486 multilaminar epithelium UBERON:0000490 unilaminar epithelium UBERON:0000922 embryo UBERON:0000923 germ layer UBERON:0000924 ectoderm UBERON:0000926 mesoderm UBERON:0001007 digestive system UBERON:0001015 musculature UBERON:0001016 nervous system UBERON:0001017 central nervous system UBERON:0001019 nerve fasciculus UBERON:0001021 nerve UBERON:0001032 sensory system UBERON:0001046 hindgut UBERON:0001062 anatomical entity UBERON:0001135 smooth muscle tissue UBERON:0001169 wall of large intestine UBERON:0001207 mucosa of large intestine UBERON:0001208 submucosa of large intestine UBERON:0001242 intestinal mucosa UBERON:0001262 wall of intestine UBERON:0001277 intestinal epithelium UBERON:0001278 epithelium of large intestine UBERON:0001353 anal region UBERON:0001555 digestive tract UBERON:0001630 muscle organ UBERON:0002036 striated muscle tissue UBERON:0002050 embryonic structure UBERON:0002072 hypodermis UBERON:0002097 skin of body UBERON:0002199 integument UBERON:0002204 musculoskeletal system UBERON:0002329 somite UBERON:0002384 UBERON:0002385 muscle tissue UBERON:0002416 integumental system UBERON:0002532 epiblast (generic) UBERON:0002548 larva UBERON:0003059 presomitic mesoderm UBERON:0003077 paraxial mesoderm UBERON:0003082 myotome UBERON:0003102 surface structure UBERON:0003104 mesenchyme UBERON:0003329 submucosa of anal canal UBERON:0003342 mucosa of anal canal UBERON:0003350 epithelium of mucosa UBERON:0003353 epithelium of hindgut UBERON:0003929 digestive tract epithelium UBERON:0004111 anatomical conduit UBERON:0004120 mesoderm-derived structure UBERON:0004121 ectoderm-derived structure UBERON:0004220 large intestine smooth muscle UBERON:0004221 intestine smooth muscle UBERON:0004226 gastrointestinal system smooth muscle UBERON:0004231 anal region smooth muscle UBERON:0004253 skin muscle UBERON:0004290 dermomyotome UBERON:0004456 entire sense organ system UBERON:0004734 gastrula UBERON:0004735 archenteron UBERON:0004786 gastrointestinal system mucosa UBERON:0004808 gastrointestinal system epithelium UBERON:0004906 ectodermal part of digestive tract UBERON:0004907 lower digestive tract UBERON:0004921 subdivision of digestive tract UBERON:0004923 organ component layer UBERON:0005090 muscle structure UBERON:0005162 multi cell part structure UBERON:0005291 embryonic tissue UBERON:0005409 alimentary part of gastrointestinal system UBERON:0005423 developing anatomical structure UBERON:0006134 nerve fiber UBERON:0006135 myelinated nerve fiber UBERON:0006136 unmyelinated nerve fiber UBERON:0006562 pharynx UBERON:0006582 statolith UBERON:0006583 statocyst UBERON:0006598 presumptive structure UBERON:0006846 surface groove UBERON:0007010 cleaving embryo UBERON:0007023 adult organism UBERON:0007026 presumptive gut UBERON:0007233 4 cell stage UBERON:0007236 8 cell stage UBERON:0007271 appendage musculature UBERON:0007503 epithelial vesicle UBERON:0007524 dense mesenchyme tissue UBERON:0008876 hypodermis skeletal muscle layer UBERON:0009503 mesenchyme of hindgut UBERON:0009566 intestinal submucosa UBERON:0010000 multicellular anatomical structure UBERON:0010316 germ layer / neural crest UBERON:0010371 ecto-epithelium UBERON:0011215 central nervous system cell part cluster UBERON:0011216 organ system subdivision UBERON:0011272 embryonic skin basal layer UBERON:0012125 dermatological-muscosal system UBERON:0012274 columnar epithelium UBERON:0012275 meso-epithelium UBERON:0013522 subdivision of tube UBERON:0013754 integumentary system layer UBERON:0013765 digestive system element UBERON:0014703 anal membrane ectodermal component UBERON:0014892 skeletal muscle organ UBERON:0015212 lateral structure UBERON:0015716 anal canal epithelium UBERON:0015783 smooth muscle layer in fatty layer of subcutaneous tissue UBERON:0016888 transitional anatomical structure UBERON:0017650 developing mesenchymal structure UBERON:0018254 skeletal musculature UBERON:0018257 submucosa of digestive tract UBERON:0019304 sensory organ epithelium UBERON:3000961 external integument structure owl:Nothing owl:Thing example to be eventually removed example to be eventually removed failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting placeholder removed placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. https://github.com/information-artifact-ontology/ontology-metadata/issues/77 https://orcid.org/0000-0001-5208-3432 out of scope 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/ 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 spatial has_part has_part has part has part x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:0000096 rostral_to spatial anterior_to anterior_to anterior to x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:cjm x distal to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). BSPO:0000097 spatial distal_to distal_to distal to x distal to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). BSPO:cjm x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000098 spatial dorsal_to dorsal_to dorsal to x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:cjm x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:0000099 caudal to spatial posterior_to posterior_to posterior to x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:cjm caudal to Crosses at an angle that is 90 degrees, or close to 90 degrees. In any non-linear organism, the main axes are rarely perpendicular when taken through the organism as a whole. BSPO:0000104 spatial approximately_perpendicular_to approximately_perpendicular_to approximately perpendicular to Crosses at an angle that is 90 degrees, or close to 90 degrees. In any non-linear organism, the main axes are rarely perpendicular when taken through the organism as a whole. BSPO:cjm Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:0000107 spatial deep_to deep_to deep to Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:cjm Closer to the left side of the organism. Example: The dorsal fin is right of the left pectoral fin, but is left of the right eye. On the type level: X left of Y <=> every instance x of X is left of some instance y of Y, and there exists some organism o such that x part of o and y part of o. BSPO:0000110 spatial left_of left_of left of Closer to the left side of the organism. Example: The dorsal fin is right of the left pectoral fin, but is left of the right eye. On the type level: X left of Y <=> every instance x of X is left of some instance y of Y, and there exists some organism o such that x part of o and y part of o. BSPO:cjm Direcly opposite to. i.e. on the opposite side through the axis. BSPO:0000113 spatial opposite_to opposite_to opposite to Direcly opposite to. i.e. on the opposite side through the axis. BSPO:cjm x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. spatial parallel_to parallel to x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. BSPO:curators BSPO:0015001 spatial finishes_axis finishes_axis A directional axis can be divided by a plane. Following Allen Interval Algebra terminology we say that the side on which the axis initiates starts the axis, with the other side finishing the axis. If s finishes axis x, and x has end point p, then x overlaps p finishes axis BSPO:0015002 spatial follows_axis follows_axis follows axis BSPO:0015003 spatial has_axis has_axis has axis crossing at right angles BSPO:0015005 spatial orthogonal_to orthogonal_to orthogonal to crossing at right angles BSPO:cjm Intersects at two points. BSPO:0015006 spatial passes_through passes_through passes through passes_through Intersects at two points. BSPO:cjm BSPO:0015007 spatial starts_axis starts_axis A directional axis can be divided by a plane. Following Allen Interval Algebra terminology we say that the side on which the axis initiates starts the axis, with the other side finishing the axis. . If s starts axis x, and x has start point p, then x overlaps p starts axis BSPO:0015008 spatial surface_of surface_of placeholder. used for relation between anatomical surface and an anatomical side. surface of bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of 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 bearer_of has characteristic David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by RO:0002104 has_plasma_membrane_part x overlaps y if and only if there exists some z such that x has part z and z part of y x overlaps y iff they have some part in common. http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 spatial overlaps overlaps "(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF [] overlaps overlaps x overlaps y iff they have some part in common. BSPO:cjm RO:0002203 develops_into mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO:0002215 capable_of capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. has function in RO:0002216 capable_of_part_of capable of part of A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO RO:0002220 spatial adjacent_to adjacent_to adjacent to adjacent to A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies. Biological Spatial Ontology * BSPO:$sequence(7,0,999999999)$ spatial based on FBql 2023-05-27 CTENO is an ontology describing the anatomy and developmet of ctenophores. lacks_plasma_membrane_part lacks_plasma_membrane_part lacks_plasma_membrane_part true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z infer input from direct reg GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' enabling an MF enables its parts true GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' involved in BP This can't be added as a property chain because it causes a circularity violation for 'part of'. This can't be added as a property chain because it causes a circularity violation for 'part of'. This can't be added as a property chain because it causes a circularity violation for 'part of'. If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction inferring direct neg reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction effector input is compound function input Input of effector is input of its parent MF if effector directly regulates X, its parent MF directly regulates X if effector directly positively regulates X, its parent MF directly positively regulates X if effector directly negatively regulates X, its parent MF directly negatively regulates X 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).