en Contributors are those that engage in discussions in the context of SIO (in alphabetical order): sivaram arabandi christopher baker joachim baran jerven bolleman matthew brush alison callahan leonid chepelev kevin cohen melanie courtot geraint duck laura furlong elisa kendall tatsuya kushida luke mccarthy jim mccusker jose miguel cruz-toledo chris mungall robert hoehndorf simon jupp jin-dong kim dana klassen thomas luetteke james malone chris mungall david osumi-sutherland tazro ohta nuria queralt stephen reed alexandre riazanov matthias samwald robert stevens mark wilkinson karin verspoor natalia villanueva-rosales Michel Dumontier sio.owl Kelsey Rook http://orcid.org/0000-0003-4727-9435 The Psychometric Ontology of Experience and Measures provides an ontology of domain concepts for the measurement of symptoms and syndromes related to psychiatric conditions. The semanticscience integrated ontology (SIO) provides a simple, integrated ontology (types, relations) for objects, processes and their attributes. This project provides foundational support for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects. website: http://semanticscience.org email: sio-ontology@googlegroups.com mailing list: http://groups.google.com/group/sio-ontology 2010-03-29 2023-11-20 2024-03-25 free to use,share,modify. modify with attribution [http://creativecommons.org/licenses/by/4.0/]. Psychometric Ontology of Experience and Measures Semanticscience Integrated Ontology (SIO) http://www.jbiomedsem.com/content/5/1/14 sio http://semanticscience.org/resource/ general class inclusion axioms: 'is part of' some 'physical entity' subClassOf 'is located in' some 'physical entity' role chains: 'has capability' o 'is realized in' -> 'is participant in' http://purl.org/ontology/POEM Psychometric Ontology of Experience and Measures (POEM) http://sio.semanticscience.org 1.59 protege#defaultLanguage The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. definition contributor creator description alternative contributor creator description issued license modified rights title citesAsAuthority preferredNamespacePrefix preferredNamespaceUri comment broaderThan equivalentTo example hasSynonym similarTo subset core#exactMatch core#example core#notation homepage can respond to detects has scale has subject has subscale has symptom has variable is about disorder is about source is about target is detected by is scale in is subject of is subject of scale is subscale of is symptom of is variable of SIO_000001 A is related to B iff there is some relation between A and B. 'is related to' is the top level relation in SIO core relations+ is related to SIO_000008 has attribute is a relation that associates a entity with an attribute where an attribute is an intrinsic characteristic such as a quality, capability, disposition, function, or is an externally derived attribute determined from some descriptor (e.g. a quantity, position, label/identifier) either directly or indirectly through generalization of entities of the same type. core has attribute SIO_000011 is attribute of is a relation that associates an attribute with an entity where an attribute is an intrinsic characteristic such as a quality, capability, disposition, function, or is an externally derived attribute determined from some descriptor (e.g. a quantity, position, label/identifier) either directly or indirectly through generalization of entities of the same type. is attribute of SIO_000020 denotes is a relation between an entity and what it is a sign or indication of, or what specifically means. denotes the symbol '%' denotes a proportion in relation to a whole. SIO_000028 has part is a transitive, reflexive and antisymmetric relation between a whole and itself or a whole and its part. has part a collection of cars has as a car as a part;a car has an engine as a part; a car has a piston as a part; SIO_000029 is time boundary of SIO_000053 has proper part is an antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part. has proper part a car has an engine as a proper part; a car has a piston as a proper part; SIO_000054 has boundary is a mereological relation between a whole and boundary located at its periphery. has boundary the surface of an apple is a 2D boundary of the apple. SIO_000059 has member is a mereological relation between a collection and an item. core has member a collection of cars has as a car as a member SIO_000060 is denoted by SIO_000061 A is located in B iff the spatialtemporial region occupied by A is part of the spatialtemporal region occupied by B. [T][R] OBO_REL:located_in core is located in A parasite in the interior of a person's intestine is located in their intestinal lumen. SIO_000062 is participant in is a relation that describes the participation of the subject in the (processual) object. is participant in a car is a participant in a car race; glucose is a participant in glycolysis SIO_000063 is agent in is a relation between an entity and a process, where the entity is present throughout the process, no permanent material change occurs, and is a causal participant in the process. sadi is agent in hexokinase is an agent in the conversion of glucose to glucose-6-phosphate SIO_000064 is provider of is a relation between a source and the entity it makes available. is provider of SIO_000066 is provided by is a relation between an entity and the entity that provides it. dc:source has provider SIO_000068 is part of is a transitive, reflexive and anti-symmetric mereological relation between a whole and itself or a part and its whole. OBO_REL:part_of core is part of SIO_000093 is proper part of is an asymmetric, irreflexive (normally transitive) relation between a part and its distinct whole. OBO_REL:proper_part_of core is proper part of SIO_000095 is member of is a mereological relation between a item and a collection. is member of SIO_000096 is boundary of is a mereological relation between a boundary located at the periphery of a whole. is boundary of SIO_000128 A is contained in B iff the spatial region occupied by A is part of the spatial region occupied by B and A is not part of B. [T] OBO_REL:contained_in core is contained in SIO_000132 has participant is a relation that describes the participation of the object in the (processual) subject. OBO_REL:has_participant core has participant SIO_000139 has agent is a relation between a process and an entity, where the entity is present throughout the process and is a causal participant in the process. OBO_REL:has_agent core sadi has agent SIO_000145 A is location of B iff the spatialtemporal region occupied by A has the spatialtemporal region occupied by B as a part. [T][R] nlp+ is location of SIO_000202 A contains B iff the spatial region occupied by A has the spatial region occupied by B as a part, and B is not part of A. [T] contains SIO_000203 interacts with A is connected to B iff there exists a fiat, material or temporal path between A and B. [S][T] core nlp is connected to SIO_000204 A is adjacent to B iff there is a small, but non-zero distance between A and B OBO_REL:adjacent_to core nlp is adjacent to SIO_000205 is represented by: a relation between an entity and some symbol. is represented by SIO_000206 is supported by is a relation between a proposition and something that supports the truth of the assertion. is supported by SIO_000207 has disputing evidence is a relation between a proposition and something that disputes (does not directly support) the truth of the assertion. is disputed by SIO_000208 is supporting evidence for SIO_000209 is disputing evidence for SIO_000210 a represents b when a serves as a sign, symbol or model of b. core represents SIO_000211 is positionally after is a relation between entities placed on a dimensional axis in which the projection of the position of the first entity is numerically greater than the projection of the position of the second entity. is positionally after SIO_000212 A is referred to by B iff B is an informational entity that makes reference to A. is referred to by SIO_000213 A has concretization B iff A is an informational entity and B is the a quality of some material entity. has concretization SIO_000214 A is concretization of B iff A is a quality of a material entity and B is an informational entity. is concretization of SIO_000215 is measurement value of is a relation between a value and the entity that it is a measurement of. is measurement value of SIO_000216 has measurement value is a relation between a quality/realizable and a measurement value. core has measurement value SIO_000217 has quality is a relation between an entity and the quality that it bears. has quality SIO_000218 is quality of is a relation between a quality and the entity that it is a property of. is quality of SIO_000219 is source of is a relation between a source of information about some entity. is source of SIO_000221 has unit is a relation between a quantity and the unit it is a multiple of. core has unit SIO_000222 is unit of is a relation between a unit and a quantity that it is a multiple of. is unit of SIO_000223 has property is a relation between an entity and the quality, capability or role that it and it alone bears. has property michel's hair has the quality of being brown in colour. SIO_000224 is property of is a relation betweena quality, capability or role and the entity that it and it alone bears. is property of SIO_000225 has function is the relation between an entity and a function that is ascribed to it. has function SIO_000226 is function of is a relation between a function and an entity that it is a property of. is function of SIO_000227 is role of is a relation between a role and the entity that it is a property of. is role of SIO_000228 has role is a relation between an entity and a role that it bears. has role SIO_000229 has output is a relation between an process and an entity, where the entity is present at the end of the process. core sadi has output SIO_000230 has input is a relation between a process and an entity, where the entity is present at the beginning of the process. core sadi has input SIO_000231 is input in is a relation between an entity and a process, where the entity is present at the beginning of the process. sadi is input in glucose and ATP are inputs in the hexokinase-mediated conversion of glucose to glucose-6-phosphate. SIO_000232 is output of is a relation between an entity and a process, where the entity is present at the end of the process. sadi is output of glucose-6-phosphate and ADP are outputs in the hexokinase-mediated conversion of glucose to glucose-6-phosphate. SIO_000233 is implementation of is a relation between an information entity and a specification that it conforms to. is implementation of SIO_000234 has implementation is a relation between a specification and an implementation that conforms to it. has implementation SIO_000235 has disposition is the relation between an entity and a disposition that it bears. has disposition SIO_000236 is disposition of is a relation between a disposition and the entity that it is a property of. is disposition of SIO_000240 is positionally before is a relation between entities placed on a dimensional axis in which the projection of the position of the first entity is numerically less than the projection of the position of the second entity. is positionally before SIO_000241 is directly after is a relation between entities placed on a dimensional axis in which the projection of the position of the first entity is numerically greater than the projection of the position of the second entity, and the entities are adjacent to one another. is directly after SIO_000242 is directly before is a relation between entities placed on a dimensional axis in which the projection of the position of the first entity is numerically less than the projection of the position of the second entity, and the entities are adjacent to one another. is directly before SIO_000243 A transitive, symmetric, temporal relation in which one entity is causally related with another non-identical entity. core is causally related with SIO_000244 A transitive temporal relation in which one entity was materially formed from another non-identical entity. OBO_REL:derives_from core is derived from SIO_000245 a derives to b if and only if a or some part thereof is consumed in the formation of b. derives into SIO_000246 a immediately derives into b if and only if a or some significant part thereof is consumed in the formation of b and there are no identifiable intermediate entities between a and b. immediately derives into SIO_000247 A non-transitive temporal relation in which one entity is immediately derived from a non-identical entity such that there are no intermediate entities between them. is immediately derived from SIO_000248 A transitive, temporal relation in which one process precedes (has occured earlier than) another process. core precedes SIO_000249 OBO_REL:preceded_by is preceded by SIO_000250 A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes. immediately precedes SIO_000251 A non-transitive temporal relation in which one process is immediately preceded by another process, such that there is no interval of time between the two processes. is immediately preceded by SIO_000252 is reference for is a relation between a document that provides information about an entity. is referenced by SIO_000253 has source is a relation between an entity and another entity from which it stems from. has source SIO_000254 is annotation of is a relation between some textual entity and the entity that it annotates. is annotation of SIO_000255 is annotated with was annotated with has annotation is a relation between an entity and some textual anntotation. has annotation document x is annotated with the keywords 'ontology','semantic web' SIO_000272 is variant of: a relationship indicating that two entities are different (by some measure), but either achieve the same objectives in different ways or are permutations of one another (temporal, logical or otherwise) core is variant of SIO_000273 has direct part is a relation to specify a part at a particular level of granularity has direct part a car has an engine as a direct part SIO_000274 A is prior version of B iff A is a variant of B and B derives from A. is prior version of SIO_000277 cites is a relation to refer to by way of example, authority or proof. cites SIO_000278 is cited by is a relation from an object that is referred to by way of example, authority or proof. is cited by SIO_000283 is similar to is a relation between two entities that share one or more features. is similar to SIO_000286 A is subsequent version of B iff A is a variant of B and A derives from B. is subsequent version of SIO_000288 is covalently connected to (transitive) SIO_000291 has target is a relation between a process and an entity, where the entity is present at the beginning of the process and undergoes a change or transformation in the process. has target SIO_000292 is target in is a relation between an entity and a process, where the entity is present at the beginning of the process and undergoes a change or transformation in the process. is target in glucose is a target in the hexokinase-mediated conversion of glucose to glucose-6-phosphate. SIO_000293 is weakly interacting with is a symmetric relation between two molecular entities (or any part thereof) that are interacting through some weak force (van der waals, hydrogen bonds, electrostatic interactions) is weakly interacting with (transitive) SIO_000294 a is causally related to b iff there is a causal chain of events from a to b is causally related to SIO_000310 is direct part of is a relation between a specific part (at some level of granularity) and its whole. core is direct part of SIO_000311 is product of is a relation between an entity and a process, where the entity is present at the end of the process as a result of a transformation in the process target. sadi is product of glucose-6-phosphate is the product of the hexokinase-mediated conversion of glucose to glucose-6-phosphate. SIO_000312 has product is a relation between an process and an entity, where a new entity exists at the end of the process. sadi has product SIO_000313 is component part of is a relation between a component and a whole, where the component is instrinsic to the whole, and loss of the part would change the kind that the whole is. core is component part of SIO_000322 A is spatiotemporally related to B iff A is in the spatial or temporal vicinity of B core is spatiotemporally related to SIO_000323 A 'is surrounded by' B iff the A 'is contained by' B and A 'is adjacent to' B or A 'is directly connected to' B. is surrounded by SIO_000324 A 'surrounds' B iff the A 'contains' B and A 'is adjacent to' B or A 'is directly connected to' B. surrounds SIO_000325 A overlaps with B iff there is some C that is part of both A and B. [S][R] overlaps with SIO_000332 is about is a relation between an information content entity and the entity that its primary subject. is about SIO_000334 is covalently connected to is a relation between an atom and another atom. is covalently connected to SIO_000335 is weakly interacting with SIO_000338 A relation between an information content entity and a product that it (directly/indirectly) specifies specifies SIO_000339 a relation between a product and the information content entity that specifies it. is specified by SIO_000341 is manifested as is a relation between an expression and its manifestations. is manifested as the english language version of 'war of the worlds' is manifested as a collection of english language versions of the book. SIO_000352 a is causally related from b iff there is a causal chain of events from b to a core is causally related from SIO_000355 realizes is a relation between a process and a realizable entity (role, function, disposition). core realizes SIO_000356 is realized in the role of a patient is realized in medical examination SIO_000362 satisfies is a relation between an entity and the specification or objective that it conforms to. satisfies SIO_000363 is satisfied by SIO_000364 is created by was created by has creator is a relation between an entity and that which created it. dc:creator has creator the iPhone was created by Apple Inc SIO_000365 is created by is creator of is a relation between a creator and an entity.. is creator of SIO_000369 has component part is a relation between a whole and a component part where the component is instrinsic to the whole, and loss of the part would change the kind that it is. has component part a human has blood as a component part SIO_000420 has expression the story 'war of worlds' is expressed as every language edition of the book 'war of the worlds' SIO_000421 is expression of is a relation between more concrete expression of some conceptualization. is expression of every language edition of 'war of the worlds' are expressions of the story of 'war of the worlds' SIO_000422 A is broader than B (t) iff for A is broader than B. http://www.w3.org/2004/02/skos/core#narrowerTransitive is broader than (t) SIO_000424 A is narrower than B (t) iff for A is narrower than B. http://www.w3.org/2004/02/skos/core#broaderTransitive is narrower than (t) SIO_000425 A is generically related with B iff A is an abstract entity or an information content entity and B is a information content entity or a physical entity, respectively. is generically related with SIO_000426 is manifestation of SIO_000427 A is narrower than B iff the meaning of term A is narrower in scope than the meaning of term B http://www.w3.org/2004/02/skos/core#broader is narrower than SIO_000477 http://www.w3.org/2004/02/skos/core#narrower is broader than SIO_000482 A is match to B iff A and B are terms with similar (related, broad, close, exact) meanings http://www.w3.org/2004/02/skos/core#relatedMatch is match to SIO_000484 http://www.w3.org/2004/02/skos/core#exactMatch is exact match to SIO_000490 http://www.w3.org/2004/02/skos/core#closeMatch is close match to SIO_000491 http://www.w3.org/2004/02/skos/core#broadMatch is broad match to SIO_000495 is dissimilar to is a relation between two entities in which one is considered dissimilar to the other based on some criteria. is dissimilar to SIO_000496 is opposite to is a relation between two entities in which one is diametrically opposed to the other. is opposite to hot is the opposite of cold; left is opposite of right SIO_000497 is version of is a relation that holds between any two versions in which one is a subsequent or alternate version of (through a branch). is version of SIO_000552 has parameter is a relation between a process and an information content entity which modulates the behaviour of some participant. sadi has parameter SIO_000553 is parameter in is a relation between a data item and some data transformation process. is parameter in SIO_000557 is described by is a relation between one entity and another entity that provides a description (detailed account) of it. is described by SIO_000558 is orthologous to is a relation between two biological entities that share a common ancestor and occur in different species. is orthologous to SIO_000563 describes is a relation between one entity and another entity that it provides a description (detailed account of). core describes SIO_000586 has capability is a relation between an entity and the capability that it bears. has capability SIO has the capability to semantically integrate data. SIO_000628 refers to is a relation between one entity and the entity that it makes reference to. core nlp+ refers to SIO_000629 is subject of SIO_000630 is paralogous to is a relation between two entities which indicates their common ancestry as a result of a gene duplication. is paralogous to SIO_000631 mentions references is a relation between one entity and the entity that it makes reference to by name, but is not described by it. core references SIO_000632 is model of is a relation between a model (an artifact) and the entity it purports to represent. is model of the architect builds a model that represents the building she envisions. SIO_000633 is modelled by SIO_000634 a relation between two entities which indicates their common ancestry but due to horizontal gene transfer. is xenologous to SIO_000635 has trigger is a relation between a realizable and the factor that causes it to be realized. has trigger SIO_000636 is trigger for SIO_000641 has basis is a relation between a realizable entity and the quality that forms the basis for it. has basis the solubility of salt (the disposition) is based on the molecular structure of NaCl (the quality) that allows the polarized water-molecules (the trigger) to break the ion bonds (the realization). SIO_000642 is base for is a relation between a quality and the realizable entity that it is the basis for. is base for the solubility of salt (the disposition) is based on the molecular structure of NaCl (the quality) that allows the polarized water-molecules (the trigger) to break the ion bonds (the realization). SIO_000643 is realizable property of SIO_000644 has realizable property SIO_000646 is capability of is a relation between a capability and the entity that bears it. is capability of SIO_000652 A is directly connected to B iff there exists a path direclty between A and B. is directly connected to SIO_000655 A transitive temporal relation in which an entity mainstains identity from one state to another. transforms into SIO_000656 A temporal relation in which an entity mainstains identity from one state to another. immediately transforms into SIO_000657 A transitive temporal relation in which an entity mainstains identity from one state to another. is transformed from SIO_000658 A temporal relation in which an entity mainstains identity from one state to another. is immediately transformed from SIO_000668 in relation to is a comparative relation to indicate that the instance of the class holding the relation exists in relation to another entity. core in relation to SIO_000671 a relation between an entity and an identifier. has identifier SIO_000672 identifies a relation between an identifier and an entity. is identifier for SIO_000673 has unique identifier is an inverse functional relation between an entity and an identifier that uniquely identifies it. has unique identifier SIO_000674 is unique identifier for is a relation between an identifier and an entity that it uniquely identifies is unique identifier for SIO_000679 has time boundary SIO_000680 has start time SIO_000681 has end time SIO_000682 is start time of SIO_000684 is end time of SIO_000687 exists at is a relation between an entity and a time measurement. core exists at SIO_000697 a is mutual disposition of b if and only if the realization of the disposition a necessarily causes the realization of the disposition b. is mutual disposition of SIO_000699 is greater than or equal to is a comparison relation between two quantities in which the first has a value larger or equal to the second. is greater than or equal to SIO_000709 a is mutually related to b if and only if the realization of the relation of a necessarily causes the realization of a relation to b. is mutually related to SIO_000710 a is mutual role of b if and only if the realization of role a necessarily causes the realization of role b. is mutual role of SIO_000733 is greater than to is a comparison relation between two quantities in which the first has a value smaller or equal to the second. is lesser than or equal to SIO_000734 is greater than to is a comparison relation between two quantities in which the first has a value larger than the second. is greater than SIO_000735 is lesser than to is a comparison relation between two quantities in which the first has a value smaller than the second. is lesser than SIO_000736 is comparable to is a relation between two entities that share at least one feature whose value can be compared. core is comparable to SIO_000737 is numerically comparable to is a comparison relation between two quantities whose datatype value can be compared. is numerically comparable to SIO_000738 is equal to is a comparison relation between two quantities whose value are exactly the same. is equal to SIO_000749 is inequal to is a comparison relation between two quantities whose value are not the same. is inequal to SIO_000772 has evidence is a relation between a proposition and something that demonstrates the truth of the assertion. has evidence SIO_000773 is evidence for SIO_000774 has evidence is a relation between a proposition and something that refutes (is incompatible with) the truth of the assertion. is refuted by SIO_000775 is refuting evidence for SIO_000793 measured at is a relation between a measurement value and the time measurement. core measured at SIO_000892 a in relation from b is a comparative relation in a is the object of reference in a relation with b. in relation from SIO_000900 has frequency is a relation that specifies the occurence of an object or event has frequency SIO_000901 is frequency of is a relation between a temporal unit and an object or event is frequency of SIO_000905 has substrate is a relation between a process and an object where the object is destroyed by its participation in the process. has substrate SIO_000970 is first part of is a proper part relation in which the part is the first of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system. is first part of SIO_000971 has first part is a proper part relation in which the part is the first of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system. has first part SIO_000972 has last part is a proper part relation in which the part is the last of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system. has last part SIO_000973 is last part of is a proper part relation in which the part is the last of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system. is last part of SIO_000974 has ordered part of is a proper part relation in which the part is one of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system. has ordered part SIO_000975 is ordered part of is a proper part relation in which the part is one of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system. is ordered part of SIO_001096 is specialization of is a relation between a more specific instance (in terms of spatial/temporal localization & other attributres) than the other. http://www.w3.org/ns/prov#specializationOf is specialization of a weather forecast for the city of London produced at a specific time is a specialization of a weather forecast for the city of London. SIO_001097 is generalization of is a relation between a more general instance (in terms of spatial/temporal localization & other attributres) than the other. is generalization of SIO_001098 is alternate of relates two specialized instances. http://www.w3.org/ns/prov#alternateOf is alternate of two weather forecasts for the city of London produced at different times or by different organizations (etc) are alternates of each other, and instances of / specializations of forecasts for the city of London. SIO_001101 a is mutual capability of b if and only if the realization of capability a necessarily causes the realization of capability b. is mutual capability of SIO_001154 x regulates y if and only if x is a process and y is either a process or a quality, and the progression of x exerts an effect on the frequency, rate or extent of y regulates SIO_001155 is regulated by SIO_001156 results in SIO_001157 is result of SIO_001158 affects SIO_001159 is affected by SIO_001242 is identical to is a relation between two objects that are conceptually the same notwithstanding provenance or other non-intrinsic attributes. is identical to SIO_001247 not implemented in standard distribution ovopub is transitively related to SIO_001277 has data item is a relation between a dataset and any described / referrenced entity. core has data item SIO_001278 'is data item in' is a relation between an entity that is described or referenced in a dataset. core is data item in SIO_001279 has phenotype is a relation between an object and an observable/measurable characteristic. has phenotype SIO_001280 is phenotype of is a relation between an observable/measurable characteristic and an object. is phenotype of x positively regulates y if and only if x is a process and y is either a process or a quality, and the progression of x exerts an effect that increases the frequency, rate or extent of y SIO_001401 positively regulates x negatively regulates y if and only if x is a process and y is either a process or a quality, and the progression of x exerts an reduced effect on the frequency, rate or extent of y SIO_001402 negatively regulates x is associated with y when x and y are logically or statistically related to one another. SIO_001403 is associated with x is correlated with y when x holds a statistical relationship with y SIO_001404 is correlated with SIO_010078 A relation between two objects, in which the first object contains information that is used to produce the second object. encodes an open reading frame encodes a protein (it contains information that specifies the amino acid composition and topology) SIO_010079 A relation between two objects, in which the first object is produced from the information contained in the second object. is encoded by SIO_010080 a relation between two information content entities in which one is transcribed into (an exact or similar kind) another through some process. is transcribed into DNA is transcribed into RNA SIO_010081 is transcribed from SIO_010082 is translated into RNA is translated into Protein a relation between two information content entities in which one is translated into (a completely different kind of entity) another through some process. SIO_010083 is translated from SIO_010302 a relation between two entities which indicates their common ancestry. is homologous to is significant SIO_000300 A relation between a informational entity and its actual value (numeric, date, text, etc). core nlp relations sadi has value 1 1 hasco:SemanticVariable ECO:0000000 A type of information that is used to support an assertion. evidence IAO:0000027 data item OBI:0000175 p-value STATO:0000193 is a population whose individual members realize (may be expressed as) a combination of inclusion rule values specifications or resulting from a sampling process (e.g. recruitment followed by randomization to group) on which a number of measurements will be carried out, which may be used as input to statistical tests and statistical inference. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra STATO statistical sample study group population STATO:0000203 a cohort is a study group population where the members are human beings which meet inclusion criteria and undergo a longitudinal design cohort STATO:0000280 Pearson's correlation coefficient 1 item stem concept 1 CompositeScale composite scale Construct construct Disorder disorder a disease entity typically representing a non-normative elevation on a syndrome in conjuction with marked distress or impairment 1 Experience symptom experience InstrumentCollection instrument collection PsychometricQuestionnaire psychometric questionnaire 1 1 QuestionnaireScale questionnaire scale a collection of indicators designed to be related to a shared construct Symptom symptom a type of behavior, emotion, or thought that is indicative of a syndrome (or a disorder, indirectly) 1 vstoi:Codebook vstoi:Detector Detector A device which detects measurements, such as temperature or wind velocity vstoi:Informant Informant (Respondent) vstoi:Instrument Instrument A device or mechanism that is used to achire attribute values of entities of interest. An instrument does not necessarily require a way to store its measured quantity (e.g, a hard disk). 1 1 vstoi:Item item 1 1 vstoi:ItemStem item stem 1 1 1 vstoi:Questionnaire Questionnaire 1 vstoi:ResponseOption response option resource:SIO_000000 sio:SIO_000000 SIO_000000 Every thing is an entity. core entity sio:SIO_000004 SIO_000004 A material entity is a physical entity that is spatially extended, exists as a whole at any point in time and has mass. core material entity resource:SIO_000005 sio:SIO_000005 SIO_000005 A quality is an attribute that is intrinsically associated with its bearer (or its parts), but whose presence/absence and observed/measured value may vary. core quality sio:SIO_000006 SIO_000006 A process is an entity that is identifiable only through the unfolding of time, has temporal parts, and unless otherwise specified/predicted, cannot be identified from any instant of time in which it exists. core process+ process sio:SIO_000009 SIO_000009 A social entity pertains to the interaction among individuals and groups. social entity sio:SIO_000010 SIO_000010 A social structure is a social entity which consists of relationships between two or more entities. social structure sio:SIO_000012 SIO_000012 An organization is a collective with a complex articulation of tasks, roles and responsibilities. organization sio:SIO_000013 SIO_000013 A geographic position is the coordinate of an entity against some geographic coordinate system. geographic position sio:SIO_000014 SIO_000014 A disposition is the tendency of a capability to be exhibited under certain conditions or in response to a certain stimulus (trigger). core disposition solubility (to dissolve when put in fluid); fragility (disposition to break when dropped) sio:SIO_000015 SIO_000015 information content entity is an object that requires some background knowledge or procedure to correctly interpret. core ice+ information content entity sio:SIO_000016 SIO_000016 A role is a realizable entity that describes behaviours, rights and obligations of an entity in some particular circumstance. core role sio:SIO_000017 SIO_000017 A function is a capability that satisfies some agentive objective, or (evolutionary) optimization. core function sio:SIO_000019 SIO_000019 A site is a spatial region bounded (in part or in whole) by material entities and may be occupied by material entities. site A nostril; the interior of the heart valve; the interior of a bottle. sio:SIO_000022 SIO_000022 A material boundary is the boundary of a material entity which exists as a lower dimensional entity at exactly the location where its parts no longer extend into space. Every material entity has a boundary, and a boundary is the boundary of exactly 1 material entity. material boundary the external surface of the window; the surface of the p52 protein sio:SIO_000026 SIO_000026 An object quality is quality of an object. object quality sio:SIO_000027 SIO_000027 A process quality is quality that is associated with a process. process quality sio:SIO_000030 SIO_000030 A sequence is a primary structure descriptor in which each of the letters in the string represents a monomeric unit (residue) in which adjacent letters represent the connectivity between the monomeric units. biopolymer sequence sio:SIO_000031 SIO_000031 A start date is a time instant pertaining to the date of the beginning of a process. start date sio:SIO_000032 SIO_000032 An end date is a time instant pertaining to date of the end of a process. end date sio:SIO_000033 SIO_000033 process status is a process quality that describes the state of a process. process status sio:SIO_000034 SIO_000034 completed is that status of a process that successfully unfolds. completed sio:SIO_000035 SIO_000035 ongoing is the status of a process that is not yet complete. ongoing sio:SIO_000036 SIO_000036 predicted is the quality of an entity that is thought to exist, as evidenced by some rational procedure. predicted sio:SIO_000037 SIO_000037 physical dimensional quantity A spatial quantity is a quantity obtained from measuring the spatial extent of an entity spatial quantity sio:SIO_000038 SIO_000038 A quantity that extends in single dimension. 1D extent quantity sio:SIO_000039 SIO_000039 depth is the dimensional extent into a plane of a 3D projection of the object. depth sio:SIO_000040 SIO_000040 height is the one dimensional extent along the vertical projection of a 3D object from a base plane of reference. height sio:SIO_000041 SIO_000041 length is the longer dimensional extent along a 2D projection of the object. length sio:SIO_000042 SIO_000042 width is the shorter dimensional extent perpendicular to a 2D projection of the object. width sio:SIO_000043 SIO_000043 thickness is the shortest dimensional extent of a 3D projection of an object. thickness sio:SIO_000044 SIO_000044 A quantity that extends in two dimensions. 2D extent quantity sio:SIO_000045 SIO_000045 area is a quantity that pertains to the extent of a two-dimensional surface or shape, or planar lamina, in the plane. area sio:SIO_000046 SIO_000046 A perimeter is a length of the outline that surrounds a two-dimensional shape. length of perimeter sio:SIO_000047 SIO_000047 circumference is the length of the outline of a circle or ellipse. it is defined as c = 2*pi*r, where r is the radius. circumference sio:SIO_000048 SIO_000048 A quantity that extends in three dimensions. 3D extent quantity sio:SIO_000049 SIO_000049 volume is the quantity of three-dimensional space enclosed by some closed boundary. volume sio:SIO_000051 SIO_000051 composition quality is a quality that describes its composition or anatomy. compositional quality sio:SIO_000052 SIO_000052 A quantity is an informational entity that gives the magnitude of a property. quantity sio:SIO_000055 SIO_000055 shape is the quality of a bearer that relates to its spatial extent. shape sio:SIO_000056 SIO_000056 A measurement of a spatial location relative to a frame of reference or other objects. position sio:SIO_000057 SIO_000057 orientation is an angle between the bearer and an axis, or the angle between the bearer and another object. orientation sio:SIO_000067 SIO_000067 A namespace is an informational entity that defines a logical container for a set of symbols or identifiers. namespace sio:SIO_000069 SIO_000069 A data item consists of information that has been collected/generated towards some purpose. data item sio:SIO_000070 SIO_000070 A measurement value is a quantitative description that reflects the magnitude of some attribute. measurement value sio:SIO_000071 SIO_000071 A coordinate is a measurement of position in n-dimensional space. coordinate sio:SIO_000072 SIO_000072 A Cartesian coordinate is the signed distance of a point to some referent line. cartesian coordinate sio:SIO_000073 SIO_000073 A polar coordinate is a position characterized by a distance from a fixed point and an angle from a fixed direction. polar coordinate sio:SIO_000074 SIO_000074 A unit of measurement is a definite magnitude of a physical quantity, defined and adopted by convention and/or by law, that is used as a standard for measurement of the same physical quantity. unit of measurement sio:SIO_000075 SIO_000075 A mathematical entity is an information content entity that are components of a mathematical system or can be defined in mathematical terms. math+ mathematical entity sio:SIO_000076 SIO_000076 A plan is a set of intended actions, through which one expects to achieve a goal. plan sio:SIO_000077 SIO_000077 A generic name is the preferred name provided by manufacturer. generic name sio:SIO_000078 SIO_000078 A language entity implements some language specification for the visual interpretation and is part of some document. nlp+ language entity sio:SIO_000079 SIO_000079 A visual language entity is a language entity that is manifested within the spectrum of light and can be pereceived and processed by a visual system. visual language entity sio:SIO_000080 SIO_000080 diagram A figure is a graphical entity which consists of a visual (n-dimentional) arrangement of information entities. figure sio:SIO_000081 SIO_000081 depiction An image is an affine projection of a visual entity to a two dimensional surface. image sio:SIO_000082 SIO_000082 photo A photograph is an image created by light falling on a light-sensitive surface. photograph sio:SIO_000083 SIO_000083 chart A statistical graph is a figure that displays the relationship among numeric data and/or mathematical functions. statistical graph sio:SIO_000085 SIO_000085 A question is a linguistic expression used to make a request for information. question sio:SIO_000087 SIO_000087 A publication is a document that has been made available by a publisher. publication sio:SIO_000088 SIO_000088 A record is a document containing a collection of statements about some entity. record sio:SIO_000089 SIO_000089 data set A dataset is a data item that is a collection of data items. http://www.w3.org/ns/dcat#Dataset dataset sio:SIO_000090 SIO_000090 A specification is a description of the essential technical attributes/requirements for an object or procedure, and may be used to determine that the object / procedure meets its requirements/attributes. specification sio:SIO_000091 SIO_000091 effective specification An action specification is a specification composed of a sequence of instructions to achieve some objective. action specification sio:SIO_000092 SIO_000092 A biopolymer is an organic polymer that are typically produced by the cells of living organisms. biopolymer sio:SIO_000094 SIO_000094 An algorithm is an effective method expressed as a finite list of well-defined instructions for calculating a function. algorithm sio:SIO_000097 SIO_000097 A software entity is a computational entity that can be interpreted by or directly executed by a processing unit. software entity sio:SIO_000098 SIO_000098 A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. software method sio:SIO_000099 SIO_000099 A software module is software composed of a collection of software methods. software module sio:SIO_000100 SIO_000100 A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application. software library sio:SIO_000101 SIO_000101 A software application is software that can be directly executed by some processing unit. software application sio:SIO_000102 SIO_000102 A software interpreter is a software application that executes some specified input software. software interpreter sio:SIO_000103 SIO_000103 A software script is software whose instructions can be executed using a software interpreter. software script sio:SIO_000104 SIO_000104 Language is a language entity which is the result of encoding and decoding information through systematic creation and usage of systems of symbols, each pairing a specific sign with an intended meaning, established through social conventions language sio:SIO_000105 SIO_000105 A symbol is a proposition about what an entity represents. symbol sio:SIO_000106 SIO_000106 A book is a publication composed of a large number of entries. book sio:SIO_000107 SIO_000107 A chapter is a document section of a book or thesis. chapter sio:SIO_000108 SIO_000108 A character is a language symbol used to construct words. character sio:SIO_000109 SIO_000109 A novel is a fictitious prose narrative of book length, typically representing character and action with some degree of realism. novel sio:SIO_000110 SIO_000110 A paragraph is a self-contained unit of written discourse consisting of one or more sentences. paragraph sio:SIO_000111 SIO_000111 A document section is a component of a document. document section sio:SIO_000112 SIO_000112 A capability is a realizable entity whose basis lies in one or more parts or qualities and reflects possibility of an entity to behave in a specified way under certain conditions or in response to a certain stimulus (trigger). capability+ core capability sio:SIO_000113 SIO_000113 A sentence is a grammatical unit consisting of one or more words that bear minimal syntactic relation to the words that precede or follow it. sentence sio:SIO_000114 SIO_000114 A word is the smallest free form (an item that may be expressed in isolation with semantic or pragmatic content) in a language. word sio:SIO_000115 SIO_000115 An identifier is a label that specifically refers to (identifies) an entity (instance/type). identifier sio:SIO_000116 SIO_000116 A name is a label used to identify an entity. name sio:SIO_000117 SIO_000117 A preferred name is the name that is generally used by some organization. preferred name sio:SIO_000118 SIO_000118 A common name is a name that is commonly used. common name sio:SIO_000119 SIO_000119 A brand name is a trademarked and marketed name of a product. brand name sio:SIO_000120 SIO_000120 A scientific name is a name given through scientific nomenclature. scientific name sio:SIO_000121 SIO_000121 A magazine is a periodical that typically contains essays, stories, poems, etc., by many writers, and often photographs and drawings, frequently specializing in a particular subject or area, as hobbies, news, or sports. http://purl.org/ontology/bibo/Magazine magazine sio:SIO_000122 SIO_000122 A synonym is a word with the same or very similar meanings. synonym sio:SIO_000123 SIO_000123 An antonym is a word with opposite or nearly opposite meaning. antonym sio:SIO_000124 SIO_000124 A hypernym is a term with a broader meaning. hypernym sio:SIO_000125 SIO_000125 A hyponym is a term with a narrower meaning. hyponym sio:SIO_000126 SIO_000126 A homonym is a word that sounds the same but has different meaning. homonym sio:SIO_000127 SIO_000127 A workflow is an algorithm that is is a depiction of a sequence of operations to achieve one or more objectives. workflow sio:SIO_000129 SIO_000129 An ontology document is a document that contains an ontology. ontology document sio:SIO_000130 SIO_000130 A pattern is a generalized representation of some repeatable concrete or informational item. pattern sio:SIO_000131 SIO_000131 A sequence motif is a pattern of nucleotides in a DNA sequence or amino acids in a protein. sequence motif sio:SIO_000133 SIO_000133 A descriptor (index term, subject term, subject heading) is a term that captures the essence of the topic of a document. descriptor sio:SIO_000135 SIO_000135 A definition is a description that succintly characterizes an entity. definition sio:SIO_000136 SIO_000136 A description is language entity in which elements of a language (formal or natural) are used to characterize an entity. description sio:SIO_000137 SIO_000137 A category is a class of entities having particular shared characteristics. category sio:SIO_000138 SIO_000138 A class is a collection of sets which can be unambiguously defined by a property that all its members share. class sio:SIO_000140 SIO_000140 A web service is a software application that can be accessed over a network, such as the Internet, and executed on a remote system hosting the requested services. web service sio:SIO_000141 SIO_000141 A criterion is a specification to describe properties used for evaluation. criterion sio:SIO_000142 SIO_000142 An inclusion criterion is a criterion that must be present to satisfy some objective. inclusion criterion sio:SIO_000143 SIO_000143 An exclusion criterion is a criterion that must be absent to satistify the objective. exclusion criterion sio:SIO_000144 SIO_000144 A parameter is variable whose value changes the characteristics of a system or a function. parameter sio:SIO_000146 SIO_000146 A monomer is a submolecule that is proper part of some polymer, and is a building block for such polymer. monomer sio:SIO_000147 SIO_000147 A keyword is a descriptor in which the association of the word with the entity facilitates information retrieval. keyword sio:SIO_000148 SIO_000148 A document is a bounded physical or digital representation of a body of information designed with the capacity (and usually intent) to communicate. document sio:SIO_000150 SIO_000150 A list is any enumeration of a set of items. list sio:SIO_000151 SIO_000151 A manuscript is a document prior to publication. manuscript sio:SIO_000152 SIO_000152 A note is a brief document. note sio:SIO_000153 SIO_000153 A patent is an information entity granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time. patent sio:SIO_000154 SIO_000154 An article is a publication that is stand-alone section of a larger work. article sio:SIO_000155 SIO_000155 A blog is a publication accessible at some website and is typically about various experiences. blog sio:SIO_000156 SIO_000156 A book volume is a book that is part of a collection. book volume sio:SIO_000157 SIO_000157 A conference proceedings is a book composed of papers presented at a conference. conference proceedings sio:SIO_000158 SIO_000158 A book series is a collection of books that have been sequentially published. book series sio:SIO_000159 SIO_000159 An edited publication is a publication that has been examined and potentially changed by an editor. edited publication sio:SIO_000160 SIO_000160 A journal is a a peer-reviewed periodical in which scholarship relating to a particular academic discipline is published. http://purl.org/ontology/bibo/Journal journal sio:SIO_000161 SIO_000161 A manual is a document that instructs on the usage of a device. manual sio:SIO_000162 SIO_000162 A periodical is a publication that appears on a regular schedule. http://purl.org/ontology/bibo/Periodical periodical sio:SIO_000163 SIO_000163 A newspaper is a periodical publication containing news regarding current events, informative articles, diverse features, editorials, and advertising. http://purl.org/ontology/bibo/Newspaper newspaper sio:SIO_000164 SIO_000164 A technical report is a publication published by a school or other institution, usually numbered within a series. technical report sio:SIO_000165 SIO_000165 A thesis document is the written research component of a post-secondary institution that contains a statement supported by arguments. thesis document sio:SIO_000166 SIO_000166 An honor's thesis is a thesis prepared as a requirement for an honor's undergraduate degree. honor's thesis sio:SIO_000167 SIO_000167 A Master's thesis is a thesis prepared as a requirement for a Master's degree. master's thesis sio:SIO_000168 SIO_000168 A PhD thesis is a thesis prepared as a requirement for a doctoral degree. phd thesis sio:SIO_000169 SIO_000169 A booklet is a document that lacks a named publisher or sponsoring institution. booklet sio:SIO_000170 SIO_000170 A diary is a document which describes day-to-day experiences. diary sio:SIO_000171 SIO_000171 A bibliographic attribute is an attribute related to publications. document component sio:SIO_000172 SIO_000172 An address is a position that indicates the physical location of some entity using a social convention. address sio:SIO_000173 SIO_000173 An affiliation is a social relation which indicates the partnership between two or more entities. affiliation sio:SIO_000174 SIO_000174 A citation is a textual entity which denotes a source described in the bibliography or reference section of a document. citation sio:SIO_000175 SIO_000175 A document title is a textual entity that summarizes the topic of the document in one sentence. document title sio:SIO_000176 SIO_000176 A reference is a textual entity that describes a single source used in the preparation or development of the work. reference sio:SIO_000177 SIO_000177 A page range denotes the start and end page in some document. page range sio:SIO_000178 SIO_000178 A page total is a textual entity that is about the number of pages in some informational entity. page total sio:SIO_000179 SIO_000179 a label is a term that is associated with some entity label sio:SIO_000180 SIO_000180 A language label is a label that denotes the language of a textual entity. language label sio:SIO_000181 SIO_000181 A first name is a name that denotes a specific individual between members of a group of individuals, whose members usually share the same surname. first name sio:SIO_000182 SIO_000182 A last name (surname) is a name added to a given name and is part of a personal name and is often the family name. last name sio:SIO_000183 SIO_000183 full name A personal name is a name to identify an individual person and usually comprises of a first name and a last name. personal name sio:SIO_000184 SIO_000184 A legal name is a name given at birth, or which appears on their birth certificate, marriage certificate, or change of name certificate. legal name sio:SIO_000185 SIO_000185 A title is a textual entity that summarily describes some entity. title sio:SIO_000186 SIO_000186 A document version is a version of a work in some sequence of derivative works. document version sio:SIO_000188 SIO_000188 An abstract section is a document section that provides brief summary of a document that explains the main argument(s), topic(s) or findings. abstract section sio:SIO_000189 SIO_000189 An acknowledgements section is a document section that identifies individuals, groups or organizations for their support in the development of the work. acknowledgements section sio:SIO_000190 SIO_000190 An author contribution section is a document section that describes the contribution of the authors. author contribution section sio:SIO_000191 SIO_000191 An author section is a document section that lists the contributing authors. author section sio:SIO_000192 SIO_000192 A bibliography section is a document section that is composed of a list of references used in the development of the work. bibliography section sio:SIO_000193 SIO_000193 A copyright section is a document section that contains a notice of copyright. copyright section sio:SIO_000194 SIO_000194 A correspondence section is a document section that contains the details for contacting the corresponding author. correspondence section sio:SIO_000195 SIO_000195 The discussion section is a document section containing a summary of the findings, a reflection on the significance of findings, comparison with related work, among others. discussion section sio:SIO_000196 SIO_000196 An introduction section is a document section that generally provides background, motivation and goals of the work. introduction section sio:SIO_000197 SIO_000197 The materials and methods section is a document section containing a description of the materials and methods used in the study. materials and methods section sio:SIO_000198 SIO_000198 The materials section is a document section containing a description of the materials used in the study. materials section sio:SIO_000199 SIO_000199 The methods section is a document section containing a description of the methods used in the study. methods section sio:SIO_000200 SIO_000200 The results section is a document section describing the main findings of the study. results section sio:SIO_000201 SIO_000201 The table of contents is a document section that lists all sections (and optionally subsections) in a sequential order along with their page number. table of contents sio:SIO_000220 SIO_000220 Implication is a logical operator that holds between a set T of propositions and a proposition B, when every model (or interpretation or valuation) of T is also a model of B. implies (->) sio:SIO_000237 SIO_000237 A namespace label is a short name for a namespace. namespace label sio:SIO_000238 SIO_000238 A logical operator is a unary or binary relation to construct logical expressions. logical operator sio:SIO_000239 SIO_000239 AND is a logical operator that has the value true if both of its operands are true, otherwise a value of false. conjunction (and) sio:SIO_000256 SIO_000256 A proposition is a sentence expressing something true or false. proposition sio:SIO_000257 SIO_000257 A dimensionless quantity is a quantity that has no associated unit. dimensionless quantity sio:SIO_000258 SIO_000258 A dimensional quantity is a quantity that has an associated unit. dimensional quantity sio:SIO_000259 SIO_000259 An argument is a set of one or more declarative sentences (or propositions) known as the premises along with another declarative sentence (or proposition) known as the conclusion. argument sio:SIO_000261 SIO_000261 A premise is a proposition of an argument from which the conclusion is drawn. premise sio:SIO_000262 SIO_000262 A conclusion is a proposition which is reached after considering the evidence, arguments or premises. conclusion sio:SIO_000263 SIO_000263 A deductive argument is an argument that asserts that the truth of the conclusion is a logical consequence of the premises. deductive argument sio:SIO_000264 SIO_000264 An inductive argument is an argument that asserts that the truth of the conclusion is supported by the premises. inductive argument sio:SIO_000265 SIO_000265 A sound argument is a valid argument with true premises. sound argument sio:SIO_000266 SIO_000266 A valid argument is an argument where the truth of the conclusion is a logical consequence of the premises and (consequently) its corresponding conditional is a necessary truth. valid argument sio:SIO_000267 SIO_000267 An invalid argument is an argument where the truth of the conclusion is false because it is not a logical consequence of the premises. invalid argument sio:SIO_000268 SIO_000268 truth value is a quality of information that is claimed/verified to be true or false. truth value true sio:SIO_000269 SIO_000269 true is a truth value that indicates that it holds under all possible worlds. true false sio:SIO_000270 SIO_000270 false is a truth value in that indicates that it is not true. false sio:SIO_000275 SIO_000275 A term is a word or phrase used to denote one or more entities. term sio:SIO_000276 SIO_000276 An emotion is a process (experience) that arises internally or from an involuntary physiological response to a stimulus. emotion++ emotion sio:SIO_000279 SIO_000279 mass is the quality of the amount of substance. mass sio:SIO_000280 SIO_000280 OR is a logical operator that results in true whenever one or more of its operands are true. disjunction (or) sio:SIO_000281 SIO_000281 NOT is a logical operator in that has the value true if its operand is false. negation (not) sio:SIO_000282 SIO_000282 XOR, also called exclusive disjunction or (symbolized XOR, EOR, EXOR, or ⊕), is a type of logical disjunction on two operands that results in a value of true if exactly one of the operands has a value of true. exclusive disjunction (xor) sio:SIO_000284 SIO_000284 A hypothesis is a proposed explanation for a phenomenon. hypothesis sio:SIO_000285 SIO_000285 An academic organization is a lawfully recognized organization that confers diplomas, degrees and other forms of recognition of academic achievement. academic organization sio:SIO_000287 SIO_000287 A social relation is a social entity that describes a relationship between two or more individuals or groups. social relation sio:SIO_000289 SIO_000289 A set is a collection of entities, for which there may be zero members. set sio:SIO_000290 SIO_000290 A university is an institution of higher education and research which grants academic degrees in a variety of subjects and provides both undergraduate education and postgraduate education. university 2 sio:SIO_000295 SIO_000295 A collection of documents is a non-zero set of documents. http://purl.org/ontology/bibo/Collection collection of documents sio:SIO_000296 SIO_000296 A website is a collection of documents published on the World Wide Web. website sio:SIO_000297 SIO_000297 film moving pictures A movie is a series of images that are displayed in rapid succession to give the impression of movement. movie sio:SIO_000298 SIO_000298 An excerpt is a contiguous or discontiguous portion of a document. excerpt sio:SIO_000299 SIO_000299 A quote is a excerpt that is attributed to a particular source. quote sio:SIO_000301 SIO_000301 A geographic image is a photograph of some geographical area. geographic image sio:SIO_000302 SIO_000302 A web page is a document that is published according to World Wide Web standards. web page sio:SIO_000304 SIO_000304 Email message is a digital document that is composed of a header and a body and is transmitted using the SMTP protocol. email sio:SIO_000305 SIO_000305 process number is a number associated with a process that denotes its ordinal position in a set of processes. process number sio:SIO_000306 SIO_000306 A letter is a document that contains a personal communication from one part to another. letter sio:SIO_000307 SIO_000307 normality is the quality in which the value may differ from normal or average normality sio:SIO_000308 SIO_000308 An edition number is count of a literary work edited and published, as by a certain editor or in a certain manner including being printed during some interval of time. edition number sio:SIO_000309 SIO_000309 volume number is a count of a sequence of periodicals. volume number sio:SIO_000314 SIO_000314 A polymer is a molecule composed of a connected set of monomeric residues. polymer sio:SIO_000315 SIO_000315 A functional specification is a specification that describes the characteristics of an object. functional specification sio:SIO_000316 SIO_000316 A design specification is a specification that provides precise and explicit information about the requirements for a product design. design specification sio:SIO_000317 SIO_000317 A specification for spatial location is an effective specification towards representation spatial position or spatial data. spatial specification sio:SIO_000318 SIO_000318 Longitude is a geographic position that refers to the angle east or west of a reference meridian between the two geographical poles to another meridian that passes through an arbitrary point. longitude sio:SIO_000319 SIO_000319 Latitude is a geographic coordinate which refers to the angle from a point on the Earth's surface to the equatorial plane latitude sio:SIO_000320 SIO_000320 A coordinate system is a specification for spatial location that uses a set of numbers, or coordinates, to uniquely determine the position of a point or other geometric element. coordinate system sio:SIO_000321 SIO_000321 A Cartesian coordinate system specifies each point uniquely in a plane by a pair of numerical coordinates, which are the signed distances from the point to two fixed perpendicular directed lines, measured in the same unit of length. cartesian coordinate system sio:SIO_000326 SIO_000326 A concept is term that refers to a generalization of a set of attributes or entities. concept sio:SIO_000327 SIO_000327 A polar coordinate system is a two-dimensional coordinate system in which each point on a plane is determined by a distance from a fixed point and an angle from a fixed direction. polar coordinate system sio:SIO_000328 SIO_000328 A positional description is a description of location using some system or frame of reference. positional identifier sio:SIO_000329 SIO_000329 A cylindrical coordinate system is a three-dimensional coordinate system that specifies point positions by the distance from a chosen reference axis, the direction from the axis relative to a chosen reference direction, and the distance from a chosen reference plane perpendicular to the axis. cylindrical coordinate system sio:SIO_000330 SIO_000330 A spherical coordinate system is a coordinate system for three-dimensional space where the position of a point is specified by three numbers: the radial distance of that point from a fixed origin, its polar angle measured from a fixed zenith direction, and the azimuth angle of its orthogonal projection on a reference plane that passes through the origin and is orthogonal to the zenith, measured from a fixed reference direction on that plane. spherical coordinate system sio:SIO_000331 SIO_000331 An OWL ontology is an ontology as specified by the W3C OWL specification. OWL ontology 1 1 1 sio:SIO_000333 SIO_000333 A 3D cartesian coordinate is a coordinate that is composed of an x, y and z coordinate. 3D cartesian coordinate sio:SIO_000337 SIO_000337 An objective is a proposition that indicates a planned or anticipated outcome. objective sio:SIO_000340 SIO_000340 A realizable entity is an attribute that is exhibited under some condition and is realized in some process. core realizable entity sio:SIO_000342 SIO_000342 A term variant is a term that is a variant of another term. term variant sio:SIO_000343 SIO_000343 to modify is the capability to change some entity. to modify sio:SIO_000344 SIO_000344 to record is the capability to detect and transcribe information in a specified format on some physical medium. to record http://purl.obolibrary.org/obo/OBI_0000368 sio:SIO_000345 SIO_000345 to magnify is the capability to increase the appearance of the size of an object. to magnify sio:SIO_000346 SIO_000346 to heat is a capability to increase the internal kinetic energy of a material. to heat sio:SIO_000347 SIO_000347 to cool is the capability to decrease the internal kinetic energy of a material. to cool http://purl.obolibrary.org/obo/OBI_0000387 sio:SIO_000348 SIO_000348 to freeze is the capability to decrease the internal kinetic energy of a material such that it changes state from a gas or liquid to a solid. to freeze http://purl.obolibrary.org/obo/OBI_0000375 sio:SIO_000349 SIO_000349 to separate is the capability to i) distinguish some entities based on some attribute(s) and ii) subsequently physically displace them. to separate sio:SIO_000350 SIO_000350 to ionize is the capability to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. to ionize sio:SIO_000351 SIO_000351 to supply energy is the capability to transfer energy from a source to a sink. to supply energy sio:SIO_000353 SIO_000353 to observe is the capability to watch attentively. to observe sio:SIO_000354 SIO_000354 dysfunction is a capability to act in a manner that is abnormal or opposite to the object's typical function. dysfunction sio:SIO_000357 SIO_000357 fitness is the quality of an object with respect to some stated functions or evolutionary adaptation. fitness sio:SIO_000358 SIO_000358 intent is a desire to realize a particular outcome. intent sio:SIO_000359 SIO_000359 purpose is the reason for which something is done or created or for which something exists. purpose sio:SIO_000360 SIO_000360 A belief is a proposition that is believed to be true. belief sio:SIO_000366 SIO_000366 rank 0 tensor A number is a tensor of rank 0. number sio:SIO_000367 SIO_000367 A variable is a value that may change within the scope of a given problem or set of operations. variable sio:SIO_000368 SIO_000368 An equation is a mathematical statement that asserts the equality of two expressions. equation sio:SIO_000370 SIO_000370 region A spatial region is an object contained in some region of space. spatial region The airspace above Ottawa airport; the band around the northern hemisphere between 50 degrees N and 60 degrees N; the spatial region occupied by a bottle. sio:SIO_000371 SIO_000371 to measure is the capability to obtain information about some entity by examining its attributes in relation to some reference metric. to measure sio:SIO_000372 SIO_000372 to inject is the capability to administer a substance into some object through its external barrier. to inject sio:SIO_000373 SIO_000373 to boil is the capability to increase the internal kinetic energy of a material such that it changes state from a solid or liquid to a gas. to boil sio:SIO_000374 SIO_000374 to reduce energy is the capability to remove energy from a source. to reduce energy sio:SIO_000375 SIO_000375 to supply electricity is the capability to transfer electricity from a source to a sink. to supply electricity sio:SIO_000376 SIO_000376 to change appearance is the capability to change the material composition of an object. to change materially sio:SIO_000377 SIO_000377 to demagnify is the capability to decrease the appearance of the size of an object. to demagnify sio:SIO_000378 SIO_000378 to change appearance is the capability to change the visual attributes of an object. to change appearance sio:SIO_000379 SIO_000379 perception is the organization, identification, and interpretation of sensory information in order to fabricate a mental representation through the process of transduction, which sensors in the body transform signals from the environment into encoded neural signals. perception sio:SIO_000380 SIO_000380 to contain is the capability to bound or constrain a physical entity in some site. to contain sio:SIO_000381 SIO_000381 to immobilize is the capability to contain an entity in such a way that it may not move in space. to immobilize sio:SIO_000382 SIO_000382 to filter is the capability to retain certain entities based on selected attribute(s) while allowing other entities to pass through. to filter sio:SIO_000383 SIO_000383 to excite is the capability to supply energy to a materila by bombarding it with energetic particles (e.g., photons). to excite sio:SIO_000384 SIO_000384 to emit is the capability to release some physical entity (light, pollution, etc). to emit sio:SIO_000385 SIO_000385 to change energetically is the capability to change the energetic aspects of an object. to change energetically sio:SIO_000386 SIO_000386 to positively charge is the capability to remove an electron or add a positively charged ion to a chemical entity. to positively charge sio:SIO_000387 SIO_000387 to negatively charge is the capability to add an electron or negatively charged ion to a chemical entity. to negatively charge sio:SIO_000388 SIO_000388 to assemble is the capability to combine entities together into a larger object that persists in time. to assemble sio:SIO_000389 SIO_000389 to extract is the capability to remove certain entities based on selected attribute(s) while allowing other entities to remain. to extract sio:SIO_000390 SIO_000390 to transport is the capability to displace a material from one location to another. to transport sio:SIO_000391 SIO_000391 time measurement is a measurement value of the duration of some interval of time or a particular instant of time (against some frame of reference). Time intervals are specified as date/datetime ranges. time measurement the duration of my life; the duration of a surgical procedure, the moment of death sio:SIO_000392 SIO_000392 to change spatially is the capability to affect the physical movement of some entity. to change spatially sio:SIO_000393 SIO_000393 A patient is an individual that is the recepient of medical care. patient sio:SIO_000394 SIO_000394 A doctor is an individual who practices medicine, which is concerned with promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury, and other physical and mental impairments. doctor sio:SIO_000395 SIO_000395 to modulate to regulate is to control or maintain the rate or speed of an object or process. to regulate sio:SIO_000396 SIO_000396 A file is an information-bearing object that contains a physical embodiment of some information using a particular character encoding. http://www.w3.org/ns/dcat#Distribution file sio:SIO_000397 SIO_000397 to provide is the capability to make available some object to another that requires it. to provide sio:SIO_000398 SIO_000398 A nurse is an individual that is involved in the protection, promotion, and optimization of health and abilities, prevention of illness and injury, alleviation of suffering through the diagnosis and treatment of human response, and advocacy in the care of individuals, families, communities, and populations. nurse sio:SIO_000399 SIO_000399 A study subject is an individual that is the subject of the study. study subject sio:SIO_000400 SIO_000400 An x cartesian coordinate is the coordinate of an object onto the x-axis of a cartesian coordinate system. x cartesian coordinate sio:SIO_000401 SIO_000401 An y cartesian coordinate is the coordinate of an object onto the y-axis of a cartesian coordinate system. y cartesian coordinate sio:SIO_000402 SIO_000402 A z cartesian coordinate is the coordinate of an object onto the z-axis of a cartesian coordinate system. z cartesian coordinate sio:SIO_000403 SIO_000403 A study group is a group of individuals that are subjects in an observational or intervention study. study group sio:SIO_000404 SIO_000404 A professor is an individual that is a scholarly teacher. professor sio:SIO_000405 SIO_000405 A student is an individual who is attends an educational institution. student sio:SIO_000406 SIO_000406 An academic is an individual that participates in education and scholarship. academic sio:SIO_000407 SIO_000407 to increase the rate of formation is to regulate the rate of formation in a manner that increases this rate relative to a reference process. to increase the rate of formation sio:SIO_000408 SIO_000408 to investigate is the capability to uncover facts. to investigate sio:SIO_000409 SIO_000409 A mutual disposition is a disposition that simulataneously invokes another disposition when realized. mutual disposition sio:SIO_000410 SIO_000410 anger is disgust directed toward an equal status individual. anger sio:SIO_000411 SIO_000411 Hate is a deep and emotional extreme dislike, directed against a certain object or class of objects. hate sio:SIO_000412 SIO_000412 love is an emotion of a strong affection and personal attachment. love sio:SIO_000413 SIO_000413 A geolegal region is a geographic region which has causal powers confered by a legal entity. geolegal region The 50 kph zones in Ottawa; the geographic region occupied by France. sio:SIO_000414 SIO_000414 A geographic region is a spatial region whose boundaries are typically defined against some material frame of reference (like the earth). geographic region The spatial region occupied by the province of ontario; the spatial region occupied by a lake. sio:SIO_000415 SIO_000415 a geopolitical region is a geographic region recognized by social or legal convention. geopolitical region The geographic region bounded by Canada; the spatial region occupied by the US embassy in Ottawa. sio:SIO_000417 SIO_000417 A time internval is a contiguous temporal region having some duration. time interval sio:SIO_000418 SIO_000418 A time instant is a temporal region which occurs instantaneously, e.g. having no duration. time instant at this moment; the moment at which a finger is detached in an industrial accident; the moment at which a child is born; the moment of death sio:SIO_000419 SIO_000419 A table is a figure that consists of an ordered arrangement of columns and rows. table sio:SIO_000423 SIO_000423 scatter chart scatter diagram scatter graph A scatterplot is a statistical graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. scatterplot sio:SIO_000428 SIO_000428 A year is a period of time taken by a planet to make one revolution around the sun. year sio:SIO_000429 SIO_000429 A month is a period of time that divides the year. month sio:SIO_000430 SIO_000430 A day is a period of 24 hours. day sio:SIO_000431 SIO_000431 A century is a period of one hundred years. century sio:SIO_000432 SIO_000432 A millenium is a period of 1000 years millennium sio:SIO_000433 SIO_000433 An hour is a period of 60 minutes. hour sio:SIO_000434 SIO_000434 A minute is a period of 60 seconds. minute sio:SIO_000435 SIO_000435 A second (symbol: s) is the base unit of time in the International System of Units (SI) and is the second division of the hour by sixty, the first division by 60 being the minute. second sio:SIO_000436 SIO_000436 An informational quality is a quality that pertains to information. informational quality 1 1 sio:SIO_000437 SIO_000437 A 2D cartesian point is a point whose position is specified along two dimensions using Cartesian coordinates. 2D cartesian point sio:SIO_000438 SIO_000438 Altitude is a distance above sea level. altitude sio:SIO_000439 SIO_000439 The center of mass (aka barycenter) is the weighted average location of all the mass in a body or group of bodies. center of mass 1 1 1 sio:SIO_000440 SIO_000440 A 3D cartesian point is a point whose position is specified along three dimensions using Cartesian coordinates. 3D cartesian point 1 sio:SIO_000441 SIO_000441 A 1D cartesian point is a point whose position is specified along a single dimension using Cartesian coordinates. 1D cartesian point sio:SIO_000442 SIO_000442 line chart A line graph is a statistical graph in which lines contains the evaluation of functions or individual points connected by line segments. line graph Graph 1 in http://tinyurl.com/opwnvm sio:SIO_000443 SIO_000443 A bar graph is a statistical graph with rectangular bars of lengths proportional to that value that they represent. bar graph Graphs 3,4,5 in http://tinyurl.com/opwnvm sio:SIO_000444 SIO_000444 A horizontal bar graph is a bar graph in which the rectangular bars are horizontally oriented in space. horizontal bar graph Graph 3 in http://tinyurl.com/opwnvm sio:SIO_000445 SIO_000445 A vertical bar graph is a bar graph in which the rectangular bars are vertically oriented in space. vertical bar graph Graph 4,5 in http://tinyurl.com/opwnvm sio:SIO_000446 SIO_000446 A stacked bar graph is a bar graph in which each rectangular bar is partioned by the categorical value of each series of data. stacked bar graph Graphs 6,7 in http://tinyurl.com/opwnvm sio:SIO_000447 SIO_000447 A line-bar graph statistical graph that contains both lines and bars. line-bar graph Graph 8 in http://tinyurl.com/opwnvm sio:SIO_000448 SIO_000448 A figure part is a part of a figure. figure part sio:SIO_000449 SIO_000449 A plot is a part of a figure that corresponds to the spatial region between the set of axes. plot The square portion of the chart bounded by lines that overlap with the two axes in Graph 1 of http://tinyurl.com/opwnvm sio:SIO_000450 SIO_000450 An axis is a line segment that is part of a statistical graph in which the position along the line corresponds to a numeric or categorical value. The value of a plotted geometric objects (e.g. point) can be obtained from the perpendicular projection of the position of the object onto the axis. Axis may also be associated with a textual description of what the values on the axis represents. axis The left vertical and bottom horizontal lines with tickmarks in Graph 1 http://tinyurl.com/opwnvm sio:SIO_000451 SIO_000451 A Cartesian coordinate axis is an axis whose behavior follows that of a Cartesian coordinate system. Cartesian coordinate axis sio:SIO_000452 SIO_000452 horizontal axis An x-axis is a Cartesian coordinate axis that is aligned with the horizon. In most figures, this axis represents categories, such as months, market segments, or other non-numeric data. x-axis The horizontal axis in http://tinyurl.com/opwnvm sio:SIO_000453 SIO_000453 vertical axis A y-axis is a Cartesian coordinate axis that is spatially oriented perpendicular to the x-axis. y-axis sio:SIO_000454 SIO_000454 A z-axis is a Cartesian coordinate axis that is spatially oriented normal to the plane formed by the x- and y-axes. z-axis sio:SIO_000455 SIO_000455 A category axis is an axis in which the position along the line is partioned into categories. category axis The horizontal axis corresponding to months of the year in graph 4 of http://tinyurl.com/opwnvm sio:SIO_000456 SIO_000456 A primary category axis is a category axis that either defines the sole value range or holds the larger set of categorical values specified by the secondary category axis. primary category axis The category axis that corresponds to years in Graph 1 of http://tinyurl.com/opwnvm sio:SIO_000457 SIO_000457 A secondary category axis is a category axis that defines a finer granular part (or subset) of the value range of the primary category axis. secondary category axis The category axis that corresponds to months in Graph 1 of http://tinyurl.com/opwnvm sio:SIO_000458 SIO_000458 A value axis is an axis in which the position along the line is partioned into numeric values. A value axis holds the properties of having a minimum and a maximum value, and is usually associated with tickmarks that indicate intervals along the axis. value axis The value axis that ranges from 3.0 to 7.4 and corresponds to billions of dollars in Graph 1 of http://tinyurl.com/opwnvm sio:SIO_000459 SIO_000459 A left value axis is a value axis that is spatially positioned to the left of the plot area. left value axis The value axis that ranges from 3.0 to 7.4 and corresponds to billions of dollars in Graph 1 of http://tinyurl.com/opwnvm sio:SIO_000460 SIO_000460 A right value axis is a value axis that is spatially positioned to the right of the plot area. right value axis sio:SIO_000461 SIO_000461 A scaled value axis is a value axis in which the value range was subject to a mathematic transformation. scaled value axis sio:SIO_000462 SIO_000462 A linear value axis is a value axis that corresponds to a scaling factor of 1 of the value range. linear value axis sio:SIO_000463 SIO_000463 A logarithmic value axis is a scaled value axis that corresponds to a scaling factor of the logarithm of the value range. logarithmic value axis sio:SIO_000464 SIO_000464 A data series is a data set composed of related values displayed in a statistical graph. data series Example: The two series that correspond to "Seasonally adjusted" and "Trend" are composed of the seasonally adjusted value of permits in each month and values from a trend derived from some mathematical tranformation across those values, respectively, in Graph 1 of http://tinyurl.com/opwnvm sio:SIO_000465 SIO_000465 A data point is a point that which corresponds to the projection of the values of measurement data against the axes of a statistical graph. data point sio:SIO_000466 SIO_000466 A global maximum stationary point is a data point that corresponds to a measurement value is larger than that of all other plotted datapoints. global maximal stationary point sio:SIO_000467 SIO_000467 A global minimum data point is a data point that corresponds to a measurement value is smaller than that of all other plotted datapoints. global minimal stationary point sio:SIO_000468 SIO_000468 A legend is a part of a figure that associates textual descriptions with symbols pertaining to plotted entities. legend The colored line segments and the adjacent textual descriptions in Graph 1 of http://tinyurl.com/opwnvm sio:SIO_000469 SIO_000469 A graph title is a title that describes a graph. graph title Total value of permits increased slightly in December" in Graph 1 of http://tinyurl.com/opwnvm sio:SIO_000470 SIO_000470 A primary title is a title that should be first used in describing some entity. primary title sio:SIO_000471 SIO_000471 subtitle, alternative title A secondary title is a title of lesser importance that should be used after the first title in describing some entity. secondary title sio:SIO_000472 SIO_000472 scientific data is data obtained from some scientific procedure. scientific data sio:SIO_000473 SIO_000473 A primary graph title is a primary title that describes a statistical graph. primary graph title "Total value of permits increased slightly in December" in Graph 1 of http://tinyurl.com/opwnvm sio:SIO_000474 SIO_000474 A secondary graph title is a secondary title that describes a statistical graph. secondary graph title sio:SIO_000475 SIO_000475 A biological quality is a quality held by a biological entity. biological quality sio:SIO_000476 SIO_000476 cellular quality is the quality of a cell cellular quality sio:SIO_000478 SIO_000478 A sequence variant role is a comparative role in which the composition of characters in a sequence differs when compared to another entity of similar type. sequence variant role sio:SIO_000479 SIO_000479 A variant role is a comparative role in which the value of an attribute differs when compared to another entity variant role sio:SIO_000480 SIO_000480 An insertion variant role is the role of an sequence that contains a sub-sequence that is considered to be an addition relative to the frame of reference. insertion variant role sio:SIO_000481 SIO_000481 A deletion variant role is the role of an sequence that lacks a sub-sequence relative to the frame of reference. deletion variant role 2 sio:SIO_000483 SIO_000483 A phrase is a group of words functioning as a single unit in the syntax of a sentence. phrase resource:SIO_000485 sio:SIO_000485 SIO_000485 A human is a primates of the family Hominidae and are characterized by having a large brain relative to body size, with a well developed neocortex, prefrontal cortex and temporal lobes, making them capable of abstract reasoning, language, introspection, problem solving and culture through social learning. human sio:SIO_000486 SIO_000486 A mouse is a small mammal belonging to the order of rodents, characteristically having a pointed snout, small rounded ears, and a long naked or almost hairless tail. mouse sio:SIO_000487 SIO_000487 A rat is a medium-sized, long-tailed rodent of the superfamily Muroidea. rat sio:SIO_000488 SIO_000488 A worm is a non-arthropod invertebrate animal that typically have a long cylindrical tube-like body and no legs. worm sio:SIO_000489 SIO_000489 Escherichia coli (e coli) is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms. e.coli sio:SIO_000492 SIO_000492 to consume is the capability to internalize a material entity. to consume sio:SIO_000493 SIO_000493 A clause consists of a subject and a predicate. clause sio:SIO_000494 SIO_000494 to actively interact with is the capability to interact with another entity in a way that requires physical contact. to actively interact with resource:SIO_000498 sio:SIO_000498 SIO_000498 A person is an object that has certain capacities or attributes constituting personhood. person sio:SIO_000499 SIO_000499 to decrease the rate of formation is to regulate the rate of formation in a manner that decreases this rate relative to a reference process. to decrease the rate of formation 2 1 sio:SIO_000500 SIO_000500 A polygon vertex is a terminal point at which two polygon edges meet and are part of a polygon. polygon vertex 2 sio:SIO_000501 SIO_000501 A polygon edge is a line segment joining two polygon vertices. polygon edge sio:SIO_000502 SIO_000502 A polyhedral skeleton is a collection of polygon edges. polyhedral skeleton sio:SIO_000503 SIO_000503 A polygonal face is a polygon bounded by a circuit of polygon edges, and includes the flat (plane) region inside the boundary. polygonal face sio:SIO_000504 SIO_000504 A polyhedral surface is composed of polygonal faces. polyhedral surface sio:SIO_000505 SIO_000505 A polygon is a planar entity that is bounded by a closed path or circuit, composed of a finite connected sequence3 of straight line segments. polygon sio:SIO_000506 SIO_000506 A geometric entity is an information content entity that pertains to the structure and topology of a space. geometry+ geometric entity sio:SIO_000507 SIO_000507 A point is a geometric entity that is located in a zero-dimensional spatial region and whose position is defined by its coordinates in some coordinate system. point sio:SIO_000508 SIO_000508 An endpoint is a terminal point that is the last of an ordered pair of points. endpoint sio:SIO_000509 SIO_000509 A start point is a terminal point which is the first of an ordered pair of points. start point sio:SIO_000510 SIO_000510 A model is a representation of some thing. model sio:SIO_000511 SIO_000511 A line is curve that extends in a single dimension (e.g. straight line; exhibits no curvature), and is composed of at least two fully connected points. line 2 sio:SIO_000512 SIO_000512 A line segment is a line and a part of a curve that is (inclusively) bounded by two terminal points. line segment sio:SIO_000513 SIO_000513 A tick mark is a line segment that is spatially positioned perpendicular to the axis of a statistical graph and indicates the position of a specific numeric value (which may be indicated by an adjacent value label) on a value axis, or is one of a pair of tick marks that delineates the boundary of a categorical value (which may be indicated by an adjacent category label) on the categorical axis. tick mark sio:SIO_000514 SIO_000514 A major tick mark is a tick mark that indicates the position of a specific numeric value and is adjacent to its value label on the value axis, or is one of a pair of tick marks that delineates the boundary of a categorical value indicated by an adjacent category label on the categorical axis. major tick mark sio:SIO_000515 SIO_000515 A minor tick mark is a tick mark that indicates the position of a specific numeric value but has no adjacent value label, or is one of a pair of tick marks that delineates the boundary of a categorical value but has no adjacent category label on the categorical axis. minor tick mark sio:SIO_000516 SIO_000516 A ray is a line which that is bounded by a startpoint and extends outwards infinitely along one dimension. ray sio:SIO_000517 SIO_000517 A quadrilateral is a polygon with composed of four points and four line segments, in which each point is fully connected to two other points. quadrilateral sio:SIO_000518 SIO_000518 A rectangle is a quadrilateral in which one pair of line segments are parallel and the other pair are perpendicular to the first pair. rectangle sio:SIO_000519 SIO_000519 A bar is a rectangle that is located in the plot of a statistical graph in which its length is proportional to the values that it represents. bar sio:SIO_000520 SIO_000520 A triangle is a polygon composed of three points and three line segments, in which each point is fully connected to another point along through the line segment. triangle 1 1 sio:SIO_000521 SIO_000521 A directed line segment is a line segment that is contained by an ordered pair of endpoints (a start point and an endpoint). directed line segment 2 sio:SIO_000522 SIO_000522 An arrowed line is a directed line segment in which one or both endpoints is tangentially part of a triangle that bisects the line. arrowed line segment 1 sio:SIO_000523 SIO_000523 A single arrowed line is directed line in which the endpoint is tangentially part of a triangle that bisects the line. single arrowed line segment 2 sio:SIO_000524 SIO_000524 A double arrowed line is an arrowed line in which both terminal points are tangentially part of different triangles that bisect the line. double arrowed line segment sio:SIO_000525 SIO_000525 A horizontal line is a line that is positionally oriented with the horizon. horizontal line sio:SIO_000526 SIO_000526 A vertical line is a line that is positionally oriented perpendicular to the horizon. vertical line sio:SIO_000527 SIO_000527 A trend line is a line, line segment or ray that is part of a statistical graph which indicates a statistical or visual direction across categorical or value data. trend line sio:SIO_000528 SIO_000528 An increasing line is a line segment in which the startpoint and endpoint are ordered along one dimension and the difference of values in a second dimension is positive. increasing line sio:SIO_000529 SIO_000529 An decreasing line is a line segment in which the startpoint and endpoint are ordered along one dimension and the difference of values in a second dimension is negative. decreasing line sio:SIO_000530 SIO_000530 An plateau line is a line segment in which the startpoint and endpoint are ordered along one dimension and the difference of values in a second dimension is zero. plateau line sio:SIO_000531 SIO_000531 A drop line is a statistical graph line that vertically or horizontally connects a data series line with a value axis in a statistical graph. drop line sio:SIO_000532 SIO_000532 A terminal point is a point that defines the finite extension of a line. terminal point sio:SIO_000533 SIO_000533 A surface normal is a vector that is perpendicular to a flat surface. surface normal sio:SIO_000534 SIO_000534 A positionally oriented line is a line that is positioned against some axis of reference. positionally oriented line sio:SIO_000535 SIO_000535 A statistical graph line is a line used in a statistical graph to communicate some trend or feature of the embedded data. statistical graph line sio:SIO_000536 SIO_000536 to regulate the rate of formation is to modify the rate at which an object is formed. to regulate the rate of formation sio:SIO_000537 SIO_000537 curvature is a quality of a bearer that relates to the presence of curves, bends, or angles. curvature sio:SIO_000538 SIO_000538 straight is a quality of a bearer that is free of curves, bends, or angles. straight PATO:0002180 [for material entities] sio:SIO_000539 SIO_000539 An infinite line is a line that extends outwards in both directions of a single dimensional and is not bounded by terminal points. infinite line sio:SIO_000540 SIO_000540 A vector line is a line which that is bounded by a startpoint and extends outwards along one dimension. vector line sio:SIO_000541 SIO_000541 A vertext normal is the normalized average of the surface normals of the faces that contain that vertex. vertex normal sio:SIO_000542 SIO_000542 to serve as is the capability to act in a manner corresponding to some role. to serve as sio:SIO_000543 SIO_000543 to serve as host is the capability to act in a manner that provides hospitality, serves to harbour an organism in or on itself. to serve as a host sio:SIO_000544 SIO_000544 to infect is the capability to administer a disease-causing organism into some object. to infect 2 sio:SIO_000545 SIO_000545 polygonal chain, polygonal curve, polygonal path, piecewise linear curve A polyline is a connected sequence of line segments. polyline sio:SIO_000546 SIO_000546 A collection of points is a geometric entity that contains a non-zero set of geometric points. collection of points sio:SIO_000547 SIO_000547 to cause disease is the capability to materially change a biological object in that it functions abnormally. to cause disease sio:SIO_000549 SIO_000549 to activate to reduce the activation energy is to require a smaller amount of energy in order to form or break a chemical bond. to reduce the activation energy sio:SIO_000550 SIO_000550 to inhibit to increase the activation energy is to require a larger amount of energy in order to form or break a chemical bond. to increase the activation energy sio:SIO_000551 SIO_000551 to change the activation energy is to change the amount of energy required to form or break a chemical bond. to change the activation energy sio:SIO_000554 SIO_000554 A quality that has a value that is normal or average. PATO:0000461 normal sio:SIO_000555 SIO_000555 A quality that has a value that is outside normal or average. abnormal sio:SIO_000556 SIO_000556 A lipid residue is a part of an organic molecule that was derived from a lipid molecule. lipid residue sio:SIO_000559 SIO_000559 chemical synthesis is synthesis of a chemical entity from physical precursors through one or more chemical interactions or reactions. chemical synthesis sio:SIO_000561 SIO_000561 A molecular orbital (or MO) is a mathematical function describing the wave-like behavior of an electron in a molecule. molecular orbital sio:SIO_000562 SIO_000562 passive transport is the movement of a substance across a membrane and does not require chemical energy. passive transport sio:SIO_000564 SIO_000564 diffusion is motion of particles at temperatures above absolute zero. diffusion sio:SIO_000565 SIO_000565 A diffusion equation describes density fluctuations in a material undergoing diffusion. diffusion equation sio:SIO_000566 SIO_000566 A movement equation describes the displacement of an object in space over time. movement equation sio:SIO_000567 SIO_000567 An ordinary differential equation (ODE) is a differential equation in which the unknown function (also known as the dependent variable) is a function of a single independent variable. ordinary differential equation sio:SIO_000568 SIO_000568 A partial differential equation (PDE) is a differential equation in which the unknown function is a function of multiple independent variables and the equation involves its partial derivatives. partial differential equation sio:SIO_000569 SIO_000569 A differential equation is a mathematical equation for an unknown function of one or several variables that relates the values of the function itself and its derivatives of various orders. differential equation sio:SIO_000570 SIO_000570 movement is the process in which an object is spatially displaced. core movement sio:SIO_000571 SIO_000571 Brownian motion is the seemlingly random movement of particles suspended in a fluid. brownian motion sio:SIO_000572 SIO_000572 osmosis is the movement of water molecules through a selectively-permeable membrane down a water potential gradient. osmosis sio:SIO_000573 SIO_000573 passive movement is the process in which an object is spatially displaced without an expenditure of energy contained in molecular bonds. passive movement sio:SIO_000574 SIO_000574 active movement is the process in which an object is spatially displaced using some chemical energy. active movement sio:SIO_000575 SIO_000575 transporting is a process in which one object physically moves another object from one location to another. transporting sio:SIO_000576 SIO_000576 membrane transport is the movement of molecules across a membrane. membrane transport sio:SIO_000577 SIO_000577 primary active transport, also called direct active transport, directly uses energy to transport molecules across a membrane. primary active transport sio:SIO_000578 SIO_000578 secondary active transport or co-transport uses electrochemical potential difference created by pumping ions out of the cell to transport molecules across a membrane. secondary active transport sio:SIO_000579 SIO_000579 symport enabled secondary active transport is a secondary active transfort in which both ion and molecule are transported in the same direction simultaneously. symport enabled secondary active transport sio:SIO_000580 SIO_000580 antiport enabled secondary active transport is a secondary active transfort in which both ion and molecule are transported in opposite directions simultaneously. antiport enabled secondary active transport sio:SIO_000581 SIO_000581 The self-propelled movement of an object. GO:0040011 locomotion sio:SIO_000582 SIO_000582 birthing is the process by which a biological organism is brought into existence. birthing sio:SIO_000583 SIO_000583 dying is a process in which a biological entity ceases to exist. dying sio:SIO_000585 SIO_000585 An idea is a proposition about some object of conceptual thought. idea sio:SIO_000587 SIO_000587 biological reproduction is the biological process by which one or more biological organisms are produced from their "parents". biological reproduction sio:SIO_000588 SIO_000588 creation development formulation production synthesis creating is the process in which an entity comes into existence. creating sio:SIO_000589 SIO_000589 regulation regulating is a process that modulates the attributes of an object or process. regulating sio:SIO_000590 SIO_000590 biosynthesis is the synthesis of an organic compound in a living organism, usually aided by enzymes. biosynthesis sio:SIO_000591 SIO_000591 destruction destroying is a process in which something is broken down and/or ceases to exist. destroying sio:SIO_000592 SIO_000592 chemical destruction is destruction of a chemical entity to its chemical constituents through one ormore chemical interactions or reactions. chemical destruction 2 2 sio:SIO_000593 SIO_000593 interacting is a process characterized by the interaction between two or more entities. core interacting sio:SIO_000594 SIO_000594 data transformation is the process of applying an algorithmic procedure to some input data and producing some output data. data transformation sio:SIO_000595 SIO_000595 A parameterized data transformation is a data transformation whose behaviour may be modified by one or more parameters. parameterized data transformation sio:SIO_000596 SIO_000596 A data storage device is a device that is capable of storing information. data storage device sio:SIO_000597 SIO_000597 A solid-state drive (SSD) is a data storage device that uses solid-state memory to store persistent data. solid state hard drive sio:SIO_000598 SIO_000598 A hard disk drive (HDD) is a non-volatile, random access device for digital data. It features rotating rigid platters on a motor-driven spindle within a protective enclosure. Data is magnetically read and written on the platter by read/write heads that float on a film of air above the platters. hard disk drive sio:SIO_000600 SIO_000600 structure is the specification that refers to the composition and arrangement of parts of an object. structure sio:SIO_000602 SIO_000602 A computational entity is an information content entity operated on using some computational system. computational entity sio:SIO_000605 SIO_000605 A sound wave is a mechanical wave that is an oscillation of pressure transmitted through a solid, liquid, or gas, composed of frequencies within the range of hearing. sound wave sio:SIO_000608 SIO_000608 A curve is a geometric entity that may be located in n-dimensional spatial region whose extension may be n-dimensional, is composed of at least two fully connected points and does not intersect itself. curve sio:SIO_000609 SIO_000609 regulation of a process is a process that modulates the duration, frequency, spatial extent of a target process. regulation of process sio:SIO_000610 SIO_000610 regulation of capability is the regulation of the ability of one party by another. regulation of capability sio:SIO_000611 SIO_000611 the regulation of the enzymatic activity. regulation of catalytic capability sio:SIO_000612 SIO_000612 A representation is a entity that in some way represents another entity (or attribute thereof). representation resource:SIO_000613 sio:SIO_000613 SIO_000613 offset A ordinal position is a number that designates the position of an entity from the first entity in an ordered sequence of entities. ordinal position resource:SIO_000614 sio:SIO_000614 SIO_000614 An attribute is a characteristic of some entity. core attribute sio:SIO_000616 SIO_000616 A collection is a set for which there exists at least one member, although any member need not to exist at any point in the collection's existence. collection 0 sio:SIO_000617 SIO_000617 An empty set is a set for which there are exactly 0 members. empty set sio:SIO_000618 SIO_000618 A standard is a socially-agreed upon specification. standard sio:SIO_000619 SIO_000619 A regulatory authority is an organization responsible for exercising regulatory or supervisory capacity in some area of human activity. regulatory authority sio:SIO_000620 SIO_000620 group A collective is a group of entities that share or are motivated by at least one common issue or interest, or work together on a specific project(s) to achieve a common objective. collective sio:SIO_000621 SIO_000621 A formal specification is a mathematical description of software or hardware that may be used to develop an implementation. formal specification sio:SIO_000622 SIO_000622 An RDFS ontology is an ontology that conforms to the syntax and semantics of the Resource Description Framework Schema (RDFS). RDFS ontology sio:SIO_000623 SIO_000623 An OBO ontology is an ontology document as specified by the Open Biological Ontology community. OBO ontology sio:SIO_000624 SIO_000624 chemical group A chemical functional group is a submolecule that confers specific chemical properties. chemical functional group sio:SIO_000625 SIO_000625 chemical structure is the structure of a chemical entity in terms of its molecular geometry and electronic structure. chemical structure sio:SIO_000626 SIO_000626 molecular geometry molecular structure is the spatial arrangement of atoms in a molecule and the chemical bonds that hold the atoms together. molecular structure sio:SIO_000638 SIO_000638 A probability measure is quantity of how likely it is that some event will occur. probability measure sio:SIO_000639 SIO_000639 to passively interact with is the capability to interact with another entity in a way that does not require physical contact. to passively interact with sio:SIO_000640 SIO_000640 A quality that has a value that is increased compared to normal or average. PATO:0002300 increased sio:SIO_000647 SIO_000647 A process model is a representation of some process. process model sio:SIO_000648 SIO_000648 An object model is a representation of an object. object model sio:SIO_000649 SIO_000649 information processing is a process that involves the generation or use of information. information processing sio:SIO_000650 SIO_000650 A wave is a physical entity that travels through space and time, consist of oscillations or vibrations and may be accompanied by the transfer of energy. wave sio:SIO_000651 SIO_000651 A textual entity is language entity that is manifested as a sequence of one or more distinct characters. textual entity sio:SIO_000653 SIO_000653 A version label is a label for a particular form or variation of an earlier or original type. version label sio:SIO_000654 SIO_000654 A software version label is a version label for a piece of software. software version label major.minor[.build[.revision]] sio:SIO_000660 SIO_000660 A hole is a site that is opening into or through something. hole sio:SIO_000661 SIO_000661 A province is a territorial unit, almost always an administrative division, within a country or state. province sio:SIO_000662 SIO_000662 A state is a set of governing and supportive institutions that have sovereignty over a definite territory and population. state sio:SIO_000663 SIO_000663 A territory is a non-sovereign geographic region. territory sio:SIO_000664 SIO_000664 A country is a region legally identified as a distinct entity in political geography. country sio:SIO_000665 SIO_000665 A city is a relatively large and permanent settlement. city sio:SIO_000666 SIO_000666 A township is a rural or sub-urban settlement. township sio:SIO_000667 SIO_000667 software execution is the process of executing software on a computing device. software execution sio:SIO_000669 SIO_000669 A start time is a time instant pertaining to the time at which a process begins. start time sio:SIO_000670 SIO_000670 An end time is a time instant pertaining to the time at which a process ends. end time sio:SIO_000675 SIO_000675 A unique identifier is an identifier that uniquely identifies some thing. unique identifier sio:SIO_000676 SIO_000676 A social role is a role that is ascribed to individuals in a community. social role sio:SIO_000677 SIO_000677 A processual role is a role that can only be realized in a process. processual role sio:SIO_000678 SIO_000678 An abstract role is a role whose basis lies in spatial/temporal or comparative relations. abstract role sio:SIO_000683 SIO_000683 A justification is a proposition that defends, explains or excuses some argument. justification sio:SIO_000686 SIO_000686 An academic department is a division of a university or school faculty devoted to a particular academic discipline. academic department sio:SIO_000688 SIO_000688 institute is a society or organization having a object or common factor, and is normally applied to those with a scientific, educational, or social objective. institute sio:SIO_000689 SIO_000689 to be a part of is the capability to be assembled into a larger structure that persists in time. to be a part of sio:SIO_000690 SIO_000690 to associate is the capability to physically interact with another object. to associate sio:SIO_000692 SIO_000692 to be actively interacted with is the capability to be manipulated by some device or agent. to be actively interacted with sio:SIO_000693 SIO_000693 A corporation is an organization that is granted a charter recognizing it as a separate legal entity. corporation sio:SIO_000694 SIO_000694 to be passively interacted with is the capability of an object to be observed. to be passively interacted with sio:SIO_000695 SIO_000695 to be recorded is the capability of an object to be observed in such a way that information about it can be transcribed in a specified format on some physical medium. to be recorded sio:SIO_000696 SIO_000696 to be observed is the capability of an object to be perceived. to be observed sio:SIO_000698 SIO_000698 to disassemble is to physically separate the parts of an object. to disassemble sio:SIO_000700 SIO_000700 to disassociate is to cease or break association with some thing. to disassociate sio:SIO_000701 SIO_000701 to interact with is a capabililty that involves another object. to interact with sio:SIO_000702 SIO_000702 to be interacted with is the capability of an object to be target of a physical interaction. to be interacted with sio:SIO_000703 SIO_000703 evolving is a process that elicits change across successive generations in the inherited characteristics of biological populations. evolving sio:SIO_000704 SIO_000704 A positional role is an abstract role which holds by comparing position to another object of reference. positional role sio:SIO_000705 SIO_000705 A specification of an object, manifested by an agent, intended to accomplish goals, in a particular environment, using a set of primitive components, satisfying a set of requirements, subject to constraints. design sio:SIO_000706 SIO_000706 An occupational role is a social role that pertains to an organizational structure. occupational role sio:SIO_000707 SIO_000707 A student role is the role of an individual that is enrolled in courses at an academic institution. student role sio:SIO_000708 SIO_000708 A professor role is the role of an individual that is involved in teaching of students (undergraduate and/or graduate) at a post-secondary academic institution. professor role sio:SIO_000711 SIO_000711 An academic role is a social role that pertains to the academic institution. academic role sio:SIO_000712 SIO_000712 A medical role is the role of an individual that is a participant in the delivery of medical care. medical role sio:SIO_000713 SIO_000713 physician A doctor role is the role of an individual who practices medicine, which is concerned with promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury, and other physical and mental impairments. doctor role sio:SIO_000714 SIO_000714 A nurse role is the role of an individual that is involved in the protection, promotion, and optimization of health and abilities, prevention of illness and injury, alleviation of suffering through the diagnosis and treatment of human response, and advocacy in the care of individuals, families, communities, and populations. nurse role sio:SIO_000715 SIO_000715 A patient role is the role of an individual that is the recepient of medical care. patient role sio:SIO_000716 SIO_000716 A medical practioner is an individual that provides medical care. medical practitioner sio:SIO_000717 SIO_000717 A dentist role is the role of an individual that that specializes in the diagnosis, prevention, and treatment of diseases and conditions of the oral cavity. dentist role sio:SIO_000719 SIO_000719 to move to translocate is the capability to displace oneself from one location to another. to translocate sio:SIO_000720 SIO_000720 to be moved to be translocated is the capability to be physically displaced from one location to another to be translocated sio:SIO_000721 SIO_000721 A comparative role is an abstract role which holds by comparing some attribute of another object of reference. comparative role sio:SIO_000722 SIO_000722 to be compared is the capability of an object to be examined in order to note the similarities or differences among a set of objects. to be compared sio:SIO_000723 SIO_000723 to compare is the capability to examine in order to note the similarities or differences among a set of objects. to compare sio:SIO_000724 SIO_000724 to examine is the capability to make detailed observation. to examine sio:SIO_000725 SIO_000725 to be examined is the capability of an object to be observed in a detailed manner. to be examined sio:SIO_000726 SIO_000726 An administrative role is the role of an individual that performs administrative tasks for some organization. administrative role sio:SIO_000727 SIO_000727 A secretary role is the role of an individual that performs administrative tasks to support one or more individuals of the same organization. secretary role sio:SIO_000728 SIO_000728 A chemical identifier is an identifier for a chemical entity chemical identifier sio:SIO_000729 SIO_000729 A record identifier is an identifier for a database entry. record identifier sio:SIO_000730 SIO_000730 A physical entity identifier is an identifier for a physical entity. physical entity identifier sio:SIO_000731 SIO_000731 An informational entity identifier is an identifier for an informational entity. informational entity identifier sio:SIO_000732 SIO_000732 A molecular identifier is an identifier for a molecular entity. molecular identifier sio:SIO_000739 SIO_000739 planning is the agentive process of developing a plan that specifies a set of actions in order to meet a set of goals or objectives. planning sio:SIO_000740 SIO_000740 A curve segment is a part of a curve that consists of at least three points. curve segment sio:SIO_000741 SIO_000741 A stationary point is a point that is part of a curve in which the derivative at that point is zero, and hence its value is at least a local maximum or minimum. stationary point sio:SIO_000742 SIO_000742 A local maximum stationary point is a point that has a higher value in some axis than adjacent points. local maximum stationary point sio:SIO_000743 SIO_000743 A local minimum stationary point is a point that has a lower value in some axis than adjacent points. local minimum stationary point sio:SIO_000744 SIO_000744 learning is the agentive process of acquiring knowledge. learning sio:SIO_000745 SIO_000745 comparison comparing is the process of examining a set of objects and determining their equality or inequality based on one or more features. comparing sio:SIO_000746 SIO_000746 reasoning is the agentive process of using knowledge to evaluate the truth value of a proposition. reasoning sio:SIO_000747 SIO_000747 study investigation is the process of carrying out a plan or procedure so as to discover facts or information about the object of study. investigation sio:SIO_000748 SIO_000748 predicting is the process of formulating a proposition about a state of affairs which might be realized in the future. predicting sio:SIO_000750 SIO_000750 A database is a set of tables. database sio:SIO_000751 SIO_000751 A quality that has a value that is decreased compared to normal or average. PATO:0002301 decreased sio:SIO_000752 SIO_000752 A row represents a single, implicitly structured data item in a table. row 0 sio:SIO_000753 SIO_000753 A column is a vertical sequence of cells in a cellular automata. column sio:SIO_000754 SIO_000754 A database table is a set of named columns with zero or more rows composed of cells that contain column values and is part of a database. database table sio:SIO_000755 SIO_000755 The minimal unit of a cellular automaton that can change state and has an associated behavior. cell (informational) sio:SIO_000756 SIO_000756 database record A database entry is a single, implicitly structured data item in a table. database entry sio:SIO_000757 SIO_000757 A database collumn is a column in a database table. database column sio:SIO_000758 SIO_000758 disordered is a structural quality in which the parts of an object are non-rigid. disordered sio:SIO_000759 SIO_000759 A unique cell is a cell that contains a unique value in the cellular automaton. unique cell sio:SIO_000760 SIO_000760 A referenceing cell is a cell of a cellular automata that refers to another cell. referencing cell sio:SIO_000761 SIO_000761 A referent cell is a cell that is the referent of some function or pointer. referent cell sio:SIO_000762 SIO_000762 A database key is an informational entity whose value is constructed from one or more database columns. database key null sio:SIO_000763 SIO_000763 A primary database key is a database key that identifies every row of a table. primary database key sio:SIO_000764 SIO_000764 A foreign database key is a database key that refers to a key in some table. foreign database key 0.0 1.0 sio:SIO_000765 SIO_000765 p-value A p-value or probability value is the probability of obtaining a test statistic at least as extreme as the one that was actually observed, assuming that the null hypothesis is true probability value sio:SIO_000766 SIO_000766 A street name is the token given to identify a particular street. street name sio:SIO_000767 SIO_000767 A postal code is a geographic coordinate composed of a series of letters and/or digits appended to a postal address for the purpose of sorting mail. postal code sio:SIO_000768 SIO_000768 An apartment number is the number assigned to identify an apartment in a building of apartments. apartment number sio:SIO_000769 SIO_000769 The uncertainty value (margin of error) of a measurement is a range of values likely to enclose the true value. uncertainty value sio:SIO_000770 SIO_000770 A standard deviation (represented by the symbol σ) is the quantity of variation from the average (mean, or expected value). standard deviation sio:SIO_000771 SIO_000771 A versioned record is a record for which there exists another variant based that was derived via modification of the facts. versioned record resource:SIO_000776 sio:SIO_000776 SIO_000776 An object is an entity that is wholly identifiable at any instant of time during which it exists. core object sio:SIO_000777 SIO_000777 to be a member of is the capability to be considered a part of a collection. to be a member of sio:SIO_000778 SIO_000778 to distort is the capability to change the appearance of an entity by some transformation. to distort sio:SIO_000779 SIO_000779 A primer is a nucleic acid that enables the synthesis of a complement strand of DNA by binding to it and acting as a point of transcription initiation. primer sio:SIO_000780 SIO_000780 to bind to is the capability to physically interact with another object through a set of non-covalent interactions. to bind to sio:SIO_000783 SIO_000783 A spatial boundary is the closure minus the interior of a subset of a topological space. spatial boundary sio:SIO_000784 SIO_000784 hermaphrodite is a biological sex of an individual with both male and female sexual organs. PATO:0001827 hermaphrodite sio:SIO_000785 SIO_000785 An answer is a reply to a question. answer sio:SIO_000786 SIO_000786 A verbal language entity is a language entity that is manifested through sound. verbal language entity sio:SIO_000787 SIO_000787 A page number is the count of a page in a sequence of pages. page number sio:SIO_000788 SIO_000788 A linear position is the position of some object against a linear positioning system. linear position sio:SIO_000789 SIO_000789 A sequence element position is the position of an element of a linear sequence. sequence element position sio:SIO_000790 SIO_000790 ncRNA gene A non-protein coding RNA (ncRNA) gene is a gene that encodes for a RNA transcript that is not further translated into a protein product. http://purl.obolibrary.org/obo/SO_0001263 non-protein coding RNA (ncRNA) gene sio:SIO_000791 SIO_000791 A sequence start position is the start position for a sequence of characters. sequence start position sio:SIO_000792 SIO_000792 A sequence end position is the position of the last character in a sequence of characters relative to some linear frame of reference. sequence end position sio:SIO_000794 SIO_000794 The number of elements of a finite set of objects. count sio:SIO_000795 SIO_000795 A chemical role is a processual role held by a chemical entity. chemical entity role sio:SIO_000796 SIO_000796 The role of a chemical participant that serves to increase the rate of reaction by lowering the activiation energy. catalytic role sio:SIO_000797 SIO_000797 The role of a chemical entity that is modified in a chemical reaction. substrate role sio:SIO_000798 SIO_000798 The role of a chemical entity present at the end of a chemical reaction. product role sio:SIO_000799 SIO_000799 The role of a chemical entity involved in the mechanism for enzyme-mediated catalysis. cofactor role sio:SIO_000800 SIO_000800 A co-factor role in which the chemical entity is modified during catalysis and must be regenerated. co-enzyme role sio:SIO_000801 SIO_000801 A coenzyme role of a chemical entity that is covalently bonded to the enzyme. prosthetic group role sio:SIO_000802 SIO_000802 A co-enzyme role of a chemical entity that is transiently associated, and is regenerated in a separate reaction. co-substrate role sio:SIO_000803 SIO_000803 The role of a chemical entity that reduces the rate of reaction. inhibitor role sio:SIO_000804 SIO_000804 The role of a chemical entity that increases the rate of reaction. activator role sio:SIO_000805 SIO_000805 The quality of having a charge. charged sio:SIO_000806 SIO_000806 The quality of not having a charge. uncharged sio:SIO_000807 SIO_000807 A partial negative charge is a negative charge where the value of the charge is negative. partial positive charge sio:SIO_000808 SIO_000808 A partial positive charge is a partial charge where the value of the charge is positive. partial negative charge sio:SIO_000809 SIO_000809 The quality of having a charge that is not a full multiple of 1 unit charge. partial charge sio:SIO_000810 SIO_000810 A complete charge is a charge where the value of the charge is a multiple of 1. complete charge sio:SIO_000811 SIO_000811 Uniform Resource Locator A Uniform Resource Locator or Universal Resource Locator (URL) is a specific character string that constitutes a reference to an Internet resource. URL sio:SIO_000812 SIO_000812 affection is an emotion characterized with a feeling or type of love for another living thing. affection sio:SIO_000813 SIO_000813 angst is the intense feeling of apprehension, anxiety or inner turmoil. angst sio:SIO_000814 SIO_000814 Annoyance is an unpleasant emtion that is characterized by a abnormal or excessive sensitivity to some external stimulus. annoyance sio:SIO_000815 SIO_000815 anxiety is an emotion charactersized by intense feeling of fear and concern coupled with a physical response. anxiety sio:SIO_000816 SIO_000816 apathy is an emotion characterized by lack of interest, enthusiasm, or concern. apathy sio:SIO_000817 SIO_000817 arousal is an emotion characterized by state of reactive to stimuli. It involves the activation of the reticular activating system in the brain stem, the autonomic nervous system and the endocrine system, leading to increased heart rate and blood pressure and a condition of sensory alertness, mobility and readiness to respond. arousal sio:SIO_000818 SIO_000818 awe is an emotion produced by that which is grand, sublime or powerful and is characterized by a combination of joy, fear and admiration/reverence/respect. awe sio:SIO_000819 SIO_000819 boldness is the trait of being willing to undertake things that involve risk or danger. boldness sio:SIO_000820 SIO_000820 boredom is the emotion experience by those not interested in their surroundings or available activities. boredom sio:SIO_000821 SIO_000821 contempt is disgust towards a lower status individual. contempt sio:SIO_000822 SIO_000822 contentment is an emotion characterized by acknowledgement and satisfaction of the current state of affairs. contentment sio:SIO_000823 SIO_000823 curiosity is the strong desire to know or learn something. curiosity sio:SIO_000824 SIO_000824 depressed depression is an unpleasant emotion linked to aversion to activity that can affect a person's thoughts, behavior, feelings and physical well-being. Depressed individuals may feel sad, anxious, empty, hopeless, worried, helpless, worthless, guilty, irritable, or restless. depression sio:SIO_000825 SIO_000825 desire is a strong emotion of wanting to have something or wishing for something to happen. desire sio:SIO_000826 SIO_000826 despair is depression, hopelessness or lack of hope. despair sio:SIO_000827 SIO_000827 disappointed disappointing disappointment is the feeling of dissatisfaction that follows the failure of expectations or hopes to manifest. disappointment sio:SIO_000828 SIO_000828 Disgust is a feeling of revulsion or profound disapproval aroused by something unpleasant or offensive. disgust sio:SIO_000829 SIO_000829 dread is the instense negative emotion that induces fear and apprehension. dread sio:SIO_000830 SIO_000830 ecstacy is an emotion characterized by a heightened state of consciousness with total involvement of a subject. ecstasy sio:SIO_000831 SIO_000831 A positive emotion is an emotion that feels good. positive emotion sio:SIO_000832 SIO_000832 negative emotion is an emotion that does not feel good. negative emotion sio:SIO_000833 SIO_000833 Embarrassment is the emotion of intense discomfort with oneself, experienced upon having a socially unacceptable act or condition witnessed by or revealed to other. embarassment sio:SIO_000834 SIO_000834 envy is an emotion that occurs when a person lacks another's (perceived) superior quality, achievement or possession and wishes that the other lacked it. envy sio:SIO_000835 SIO_000835 euphoria is an emotion characterized by intense feelings of well-being, elation, happiness, ecstasy, excitement, and joy. euphoria sio:SIO_000836 SIO_000836 excitement is a positive emotion of feeling great enthusiasm and eagerness. excitement sio:SIO_000837 SIO_000837 Fear is a negative emotion induced by a perceived threat that induces one to hide or move quickly away from the location of the perceived threat. fear sio:SIO_000838 SIO_000838 Frustration is an emotion that arises from the perceived resistance to the fulfillment of individual will. frustration sio:SIO_000839 SIO_000839 appreciation gratefulness gratification thankfullness Gratitude, thankfulness, gratefulness, or appreciation is a feeling, emotion or attitude in acknowledgment of a benefit that one has received or will receive. gratitude sio:SIO_000840 SIO_000840 happiness is an emotion characterized by positive or pleasant emotions ranging from contentment to intense joy. happiness sio:SIO_000841 SIO_000841 guilty Guilt is the emotion borne from feeling responsible for the commission of an offense and arises out of public humiliation. guilt sio:SIO_000842 SIO_000842 grief is an emotion in response to loss, whether physical or abstract including death, unemployment, ill health or the end of a relationship. grief sio:SIO_000843 SIO_000843 hope is an emotion of belief in a positive outcome related to events and circumstances in one's life. hope sio:SIO_000844 SIO_000844 Hostility is the intense negative emotion of being in conflict or opposition to someone or something. hostility sio:SIO_000845 SIO_000845 hurt is an unpleasant feeling, emotion or sensation. hurt sio:SIO_000846 SIO_000846 Hysteria is an unmanageable emotion. hysteria sio:SIO_000847 SIO_000847 indifference is an emotion characterized by lack of interest, concern, or sympathy. indifference sio:SIO_000848 SIO_000848 interest is the emotion of wanting to know or learn about something or someone. interest sio:SIO_000849 SIO_000849 jealousy is an emotion and typically refers to the negative thoughts and feelings of insecurity, fear, and anxiety over an anticipated loss of something that the person values, particularly in reference to a human connection. jealousy sio:SIO_000850 SIO_000850 joy is an emotion of intense happiness. joy sio:SIO_000851 SIO_000851 loathing is an intense dislike or disgust. loathing sio:SIO_000852 SIO_000852 Loneliness is an unpleasant emotion in which a person feels a strong sense of emptiness, yearning distress and solitude resulting from inadequate quantity or quality of social relationships. loneliness sio:SIO_000853 SIO_000853 lust is the strong desire for sex. lust sio:SIO_000854 SIO_000854 misery is a feeling of great unhappiness, suffering and/or pain. misery sio:SIO_000855 SIO_000855 Panic is a sudden emotion of fear which is so strong as to dominate or prevent reason and logical thinking, replacing it with overwhelming feelings of anxiety and frantic agitation consistent with an animalistic fight-or-flight reaction. panic sio:SIO_000856 SIO_000856 passion is the intense desire for something. passion sio:SIO_000857 SIO_000857 Pity is the emotion of sadness or sorrow for another. pity sio:SIO_000858 SIO_000858 pleasure is an emotion of happy satisfaction and enjoyment. pleasure sio:SIO_000859 SIO_000859 pride is an emotion of satisfaction of attachment toward one's own or another's choices and actions, or toward a whole group of people, and is a product of praise, independent self-reflection, or a fulfilled feeling of belonging. pride sio:SIO_000860 SIO_000860 Rage is a feeling of intense anger that is associated with the Fight-or-flight response. rage sio:SIO_000861 SIO_000861 regret is a feeling of sadness, repentance, or disappointment over something that has happened or been done. regret sio:SIO_000862 SIO_000862 remorse is an emotion of personal regret felt by a person after he or she has committed an act which they deem to be shameful, hurtful, or violent. remorse sio:SIO_000863 SIO_000863 sad unhappiness unhappy sadness is emotional pain associated with, or characterized by feelings of disadvantage, loss, despair, helplessness, sorrow, and rage. sadness sio:SIO_000864 SIO_000864 satisfaction is an emotion of fulfillment of one's wishes, expectations, or needs, or the pleasure derived from this. satisfaction sio:SIO_000865 SIO_000865 shame is the emotion borne from feeling responsible for the commission of an offense. shame sio:SIO_000866 SIO_000866 shock is an emotion of sudden upset or surprise. shock sio:SIO_000867 SIO_000867 shyness is an emotion of apprehension, lack of comfort, or awkwardness experienced when in proximity to, approaching, or being approached by other individuals, especially in new situations or with unfamiliar individuals. shyness sio:SIO_000868 SIO_000868 sorrow is the emotion that is characterized by a long term state of intense sadness, distress and a degree of resignation (not accepting). sorrow sio:SIO_000869 SIO_000869 Suffering is the unpleasant emotion and aversion associated with the perception of harm or threat of harm in an individual. suffering sio:SIO_000870 SIO_000870 surprise is a brief emotion experienced as the result of an unexpected event. surprise sio:SIO_000871 SIO_000871 terror is the extreme feeling of fear. terror sio:SIO_000872 SIO_000872 wonder is an emotion of perceiving something very rare or unexpected, but not threatening. wonder sio:SIO_000873 SIO_000873 worry is the emotion characterized by concer over a real or imaginary issue. worry sio:SIO_000875 SIO_000875 A department chain role is the role of an individual that heads a department at a academic organization. department chair role sio:SIO_000876 SIO_000876 A student advisor role is the role of an individual employed at an academic organization that is involved in advising students. student advisor role sio:SIO_000877 SIO_000877 An undergraduate student advisor role is the role of an individual employed at an academic organization that is involved in advising undergraduate students. undergraduate student advisor role sio:SIO_000878 SIO_000878 A graduate student advisor role is the role of an individual employed at an academic organization that is involved in advising graduate students. graduate student advisor role sio:SIO_000879 SIO_000879 The role of a chemical entity present at the beginning of a chemical reaction. reactant role sio:SIO_000880 SIO_000880 The role of a chemical entity that modifies the rate of reaction. regulator role sio:SIO_000881 SIO_000881 An investigational role is a role held by participants involved in an investigation. investigational role sio:SIO_000882 SIO_000882 The role of an organism in providing resources to maintain the survival and/or reproduction of another organism. host role sio:SIO_000883 SIO_000883 A subject role is the role of an individual that is the target of the study. subject role sio:SIO_000884 SIO_000884 A publishing role is the role of an individual that is involved in the preparation and issue of creative works for consumption by a wider audience. publishing role sio:SIO_000885 SIO_000885 A publisher role is the role of an individual that prepares and issues creative works. publisher role sio:SIO_000886 SIO_000886 An author role is the role of an individual that creates a creative, written work. author role sio:SIO_000887 SIO_000887 A buffer role is the role of a chemical substance which maintains a pH at a near constant value. buffer role sio:SIO_000888 SIO_000888 A chemical substance role is a chemical entity role held by a chemical substance. chemical substance role sio:SIO_000889 SIO_000889 A molecular entity role is a chemical entity role held by a molecule. molecular entity role sio:SIO_000890 SIO_000890 A toxin role is a toxic role of a chemical substance that is poisonous and is produced by an organism. toxin role sio:SIO_000891 SIO_000891 A toxic role is the role of a chemical substance that is poisonous. toxic role sio:SIO_000893 SIO_000893 A role of a chemical substance that participates in a chemical reaction as part of some scientific investigation. reagent role sio:SIO_000894 SIO_000894 to luminesce is to emit light through cold body radiation to luminesce sio:SIO_000895 SIO_000895 to fluoresce is to emit light as a result of absorbing light or other electromagnetic radiation. to fluoresce sio:SIO_000896 SIO_000896 A molecular tracer role is a reactant role of a molecular entity that serves as a marker for the presence, abundance, or location of a molecular target that it associates with. molecular tracer role 2 sio:SIO_000897 SIO_000897 An association is a relationship between two or more entities derived by some informational analysis. association sio:SIO_000898 SIO_000898 A statistical association is any relationship between two measured quantities that renders them statistically dependent. statistical association sio:SIO_000899 SIO_000899 A chromosome is a molecular complex of circular or linear DNA and bound proteins. chromosome sio:SIO_000902 SIO_000902 A top value axis is a value axis that is spatially positioned to the top of the plot area. top value axis sio:SIO_000903 SIO_000903 A bottom value axis is a value axis that is spatially positioned to the bottom of the plot area. bottom value axis sio:SIO_000904 SIO_000904 A chart is a figure that displays the relationship among tabular numeric data, functions or some kinds of qualitative structures. chart sio:SIO_000906 SIO_000906 A map is a a visual representation of an area that depicts the relationship between elements of that space. map sio:SIO_000907 SIO_000907 A heatmap is a graphical representation of data where the individual values contained in a matrix are represented as colors. heatmap sio:SIO_000908 SIO_000908 A streamgraph is a multi-line stacked graph that yields the appearance of continuous y-values across the x-axis. streamgraph sio:SIO_000909 SIO_000909 A boxplot (box-and-whisker diagram) is a convenient way of graphically depicting groups of numerical data through their five-number summaries: the smallest observation (sample minimum), lower quartile (Q1), median (Q2), upper quartile (Q3), and largest observation (sample maximum). boxplot sio:SIO_000910 SIO_000910 A geographic heatmap is a graphical representation of data over a geographic region where individual values are represented as colors. geographic heatmap sio:SIO_000911 SIO_000911 A histogram is a graphical representation of data which consists of tabular frequencies, shown as adjacent rectangles, over discrete intervals (bins) , with an area equal to the frequency of the observations in the interval. histogram resource:SIO_000912 sio:SIO_000912 SIO_000912 A measurement scale is a functional specification that specifies an allowed range of categories or values. measurement scale sio:SIO_000913 SIO_000913 A nominal scale of measurement only specifies a limited set of categories. nomimal scale sio:SIO_000914 SIO_000914 A binary scale is a measurement scale that specifies a choice between two values. binary scale sio:SIO_000915 SIO_000915 A numeric scale of measurement is one that only specifies numeric values. numeric scale sio:SIO_000916 SIO_000916 A decimal scale of measurement is one that only specifies decimal values. decimal scale sio:SIO_000917 SIO_000917 An integer scale of measurement is one that only specifies integer values. integer scale sio:SIO_000918 SIO_000918 modification modifying is the process by which an entity gains or loses parts, qualities, roles, dispositions, functions, etc, but maintains their identity through these changes. modifying sio:SIO_000919 SIO_000919 reproducing is a process characterized by creation of an entity that is similar or exactly the same as the template from which it is derived. reproducing sio:SIO_000920 SIO_000920 An independent variable is a variable that may take on different values independent of other elements in a system. independent variable sio:SIO_000921 SIO_000921 A dependent variable is one whose value changes as a consequence of changes in other values in the system. dependent variable sio:SIO_000922 SIO_000922 A Gantt chart is a bar chart that illustrates a project schedule. Gantt chart sio:SIO_000923 SIO_000923 A correlation is a statistical relationship involving dependence between two random variables or datasets. correlation sio:SIO_000924 SIO_000924 A television program is a audiovisual media that is produced and broadcast using a television. television program sio:SIO_000926 SIO_000926 A radio receiver is a communication device that receives its input from an antenna, uses electronic filters to separate a wanted radio signal from all other signals picked up by this antenna, amplifies it to a level suitable for further processing, and finally converts through demodulation and decoding the signal into a form usable for the consumer, such as sound, pictures, digital data, measurement values, navigational positions. radio receiver sio:SIO_000927 SIO_000927 The telephone is a communications device that transmits and receives sounds, and are minimally composed of a microphone to speak into, a speaker'which reproduces the voice of the other person and a ringer which makes a sound to alert the owner when a call is coming in. telephone sio:SIO_000928 SIO_000928 A radar is an object-detection system which uses radio waves to determine the range, altitude, direction, or speed of objects. radar sio:SIO_000929 SIO_000929 A pie chart is a circular chart divided into sectors each of whose length is proportional to the quantity it represents. pie chart sio:SIO_000930 SIO_000930 A matrix chart summarizes a multidimensional data set in a grid. matrix chart sio:SIO_000931 SIO_000931 A network diagram consists of a set of vertices connected by edges. network diagram sio:SIO_000932 SIO_000932 A block histogram contains an x-axis that is divided into bins which correspond to value ranges. Each item in the data set is drawn as a rectangular block, and the blocks are piled into the bins to show how many values in each range. block histogram sio:SIO_000933 SIO_000933 A bubble chart contains circles whose area corresponds to a value. bubble chart sio:SIO_000934 SIO_000934 A stack graph is a statistical graph which presents multiple series in which the distance between one series and another indicates the relative contribution to the total for any x-value. stack graph sio:SIO_000935 SIO_000935 A treemap is a chart that fully partitions the area into a set of rectangles whose area represents its relative value. treemap sio:SIO_000936 SIO_000936 A word tree is a chart that links phrases with contexts through a tree-like branching structure. word tree sio:SIO_000937 SIO_000937 A textual chart is a chart containing text. textual chart sio:SIO_000938 SIO_000938 word cloud A tag cloud is a visualization of word frequencies. tag cloud sio:SIO_000939 SIO_000939 A phrase net diagram illustrates the relationship between different words used in a text. phrase net diagram sio:SIO_000940 SIO_000940 A mereological chart is a chart that illustrates the parts in the context of the whole. mereological chart sio:SIO_000941 SIO_000941 conversing a form of interactive, spontaneous communication between two or more agents who are following rules of etiquette. conversing sio:SIO_000942 SIO_000942 A numeric label is a number used as a label. numeric label sio:SIO_000943 SIO_000943 A start position is the proximal position of an object relative to an origin in a linear system. start position sio:SIO_000944 SIO_000944 An interval is a set of real numbers that includes all numbers between any two numbers in the set. interval sio:SIO_000945 SIO_000945 A tree diagram is a hierarchical network diagram in which a root vertex is connected to one or more other vertices through a directed edge, which in turn may be connected to other vertices. tree diagram sio:SIO_000946 SIO_000946 A flowchart is a diagram that represents an algorithm or process, showing the steps as boxes of various kinds, and their order by connecting these with arrows. flowchart sio:SIO_000947 SIO_000947 A Venn diagram is a chart that illustrates all possible logical relations between a finite collection of sets as overlapping circles. venn diagram sio:SIO_000948 SIO_000948 A dendrogram is a tree diagram used to illustrate the arrangement of the clusters produced by hierarchical clustering. dendrogram sio:SIO_000949 SIO_000949 apprehension is the negative emotion that something unpleasant will occur. apprehension sio:SIO_000950 SIO_000950 resentment is disgust directed toward a higher status individual. resentment sio:SIO_000951 SIO_000951 Pain is an unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage. pain sio:SIO_000952 SIO_000952 A default parameter is a parameter which has a default value. default parameter sio:SIO_000953 SIO_000953 stop position An end position is the distal position of an object relative to an origin in a linear system. end position sio:SIO_000954 SIO_000954 sick is the status of a living organism that is behaving at a sub-optimal level. sick sio:SIO_000955 SIO_000955 An environment is a geographic region that hosts certain processes or objects. environment resource:SIO_000956 sio:SIO_000956 SIO_000956 A device is usually a constructed tool. device sio:SIO_000957 SIO_000957 A communication device is a device that facilitates the transmission of information through encoded in an audio or digital signal between a sender and a receiver. communication device sio:SIO_000959 SIO_000959 existence quality is the quality of an entity that describe in what environment it is known to exist. existence quality sio:SIO_000960 SIO_000960 real is the quality of an entity that exists in real space and time. real sio:SIO_000961 SIO_000961 fictional is the quality of an entity that exists only in a creative work of fiction. fictional sio:SIO_000962 SIO_000962 virtual is the quality of an entity that exists only in a virtual setting such as a simulation or game environment. virtual sio:SIO_000963 SIO_000963 not started is the status of a process that is predicted to exist but has not yet begun. not started sio:SIO_000964 SIO_000964 A standard operating procedure is a specification approved for use in specific environments. standard operating procedure sio:SIO_000965 SIO_000965 agreement quality is a quality that exhibits the degree of consensus for some set of assertions. agreement quality sio:SIO_000966 SIO_000966 agreement is the result of consensus decision making when members of the group agree. agreement sio:SIO_000967 SIO_000967 agreement is the result of consensus decision making when members of the group do not all agree. disagreement sio:SIO_000968 SIO_000968 A poison role is the role of a substance that causes some negative disturbance in an organism. poison role sio:SIO_000969 SIO_000969 communication communicating is the process of conveying information through the exchange of thoughts, messages, or information, as by speech, visuals, signals, writing, or behaviour. communicating sio:SIO_000976 SIO_000976 observational study draws inferences about the possible effect of a treatment on subjects, where the assignment of subjects into a treated group versus a control group is outside the control of the investigator observational study sio:SIO_000977 SIO_000977 A syllable is a verbal entity of language having one vowel sound, with or without surrounding consonants, forming the whole or a part of a word. syllable sio:SIO_000978 SIO_000978 A consonant is a verbal entity of language that is articulated with complete or partial closure of the vocal tract. consonant sio:SIO_000979 SIO_000979 A vowel is a verbal entity of language that is pronounced with an open vocal tract so that there is no build-up of air pressure at any point above the glottis. vowel sio:SIO_000980 SIO_000980 A sign language (also signed language) is a language that involves manual communication and body language to convey meaning. This can involve simultaneously combining hand shapes, orientation and movement of the hands, arms or body, and facial expressions to fluidly express a speaker's thoughts. sign language sio:SIO_000981 SIO_000981 A verbal language is a language that uses sounds to communicate. verbal language sio:SIO_000982 SIO_000982 written language is a language that is communicated through a writing system. written language sio:SIO_000983 SIO_000983 A gene-disease association is an association between a gene and a disease. gene-disease association sio:SIO_000984 SIO_000984 A genome is a collection of nucleic acids. genome sio:SIO_000985 SIO_000985 A gene that contains an open reading frame which codes for a protein. http://purl.obolibrary.org/obo/SO_0001217 protein coding gene sio:SIO_000986 SIO_000986 A gene that codes for a functional RNA molecule. functional rna coding gene sio:SIO_000987 SIO_000987 A predicted gene is a gene that was identified through computational method but has not been experimentally validated. predicted gene sio:SIO_000988 SIO_000988 A pseudo gene is a region of a nucleic acid that either cannot be transcribed, or its RNA transcript cannot be translated. http://purl.obolibrary.org/obo/SO_0000336 pseudogene sio:SIO_000989 SIO_000989 A sequence assembly is a sequence that is produced as by the alignment of two or more sequences. sequence assembly sio:SIO_000991 SIO_000991 An experimentally validated gene is a gene whose existence has been demonstrated through experimental methods. validated gene sio:SIO_000992 SIO_000992 unsupported is an existence quality in which there is no evidence to support the existence of the entity in any world (real or hypothetical) unsupported sio:SIO_000993 SIO_000993 A chemical-disease association is an association between a chemical and a disease. chemical-disease association sio:SIO_000994 SIO_000994 study An experiment is an investigation that has the goal of verifying, falsifying, or establishing the validity of a hypothesis. experiment sio:SIO_000995 SIO_000995 suspended is the status of a process that is no longer progressing towards completion. suspended sio:SIO_000996 SIO_000996 cancelled is a process status in which the process, while planned to occur, will not occur. cancelled sio:SIO_000997 SIO_000997 aborted is a process status in which a started process will not complete as intended. aborted sio:SIO_000998 SIO_000998 literature curation is the process of an agent selecting and extracting terms and phrases from a document. literature curation sio:SIO_000999 SIO_000999 A procedure is a process that attempts to achieve one or more objectives by following an established set of actions. procedure sio:SIO_001000 SIO_001000 A clinical trial is an intervention trial to determine the safety and efficacy of medical interventions (e.g., drugs, diagnostics, devices, therapy protocols). clinical trial sio:SIO_001001 SIO_001001 A medical diagnosis (often simply termed diagnosis) refers to the process of attempting to determine or identify a possible disease or disorder. medical diagnosis sio:SIO_001002 SIO_001002 A differential diagnosis (sometimes abbreviated DDx, ddx, DD, D/Dx, or ΔΔ) is a systematic diagnostic method used to identify the presence of an entity where multiple alternatives are possible (and the process may be termed differential diagnostic procedure), and may also refer to any of the included candidate alternatives (which may also be termed candidate condition). differential diagnosis sio:SIO_001003 SIO_001003 A diagnostic opinion is an opinion resulting from a medical diagnostic procedure. diagnostic opinion sio:SIO_001004 SIO_001004 An opinion is a belief that is the result of emotion or interpretation of facts. opinion sio:SIO_001005 SIO_001005 A chemical effect is a chemical interaction in which a chemical elicits a marked characteristic of a biological system. chemical effect 2 sio:SIO_001006 SIO_001006 A drug-drug interaction is an interaction in which two drugs interact in such a way to produce a non-additive biological response. drug drug interaction sio:SIO_001007 SIO_001007 bioassay An assay is an investigative (analytic) procedure in laboratory medicine, pharmacology, environmental biology, and molecular biology for qualitatively assessing or quantitatively measuring the presence or amount or the functional activity of a target entity (the analyte) which can be a drug or biochemical substance or a cell in an organism or organic sample. assay sio:SIO_001008 SIO_001008 toxicity is the quality of a chemical substance to cause injury to an organism in a dose dependent manner. toxicity sio:SIO_001009 SIO_001009 toxic is the quality of a substance imparing the normal functioning of a system. toxic sio:SIO_001010 SIO_001010 non toxic is the quality of a substance having no damaging effect to a system. non toxic sio:SIO_001011 SIO_001011 chemical quality is the quality of a chemical entity. chemical quality sio:SIO_001012 SIO_001012 healthy is an organismal state of complete physical, mental and social well-being. healthy sio:SIO_001013 SIO_001013 age is the length of time that a person has lived or a thing has existed. age sio:SIO_001014 SIO_001014 ethnicity is the biological quality of membership in a social group based on a common heritage. ethnicity sio:SIO_001015 SIO_001015 race is a characteristic of an individual by heritable phenotypic characteristics, geographic ancestry, physical appearance, ethnicity, and social status. race sio:SIO_001016 SIO_001016 An ethnic group is a group of people whose members identify with each other through a common heritage, consisting of a common culture, including a shared language or dialect. ethnic group resource:SIO_001017 sio:SIO_001017 SIO_001017 A syndrome is composed of a set of several clinically recognizable features, signs (observed by someone other than the patient), symptoms (reported by the patient), phenomena or characteristics that often occur together. syndrome a sufficient set of co-occuring symptoms believed to represent an underlying phenomenon with dimensional properties sio:SIO_001018 SIO_001018 A ratio is a relationship between two numbers of the same kind expressed arithmetically as a dimensionless quotient of the two which explicitly indicates how many times the first number contains the second. ratio sio:SIO_001019 SIO_001019 A dose is the quantity of a chemical substance administered to a biological system. dose sio:SIO_001020 SIO_001020 effective dose is the amount of a substance required to produce an effect on a predefined percentage of a population. effective dose sio:SIO_001021 SIO_001021 An expected value (or e-value) is the weighted average of all possible values that a random variable can take on. expected value sio:SIO_001022 SIO_001022 clinical laboratory test A diagnostic test is a procedure performed to confirm, or determine the presence of disease in an individual suspected of having the disease, usually following the report of symptoms, or based on the results of other medical tests. diagnostic test sio:SIO_001023 SIO_001023 A medical screening is a medical test or series used to detect or predict the presence of disease in individuals at risk for disease within a defined group, such as a population, family, or workforce medical screening sio:SIO_001024 SIO_001024 A medical procedure is a procedure to identify, examine, alleviate or eliminate an undesirable biological disease or disorder. medical procedure sio:SIO_001025 SIO_001025 A prognosis is a proposition about the likely course of a disease, the chance of recovery or recurrence. prognosis sio:SIO_001026 SIO_001026 A report is a textual document made that present focused, salient content to a specific audience. report sio:SIO_001027 SIO_001027 A medical health record is a record of a single patient's medical history. medical health record sio:SIO_001028 SIO_001028 A medical report is a report prepared by a health care practioner about test outcomes or health status of an individual. medical report sio:SIO_001029 SIO_001029 A peer reviewed article is an article that has undergone peer-review and deemed acceptable for publication. peer reviewed article sio:SIO_001030 SIO_001030 A major version number is a version of a software that exhibits a significant change in functionalilty from a prior version. major version number sio:SIO_001031 SIO_001031 A minor version number is a version of a software that exhibits minor features or significant fix from a prior version. minor version number sio:SIO_001032 SIO_001032 A revision number is a version of a software in which bugs have been fixed from a prior version. revision number sio:SIO_001033 SIO_001033 text quality is the quality of a textual entity. text quality sio:SIO_001034 SIO_001034 reviewed is the quality of a textual entity that has been examined and commented on by another party. reviewed sio:SIO_001035 SIO_001035 peer-reviewed is the quality of a textual entity that has been examined and commented by a peer expert reviewer. peer-reviewed sio:SIO_001036 SIO_001036 drafted draft is the quality of text that has not yet complete. draft sio:SIO_001037 SIO_001037 finalized is the quality of a textual entity that is in its final form. finalized sio:SIO_001038 SIO_001038 editor reviewed is the quality of a textual entity that has been examined and commented on by an editor. editor reviewed sio:SIO_001039 SIO_001039 written is the quality of information that is embodied as visual glyphs in some material form. written sio:SIO_001040 SIO_001040 A morpheme is the smallest semantically meaningful unit in a language. morpheme sio:SIO_001041 SIO_001041 study protocol A study design is a protocol for the proper execution of a study which normally requires a carefullly crafted research question or hypothesis and at least one variable under observation and observed values for that variable. study design sio:SIO_001042 SIO_001042 A recipe is a set of instructions that describe how to prepare or make something. recipe sio:SIO_001043 SIO_001043 An experimental protocol is an action specification with respect to the design and implementation of experiments. In addition to providing a detailed set of procedures and lists of required equipment and instruments, experimental protocols often include information on safety precautions, the calculation of results and reporting standards, including statistical analysis and rules for predefining and documenting excluded data to avoid bias. experimental protocol sio:SIO_001044 SIO_001044 A viroid is a molecule of RNA that does not code for and is not protected by a protein coat. viroid sio:SIO_001045 SIO_001045 The quality of being polar or not polar. polar quality sio:SIO_001046 SIO_001046 polar is the quality of having a dipole. polar sio:SIO_001047 SIO_001047 non-polar is the quality of not having a dipole. non-polar sio:SIO_001048 SIO_001048 An intervention study has the objective of improving the condition of an individual or a group of individuals, and demonstrates the magnitude of that capability by comparing it to a control group. intervention study sio:SIO_001049 SIO_001049 sampling is the act of obtaining a sample, whether through selection, collection or preparation. sampling sio:SIO_001050 SIO_001050 A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. sample sio:SIO_001051 SIO_001051 data analysis is a process of inspecting, cleaning, transforming, and modeling data with the goal of highlighting useful information, suggesting conclusions, and supporting decision making. data analysis sio:SIO_001052 SIO_001052 data collection is the process of acquiring information. data collection sio:SIO_001053 SIO_001053 A reason is a justification that specifies the motive for an action or a determination. reason sio:SIO_001054 SIO_001054 measurement measuring is the process of determining the size, amount, or degree of (something) by using an instrument or device marked in standard units measuring sio:SIO_001055 SIO_001055 observation observing is a process of passive interaction in which one entity makes note of attributes of one or more entities. observing sio:SIO_001056 SIO_001056 character offset The ordinal position of a character in a sequence of characters. character position sio:SIO_001057 SIO_001057 The position of the first character in a word as an offset from the first character of the text in which it is found. word start position sio:SIO_001058 SIO_001058 word end position is the position of the last character in a word as an offset from the first character of the text in which it is found. word end position sio:SIO_001059 SIO_001059 gesturing is a form of non-verbal communication in which visible bodily actions communicate particular messages, either in place of speech or together and in parallel with spoken words. Gestures include movement of the hands, face, or other parts of the body. gesturing sio:SIO_001060 SIO_001060 planned is a process status for a process that has not yet started, but is referred to in a plan. planned sio:SIO_001061 SIO_001061 A population is all the organisms that both belong to the same group or species and live in the same geographical area. population sio:SIO_001062 SIO_001062 A human population refers to a collection of human beings. human population sio:SIO_001063 SIO_001063 A group of people affiliated by consanguinity, affinity, or co-residence. family sio:SIO_001064 SIO_001064 A community is a sizeable social unit that shares common values. community sio:SIO_001065 SIO_001065 speculation is an opinion based on incomplete evidence. speculation sio:SIO_001066 SIO_001066 A study is a process that realizes the steps of a study design. study sio:SIO_001067 SIO_001067 In a controlled observational cohort study, two groups of subjects are selected from two populations that are thought to differ in only one characteristic. The groups of subjects are studied for a specific period and contrasted at the end of the study period. controlled observational cohort study sio:SIO_001068 SIO_001068 A control group is a group of individuals that are not subject to an intervention of interest, but rather serve as a baseline to compare the outcomes in the intervention group. control group sio:SIO_001069 SIO_001069 An intervention group is a group of individuals that are subject to an intervention. intervention group sio:SIO_001070 SIO_001070 controlled variable extraneous variable A control variable that is believed to alter the dependent or independent variables, but may not actually be the focus of the experiment. So that variable will be kept constant or monitored to try to minimise its effect on the experiment. control variable sio:SIO_001071 SIO_001071 text span start position is the position (offset) of the first character of a text span in relation the text it is from. text span start position sio:SIO_001072 SIO_001072 text span end position is the position (offset) of the last character of a text span in relation the text it is from. text span end position sio:SIO_001073 SIO_001073 selector A text span is a subset of contiguous sequence of characters of a textual entity. text span sio:SIO_001074 SIO_001074 A t-statistic is a ratio of the departure of an estimated parameter from its notional value and its standard error. t-statistic sio:SIO_001075 SIO_001075 A microarray probe set identifier is an identifier for a set of probe pairs selected to represent expressed sequences on an array. microarray probe set identifier sio:SIO_001076 SIO_001076 A microarray experiment is an experiment that involves a microarray device to measure the expression of one or more genes. microarray experiment sio:SIO_001077 SIO_001077 A gene expression value is a measured value obtained from a gene expression experiment. gene expression value sio:SIO_001078 SIO_001078 A differential gene expression ratio is the ratio of gene expression values from a test sample compared to a control sample. differential gene expression ratio sio:SIO_001079 SIO_001079 A genotype is a functional specification of a biological entity in terms of its genetic composition (or lack thereof). genotype sio:SIO_001080 SIO_001080 A vocabulary is a collection of terms. vocabulary 0.0 sio:SIO_001081 SIO_001081 A t-statistic based increased differential gene expression is a differential gene expression ratio in which the t-statistic is greater than zero. t-statistic based increased differential gene expression 0.0 sio:SIO_001082 SIO_001082 A t-statistic based decreased differential gene expression is a differential gene expression ratio in which the t-statistic is less than zero. t-statistic based decreased differential gene expression sio:SIO_001083 SIO_001083 A date of database submission refers to the moment in time in which some information was submitted/received to a database system. date of database submission sio:SIO_001084 SIO_001084 A liquid solution is a heterogeneous substance in a liquid state. liquid solution sio:SIO_001085 SIO_001085 to remove a covalent bond is the capability to covalently modify a chemical entity by removing a covalent bond. to remove a covalent bond sio:SIO_001086 SIO_001086 to add a covalent bond is the capability to covalently modify a chemical entity by adding a covalent bond. to add a covalent bond sio:SIO_001087 SIO_001087 to modify electronically is the capability to change the electronic properties of an object. to modify electronically sio:SIO_001088 SIO_001088 concentration is the amount of substance per unit volume of a solution concentration sio:SIO_001089 SIO_001089 pH is a measure of the activity of the (solvated) hydrogen ion. pH is defined as the decimal logarithm of the reciprocal of the hydrogen ion activity, aH+, in a solution. pH sio:SIO_001090 SIO_001090 homogeneous is a quality that describes the uniform composition of an object. homogeneous sio:SIO_001091 SIO_001091 homogeneous is a quality that describes the varied composition of an object. heterogeneous sio:SIO_001092 SIO_001092 A structural quality is a quality of an object that describes its structure. structural quality sio:SIO_001093 SIO_001093 rigid is the quality of maintaining structural integrity (and not bending) under pressure. rigid sio:SIO_001094 SIO_001094 bent is the quality of a line being sharply curved or having an angle. bent sio:SIO_001095 SIO_001095 curved is the quality of a line that deviates from straightness in a smooth, continuous fashion. curved sio:SIO_001099 SIO_001099 electronic configuration electronic structure is the electron configuration is the distribution of electrons of an atom or molecule (or other physical structure) in atomic or molecular orbitals. electronic structure the electron configuration of the neon atom is 1s2 2s2 2p6. sio:SIO_001100 SIO_001100 A crystal structure is the arrangement of atoms or molecules in a crystalline liquid or solid. crystal structure sio:SIO_001102 SIO_001102 to interact and to be interacted with is a mutual disposition of interacting objects. to interact and to be interacted with sio:SIO_001103 SIO_001103 to gain a covalent bond is the capability of a chemical entity to have bonds added. to gain a covalent bond sio:SIO_001104 SIO_001104 to lose a covalent bond is the capability of a chemical entity to have bonds removed. to lose a covalent bond sio:SIO_001105 SIO_001105 to ingest is the capability to take into the body by the mouth for digestion or absorption. to ingest sio:SIO_001106 SIO_001106 to produce is the capability to create new objects to produce sio:SIO_001107 SIO_001107 biological pathway A pathway is an effective specification that outlines a set of actions that forms a way to achieve an objective. pathway sio:SIO_001108 SIO_001108 A central tendency measure is a central value or a typical value for a probability distribution. centrality measure sio:SIO_001109 SIO_001109 arithmeritic mean average A mean is the central tendency of a collection of numbers taken as the sum of the numbers divided by the size of the collection. mean sio:SIO_001110 SIO_001110 A median is the numerical value separating the higher half of a sample, a population, or a probability distribution, from the lower half. median sio:SIO_001111 SIO_001111 A mode is the value that appears most often in a set of data. mode sio:SIO_001112 SIO_001112 A sum is the result of adding a set of values together. sum sio:SIO_001113 SIO_001113 min A minimal value is smallest value of an attribute for the entities in the defined set. minimal value sio:SIO_001114 SIO_001114 max A maximal value is largest value of an attribute for the entities in the defined set. maximal value sio:SIO_001115 SIO_001115 A count of the instances of a class or members in a collection. member count sio:SIO_001116 SIO_001116 A union is a list of all of the values of an attribute for the entities in the defined set. union sio:SIO_001117 SIO_001117 An intersection is a list of only the values of an attribute for the entities in the defined set where all entities have that value. intersection sio:SIO_001118 SIO_001118 ordered list A sequence is an ordered list of entities. Like a set, it contains members (also called elements, or terms). sequence For example, (M, A, R, Y) is a sequence of letters that differs from (A, R, M, Y), as the ordering matters, and (1, 1, 2, 3, 5, 8), which contains the number 1 at two different positions, is a valid sequence. sio:SIO_001119 SIO_001119 A gene-variant disease association in which a mutation in the gene/protein results in the development or maintenance of the disease. gene-disease association linked with causal mutation sio:SIO_001120 SIO_001120 gene-disease association arising from a therapeutic role of the gene/protein A gene disease association in which the gene is a therapeutic marker for the disease. therapeutic gene-disease association sio:SIO_001121 SIO_001121 A gene-disease association in which the gene/protein is involved in the etiology or maintenance of the disease. gene-disease biomarker association sio:SIO_001122 SIO_001122 gene variant-disease association A gene-disease association in which a sequence variation (a mutation, a SNP) is associated with the disease. gene-disease association linked with genetic variation sio:SIO_001123 SIO_001123 A gene-disease association in which the disease phenotype is associated with an altered expression of the gene. gene-disease association linked with altered gene expression sio:SIO_001124 SIO_001124 A gene-disease association in which the disease phenotype is associated with post-translational modifications in the protein product. gene-disease association linked with post-translational modification methylation or phosphorylation of protein product sio:SIO_001125 SIO_001125 A process that modulates the frequency, rate or extent of transcription. regulation of transcription sio:SIO_001126 SIO_001126 A process that modulates the frequency, rate or extent of translation. regulation of translation sio:SIO_001127 SIO_001127 A process that modulates the frequency, rate or extent of process involved in the creation or destruction of a molecule. regulation of molecular quantity sio:SIO_001128 SIO_001128 A process that modulates the frequency, rate or extent of process involved in the production of a molecule. regulation of molecular production sio:SIO_001129 SIO_001129 A process that modulates the frequency, rate or extent of process involved in the destruction of a molecule. regulation of molecular degradation sio:SIO_001130 SIO_001130 A process mediated by a protein that modulates the frequency, rate or extent of translation. protein mediated regulation of translation sio:SIO_001131 SIO_001131 A process mediated by rna that modulates the frequency, rate or extent of translation. rna mediated regulation of translation sio:SIO_001132 SIO_001132 The process of maintaining some the frequency, rate or extent of another process. process maintenance sio:SIO_001133 SIO_001133 The increase of regulation leads to a increased occurence of processes of the target type. increased frequency of process from increased regulation sio:SIO_001134 SIO_001134 The increase of regulation leads to a decreased occurence of processes of the target process type. decreased frequency of process from increased regulation sio:SIO_001135 SIO_001135 regulation of a process duration is a process that modulates the frequency of another process relative to some reference process. regulation of process frequency sio:SIO_001136 SIO_001136 regulation of a process duration is a process that modulates the duration of another process relative to some reference process. regulation of process duration sio:SIO_001137 SIO_001137 increased duration of process from increased regulation is a process in which the duration of the target process is increased as a result of increased regulation. increased duration of process from increased regulation sio:SIO_001138 SIO_001138 decreased duration of process from increased regulation is a process in which the duration of the target process is decreased as a result of increased regulation. decreased duration of process from increased regulation sio:SIO_001139 SIO_001139 regulation of a process spatial extent is a process that modulates the spatial extent of another process relative to some reference process. regulation of process spatial extent heating the solution causes greater diffusion of a chemical. sio:SIO_001140 SIO_001140 The increase of regulation leads to a increased spatial extent of the target process. increased spatial extent of process from increased regulation sio:SIO_001141 SIO_001141 The increase of regulation leads to a decreased spatial extent of the target process. decreased spatial extent of process from decreased regulation sio:SIO_001142 SIO_001142 maintenance of spatial extent of process is a regulation of a process' spatial extent within some specified parameter. maintenance of spatial extent of process sio:SIO_001143 SIO_001143 maintenance of duration of process is a process that regulates a target process to maintain its duration within an expected interval. maintenance of duration of process sio:SIO_001144 SIO_001144 maintenance of frequency of process is a process that regulates the number of occurences of a target process type to a specified number or interval. maintenance of frequency of process sio:SIO_001145 SIO_001145 regulation of a participant quantity is the regulation of a process in which the quantity of its partcipants is changed. regulation of object quantity sio:SIO_001146 SIO_001146 increased regulation leads to an increase in the number of target objects of a specified type. increased object production from increased regulation sio:SIO_001147 SIO_001147 increased regulation leads to a decrease in the number of target objects of a specified type. decreased object production from increased regulation sio:SIO_001148 SIO_001148 increased regulation leads to an increase in the consumption of an object of specified type. increased object consumption from increased regulation sio:SIO_001149 SIO_001149 increased regulation leads to an decrease in the consumption of an object of specified type. decreased object consumption from increased regulation sio:SIO_001150 SIO_001150 A process that modulates the frequency, rate or extent of process involved in the consumption of an object. regulation of object consumption sio:SIO_001151 SIO_001151 regulation of a participant quantity is the regulation of a process in which the quantity of a selected participant is increased. regulation of object production sio:SIO_001152 SIO_001152 maintenance of quantity of object production is a regulation of object production in which the number of objects produced is held more or less constant. maintenance of quantity of object production sio:SIO_001153 SIO_001153 regulation of a participant quantity is the regulation of a process in which the quantity of a selected participant is maintained at a steady level. maintenance of level of object consumption sio:SIO_001160 SIO_001160 number of objects produced is a count of objects that were produced in some process. number of objects produced sio:SIO_001161 SIO_001161 number of objects consumed is a count of objects that were consumed in some process. number of objects consumed sio:SIO_001162 SIO_001162 A difference in number of objects produced is a count of the number of objects produced with respect to a second variable (space, time, etc) difference in number of objects produced sio:SIO_001163 SIO_001163 An increase in the number of objects produced is the positive value of a difference in number of objects produced. increase in number of objects produced sio:SIO_001164 SIO_001164 An decrease in the number of objects produced is the negative value of a difference in number of objects produced. decrease in number of objects produced sio:SIO_001165 SIO_001165 user account allows a user to authenticate to system services and be granted authorization to access them. user account sio:SIO_001166 SIO_001166 An annotation is a written explanatory or critical description, or other in-context information (e.g., pattern, motif, link), that has been associated with data or other types of information. annotation sio:SIO_001167 SIO_001167 A comment is a verbal or written remark often related to an added piece of information, or an observation or statement. comment sio:SIO_001168 SIO_001168 An audio recording is an electrical or mechanical inscription and re-creation of sound waves, such as spoken voice, singing, instrumental music, or sound effects. audio recording sio:SIO_001169 SIO_001169 An issue is a single instance of a periodically published journal, magazine, or newspaper. issue sio:SIO_001170 SIO_001170 A slideshow is a visual presentation of information contained within a collection of slides. slideshow sio:SIO_001171 SIO_001171 dbxref A database cross-reference is an association between one data item and another. database cross-reference sio:SIO_001172 SIO_001172 An exact cross-reference is a database cross-reference in which one entity is equivalent to the other based on all the entitie's attributes (minus the source). exact cross-reference 2 sio:SIO_001173 SIO_001173 double stranded nucleic acid is a molecular complex composed of two weakly connected deoxyribonucleic acids. double stranded DNA sio:SIO_001174 SIO_001174 A nucleic acid strand is a single-stranded nucleic acid that is part of a double stranded nucleic acid complex. nucleic acid strand sio:SIO_001175 SIO_001175 forward strand The positive nucleic acid strand refers to the strand that is to be read 5' to 3'. positive nucleic acid strand sio:SIO_001176 SIO_001176 reverse strand The negative nucleic acid strand is the strand that is that is complimentary to the forward strand and appears from 3' to 5'. negative nucleic acid strand 2 sio:SIO_001177 SIO_001177 double stranded nucleic acid is a molecular complex composed of two weakly connected nucleic acids. double stranded nucleic acid 2 sio:SIO_001178 SIO_001178 double stranded nucleic acid is a molecular complex composed of two weakly connected ribonucleic acids. double stranded RNA sio:SIO_001179 SIO_001179 full agreement is the result of consensus decision making when members of the group unanimously agree. full agreement sio:SIO_001180 SIO_001180 A mass spectrometry experiment is an experiment that involves the use of a mass spectrometer. mass spectrometry experiment sio:SIO_001181 SIO_001181 full agreement is the result of consensus decision making when members of the group unanimously disagree. full disagreement sio:SIO_001182 SIO_001182 rRNA gene A ribosomal RNA gene is a gene that codes for a ribosomal RNA molecule. http://purl.obolibrary.org/obo/SO_0001637 ribosomal RNA gene sio:SIO_001183 SIO_001183 A statement is a proposition that is either (a) a meaningful declarative sentence that is either true or false, or (b) that which a true or false declarative sentence asserts. statement sio:SIO_001184 SIO_001184 A slope or gradient of a line describes its steepness, incline, or grade. A higher slope value indicates a steeper incline. Slope is normally described by the ratio of the "rise" divided by the "run" between two points on a line. slope sio:SIO_001185 SIO_001185 A software process identifier is an identifier for a software process in some operating system. software process identifier sio:SIO_001186 SIO_001186 hypothetical is the quality of an entity that is conjectured to exist. hypothetical sio:SIO_001187 SIO_001187 A database row is a row that is part of a database table. database row sio:SIO_001188 SIO_001188 a SADI semantic web service is a semantic web service that follows the SADI specification sadi SADI semantic web service http://en.wikipedia.org/wiki/SADI sio:SIO_001189 SIO_001189 a semantic web service is a web service that provides a formal, machine understanble description of its functionality. semantic web service sio:SIO_001190 SIO_001190 a REST web service is a web service that provides functionality according to the Representational State Transfer (REST) specification. REST web service http://en.wikipedia.org/wiki/REST sio:SIO_001191 SIO_001191 a SOAP web service is a web service that implements Simple Object Access Protocol (SOAP). SOAP web service http://en.wikipedia.org/wiki/SOAP sio:SIO_001192 SIO_001192 A web service invocation involves the execution of a web service. web service invocation sio:SIO_001193 SIO_001193 A SADI web service invocation is the excution of a SADI web service. sadi SADI web service invocation sio:SIO_001194 SIO_001194 media are audo/visual/audiovisual modes of communicating information for mass consumption. media sio:SIO_001195 SIO_001195 Behaviour is the set of actions and mannerisms made by systems (biological or otherwise) in response to stimuli or inputs, whether internal or external, conscious or subconscious, overt or covert, and voluntary or involuntary. behaviour+ core behaviour sio:SIO_001196 SIO_001196 history is a sequence of past events. history sio:SIO_001197 SIO_001197 A structural motif is a pattern in a structure formed by a spatial arrangement of objects (e.g. atoms). structural motif sio:SIO_001198 SIO_001198 consensus is an acceptable resolution, one that can be supported, even if not the preferred outcome for each individual. consensus sio:SIO_001199 SIO_001199 A process that increases the frequency, rate or extent of process involved in the destruction of a molecule as a result of increased regulation. increased molecular degradation from increased regulation sio:SIO_001200 SIO_001200 A process that decreases the frequency, rate or extent of process involved in the destruction of a molecule as a result of decreased regulation. decreased molecular degradation from decreased regulation sio:SIO_001201 SIO_001201 A process that increases the frequency, rate or extent of process involved in the destruction of a molecule as a result of decreased regulation. increased molecular degradation from decreased regulation sio:SIO_001202 SIO_001202 A process that decreases the frequency, rate or extent of process involved in the destruction of a molecule as a result of increased regulation. decreased molecular degradation from increased regulation sio:SIO_001203 SIO_001203 A process that increases the frequency, rate or extent of process involved in the production of a molecule as a result of increased regulation. increased molecular production from increased regulation sio:SIO_001204 SIO_001204 A process that decreases the frequency, rate or extent of process involved in the production of a molecule as a result of increased regulation. decreased molecular production from increased regulation sio:SIO_001205 SIO_001205 A process that increases the frequency, rate or extent of process involved in the production of a molecule as a result of decreased regulation. increased molecular production from decreased regulation sio:SIO_001206 SIO_001206 A process that decreases the frequency, rate or extent of process involved in the production of a molecule as a result of decreased regulation. decreased molecular production from decreased regulation sio:SIO_001207 SIO_001207 increased chemical destruction is a process in which there is an increase in the amount of chemical destroyed relative to some reference process increased chemical destruction sio:SIO_001208 SIO_001208 decreased chemical destruction is a process in which there is a decrease in the amount of chemical destroyed relative to some reference process decreased chemical destruction sio:SIO_001209 SIO_001209 An assertional qualifier is the quality of affirmation, either being positive or negative. assertional qualifier sio:SIO_001210 SIO_001210 positive is an assertional qualifier that expresses the validity or truth of a basic assertion. positive sio:SIO_001211 SIO_001211 negative is an assertional qualifier that expresses the falsity or lack of truth of a basic assertion. negative sio:SIO_001212 SIO_001212 intensity is a quality that represents the strength or degree of something. intensity sio:SIO_001213 SIO_001213 mild is a qualitative intensity value that is more intense than weak, but less intense than moderate. mild sio:SIO_001214 SIO_001214 moderate is a qualitative intensity value that is more intense than mild, but less intense than strong. moderate sio:SIO_001215 SIO_001215 severe is a qualitative intensity value that is more intense than strong, but less intense than fatal. severe sio:SIO_001216 SIO_001216 fatal is a qualitative intensity value that is more intense than severe, leading to the death/non-functioning of a system. fatal sio:SIO_001217 SIO_001217 strong is a qualitative intensity value that is more intense than moderate, but less intense than severe. strong sio:SIO_001218 SIO_001218 weak is a qualitative intensity value that is more intense than none, but less intense than mild. weak sio:SIO_001219 SIO_001219 to test a hypothesis is the capability to evaluate the truth value of a proposition based on gathered evidence. to test a hypothesis sio:SIO_001220 SIO_001220 to characterize is the capability to classify the attributes or features of an entity against a reference classification. to characterize sio:SIO_001221 SIO_001221 to describe is the capabilty to communicate facts about an entity. to describe sio:SIO_001222 SIO_001222 The 5' splice site is the terminal region of an exon that is 5' to the intron that is to be excised. 5' splice site sio:SIO_001223 SIO_001223 The 3' splice site is the terminal region of an exon that is 3' to the intron that is to be excised. 3' splice site sio:SIO_001224 SIO_001224 An amino acid is an organic molecule composed of a carbon bonded to four different groups: a carboxyl group, an amino group, an R group, and a hydrogen atom. In the case of glycine, the R group is another hydrogen atom. amino acid sio:SIO_001225 SIO_001225 A cisregulatory element is a DNA sequence located on the same DNA strand or chromosome as the gene whose expression it affects. cis regulatory element sio:SIO_001226 SIO_001226 A trans-regulatory element is a DNA sequence associated with the regulation of a gene located outside the genomic region supporting the corresponding structural DNA region of the trans-regulatory element (i.e., a different DNA strand or different chromosome). trans-regulatory element sio:SIO_001227 SIO_001227 A small cytoplasmic RNA (scRNA) gene is a gene that encodes a small (7S; 129 nucleotides) RNA molecule found in the cytosol and rough endoplasmic reticulum that are normally associated with proteins that are involved in specific selection and transport of other proteins. http://purl.obolibrary.org/obo/SO_0001266 small cytoplasmic RNA (scRNA) gene sio:SIO_001228 SIO_001228 A small nuclear RNA (snRNA) gene is a gene that encodes a small niuclear RNA molecule. http://purl.obolibrary.org/obo/SO_0001268 small nuclear RNA (snRNA) gene sio:SIO_001229 SIO_001229 A small nucleolar RNA (snoRNA) gene is a gene that encodes a small RNA that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. http://purl.obolibrary.org/obo/SO_0001267 small nucleolar RNA (snoRNA) gene sio:SIO_001230 SIO_001230 solube RNA (sRNA) gene tRNA gene A transfer RNA (tRNA) gene is a gene that codes for a tRNA used in the translation of a messenger RNA (mRNA) to produce a protein product. http://purl.obolibrary.org/obo/SO_0001272 transfer RNA (tRNA) gene sio:SIO_001231 SIO_001231 scRNA A small cytoplasmic RNA (scRNA) molecule is a small (7S; 129 nucleotides) RNA molecule found in the cytosol and rough endoplasmic reticulum that are normally associated with proteins that are involved in specific selection and transport of other proteins. small cytoplasmic RNA (scRNA) sio:SIO_001232 SIO_001232 tRNA A transfer RNA (tRNA) is an RNA molecule that aids in the translation of a messenger RNA (mRNA) to produce a protein product. transfer RNA (tRNA) sio:SIO_001233 SIO_001233 snRNA A small nuclear RNA (snRNA) is a small RNA molecule that is located in the nucleus of a cell. small nuclear RNA (snRNA) sio:SIO_001234 SIO_001234 snoRNA A small nucleolar RNA (snoRNA) is a small RNA that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. small nucleolar RNA (snoRNA) sio:SIO_001235 SIO_001235 A non-protein coding RNA (ncRNA) is a RNA molecular that cannot be used as a template for generating a protein product. non-protein coding RNA (ncRNA) sio:SIO_001236 SIO_001236 A data collection device is a device that collects information about one or more objects. data collection device sio:SIO_001237 SIO_001237 A mass spectrometer is a device that identifies ions based on their mass to charge ratio using an electromagnetic field. http://purl.obolibrary.org/obo/OBI_0000049 mass spectrometer sio:SIO_001238 SIO_001238 microarray platform A microarray device is a device that identifies the binding of a target substance to a physically immobile substrate placed in an array or lattice. http://purl.obolibrary.org/obo/OBI_0000052 microarray device sio:SIO_001239 SIO_001239 to identify is the capability to determine the identity of something. to identify sio:SIO_001240 SIO_001240 nuclear magnetic resonance device A nuclear magnetic resonance (NMR) device is a device that applies a magnetic field to perturb nuclei with an odd number of protons and/or of neutrons in order to hav them absort and re-emit electromagnetic radiation. http://purl.obolibrary.org/obo/OBI_0000566 nmr device sio:SIO_001241 SIO_001241 registry A catalog is a systemic collection of items of the same type. catalog sio:SIO_001243 SIO_001243 Likelihood is the hypothetical probability that an event that has already occurred would yield a specific outcome. likelihood sio:SIO_001244 SIO_001244 Log likelihood is the natural logarithm of the likelihood function log likelihood sio:SIO_001245 SIO_001245 z-value, z-score, normal score, standardadized variable. A standard score is the (signed) number of standard deviations an observation or datum is above the mean. standard score sio:SIO_001246 SIO_001246 an interval is a set of real numbers with the property that any number that lies between two numbers in the set is also included in the set. interval The set of all numbers x satisfying 0<=x<=1 is an interval which contains 0 and 1, as well as numbers between them. sio:SIO_001248 SIO_001248 an open interval is an interval that does not include its endpoints. open interval (0,1) is an open interval that is greater than 0 and less than 1. sio:SIO_001249 SIO_001249 A closed interval is an interval that includes its endpoints, and is denoted with square brackets. closed interval [0,1] is a closed interval that is greater than or equal to 0 and less than or equal to 1. sio:SIO_001250 SIO_001250 drug-pathway association a chemical-pathway association is an association between a chemical and a pathway. chemical-pathway association sio:SIO_001251 SIO_001251 a left open interval is an interval in which there is no element that is smaller than all other elements. left open interval sio:SIO_001252 SIO_001252 a right open interval is an interval in which there is no element that is greater than all other elements. right open interval sio:SIO_001253 SIO_001253 a right closed interval is an interval in which there is a real number that is larger than all of its elements. right closed interval sio:SIO_001254 SIO_001254 a left closed interval is an interval in which there is a real number that is smaller than all its elements. left closed interval sio:SIO_001255 SIO_001255 a pharmacokinetic pathway is a metabolic pathway which describes the metabolism of a drug molecule. pharmacokinetic pathway sio:SIO_001256 SIO_001256 a pharmacodynamic pathay is a regulatory pathway in which a drug molecule regulates the activity of one or more components organized in a pathway. pharmacodynamic pathway sio:SIO_001257 SIO_001257 a chemical-gene association is an association between a chemical and a gene. chemical-gene association sio:SIO_001258 SIO_001258 set item is an item in a set. set item sio:SIO_001259 SIO_001259 a collection item is an item in a collection. collection item sio:SIO_001260 SIO_001260 a list item is an item in a list. list item sio:SIO_001261 SIO_001261 an ordered list item is an item in an ordered list. ordered list item sio:SIO_001262 SIO_001262 an anatomical entity is an object that is a structural part (material or immaterial) of a biological entity. anatomical entity sio:SIO_001263 SIO_001263 zygosity is the quality pertaining to the allelic complement of a biological system at a single locus on the DNA. zygosity sio:SIO_001264 SIO_001264 homozygous is the quality of a biological organism in which there are two identical alleles at a given locus. homozygous sio:SIO_001265 SIO_001265 homozygous is the quality of a biological organism in which there are two different alleles at a given locus. heterozygous sio:SIO_001266 SIO_001266 hemizygous is the quality of a biological organism in which, based on the ploidy of the organism, there is half the number of alleles than normal at a given locus. hemizygous sio:SIO_001267 SIO_001267 nullizygous is the quality of a biological organism in which there are no allelles at a given locus. nullizygous sio:SIO_001268 SIO_001268 parental transmition is the quality of a biological organism in which the (genetic) material is transmitted from a parental unit. parental transmission sio:SIO_001269 SIO_001269 maternally transmitted is the quality of a biological organism in which the (genetic) material is transmitted from the maternal line. maternally transmitted sio:SIO_001270 SIO_001270 paternally transmitted is the quality of a biological organism in which the (genetic) material is transmitted from the paternal line. paternally transmitted sio:SIO_001271 SIO_001271 helicity is the quality of being helical helicity sio:SIO_001272 SIO_001272 a circularly helical quality is the quality of a helix that is connected in a circle or loop. circularly helical sio:SIO_001273 SIO_001273 left-handed helical quality is the quality in which a clockwise screwing motion moves the helix towards the observed along the line of sight along the helix's axis. left-handed helical sio:SIO_001274 SIO_001274 right-handed helical quality is the quality in which a clockwise screwing motion moves the helix away from the observed along the line of sight along the helix's axis. right-handed helical sio:SIO_001275 SIO_001275 a coding frame offset is a numeric value that indicates the number of bases from a reference start codon position. coding frame offset sio:SIO_001276 SIO_001276 a coding sequence is a sequence of nucleotides which encode a RNA or protein product.. coding sequence sio:SIO_001281 SIO_001281 Humiliation is the abasement of pride, which creates mortification or leads to a state of being humbled or reduced to lowliness or submission. humiliation sio:SIO_001282 SIO_001282 hunger is the craving for food. hunger sio:SIO_001283 SIO_001283 discouraged Discouragement is the emtion of having lost confidence or enthusiasm. discouragement sio:SIO_001284 SIO_001284 contentment pleasure satisfaction is the emotion of fulfillling one's wishes, expectations, or needs. satisfaction sio:SIO_001285 SIO_001285 suicidal is the emotion of being deeply unhappy or depressed with thoughts of killing one's self. suicidal sio:SIO_001286 SIO_001286 irritable irritability is the negative emotion of quick excitability to annoyance, impatience, or anger. irritability sio:SIO_001287 SIO_001287 indecisiveness indecision is the emotion of being unable to choose between two or more possible courses of action. indecision sio:SIO_001288 SIO_001288 a temporal qualifier is pertains to the frequency of the event of interest. temporal qualifier sio:SIO_001289 SIO_001289 none of the time never refers to in none of the occasions. never sio:SIO_001290 SIO_001290 some of the time some refers to in the minority of occasions some of the time sio:SIO_001291 SIO_001291 most of the time most refers to in the majority of occasions most of the time sio:SIO_001292 SIO_001292 all of the time always indicates that the event occurs at all times. always sio:SIO_001293 SIO_001293 quality descriptor sio:SIO_001294 SIO_001294 very poor quality sio:SIO_001295 SIO_001295 poor quality sio:SIO_001296 SIO_001296 neither good nor poor quality sio:SIO_001297 SIO_001297 good quality sio:SIO_001298 SIO_001298 very good quality sio:SIO_001299 SIO_001299 quantity modifier sio:SIO_001300 SIO_001300 An ovopub is an information content entity that contains and links to one or more resources and/or statements, including those describing its provenance, and is itself a dereferenceable resource. ovopub+ ovopub sio:SIO_001301 SIO_001301 A collection ovopub is an ovopub that contains and links to one or more assertion subgraphs and/or ovopubs, as well as statements describing its provenance. It is used to share a specific set of items or restrict a search to the resources contained therein. collection ovopub sio:SIO_001302 SIO_001302 An assertion ovopub is an ovopub that contains and links to an assertion subgraph with one or more statements that may be true or false, as well as statements describing its provenance. assertion ovopub sio:SIO_001303 SIO_001303 none quantifier sio:SIO_001304 SIO_001304 a little quantifier sio:SIO_001305 SIO_001305 moderately quantifier sio:SIO_001306 SIO_001306 mostly quantifier sio:SIO_001307 SIO_001307 completely quantifier sio:SIO_001308 SIO_001308 satisfaction qualifier sio:SIO_001309 SIO_001309 very dissatisfied qualifier sio:SIO_001310 SIO_001310 dissatisfied qualifier sio:SIO_001311 SIO_001311 neither satisfied or dissatisfied qualifier sio:SIO_001312 SIO_001312 satisfied qualifier sio:SIO_001313 SIO_001313 excellent quality sio:SIO_001314 SIO_001314 the date at which an information content entity was made public. date of issue sio:SIO_001315 SIO_001315 an ordered list of authors. author list sio:SIO_001316 SIO_001316 an ordered list is a list in which items are sequentially ordered. ordered list sio:SIO_001317 SIO_001317 a middle name is a name assigned to an individual that is not the first or last name. middle name sio:SIO_001318 SIO_001318 a middle initial is an abbreviated middle name. middle initial sio:SIO_001319 SIO_001319 a telephone number is an identifier used to connect to a physical device capable of transfering voice or data over a network. telephone number sio:SIO_001320 SIO_001320 a cellular phone number is a number to connect to a mobile device cellular phone number sio:SIO_001321 SIO_001321 a fax number is a number to connect to fax device fax number sio:SIO_001322 SIO_001322 IP address an IP number is an number to connect to a device on the internet. IP number sio:SIO_001323 SIO_001323 an email address is an identifier to send mail to particular electronic mailbox. email address sio:SIO_001324 SIO_001324 a work phone number is the number to connect to an phone at a place of work. work phone number sio:SIO_001325 SIO_001325 a home phone number is the number to connect to an phone at a place of residence. home phone number sio:SIO_001326 SIO_001326 status descriptor is a descriptor for the state of a process or object. status descriptor sio:SIO_001327 SIO_001327 A protein expression value is a quantity obtained from a protein expression experiment. protein expression value sio:SIO_001328 SIO_001328 CNV copy number variation refers to the number of deletions/duplications of a DNA region as compared to some reference state. copy number variation sio:SIO_001329 SIO_001329 SNP SNV single nucleotide variation a single nucleotide variation (SNV) is a nucleotide residue that is a variant compared to some reference nucleic acid sequence. single nucleotide polymorphism sio:SIO_001330 SIO_001330 metadata is data that provides information about data. metadata sio:SIO_001331 SIO_001331 A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms. diagnosis sio:SIO_001332 SIO_001332 dag a directed acyclic graph or DAG is a network digram that contains directed edges in which nodes may have multiple parents, but there are no cycles. directed acyclic graph sio:SIO_001333 SIO_001333 an arc is a closed segment of a differentiable curve. arc sio:SIO_001334 SIO_001334 an edge is a line connecting two graph vertices. edge sio:SIO_001335 SIO_001335 vertex a node or vertex is a point in a graph. node sio:SIO_001336 SIO_001336 An epimer is a stereoisomer that differs in configuration at only one stereogenic center. epimer 2 sio:SIO_001337 SIO_001337 epimer association sio:SIO_001338 SIO_001338 a mereological quality is a quality of an entity vis-a-vis containment or parthood mereological quality sio:SIO_001339 SIO_001339 empty is the quality of not containing some thing empty sio:SIO_001340 SIO_001340 full is the quality of contain an entity such that there is no more space for any additional entity. full sio:SIO_001341 SIO_001341 a containment quality is a quality of being able to contain another entity. containment quality sio:SIO_001342 SIO_001342 A gene-disease association in which a gene mutation is known to modify the clinical presentation of the disease. gene-disease association linked with modifying mutation sio:SIO_001343 SIO_001343 A gene-disease association in which a germline mutation in the gene predisposes to the development of the disease, and it is necessary but not sufficient for the manifestation of the disease. gene-disease association linked with susceptibility mutation sio:SIO_001344 SIO_001344 A gene-variant disease association in which a germline mutation in the gene/protein results in the development or maintenance of the disease, and it may be passed on to offspring. gene-disease association linked with germline causal mutation sio:SIO_001345 SIO_001345 A gene-variant disease association in which a somatic mutation in the gene/protein results in the development or maintenance of the disease, and it may not be passed on to offspring. gene-disease association linked with somatic causal mutation sio:SIO_001346 SIO_001346 A gene-variant disease association in which a somatic mutation in the gene modifies the clinical presentation of the disease, and it may not be passed on to offspring. gene-disease association linked with somatic modifying mutation sio:SIO_001347 SIO_001347 A gene-variant disease association in which a germline mutation in the gene modifies the clinical presentation of the disease, and it may be passed on to offspring. gene-disease association linked with germline modifying mutation sio:SIO_001348 SIO_001348 A gene-disease association in which the fusion between two different genes (promotor and/or other coding DNA regions) is associated with the disease. fusion gene-disease association sio:SIO_001349 SIO_001349 A gene-disease association in which the gene is included in a chromosomal rearrangement associated with a particular manifestation of the disease. gene-disease association linked with chromosomal rearrangement sio:SIO_001350 SIO_001350 a gene-disease association that is linked with some genomic alteration gene-disease association linked with genomic alterations sio:SIO_001351 SIO_001351 DisGeNET Disease specificity is a measure of disease coverage. It is calculated from the negative base 2 log of the ratio of number of diseases associated to the total number of diseases. The measure is described here: http://www.disgenet.org/web/DisGeNET/menu/dbinfo#specificity DisGeNET disease specificity sio:SIO_001352 SIO_001352 The DisGeNET pleiotropy index is a measure of specificity as it pertains to classes of disease. The disease pleotropy index is computed from the ratio of the number of disease classes associated with an entity over the total number of disease classes multplied by 100. The measure is defined here: http://www.disgenet.org/web/DisGeNET/menu/dbinfo#pleiotropy DisGeNET Pleiotropy Index sio:SIO_001353 SIO_001353 specialized object sio:SIO_001354 SIO_001354 A week is a period of 7 consecutive days. week sio:SIO_001355 SIO_001355 Specific gravity is the ratio of the density of a substance to the density of a reference substance; equivalently, it is the ratio of the mass of a substance to the mass of a reference substance for the same given volume. specific gravity sio:SIO_001356 SIO_001356 information encoding sio:SIO_001357 SIO_001357 speech is the expression of thoughts and feelings by sound. speech sio:SIO_001358 SIO_001358 the capability to retrieve a (digitial/physical/mental) object from a location. to retrieve sio:SIO_001359 SIO_001359 information translation sio:SIO_001360 SIO_001360 information decoding sio:SIO_001361 SIO_001361 to store is the capability to place an object into a medium in which it can be retrieved in the future. to store sio:SIO_001362 SIO_001362 the capability to encode information in a different representation to encode information sio:SIO_001363 SIO_001363 the capability to maintain information such that it can be retrieved in the future. to maintain information sio:SIO_001364 SIO_001364 the ability to reverse an encoding operation to decode information sio:SIO_001365 SIO_001365 The amount of change accumulated per unit time. rate of change sio:SIO_001366 SIO_001366 regulation of information the regulation or maintenance of information information maintenance sio:SIO_001367 SIO_001367 Frequency is the number of occurrences of a repeating event per unit time frequency sio:SIO_001368 SIO_001368 Speed is the rate of change of an object's position. speed sio:SIO_001369 SIO_001369 The rate of change of an object's position and the direction of that change velocity sio:SIO_001370 SIO_001370 A slide is an visual representation meant to communicate some information. slide sio:SIO_001371 SIO_001371 A statute is a formal written enactment of a legislative authority that governs a state, city or country. statute sio:SIO_001372 SIO_001372 A legal document proposing or enacting a law or a group of laws. legislation sio:SIO_001373 SIO_001373 A legal document is a formally executed written document that can be formally attributed to its author, records and formally expresses a legally enforceable act, process, or contractual duty, obligation, or right, and therefore evidences that act, process, or agreement. legal document sio:SIO_001374 SIO_001374 A brief is a written legal document used in various legal adversarial systems that is presented to a court arguing why one party to a particular case should prevail. brief sio:SIO_001375 SIO_001375 book section sio:SIO_001376 SIO_001376 A bill is proposed legislation under consideration by a legislature. bill sio:SIO_001377 SIO_001377 a versioned dataset is a dataset with a particular release date or release number. versioned dataset sio:SIO_001378 SIO_001378 an analyte is a substance or chemical constituent of interest in an analytical procedure. analyte sio:SIO_001379 A protein domain is a part of a protein that maintains its structure and function independently of the rest of the protein. SIO_001379 protein domain sio:SIO_001380 a protein family is a collection of proteins that share a common evolutionary origin, reflected by their related function and similarity in composition or structure. SIO_001380 protein family sio:SIO_001381 a genomic sequence variant is part of a nucleic acid which is compositionally different than another reference genomic part. SIO_001381 variant genomic sequence variant sio:SIO_001382 a unigene cluster is a collection of transcripts (ESTs and mRNAs) that map to a particular genomic region. SIO_001382 cluster of transcripts unigene cluster sio:SIO_001383 a gene symbol is a short name assigned to a gene. SIO_001383 gene symbol sio:SIO_001384 a statement of consequence is a statement concerning the result or effect of an action or condition. SIO_001384 statement of consequence sio:SIO_001385 a notation is a series or system of written symbols used to represent numbers, amounts, or elements. SIO_001385 notation sio:SIO_001386 a notation to describe a chemical entity SIO_001386 chemical notation sio:SIO_001387 SIO_001387 InCHI notation sio:SIO_001388 SIO_001388 sequence variation notation sio:SIO_001389 The HGVS (human genome variation society) notation is a notation to specify a sequence variation in dna, rna, proteins, and other biomolecules. SIO_001389 hgvs notation sio:SIO_001390 A protein coding sequence (CDS) is the region of DNA that is translated to form proteins. The CDS refers to those nucleotides (concatenated exons) that can be divided into codons which are actually translated into amino acids by the ribosomal translation machinery. SIO_001390 CDS coding sequence protein coding sequence sio:SIO_001391 an ontology is a formal specification of entities, their attributes and relationships. SIO_001391 ontology sio:SIO_001392 A biologic, also known as a biologic medical product, biological, or biopharmaceutical, is any pharmaceutical drug product manufactured in, extracted from, or semisynthesized from biological sources. SIO_001392 biologic sio:SIO_001393 a post-translational modification is a part of a protein that was added, removed, or modified as a result of a chemical reaction after synthesis. SIO_001393 post-translational modification sio:SIO_001394 evidence is the body of facts or information indicating whether a belief or proposition is true or valid. SIO_001394 evidence 2 sio:SIO_001395 SIO_001395 oligosaccharide saccharide a carbohydrate is an organic molecule composed of two or more monosaccharides. carbohydrate sio:SIO_001396 A terminology is a set of terms used for a specified application. SIO_001396 terminology sio:SIO_001397 A microRNA (abbreviated miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals and some viruses, that functions in RNA silencing and post-transcriptional regulation of gene expression. SIO_001397 miRNA microRNA (miRNA) sio:SIO_001398 a medical intervention is a medical procedure to treat (to cure or alleviate) a health condition. SIO_001398 medical intervention sio:SIO_001399 chemical exposure is a process to expose one or more individuals to a chemical substance. SIO_001399 chemical exposure sio:SIO_001400 SIO_001400 subcellular entity sio:SIO_001405 SIO_001405 intersex is a biological sex characterised by birth with genitalia and/or secondary sexual characteristics of indeterminate sex, or which combine features of both sexes. intersex sio:SIO_001406 SIO_001406 Density (volumetric mass density) is the quantity of mass per unit volume of a substance. density sio:SIO_001407 SIO_001407 The surface area of a is a measure of the total area that the surface of the object occupies. surface area sio:SIO_001408 SIO_001408 The aspect ratio of a geometric shape is the ratio of its sizes in different dimensions. aspect ratio sio:SIO_001409 SIO_001409 object relational quality refers to a quality in relation to one or more objects object relational quality sio:SIO_001410 SIO_001410 synthetic quality is the quality of a manufactured object that has similar properties as naturally occuring objects. synthetic quality sio:SIO_001411 SIO_001411 sample quality is the quality of an object that is drawn from a larger population. sample quality sio:SIO_001412 SIO_001412 replica quality is the quality of an object that is an exact copy of another object. replica quality sio:SIO_001413 SIO_001413 A percentage is a number that is a ratio expressed as a fraction of 100. It is denoted using the percent sign "%". percentage sio:SIO_001414 SIO_001414 A quantile is a quantity that divides the range of a probability distribution into continuous intervals with equal probabilities, or dividing the observations in a sample in the same way. quantile sio:SIO_001415 SIO_001415 A percentile (or a centile) is a quantile that divides the given probability distribution, or sample, into 100 equal-sized intervals. percentile sio:SIO_001416 SIO_001416 a duplicate role is a comparative role that holds when one item is an exact copy of another in a specific set. duplicate role sio:SIO_001417 SIO_001417 a replicate role is a comparative role that holds when one item is a reproduction, facsimile, or a copy of another. replicate role sio:SIO_001418 SIO_001418 a replicate is an object that is a facsimile, reproduction, or copy of another item. replicate sio:SIO_001419 SIO_001419 replicates a collection of replicates is a collection composed of items that are a facsimile, reproduction, or copy of other items in the collection. a collection of replicates sio:SIO_001420 SIO_001420 a duplicate is an object that is an exact copy of another item duplicate sio:SIO_001421 SIO_001421 duplicates a collection of duplicates is a collection composed of items that are an exact copy of other items in the collection. a collection of duplicates sio:SIO_001422 SIO_001422 salt a chemical salt is a molecular complex composed of an ionic assembly of cations and anions. chemical salt sio:SIO_001423 SIO_001423 a strong chemical salt is a chemical salt that is composed of strong electrolytes. Strong chemical salts contain Na,K,NH4 or NO3, CIO4, CH3COO. strong chemical salt sio:SIO_001424 SIO_001424 a weak chemical salt is a chemical salt composed of weak eletrolytes. weak chemical salt sio:SIO_001425 SIO_001425 a peptide is an organic polymer composed of between two and fifty amino acids. peptide sio:SIO_001426 SIO_001426 an oligopeptide is an organic polymer composed of fewer than 10 or 15 amino acids. oligopeptide 2 sio:SIO_001427 SIO_001427 an amino acid polymer is an organic polymer composed of two or more amino acid residues. amino acid polymer sio:SIO_001428 SIO_001428 an ingredient is a chemical substance that forms part of a mixture. ingredient sio:SIO_001429 SIO_001429 a tensor is a n-dimensional array. tensor sio:SIO_001430 SIO_001430 rank 1 tensor a vector is a rank 1 tensor that is described by n-dimension of scalars. vector sio:SIO_001431 SIO_001431 rank 0 tensor a scalar is a rank 0 tensor and is an element of a field that is used to define a vector space. scalar 0 sio:SIO_001432 SIO_001432 a vector space is a set of vectors. vector space sio:SIO_001433 SIO_001433 rank 2 tensor a matrix is a rank 2 tensor. It is represented as a rectangular array or table of numbers, symbols, or expressions arranged in rows and columns. matrix sio:SIO_001434 SIO_001434 a rank nonzero tensor is a tensor with a rank greater than zero. rank nonzero tensor 2 sio:SIO_001435 SIO_001435 A chemical-chemical association is an association between two chemical entities. chemical-chemical association 2 sio:SIO_001436 SIO_001436 A disease-disease association is an association between two diseases. disease-disease association 2 sio:SIO_001437 SIO_001437 A gene-gene association is an association between two genes. gene-gene association 2 sio:SIO_001438 SIO_001438 A protein-protein association is an association between two proteins. protein-protein association sio:SIO_001439 SIO_001439 A protein-disease association is an association between a protein and a disease. protein-disease association sio:SIO_001440 SIO_001440 A chemical-protein association is an association between a chemical and a protein. chemical-protein association sio:SIO_001441 SIO_001441 An imaginary number is a complex number whose real part is zero e.g. 0 + bi, and is expressed as a multiple of the square root of -1. 5i is an imaginary number, and its square is -25. imaginary number sio:SIO_001442 SIO_001442 a real number is a complex number whose imaginary part is zero, e.g. a + 0i. real number 1 1 sio:SIO_001443 SIO_001443 a complex number is an element of a number system that extends the real numbers with an imaginary unit i. Every complex number can be expressed in the form a + bi, where a and b are real numbers. complex number sio:SIO_001444 SIO_001444 the quality of existing only in the imagination. it can be used to describe concepts, ideas, or things that are the product of a cognitive process. imaginary sio:SIO_001445 SIO_001445 a protein isoform is a protein that is a structural variant (different sequence of amino acids and/or post-translational modifications) of another protein, but encoded by the same gene. protein isoform sio:SIO_001446 SIO_001446 a salt is a heterogeneous substance that is coposed of positively charged ions (cations) and negatively charged ions (anions) held together by electrostatic forces. salt sio:SIO_010000 SIO_010000 A biological organisn is a biological entity that consists of one or more cells and is capable of genomic replication (independently or not). organism sio:SIO_010001 SIO_010001 A cell is a biological entity that is contained by a plasma membrane. cell sio:SIO_010002 SIO_010002 A tissue is a mereologically maximal collection of cells that together perform some function. tissue sio:SIO_010003 SIO_010003 An organ is a collection of tissues joined in structural unit to serve a common function. organ sio:SIO_010004 SIO_010004 A chemical entity is a material entity that pertains to chemistry. CHEBI:23367 chemical+ chemical entity atom, ion, molecule, chemical substance, sio:SIO_010005 SIO_010005 A weak submolecular component is a submolecular component that weakly connects submolecular components. weak submolecular component 2 sio:SIO_010007 SIO_010007 A polypeptide is an organic polymer composed of amino acid residues, typically of less than 50 amino acids in length. polypeptide 2 sio:SIO_010008 SIO_010008 A nucleic acid is an organic polymer composed of a sequence of nucleotide residues. nucleic acid 2 sio:SIO_010009 SIO_010009 A ribonucleic acid is an organic polymer composed of a sequence of ribonucleotide residues. ribonucleic acid 2 sio:SIO_010010 SIO_010010 A deoxyribonucleic acid is an organic polymer composed of a sequence of deoxyribonucleotide residues. deoxyribonucleic acid sio:SIO_010011 SIO_010011 A lipid is a water-insoluable organic molecule. lipid sio:SIO_010013 SIO_010013 A chemical interaction is a biochemical process in which chemical entities interact through some set of attractive forces. biopax:Interaction chemical interaction sio:SIO_010014 SIO_010014 A primary structure descriptor describes a biomolecular object in terms of a 1D or 2D topology. primary structure descriptor sio:SIO_010015 SIO_010015 amino acid sequence polypeptide sequence A protein acid sequence is the character representation of the molecular structure of a protein. protein sequence sio:SIO_010016 SIO_010016 A nucleic acid sequence is a symbolic representation of the sequence of nucleic acid residues in a nucleic acid. nucleic acid sequence sio:SIO_010017 SIO_010017 RNA sequence A ribonucleic acid sequence is a symbolic representation of the sequence of ribonucleic acid residues in a ribonucleic acid. ribonucleic acid sequence sio:SIO_010018 SIO_010018 DNA sequence A deoxyribonucleic acid sequence is a symbolic representation of the sequence of deoxyribonucleic acid residues in a deoxyribonucleic acid. deoxyribonucleic acid sequence sio:SIO_010019 SIO_010019 biological data is scientific data relevant to biology. biological data sio:SIO_010020 SIO_010020 A submolecular entity is a chemical entity that is a part of a molecule. submolecular entity sio:SIO_010022 SIO_010022 A secondary structure descriptor describes local topological patterns in a biopolymer. secondary structure descriptor sio:SIO_010023 SIO_010023 A tertiary structure descriptor describes 3D topological patterns in a biopolymer. tertiary structure descriptor sio:SIO_010024 SIO_010024 A quaternary structure descriptor describes topological patterns in a multi-unit biopolymer complex. quaternary structure sio:SIO_010026 SIO_010026 genetic polymorphism is the description of a difference in genetic composition at some location. genetic polymorphism sio:SIO_010028 SIO_010028 genetic data is data pertaining to genetics. genetic data sio:SIO_010029 SIO_010029 biological sex is the quality of a biological organism based on reproductive function or organs. biological sex sio:SIO_010030 SIO_010030 A monosaccharide is an organic molecule that consists of a single polyhydroxy aldehyde or ketone group. monosaccharide sio:SIO_010031 SIO_010031 A PDB chain identifier is a alphabetical label to identify a molecule in a structure provided by the Protein DataBank . PDB chain identifier sio:SIO_010032 SIO_010032 A PDB record identifier is an identifier for a PDB generated record. PDB record identifier sio:SIO_010033 SIO_010033 A hydrogen bond is a weak submolecular interaction formed between a hydrogen atom and a electronegative atom. hydrogen bond sio:SIO_010034 SIO_010034 A cation pi interaction is an ionic interaction between the localized negative charge of π orbital electrons, located above and below the plane of an aromatic ring, and a positive charge. cation pi interaction sio:SIO_010035 SIO_010035 A gene is part of a nucleic acid that contains all the necessary elements to encode a functional transcript. biopax:Gene http://purl.obolibrary.org/obo/SO_0000704 gene sio:SIO_010036 SIO_010036 A biochemical reaction is a biochemical process that involves the conversion of at least one chemical participant (target) into another (product) by an enzyme (agent). biopax:BiochemicalReaction biopax:Conversion biochemical reaction sio:SIO_010037 SIO_010037 A chemical element is a (effectively) homogeneous substance composed of one type of atom. chemical element sio:SIO_010038 SIO_010038 A drug is a chemical substance that contains one or more active ingredients that regulate one or more biological processes. drug sio:SIO_010039 SIO_010039 medicine A pharmaceutical preparation is a chemical substance that is approved for use in the medical diagnosis, cure, treatment, or prevention of disease. pharmaceutical drug sio:SIO_010040 SIO_010040 A binding site is a molecular site which when occupied with particular ligands leads to structural transformations that initiatiate new moelcular processes. binding site sio:SIO_010041 SIO_010041 An active site is a molecular site in which a chemical event occurs (structural transformation or conformational change). active site sio:SIO_010042 SIO_010042 A haplotype is one of a set of genomic sequence variants. haplotype sio:SIO_010043 SIO_010043 A protein is an organic polymer that is composed of one or more linear polymers of amino acids. CHEBI:36080 protein sio:SIO_010044 SIO_010044 An atom is composed of a core of protons and/or neutrons which may be surrounded by a cloud of electrons. atom sio:SIO_010045 SIO_010045 A base pair is a weak molecular interaction composed of hydrogen bonds between nucleobases. base pair sio:SIO_010046 SIO_010046 A biological entity is a heterogeneous substance that contains genomic material or is the product of a biological process. chemical- biological entity sio:SIO_010047 SIO_010047 A strong submolecular component is a submolecular component that strongly connects submolecular components. strong submolecular component sio:SIO_010048 SIO_010048 male is a biological sex of an individual with male sexual organs. PATO:0000384 male sio:SIO_010049 SIO_010049 A moleclar site is a spatial region bounded (in part or in whole) by a molecule and may be occupied by other material entities (e.g. drugs). molecular site sio:SIO_010050 SIO_010050 An allosteric site is a binding site that when bound to particular ligand changes the conformational state and affects its functionality. allosteric site sio:SIO_010051 SIO_010051 A biological fluid is a fluid of biological origin. biological fluid sio:SIO_010052 SIO_010052 female is a biological sex of an individual with female sexual organs. female sio:SIO_010053 SIO_010053 evolutionary lineage is a sequence of species, that form a line of descent, each new species the direct result of speciation from an immediate ancestral species. evolutionary lineage sio:SIO_010054 SIO_010054 A cell line is a collection of genetically identifical cells. cell line sio:SIO_010055 SIO_010055 A strain is a genetic variant or kind of microorganism. strain sio:SIO_010056 SIO_010056 A phenotype is an observable characteristic of an individual. phenotype sio:SIO_010057 SIO_010057 life status is the quality of whether something is alive or dead. life status sio:SIO_010058 SIO_010058 alive is the state of a biological organism that exhibits biological functions. alive sio:SIO_010059 SIO_010059 dead is the quality of an object in which there is a cessation of all biological functions. dead sio:SIO_010060 SIO_010060 family history is the systematic narrative and research of past events relating to a specific family, or specific families. family history sio:SIO_010061 SIO_010061 generation number is a count of the number of biological reproduction events elapsed from some starting reference point. generation number sio:SIO_010064 SIO_010064 The five prime untranslated region (5' UTR) is a section of messenger RNA (mRNA) and the DNA that codes for it that starts at the +1 position (where transcription begins) and ends one nucleotide before the start codon (usually AUG) of the coding region. 5' untranslated region sio:SIO_010065 SIO_010065 bioinformatic data is data genereated or used for computer-based investigations of biological phenomena. bioinformatic data sio:SIO_010066 SIO_010066 A sequence alignment is the character-based alignment of sequences using some method. sequence alignment sio:SIO_010067 SIO_010067 A multiple sequence alignment is a sequence alignment involving more than two sequences. multiple sequence alignment sio:SIO_010068 SIO_010068 A pairwise sequence alignment is the alignment of exactly 2 sequences. pairwise sequence alignment sio:SIO_010070 SIO_010070 A three prime untranslated region (3'-UTR) is the section of messenger RNA (mRNA) that immediately follows the translation termination codon. 3' untranslated region sio:SIO_010071 SIO_010071 An organic submolecule is connected region of a molecule. organic submolecule sio:SIO_010072 SIO_010072 An organic molecule is a molecule composed of organic atoms (at least carbon, hydrogen, and optionally oxygen, phosphorus, nitrogen, sulfur) organic molecule 1 1 sio:SIO_010073 SIO_010073 An open reading frame (ORF) is a part of a gene that encodes a protein but does not contain a stop codon. open reading frame sio:SIO_010074 SIO_010074 An amino acid residue is a submolecule of an amino acid that is part of a larger molecule. amino acid residue sio:SIO_010075 SIO_010075 A nucleotide residue is a part of a molecule that derives from a nucleotide. nucleotide residue sio:SIO_010076 SIO_010076 A poison is a drug that is harzardous or toxic to an organism when ingested at a certain quantity. poison sio:SIO_010077 SIO_010077 An active ingredient is a molecular entity that exhibits biological activity. active ingredient sio:SIO_010084 SIO_010084 An operon is a collection of contiguous genes transcribed as a single (polycistronic) mRNA. SO:0000178 operon sio:SIO_010085 SIO_010085 A gene regulatory component is a gene component that exerts a regulatory function. gene regulatory component sio:SIO_010086 SIO_010086 A gene enhancer is a short region of DNA that can be bound with proteins to enhance transcription levels of genes in a gene cluster. gene enhancer sio:SIO_010087 SIO_010087 Aninactive ingredient is a molecular entity that does not exhibit biological activity. inactive ingredient sio:SIO_010088 SIO_010088 to serve as a template for molecular synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which another molecule may be produced. to serve as a template for molecular synthesis sio:SIO_010089 SIO_010089 to serve as a template for protein synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which a protein may be produced. to serve as a template for protein synthesis sio:SIO_010090 SIO_010090 to serve as a template for RNA synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which an RNA molecule may be produced. to serve as a template for RNA synthesis sio:SIO_010091 SIO_010091 to serve as a template for DNA synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which a DNA molecule may be produced. to serve as a template for DNA synthesis sio:SIO_010092 SIO_010092 A deoxyribonucleic acid template is a deoxyribonucleic acid that provides the template to synthesize a complementary strand of DNA through transcription. deoxyribonucleic acid template sio:SIO_010093 SIO_010093 A deoxyribonucleic acid primer is a deoxyribonucleic acid that enables the synthesis of a complement strand of DNA by binding to it and acting as a point of transcription initiation. deoxyribonucleic acid primer sio:SIO_010094 SIO_010094 to serve as a primer for DNA synthesis is the capability of a short nucleic acid to bind to the 5' end of single strand of DNA template and help initiate DNA replication. to serve as a primer for DNA synthesis sio:SIO_010095 SIO_010095 An RNA transcript component is a region of an RNA transcript. RNA transcript component sio:SIO_010096 SIO_010096 A mature RNA is a ribonucleic acid that contains an untranslated region (UTR) and protein coding sequence and lacks introns. mature mRNA sio:SIO_010097 SIO_010097 Precursor mRNA (pre-mRNA) is a single strand of messenger ribonucleic acid (mRNA) that is synthesized from a DNA template throught transcription. pre-mRNA sio:SIO_010098 SIO_010098 An mRNA splice variant is an mRNA molecule that varies from another mRNA molecule of the same gene origin but having a different final sequence due to differences in its assembly from splice sites. mRNA splice variant sio:SIO_010099 SIO_010099 A messenger RNA is a ribonucleic acid that contains an untranslated region (UTR) and protein coding sequence and lacks introns. messenger RNA sio:SIO_010100 SIO_010100 A gene that is located on DNA. dna gene sio:SIO_010101 SIO_010101 A gene that is located on RNA. rna gene sio:SIO_010277 SIO_010277 An allele is one of a set of sequence variants of a gene. allele sio:SIO_010278 SIO_010278 ploidy is the cellular quality relating to the amount of DNA contained in a cell. ploidy sio:SIO_010283 SIO_010283 chemical transport is the directed movement of a chemical entity by some agent (e.g. transporter). biopax:Transport chemical transport sio:SIO_010284 SIO_010284 active transport is the movement of a substance across a membrane against its concentration gradient (from low to high concentration) and requires chemical energy. biopax:TransportWithBiochemicalReaction active transport sio:SIO_010285 SIO_010285 molecular complex formation is the process of forming a molecular complex from its constituent parts. molecular complex formation sio:SIO_010286 SIO_010286 molecular complex disassociation is the process of dissambly of a molecular complex into its constitutent parts. molecular complex dissociation sio:SIO_010287 SIO_010287 regulation of biochemical process is a process that changes the frequency, rate or extent of a target biochemical process. regulation of biochemical process sio:SIO_010288 SIO_010288 biochemical activation is a molecular interaction that increases the catalytic rate of the target enzyme. biochemical activation sio:SIO_010289 SIO_010289 biochemical inhibition is a molecular interaction that decreases the catalytic rate of the target enzyme. biochemical inhibition sio:SIO_010295 SIO_010295 positive regulation process up-regulation is a process that increases the frequency, rate or extent of one or more processes in relation to a reference state. process up-regulation sio:SIO_010296 SIO_010296 negative regulation process down-regulation is a process that decreases the frequency, rate or extent of one or more processes in relation to a reference state. process down-regulation sio:SIO_010298 SIO_010298 medical data is data of interest to medicine. medical data sio:SIO_010299 SIO_010299 disease is the outward manifestation of one or more disorders. disease sio:SIO_010300 SIO_010300 transcription is the process of creating a complementary RNA copy of a sequence of DNA. transcription sio:SIO_010301 SIO_010301 translation is the process of producing a polypeptide from a ribonucleic acid by a ribosome. translation sio:SIO_010307 SIO_010307 Molecular modification is chemical alteration of a known and previously characterized lead compound for the purpose of enhancing its usefulness as a drug. This could mean enhancing its specificity for a particular body target site, increasing its potency, improving its rate and extent of absorption, modifying to advantage its time course in the body, reducing its toxicity, changing its physical or chemical properties (like solubility) to provide desired features. molecular modification sio:SIO_010308 SIO_010308 Metabolism is the set of chemical processes that occur within a living organism in order to maintain life. metabolism sio:SIO_010309 SIO_010309 Anabolism is the set of metabolic processes that take apart larger chemical entities units into smaller chemical entities. catabolism sio:SIO_010310 SIO_010310 Anabolism is the set of metabolic processes that construct larger chemical entities units from smaller chemical entities. anabolism sio:SIO_010334 SIO_010334 A carbohydrate residue is a part of a molecule that was derived from a monosaccharide molecule. carbohydrate residue sio:SIO_010335 SIO_010335 A nucleic acid part is a component of a nucleic acid. nucleic acid part sio:SIO_010336 SIO_010336 A deoxyribonucleotide residue is a part of a molecule that derives from a deoxyribonucleotide. deoxyribonucleotide residue sio:SIO_010337 SIO_010337 A ribonucleotide residue is a part of a molecule that derives from a ribonucleotide. ribonucleotide residue sio:SIO_010338 SIO_010338 A pharmaceutical ingredient is a part of a pharmaceutical preparation. pharmaceutical ingredient sio:SIO_010340 SIO_010340 to covalently modify is to materially change a molecule by adding or removing covalent bonds between atoms. to covalently modify sio:SIO_010342 SIO_010342 A chemical complex is a chemical substance composed of weakly connected molecules and ions in a known stoichiometry. chemical complex sio:SIO_010343 SIO_010343 An enzyme is a protein or protein complex that realizes its disposition to covalently modify some molecule during a chemical reaction. enzyme sio:SIO_010344 SIO_010344 A catalyst is a molecule that has the capability to reduce the activation energy of a reaction and hence increase the overall rate of reaction. catalyst sio:SIO_010345 SIO_010345 A chemical reaction is a process that leads to the transformation of one set of chemical substances to another. chemical reaction sio:SIO_010346 SIO_010346 An organic polymer is an organic molecule composed of connected set of monomeric units. organic polymer sio:SIO_010347 SIO_010347 to modify conformation of is to affect the spatial arrangement of an entity. to modify conformation of sio:SIO_010349 SIO_010349 to cleave is to split or sever an object along a natural line or grain. to cleave sio:SIO_010351 SIO_010351 to combine is the capability to modify a set of objects in a way that the object is merged with another object to form a new object or substance. to combine sio:SIO_010353 SIO_010353 to breathe is the capability to inhale and exhale air into the body during respiration. to breathe sio:SIO_010354 SIO_010354 to conformationally activate is to modify the conformation of an entity in such a way that it becomes activated or functional. to conformationally activate sio:SIO_010355 SIO_010355 to conformationally inhibit is to modify the conformation of an entity in such a way that it functionally is reduced or inhibited. to conformationally inhibit sio:SIO_010358 SIO_010358 to oxidize is the capability to remove an electron or an increase in oxidation state of a chemical entity. to oxidize sio:SIO_010359 SIO_010359 to reduce is the capability to add an electron or an decrease in oxidation state of a chemical entity. to reduce sio:SIO_010360 SIO_010360 to modify the oxidation state of is to change the number of electrons of a molecule, atom or ion. to modify oxidation state of sio:SIO_010362 SIO_010362 A substrate is a molecule that is consumed in the course of a biochemical reaction. substrate sio:SIO_010363 SIO_010363 product sio:SIO_010364 SIO_010364 to be modified is the capability to be actively interacted with in such a way that it leads to a physical reconfiguration. to be modified sio:SIO_010365 SIO_010365 to be cleaved is the capability to be modified in a way that splits one part of the object from the other. to be cleaved sio:SIO_010366 SIO_010366 to be covalently modified is the capability of a chemical entity to have bonds added or removed to be covalently modified sio:SIO_010367 SIO_010367 to be combined is the capability to be modified in a way that the object is merged with another object to form a new object or substance. to be combined sio:SIO_010368 SIO_010368 to be transported is the disposition to undergo motion. to be transported sio:SIO_010369 SIO_010369 to be electronically modified is the capability of a chemical entity to have electrons added or removed. to be electronically modified sio:SIO_010370 SIO_010370 to gain an electron is the capability of a chemical entity to receive an electron. to gain an electron sio:SIO_010371 SIO_010371 to lose an electron is the capability of a chemical entity to lose an electron. to lose an electron sio:SIO_010372 SIO_010372 to be activated is the capability to be modified in such a way that the conformational change leads to an increase in another capability. to be activated sio:SIO_010373 SIO_010373 to be inhibited is the capability to be modified in such a way that the conformational change leads to an decrease in another capability. to be inhibited sio:SIO_010374 SIO_010374 to be conformationally changed is the capability to be modified in such a way that the object's conformation is changed. to be conformationally changed 2 sio:SIO_010375 SIO_010375 A multi-cellular organism is an organism that consists of more than one cell. multicellular organism sio:SIO_010376 SIO_010376 A unicellular organism is a organism that is composed of a single cell. unicellular organism sio:SIO_010377 SIO_010377 A cellular organism is an organism that contains one or more cells. cellular organism sio:SIO_010378 SIO_010378 A non-cellular organism is an organism that does not contain a cell. non-cellular organism sio:SIO_010379 SIO_010379 A virus is a non-cellular organism that can replicate only inside the living cells of an organism. virus sio:SIO_010383 SIO_010383 A drug regulatory authority is a regulatory authority which acts to control what substances may be used to treat individuals. drug regulatory authority sio:SIO_010410 SIO_010410 A specialized material entity is a material entity that is defined by having some quality, role or capability. specialized material entity sio:SIO_010411 SIO_010411 A reagent is a substance that is added to a system in order to bring about a chemical reaction, or added to see if a reaction occurs. reagent sio:SIO_010412 SIO_010412 A specimen is a portion of material for use in testing, examination, or study. specimen sio:SIO_010414 SIO_010414 A pathogen or infectious agent is a microorganism that causes disease in its host. pathogen sio:SIO_010415 SIO_010415 A host is an organism that harbors a parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. host sio:SIO_010416 SIO_010416 A buffer is a dissolved chemical substance that resists change in pH upon addition of small amounts of acid or base. buffer sio:SIO_010417 SIO_010417 A solvent is a substance that can dissolve other substances (solutes). solvent sio:SIO_010418 SIO_010418 A solute is a substance that becomes dissolved in a solvent. solute sio:SIO_010419 SIO_010419 An antigen is a molecule that can be bound by a major histocompatibility complex (MHC) and presented to a T-cell receptor. antigen sio:SIO_010420 SIO_010420 A receptor molecule is a molecule that has the capability to bind to a signal and propogate a response to that signal. receptor sio:SIO_010423 SIO_010423 target sio:SIO_010424 SIO_010424 A centrifugation pellet is a solid substance that forms as a result of compaction by a centrifuge. centrifugation pellet sio:SIO_010425 SIO_010425 A supernatent is a liquid substance that remains after centrifugation. supernatant sio:SIO_010426 SIO_010426 A centrifugation substance is a substance that is the target or product of centrifugation. centrifugation substance sio:SIO_010427 SIO_010427 A liquid solution component is a part of a liquid solution. liquid solution component sio:SIO_010428 SIO_010428 An evaluation role is a processual role held by an entity during some evaluation. evaluation role sio:SIO_010429 SIO_010429 A placebo is a medically ineffectual treatment for a medical condition intended to deceive the recipient. placebo sio:SIO_010430 SIO_010430 A test role is the role of an individual that is a participant in the study and is the target of the intervention. test role sio:SIO_010431 SIO_010431 A control role is the role of an individual that is part of a study, but is not subject to the intervention that is to be tested. control role sio:SIO_010432 SIO_010432 A ligand is a molecule that is part of a complex by weakly interacting with another molecule. ligand sio:SIO_010433 SIO_010433 A low barrier hydrogen bond is a shorter, stronger hydrogen bond that is formed between both heteroatoms. low barrier hydrogen bond sio:SIO_010434 SIO_010434 A molecular activator is a molecular regulator that realizes its disposition to conformationally change a target molecule and increase its functionality. activator sio:SIO_010435 SIO_010435 A molecular inhibitor is a molecular regulator that realizes its disposition to conformationally change a target molecule and decrease its functionality. inhibitor sio:SIO_010436 SIO_010436 A molecular regulator is a molecule that regulates the function of another chemical entity. molecular regulator sio:SIO_010437 SIO_010437 A signal transducer is a molecule that responds to and amplifies a signal in a signalling system. signal transducer sio:SIO_010438 SIO_010438 A signal is an object that initiates a sequence of events. signal sio:SIO_010439 SIO_010439 A mesenger is a molecule involved in either signal detection or signal propagation from receptors on the cell surface to target molecules inside the cell, in the cytoplasm or nucleus. messenger sio:SIO_010440 SIO_010440 A second messenger is a molecule that relay signals from receptors on the cell surface to target molecules inside the cell, in the cytoplasm or nucleus. second messenger sio:SIO_010441 SIO_010441 A submolecule is any part of a molecule. submolecule sio:SIO_010442 SIO_010442 charge quality is the quality pertaining to electric charge. charge quality sio:SIO_010443 SIO_010443 An intron is a region of a gene that is removed from the final protein open reading frame. intron sio:SIO_010444 SIO_010444 A gene component is a component of a gene. gene component sio:SIO_010445 SIO_010445 An exon is a nucleotide sequence encoded by a gene that remains present within the final mature RNA product of that gene after introns have been removed by RNA splicing. exon sio:SIO_010446 SIO_010446 A gene promoter is a region of DNA that initiates transcription of a particular gene. gene promoter sio:SIO_010447 SIO_010447 A start codon is the first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon is almost always preceded by an untranslated region 5' UTR. start codon sio:SIO_010448 SIO_010448 A stop codon (or termination codon) is a nucleotide triplet within messenger RNA that signals a termination of translation. stop codon sio:SIO_010450 SIO_010450 An RNA transcript is an RNA molecule that is produced from transcription of a nucleic acid template. RNA transcript sio:SIO_010451 SIO_010451 A splice site is a region required for the excision of an intron and connection to another exon. splice site sio:SIO_010452 SIO_010452 A molecular pocket is a site on a molecule that appears as a depression into the structure. molecular pocket sio:SIO_010453 SIO_010453 An acid is a molecular entity in solution capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid). acid sio:SIO_010454 SIO_010454 A base is a molecular entity dissolved in a solvent that is capable of accepting a proton (Bronsted base) or forming a covalent bond with a hydron (Lewis base) . base sio:SIO_010455 SIO_010455 An isomer is a molecule that is compositionally identical to another molecule as a result of a different atomic connectivity. isomer sio:SIO_010456 SIO_010456 An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge. ion sio:SIO_010457 SIO_010457 An anion is an atom or molecule with a net positive electrical charge. cation sio:SIO_010458 SIO_010458 An anion is an atom or molecule with a net negative electrical charge. anion sio:SIO_010459 SIO_010459 A polar solvent is a solvent that exhibits a polar quality. polar solvent sio:SIO_010460 SIO_010460 A non-polar solvent is a solvent that exhibits a non-polar quality. nonpolar solvent sio:SIO_010461 SIO_010461 A positive charge is a charge where the value is positive. positive charge sio:SIO_010462 SIO_010462 A heterogeneous substance is a chemical substance that is composed of more than one different kind of component. heterogeneous substance sio:SIO_010463 SIO_010463 A homogeneous substance is a substance that is composed of a uniform type of entity. homogeneous substance sio:SIO_010464 SIO_010464 A negative charge is a charge where the value is negative. negative charge sio:SIO_010465 SIO_010465 An antibody (also known as immunoglobulins, abbreviated Ig) are gamma globulin proteins that are used by the immune system to identify and neutralize foreign objects. They are typically made of two large heavy chains and two small light chains. antibody sio:SIO_010468 SIO_010468 An alpha helix is structural region of a protein that is characterized by 3.6 residues per turn, a translation of 1.5 angstroms along the helical axis in which backbone N-H groups form a hydrogen bond to the backbone carboxyl group of the amino acid four residues prior. alpha helix sio:SIO_010469 SIO_010469 A beta strand is structural region of a protein that is characterized by a roughly planar sequence of amino acid residues forming hydrogen bonds between the N-O and the C=O of another part of the peptide and having their side chains perpendicular to the planar axis. beta strand sio:SIO_010471 SIO_010471 An amino acid polymer submolecule is a submolecule of an amino acid polymer. amino acid polymer submolecule sio:SIO_010496 SIO_010496 An ionic interaction is a weak submolecular interaction between a charged submolecules. ionic interaction 2 sio:SIO_010497 SIO_010497 A protein complex is a molecular complex composed of at least two polypeptide chains. protein complex sio:SIO_010498 SIO_010498 A single bond is a covalent bond between a pair of atoms in which one pair of electrons are shared. single bond sio:SIO_010499 SIO_010499 A double bond is a covalent bond between a pair of atoms in which two pairs of electrons are shared. double bond sio:SIO_010500 SIO_010500 A triple bond is a covalent bond between a pair of atoms in which three pairs of electrons are shared. triple bond sio:SIO_010501 SIO_010501 An aromatic bond is an interaction between a set of atoms across which pairs of electrons are shared. aromatic bond sio:SIO_010502 SIO_010502 A disulfide bond is a bond between two sulfur atoms. disulfide bond sio:SIO_010503 SIO_010503 A dipole-dipole interaction is a weak submolecular interaction between strongly electronegative atoms. dipole-dipole interaction sio:SIO_010504 SIO_010504 van der Waals' interaction is an a weak submolecular interaction between an instantaneous dipole and induced dipole. van der Waals interaction sio:SIO_010505 SIO_010505 A base stack is a stabilizing interaction of DNA and RNA between spatially adjacent nucleotides and possibly involving London dispersion, hydrophobic and electrostatic forces. base stack sio:SIO_010506 SIO_010506 A molecular complex is a chemical complex composed of at least one weakly interacting molecule. molecular complex sio:SIO_010507 SIO_010507 An acid-base reaction is a chemical reaction between an acid and a base. acid-base reaction sio:SIO_010508 SIO_010508 A catalyzed reaction is a chemical reaction that is facilitated by a catalyst. catalyzed reaction sio:SIO_010509 SIO_010509 A redox reaction is a chemical reaction in which there is a net movement of electrons from one reactant to another. redox reaction sio:SIO_010510 SIO_010510 An inorganic reaction is a chemical reaction that involves the transformation of inorganic molecules. inorganic reaction sio:SIO_010511 SIO_010511 A decomposition reaction is an inorganic reaction in which molecule is fragmented into submolecules or atoms. decomposition reaction sio:SIO_010512 SIO_010512 A displacement reaction is an inorganic reaction in which a elementary substance displaces and sets free a constituent atom from a molecule. displacement reaction sio:SIO_010513 SIO_010513 A double displacement reaction is a displacement reaction in which two molecules swap ions, effectively displacing each other to form two new molecules. double displacement reaction sio:SIO_010514 SIO_010514 A single displacement reaction where one atom is transferred out of one molecule and into another. single displacement reaction sio:SIO_010515 SIO_010515 A synthesis reaction is an inorganic reaction in which two or more molecules are chemically bonded together to produce a single product. synthesis reaction sio:SIO_010516 SIO_010516 An organic reaction is a chemical reaction involving at least one organic molecule. organic reaction sio:SIO_010517 SIO_010517 An isomerization reaction is a chemical reaction in which a molecule is converted into its isomer. isomerization reaction sio:SIO_010518 SIO_010518 An addition reaction is an organic reaction where two or more molecules combine to form a larger one. Addition reactions are limited to chemical compounds that have multiply-bonded atoms: * Molecules with carbon-carbon double bonds or triple bonds * Molecules with carbon - hetero double bonds like C=O or C=N addition reaction sio:SIO_010519 SIO_010519 A polar addition reaction is an addition reaction involving polar residues. polar addition reaction sio:SIO_010520 SIO_010520 A non-polar addition reaction is an addition reaction involving non-polar residues. non-polar addition reaction sio:SIO_010521 SIO_010521 A free radical addition is a non-polar addition reaction involving free radicals. free radical addition sio:SIO_010522 SIO_010522 A nucleophilic addition reaction is an addition reaction where a pi bond is removed by the creation of two new covalent bonds by the addition from a nucleophile. nucleophilic addition reaction sio:SIO_010523 SIO_010523 An electrophilic addition reaction is a polar addition reaction where a pi bond is removed by the creation of two new covalent bonds. electrophilic addition reaction sio:SIO_010525 SIO_010525 A biochemical pathway specifies a series of biochemical modifications and transformations towards achieving some biological outcome. biochemical pathway sio:SIO_010526 SIO_010526 A chemical reaction pathway specifies a series of chemical reactions towards producing some chemical product. chemical reaction pathway sio:SIO_010527 SIO_010527 A chemical synthesis pathway is a pathway involved in the assembly of a chemical. chemical synthesis pathway sio:SIO_010528 SIO_010528 A chemical degradation pathway is a pathway involved in the disassembly of a chemical. chemical degradation pathway sio:SIO_010530 SIO_010530 A 3D structure model is a representation of the spatial arrangement of one or more chemical entities. 3d structure model sio:SIO_010531 SIO_010531 A sequence profile is provides the preference for a character at each position of an abstracted sequence. sequence profile sio:SIO_010532 SIO_010532 A metabolic pathway is a series of biochemical reactions that begins with one or more substrates and ends with one or more products. metabolic pathway sio:SIO_010533 SIO_010533 A regulatory pathway is a series of biochemical reactions that lead to the increase or decrease of activity of participating molecular components. regulatory pathway sio:SIO_010673 SIO_010673 A medical history is a record of the events of a recipient of medical care. medical history 2 sio:SIO_010674 SIO_010674 A binary compound is a mereological maximum sum of two kinds of weakly connected entities. binary compound sio:SIO_010775 SIO_010775 A stereoisomer is an isomer in which the atomic connectivity is the same, but differs in its spatial arrangement of atoms. stereoisomer sio:SIO_010776 SIO_010776 A diastereomer is a stereoisomer that is not a mirror image of its isomer. diastereomer sio:SIO_010777 SIO_010777 An enantiomer is a stereoisomer that is a mirror image of its isomer. enantiomer sio:SIO_010778 SIO_010778 An optical isomer is a stereoisomer that rotates the plane of polarization of a beam of plane polarized light. optical isomer sio:SIO_010779 SIO_010779 A structural isomer is an isomer in which the atoms are joined together in different ways. structural isomer 3 sio:SIO_010780 SIO_010780 A ring is a submolecule with a circular topology. ring sio:SIO_010781 SIO_010781 An aromatic ring is a ring in which the electrons are delocalized across all atoms in the ring. aromatic ring sio:SIO_010782 SIO_010782 A heterocyclic ring is a ring containing a hetero atom. heterocyclic ring sio:SIO_010783 SIO_010783 A homocyclic ring is a ring where the atoms are of a single type. homocyclic ring 1 1 sio:SIO_010784 SIO_010784 An ionic compound is a mereological maximal sum of weakly connected paired positive and negative ions. ionic compound sio:SIO_010785 SIO_010785 An allotrope is a structural variant of a chemical element. allotrope sio:SIO_010786 SIO_010786 A carbon allotrope is a chemical substance composed of carbon. carbon allotrope sio:SIO_010787 SIO_010787 diamond is a carbon allotrope in which each carbon atom in diamond is covalently bonded to four other carbons in a tetrahedron. These tetrahedrons together form a 3-dimensional network of puckered six-membered rings of atoms. diamond sio:SIO_010788 SIO_010788 graphite is an allotrope of carbon which is a conductor, and is the most stable form of solid carbon. graphite sio:SIO_010789 SIO_010789 fullerene is a carbon allotrope which take the form of a hollow sphere, ellipsoid, or tube. fullerene sio:SIO_010790 SIO_010790 aggregate of carbon nanorods is an allotrope of carbon considered to be the least compressible material known, as measured by its isothermal bulk modulus; aggregated diamond nanorods have a modulus of 491 gigapascals (GPa), while a conventional diamond has a modulus of 442 GPa. ADNRs are also 0.3% denser than regular diamond. aggregated carbon nanorods sio:SIO_010791 SIO_010791 amorphous carbon is an allotrope of carbon that does not have any crystalline structure. As with all glassy materials, some short-range order can be observed, but there is no long-range pattern of atomic positions. amorphous carbon sio:SIO_010792 SIO_010792 carbon nanofoam is an allotrope of carbon that consists of a low-density cluster-assembly of carbon atoms strung together in a loose three-dimensional web. Each cluster is about 6 nanometers wide and consists of about 4000 carbon atoms linked in graphite-like sheets that are given negative curvature by the inclusion of heptagons among the regular hexagonal pattern. carbon nanofoam sio:SIO_010793 SIO_010793 chaoite is an allotrope of carbon that is slightly harder than graphite with a reflection colour of grey to white. chaoite sio:SIO_010794 SIO_010794 glassy carbon is an allotrope of carbon which is widely used as an electrode material in electrochemistry, as well as for high temperature crucibles and as a component of some prosthetic devices. glassy carbon sio:SIO_010795 SIO_010795 ionsdaleite is a hexagonal allotrope of the carbon allotrope diamond. ionsdaleite sio:SIO_011000 SIO_011000 boron atom CHEBI:27560 sio:SIO_011001 SIO_011001 carbon atom CHEBI:27594 sio:SIO_011002 SIO_011002 hydrogen atom CHEBI:49637 sio:SIO_011003 SIO_011003 helium atom CHEBI:30217 sio:SIO_011004 SIO_011004 lithium atom CHEBI:30145 sio:SIO_011005 SIO_011005 beryllium atom CHEBI:30501 sio:SIO_011006 SIO_011006 nitrogen atom CHEBI:25555 sio:SIO_011007 SIO_011007 oxygen atom CHEBI:25805 sio:SIO_011008 SIO_011008 fluorine atom CHEBI:24061 sio:SIO_011009 SIO_011009 neon atom CHEBI:33310 sio:SIO_011010 SIO_011010 sodium atom CHEBI:26708 sio:SIO_011011 SIO_011011 magnesium atom CHEBI:25107 sio:SIO_011012 SIO_011012 aluminium atom CHEBI:28984 sio:SIO_011013 SIO_011013 silicon atom CHEBI:27573 sio:SIO_011014 SIO_011014 phosphorus atom CHEBI:28659 sio:SIO_011015 SIO_011015 sulfur atom CHEBI:26833 sio:SIO_011016 SIO_011016 chlorine atom CHEBI:23116 sio:SIO_011017 SIO_011017 argon atom CHEBI:49475 sio:SIO_011018 SIO_011018 potassium atom CHEBI:26216 sio:SIO_011019 SIO_011019 calcium atom CHEBI:22984 sio:SIO_011020 SIO_011020 scandium atom CHEBI:33330 sio:SIO_011021 SIO_011021 titanium atom CHEBI:33341 sio:SIO_011022 SIO_011022 vanadium atom CHEBI:27698 sio:SIO_011023 SIO_011023 chromium atom CHEBI:28073 sio:SIO_011024 SIO_011024 manganese atom CHEBI:18291 sio:SIO_011025 SIO_011025 iron atom CHEBI:18248 sio:SIO_011026 SIO_011026 cobalt atom CHEBI:27638 sio:SIO_011027 SIO_011027 nickel atom CHEBI:28112 sio:SIO_011028 SIO_011028 copper atom CHEBI:28694 sio:SIO_011029 SIO_011029 zinc atom CHEBI:27363 sio:SIO_011030 SIO_011030 gallium atom CHEBI:49631 sio:SIO_011031 SIO_011031 germanium atom CHEBI:30441 sio:SIO_011032 SIO_011032 arsenic atom CHEBI:27563 sio:SIO_011033 SIO_011033 selenium atom CHEBI:27568 sio:SIO_011034 SIO_011034 bromine atom CHEBI:22927 sio:SIO_011035 SIO_011035 krypton atom CHEBI:49696 sio:SIO_011036 SIO_011036 rubidium atom CHEBI:33322 sio:SIO_011037 SIO_011037 strontium atom CHEBI:33324 sio:SIO_011038 SIO_011038 yttrium atom CHEBI:33331 sio:SIO_011039 SIO_011039 zirconium atom CHEBI:33342 sio:SIO_011040 SIO_011040 niobium atom CHEBI:33344 sio:SIO_011041 SIO_011041 molybdemum atom CHEBI:28685 sio:SIO_011042 SIO_011042 technetium atom CHEBI:33353 sio:SIO_011043 SIO_011043 ruthenium atom CHEBI:30682 sio:SIO_011044 SIO_011044 rhodium atom CHEBI:33359 sio:SIO_011045 SIO_011045 palladium atom CHEBI:33363 sio:SIO_011046 SIO_011046 silver atom CHEBI:30512 sio:SIO_011047 SIO_011047 cadmium atom CHEBI:22977 sio:SIO_011048 SIO_011048 indium atom CHEBI:30430 sio:SIO_011049 SIO_011049 tin atom CHEBI:27007 sio:SIO_011050 SIO_011050 antimony atom CHEBI:30513 sio:SIO_011051 SIO_011051 tellurium atom CHEBI:30452 sio:SIO_011052 SIO_011052 iodine atom CHEBI:24859 sio:SIO_011053 SIO_011053 xenon atom CHEBI:49957 sio:SIO_011054 SIO_011054 caesium atom CHEBI:30514 sio:SIO_011055 SIO_011055 barium atom CHEBI:32594 sio:SIO_011056 SIO_011056 lanthanum atom CHEBI:33336 sio:SIO_011057 SIO_011057 hafnium atom CHEBI:33343 sio:SIO_011058 SIO_011058 tantalum atom CHEBI:33348 sio:SIO_011059 SIO_011059 tungsten atom CHEBI:27998 sio:SIO_011060 SIO_011060 rhenium atom CHEBI:49882 sio:SIO_011061 SIO_011061 osmium atom CHEBI:30687 sio:SIO_011062 SIO_011062 iridium atom CHEBI:49666 sio:SIO_011063 SIO_011063 platinum atom CHEBI:33364 sio:SIO_011064 SIO_011064 gold atom CHEBI:29287 sio:SIO_011065 SIO_011065 mercury atom CHEBI:25195 sio:SIO_011066 SIO_011066 thallium atom CHEBI:49920 sio:SIO_011067 SIO_011067 lead atom CHEBI:25016 sio:SIO_011068 SIO_011068 bismuth atom CHEBI:33301 sio:SIO_011069 SIO_011069 polonium atom CHEBI:33313 sio:SIO_011070 SIO_011070 astatine atom CHEBI:30415 sio:SIO_011071 SIO_011071 radon atom CHEBI:33314 sio:SIO_011072 SIO_011072 francium atom CHEBI:33323 sio:SIO_011073 SIO_011073 radium atom CHEBI:33325 sio:SIO_011074 SIO_011074 actinium atom CHEBI:33337 sio:SIO_011075 SIO_011075 rutherfordium atom CHEBI:33346 sio:SIO_011076 SIO_011076 dubnium atom CHEBI:33349 sio:SIO_011077 SIO_011077 seaborgium atom CHEBI:33351 sio:SIO_011078 SIO_011078 bohrium atom CHEBI:33355 sio:SIO_011079 SIO_011079 hassium atom CHEBI:33357 sio:SIO_011080 SIO_011080 meitnerium atom CHEBI:33361 sio:SIO_011081 SIO_011081 darmstadtium atom CHEBI:33367 sio:SIO_011082 SIO_011082 roentgenium atom CHEBI:33368 sio:SIO_011083 SIO_011083 copernicium atom CHEBI:33517 sio:SIO_011084 SIO_011084 unutrium atom sio:SIO_011085 SIO_011085 ununquadium atom sio:SIO_011086 SIO_011086 ununpentium atom sio:SIO_011087 SIO_011087 ununhexium atom sio:SIO_011088 SIO_011088 ununseptium atom sio:SIO_011089 SIO_011089 ununoctium atom sio:SIO_011090 SIO_011090 cerium atom CHEBI:33369 sio:SIO_011091 SIO_011091 praseodymium atom CHEBI:49828 sio:SIO_011092 SIO_011092 neodymium atom CHEBI:33372 sio:SIO_011093 SIO_011093 promethium atom CHEBI:33373 sio:SIO_011094 SIO_011094 samarium atom CHEBI:33374 sio:SIO_011095 SIO_011095 europium atom CHEBI:32999 sio:SIO_011096 SIO_011096 gadolinium atom CHEBI:33375 sio:SIO_011097 SIO_011097 terbium atom CHEBI:33376 sio:SIO_011098 SIO_011098 dysprosium atom CHEBI:33377 sio:SIO_011099 SIO_011099 holmium atom CHEBI:49648 sio:SIO_011100 SIO_011100 erbium atom CHEBI:33379 sio:SIO_011101 SIO_011101 thulium atom CHEBI:33380 sio:SIO_011102 SIO_011102 ytterbium atom CHEBI:33381 sio:SIO_011103 SIO_011103 lutetium atom CHEBI:33382 sio:SIO_011104 SIO_011104 thorium atom CHEBI:33385 sio:SIO_011105 SIO_011105 protactinium atom CHEBI:33386 sio:SIO_011106 SIO_011106 uranium atom CHEBI:27214 sio:SIO_011107 SIO_011107 neptunium atom CHEBI:33387 sio:SIO_011108 SIO_011108 plutonium atom CHEBI:33388 sio:SIO_011109 SIO_011109 americium atom CHEBI:33389 sio:SIO_011110 SIO_011110 curium atom CHEBI:33390 sio:SIO_011111 SIO_011111 berkelium atom CHEBI:33391 sio:SIO_011112 SIO_011112 californium atom CHEBI:33392 sio:SIO_011113 SIO_011113 einsteinium atom CHEBI:33393 sio:SIO_011114 SIO_011114 fermium atom CHEBI:33394 sio:SIO_011115 SIO_011115 mendelevium atom CHEBI:33395 sio:SIO_011116 SIO_011116 nobelium atom CHEBI:33396 sio:SIO_011117 SIO_011117 lawrencium atom CHEBI:33397 2 sio:SIO_011118 SIO_011118 A covalent bond is a strong submolecular interaction between atoms. covalent bond CHEMINF:000063 sio:SIO_011119 SIO_011119 A biomolecular structure descriptor is structure description for organic compounds. biomolecular structure descriptor sio:SIO_011120 SIO_011120 A molecular structure file is a file that contains a description of molecular structure. molecular structure file sio:SIO_011121 SIO_011121 molecular structure descriptor is data that describes some aspect of the molecular structure (composition) and is about some chemical entity. molecular structure descriptor CHEMINF:000085 sio:SIO_011123 SIO_011123 A chemical datum is a scientific data item which conforms to some specification, either for how it is calculated or for how it is measured, and is commonly used in the domain of chemistry to name and differentiate different numeric properties (both calculated and measured) which are about chemical entities. chemical data CHEMINF:000123 sio:SIO_011125 SIO_011125 A molecule is a single chemical entity composed of fully covalently bonded atoms. molecule CHEBI:23367 sio:SIO_011126 SIO_011126 mixture A chemical substance is a chemical entity composed of two or more weakly (non-covalently) interacting chemical entities. chemical substance CHEMINF:440533 sio:SIO_011130 SIO_011130 A PDB file is a molecular structure file specified by the Protein DataBank (PDB). PDB file sio:SIO_011131 SIO_011131 A collection of 3D molecular structure models is just that. collection of 3d molecular structure models :arc9cacb849 :arc9cacb847 :arc9cacb848 :arc9cacb845 :arc9cacb846 :arc9cacb843 :arc9cacb844 :arc9cacb852 :arc9cacb853 :arc9cacb850 :arc9cacb851 :arc9cacb858 :arc9cacb859 :arc9cacb856 :arc9cacb857 :arc9cacb854 :arc9cacb855 :arc9cacb863 :arc9cacb864 :arc9cacb861 :arc9cacb862 :arc9cacb860 :arc9cacb869 :arc9cacb867 :arc9cacb868 :arc9cacb865 :arc9cacb866 :arc9cacb874 :arc9cacb875 :arc9cacb872 :arc9cacb873 :arc9cacb870 :arc9cacb871 :arc9cacb878 :arc9cacb879 :arc9cacb876 :arc9cacb877 :arc9cacb401 :arc9cacb885 :arc9cacb402 :arc9cacb886 :arc9cacb883 :arc9cacb400 :arc9cacb884 :arc9cacb881 :arc9cacb882 :arc9cacb880 :arc9cacb809 :arc9cacb807 :arc9cacb808 :arc9cacb805 :arc9cacb806 :arc9cacb803 :arc9cacb804 :arc9cacb801 :arc9cacb802 :arc9cacb800 :arc9cacb1013 :arc9cacb1016 :arc9cacb1015 :arc9cacb1018 :arc9cacb1017 :arc9cacb1010 :arc9cacb1012 :arc9cacb1011 :arc9cacb818 :arc9cacb819 :arc9cacb816 :arc9cacb817 :arc9cacb814 :arc9cacb815 :arc9cacb812 :arc9cacb813 :arc9cacb810 :arc9cacb811 :arc9cacb1025 :arc9cacb820 :arc9cacb1024 :arc9cacb1026 :arc9cacb1029 :arc9cacb1028 :arc9cacb1021 :arc9cacb1020 :arc9cacb1023 :arc9cacb1022 :arc9cacb829 :arc9cacb827 :arc9cacb828 :arc9cacb825 :arc9cacb826 :arc9cacb823 :arc9cacb824 :arc9cacb821 :arc9cacb822 :arc9cacb830 :arc9cacb831 :arc9cacb838 :arc9cacb839 :arc9cacb836 :arc9cacb837 :arc9cacb834 :arc9cacb835 :arc9cacb832 :arc9cacb833 :arc9cacb841 :arc9cacb1003 :arc9cacb842 :arc9cacb1002 :arc9cacb840 :arc9cacb1004 :arc9cacb1007 :arc9cacb1006 :arc9cacb1009 :arc9cacb1008 :arc9cacb1000 :arc9cacb449 :arc9cacb447 :arc9cacb448 :arc9cacb456 :arc9cacb457 :arc9cacb454 :arc9cacb455 :arc9cacb452 :arc9cacb453 :arc9cacb450 :arc9cacb451 :arc9cacb458 :arc9cacb459 :arc9cacb467 :arc9cacb468 :arc9cacb465 :arc9cacb466 :arc9cacb463 :arc9cacb464 :arc9cacb461 :arc9cacb462 :arc9cacb460 :arc9cacb469 :arc9cacb478 :arc9cacb479 :arc9cacb476 :arc9cacb477 :arc9cacb474 :arc9cacb475 :arc9cacb472 :arc9cacb473 :arc9cacb470 :arc9cacb471 :arc9cacb489 :arc9cacb487 :arc9cacb488 :arc9cacb485 :arc9cacb486 :arc9cacb483 :arc9cacb484 :arc9cacb481 :arc9cacb482 :arc9cacb480 :arc9cacb409 :arc9cacb407 :arc9cacb408 :arc9cacb405 :arc9cacb889 :arc9cacb406 :arc9cacb403 :arc9cacb887 :arc9cacb404 :arc9cacb888 :arc9cacb412 :arc9cacb896 :arc9cacb413 :arc9cacb897 :arc9cacb410 :arc9cacb894 :arc9cacb411 :arc9cacb895 :arc9cacb892 :arc9cacb893 :arc9cacb890 :arc9cacb891 :arc9cacb418 :arc9cacb419 :arc9cacb416 :arc9cacb417 :arc9cacb414 :arc9cacb898 :arc9cacb415 :arc9cacb899 :arc9cacb423 :arc9cacb424 :arc9cacb421 :arc9cacb422 :arc9cacb420 :arc9cacb429 :arc9cacb427 :arc9cacb428 :arc9cacb425 :arc9cacb426 :arc9cacb434 :arc9cacb435 :arc9cacb432 :arc9cacb433 :arc9cacb430 :arc9cacb431 :arc9cacb438 :arc9cacb439 :arc9cacb436 :arc9cacb437 :arc9cacb445 :arc9cacb446 :arc9cacb443 :arc9cacb444 :arc9cacb441 :arc9cacb442 :arc9cacb440 :arc9cacb498 :arc9cacb499 :arc9cacb496 :arc9cacb497 :arc9cacb494 :arc9cacb495 :arc9cacb492 :arc9cacb493 :arc9cacb490 :arc9cacb491 :arc9cacb1057 :arc9cacb1059 :arc9cacb1050 :arc9cacb1052 :arc9cacb1051 :arc9cacb1054 :arc9cacb1056 :arc9cacb1055 :arc9cacb1068 :arc9cacb1061 :arc9cacb1060 :arc9cacb1062 :arc9cacb1065 :arc9cacb1064 :arc9cacb1067 :arc9cacb1066 :arc9cacb908 :arc9cacb909 :arc9cacb906 :arc9cacb907 :arc9cacb904 :arc9cacb905 :arc9cacb902 :arc9cacb903 :arc9cacb900 :arc9cacb901 :arc9cacb1036 :arc9cacb1038 :arc9cacb1037 :arc9cacb1030 :arc9cacb1032 :arc9cacb1034 :arc9cacb1033 :arc9cacb919 :arc9cacb917 :arc9cacb918 :arc9cacb915 :arc9cacb916 :arc9cacb913 :arc9cacb914 :arc9cacb911 :arc9cacb912 :arc9cacb910 :arc9cacb1047 :arc9cacb1049 :arc9cacb1048 :arc9cacb1041 :arc9cacb1040 :arc9cacb1043 :arc9cacb1042 :arc9cacb1045 :arc9cacb1044 :arc9cacb1070 :arc9cacb1072 :arc9cacb1071 :arc9cacb1074 :arc9cacb1076 :arc9cacb1075 :arc9cacb728 :arc9cacb729 :arc9cacb726 :arc9cacb727 :arc9cacb724 :arc9cacb725 :arc9cacb722 :arc9cacb723 :arc9cacb731 :arc9cacb732 :arc9cacb730 :arc9cacb739 :arc9cacb737 :arc9cacb738 :arc9cacb735 :arc9cacb736 :arc9cacb733 :arc9cacb734 :arc9cacb742 :arc9cacb743 :arc9cacb740 :arc9cacb741 :arc9cacb748 :arc9cacb749 :arc9cacb746 :arc9cacb747 :arc9cacb744 :arc9cacb745 :arc9cacb753 :arc9cacb754 :arc9cacb751 :arc9cacb752 :arc9cacb750 :arc9cacb759 :arc9cacb757 :arc9cacb758 :arc9cacb755 :arc9cacb756 :arc9cacb764 :arc9cacb765 :arc9cacb762 :arc9cacb763 :arc9cacb760 :arc9cacb761 :arc9cacb708 :arc9cacb709 :arc9cacb706 :arc9cacb707 :arc9cacb704 :arc9cacb705 :arc9cacb702 :arc9cacb703 :arc9cacb700 :arc9cacb701 :arc9cacb710 :arc9cacb719 :arc9cacb717 :arc9cacb718 :arc9cacb715 :arc9cacb716 :arc9cacb713 :arc9cacb714 :arc9cacb711 :arc9cacb712 :arc9cacb720 :arc9cacb721 :arc9cacb328 :arc9cacb329 :arc9cacb326 :arc9cacb327 :arc9cacb335 :arc9cacb336 :arc9cacb333 :arc9cacb334 :arc9cacb331 :arc9cacb332 :arc9cacb330 :arc9cacb339 :arc9cacb337 :arc9cacb338 :arc9cacb346 :arc9cacb347 :arc9cacb344 :arc9cacb345 :arc9cacb342 :arc9cacb343 :arc9cacb340 :arc9cacb341 :arc9cacb348 :arc9cacb349 :arc9cacb357 :arc9cacb358 :arc9cacb355 :arc9cacb356 :arc9cacb353 :arc9cacb354 :arc9cacb351 :arc9cacb352 :arc9cacb350 :arc9cacb359 :arc9cacb368 :arc9cacb369 :arc9cacb366 :arc9cacb367 :arc9cacb364 :arc9cacb365 :arc9cacb362 :arc9cacb363 :arc9cacb360 :arc9cacb361 :arc9cacb768 :arc9cacb769 :arc9cacb766 :arc9cacb767 :arc9cacb775 :arc9cacb776 :arc9cacb773 :arc9cacb774 :arc9cacb771 :arc9cacb772 :arc9cacb770 :arc9cacb779 :arc9cacb777 :arc9cacb778 :arc9cacb302 :arc9cacb786 :arc9cacb303 :arc9cacb787 :arc9cacb300 :arc9cacb784 :arc9cacb301 :arc9cacb785 :arc9cacb782 :arc9cacb783 :arc9cacb780 :arc9cacb781 :arc9cacb308 :arc9cacb309 :arc9cacb306 :arc9cacb307 :arc9cacb304 :arc9cacb788 :arc9cacb305 :arc9cacb789 :arc9cacb313 :arc9cacb797 :arc9cacb314 :arc9cacb798 :arc9cacb311 :arc9cacb795 :arc9cacb312 :arc9cacb796 :arc9cacb793 :arc9cacb310 :arc9cacb794 :arc9cacb791 :arc9cacb792 :arc9cacb790 :arc9cacb319 :arc9cacb317 :arc9cacb318 :arc9cacb315 :arc9cacb799 :arc9cacb316 :arc9cacb324 :arc9cacb325 :arc9cacb322 :arc9cacb323 :arc9cacb320 :arc9cacb321 :arc9cacb379 :arc9cacb377 :arc9cacb378 :arc9cacb375 :arc9cacb376 :arc9cacb373 :arc9cacb374 :arc9cacb371 :arc9cacb372 :arc9cacb370 :arc9cacb388 :arc9cacb389 :arc9cacb386 :arc9cacb387 :arc9cacb384 :arc9cacb385 :arc9cacb382 :arc9cacb383 :arc9cacb380 :arc9cacb381 :arc9cacb399 :arc9cacb397 :arc9cacb398 :arc9cacb395 :arc9cacb396 :arc9cacb393 :arc9cacb394 :arc9cacb391 :arc9cacb392 :arc9cacb390 :arc9cacb609 :arc9cacb607 :arc9cacb608 :arc9cacb605 :arc9cacb606 :arc9cacb603 :arc9cacb604 :arc9cacb601 :arc9cacb602 :arc9cacb610 :arc9cacb611 :arc9cacb618 :arc9cacb619 :arc9cacb616 :arc9cacb617 :arc9cacb614 :arc9cacb615 :arc9cacb612 :arc9cacb613 :arc9cacb621 :arc9cacb622 :arc9cacb620 :arc9cacb629 :arc9cacb627 :arc9cacb628 :arc9cacb625 :arc9cacb626 :arc9cacb623 :arc9cacb624 :arc9cacb632 :arc9cacb633 :arc9cacb630 :arc9cacb631 :arc9cacb638 :arc9cacb639 :arc9cacb636 :arc9cacb637 :arc9cacb634 :arc9cacb635 :arc9cacb643 :arc9cacb644 :arc9cacb641 :arc9cacb642 :arc9cacb640 :arc9cacb5 :arc9cacb6 :arc9cacb3 :arc9cacb4 :arc9cacb1 :arc9cacb2 :arc9cacb9 :arc9cacb7 :arc9cacb8 :arc9cacb600 :arc9cacb209 :arc9cacb207 :arc9cacb208 :arc9cacb205 :arc9cacb689 :arc9cacb206 :arc9cacb214 :arc9cacb698 :arc9cacb215 :arc9cacb699 :arc9cacb212 :arc9cacb696 :arc9cacb213 :arc9cacb697 :arc9cacb210 :arc9cacb694 :arc9cacb211 :arc9cacb695 :arc9cacb692 :arc9cacb693 :arc9cacb690 :arc9cacb691 :arc9cacb218 :arc9cacb219 :arc9cacb216 :arc9cacb217 :arc9cacb225 :arc9cacb226 :arc9cacb223 :arc9cacb224 :arc9cacb221 :arc9cacb222 :arc9cacb220 :arc9cacb229 :arc9cacb227 :arc9cacb228 :arc9cacb236 :arc9cacb237 :arc9cacb234 :arc9cacb235 :arc9cacb232 :arc9cacb233 :arc9cacb230 :arc9cacb231 :arc9cacb238 :arc9cacb239 :arc9cacb247 :arc9cacb248 :arc9cacb245 :arc9cacb246 :arc9cacb243 :arc9cacb244 :arc9cacb241 :arc9cacb242 :arc9cacb240 :arc9cacb649 :arc9cacb647 :arc9cacb648 :arc9cacb645 :arc9cacb646 :arc9cacb654 :arc9cacb655 :arc9cacb652 :arc9cacb653 :arc9cacb650 :arc9cacb651 :arc9cacb658 :arc9cacb659 :arc9cacb656 :arc9cacb657 :arc9cacb665 :arc9cacb666 :arc9cacb663 :arc9cacb664 :arc9cacb661 :arc9cacb662 :arc9cacb660 :arc9cacb669 :arc9cacb667 :arc9cacb668 :arc9cacb676 :arc9cacb677 :arc9cacb674 :arc9cacb675 :arc9cacb672 :arc9cacb673 :arc9cacb670 :arc9cacb671 :arc9cacb678 :arc9cacb679 :arc9cacb203 :arc9cacb687 :arc9cacb204 :arc9cacb688 :arc9cacb201 :arc9cacb685 :arc9cacb202 :arc9cacb686 :arc9cacb683 :arc9cacb200 :arc9cacb684 :arc9cacb681 :arc9cacb682 :arc9cacb680 :arc9cacb298 :arc9cacb299 :arc9cacb296 :arc9cacb297 :arc9cacb294 :arc9cacb295 :arc9cacb292 :arc9cacb293 :arc9cacb290 :arc9cacb291 :arc9cacb249 :arc9cacb258 :arc9cacb259 :arc9cacb256 :arc9cacb257 :arc9cacb254 :arc9cacb255 :arc9cacb252 :arc9cacb253 :arc9cacb250 :arc9cacb251 :arc9cacb269 :arc9cacb267 :arc9cacb268 :arc9cacb265 :arc9cacb266 :arc9cacb263 :arc9cacb264 :arc9cacb261 :arc9cacb262 :arc9cacb260 :arc9cacb278 :arc9cacb279 :arc9cacb276 :arc9cacb277 :arc9cacb274 :arc9cacb275 :arc9cacb272 :arc9cacb273 :arc9cacb270 :arc9cacb271 :arc9cacb289 :arc9cacb287 :arc9cacb288 :arc9cacb285 :arc9cacb286 :arc9cacb283 :arc9cacb284 :arc9cacb281 :arc9cacb282 :arc9cacb280 :arc9cacb968 :arc9cacb969 :arc9cacb966 :arc9cacb967 :arc9cacb964 :arc9cacb965 :arc9cacb17 :arc9cacb973 :arc9cacb16 :arc9cacb974 :arc9cacb19 :arc9cacb971 :arc9cacb18 :arc9cacb972 :arc9cacb13 :arc9cacb12 :arc9cacb970 :arc9cacb15 :arc9cacb14 :arc9cacb11 :arc9cacb10 :arc9cacb979 :arc9cacb977 :arc9cacb978 :arc9cacb975 :arc9cacb976 :arc9cacb500 :arc9cacb984 :arc9cacb501 :arc9cacb985 :arc9cacb983 :arc9cacb980 :arc9cacb981 :arc9cacb508 :arc9cacb509 :arc9cacb506 :arc9cacb507 :arc9cacb504 :arc9cacb988 :arc9cacb505 :arc9cacb989 :arc9cacb502 :arc9cacb503 :arc9cacb987 :arc9cacb39 :arc9cacb511 :arc9cacb995 :arc9cacb38 :arc9cacb512 :arc9cacb993 :arc9cacb510 :arc9cacb994 :arc9cacb35 :arc9cacb991 :arc9cacb34 :arc9cacb37 :arc9cacb36 :arc9cacb990 :arc9cacb31 :arc9cacb30 :arc9cacb33 :arc9cacb32 :arc9cacb519 :arc9cacb517 :arc9cacb518 :arc9cacb515 :arc9cacb999 :arc9cacb516 :arc9cacb513 :arc9cacb997 :arc9cacb514 :arc9cacb998 :arc9cacb28 :arc9cacb522 :arc9cacb27 :arc9cacb523 :arc9cacb520 :arc9cacb29 :arc9cacb521 :arc9cacb24 :arc9cacb23 :arc9cacb26 :arc9cacb25 :arc9cacb20 :arc9cacb22 :arc9cacb21 :arc9cacb928 :arc9cacb929 :arc9cacb926 :arc9cacb927 :arc9cacb924 :arc9cacb925 :arc9cacb922 :arc9cacb923 :arc9cacb920 :arc9cacb921 :arc9cacb930 :arc9cacb57 :arc9cacb56 :arc9cacb59 :arc9cacb58 :arc9cacb53 :arc9cacb52 :arc9cacb55 :arc9cacb54 :arc9cacb51 :arc9cacb50 :arc9cacb939 :arc9cacb937 :arc9cacb938 :arc9cacb935 :arc9cacb936 :arc9cacb933 :arc9cacb934 :arc9cacb931 :arc9cacb932 :arc9cacb940 :arc9cacb49 :arc9cacb941 :arc9cacb46 :arc9cacb45 :arc9cacb48 :arc9cacb47 :arc9cacb42 :arc9cacb41 :arc9cacb44 :arc9cacb43 :arc9cacb40 :arc9cacb948 :arc9cacb949 :arc9cacb946 :arc9cacb947 :arc9cacb944 :arc9cacb945 :arc9cacb942 :arc9cacb943 :arc9cacb951 :arc9cacb952 :arc9cacb950 :arc9cacb79 :arc9cacb78 :arc9cacb75 :arc9cacb74 :arc9cacb77 :arc9cacb76 :arc9cacb71 :arc9cacb70 :arc9cacb73 :arc9cacb72 :arc9cacb959 :arc9cacb957 :arc9cacb958 :arc9cacb955 :arc9cacb956 :arc9cacb953 :arc9cacb954 :arc9cacb962 :arc9cacb963 :arc9cacb960 :arc9cacb961 :arc9cacb68 :arc9cacb67 :arc9cacb69 :arc9cacb64 :arc9cacb63 :arc9cacb66 :arc9cacb65 :arc9cacb60 :arc9cacb62 :arc9cacb61 :arc9cacb568 :arc9cacb569 :arc9cacb577 :arc9cacb578 :arc9cacb575 :arc9cacb576 :arc9cacb573 :arc9cacb574 :arc9cacb571 :arc9cacb572 :arc9cacb570 :arc9cacb579 :arc9cacb104 :arc9cacb588 :arc9cacb105 :arc9cacb589 :arc9cacb102 :arc9cacb586 :arc9cacb103 :arc9cacb587 :arc9cacb100 :arc9cacb584 :arc9cacb101 :arc9cacb585 :arc9cacb582 :arc9cacb583 :arc9cacb580 :arc9cacb581 :arc9cacb108 :arc9cacb109 :arc9cacb106 :arc9cacb107 :arc9cacb115 :arc9cacb599 :arc9cacb116 :arc9cacb113 :arc9cacb597 :arc9cacb114 :arc9cacb598 :arc9cacb111 :arc9cacb595 :arc9cacb112 :arc9cacb596 :arc9cacb593 :arc9cacb110 :arc9cacb594 :arc9cacb591 :arc9cacb592 :arc9cacb590 :arc9cacb119 :arc9cacb117 :arc9cacb118 :arc9cacb126 :arc9cacb127 :arc9cacb124 :arc9cacb125 :arc9cacb122 :arc9cacb123 :arc9cacb120 :arc9cacb121 :arc9cacb528 :arc9cacb529 :arc9cacb526 :arc9cacb527 :arc9cacb524 :arc9cacb525 :arc9cacb533 :arc9cacb534 :arc9cacb531 :arc9cacb532 :arc9cacb530 :arc9cacb539 :arc9cacb537 :arc9cacb538 :arc9cacb535 :arc9cacb536 :arc9cacb544 :arc9cacb545 :arc9cacb542 :arc9cacb543 :arc9cacb540 :arc9cacb541 :arc9cacb548 :arc9cacb549 :arc9cacb546 :arc9cacb547 :arc9cacb555 :arc9cacb556 :arc9cacb553 :arc9cacb554 :arc9cacb551 :arc9cacb552 :arc9cacb550 :arc9cacb559 :arc9cacb557 :arc9cacb558 :arc9cacb566 :arc9cacb567 :arc9cacb564 :arc9cacb565 :arc9cacb562 :arc9cacb563 :arc9cacb560 :arc9cacb561 :arc9cacb179 :arc9cacb177 :arc9cacb178 :arc9cacb175 :arc9cacb176 :arc9cacb173 :arc9cacb174 :arc9cacb171 :arc9cacb172 :arc9cacb170 :arc9cacb188 :arc9cacb189 :arc9cacb186 :arc9cacb187 :arc9cacb184 :arc9cacb185 :arc9cacb182 :arc9cacb183 :arc9cacb180 :arc9cacb181 :arc9cacb199 :arc9cacb197 :arc9cacb198 :arc9cacb195 :arc9cacb196 :arc9cacb193 :arc9cacb194 :arc9cacb191 :arc9cacb192 :arc9cacb190 :arc9cacb128 :arc9cacb129 :arc9cacb137 :arc9cacb138 :arc9cacb135 :arc9cacb136 :arc9cacb133 :arc9cacb134 :arc9cacb131 :arc9cacb132 :arc9cacb130 :arc9cacb139 :arc9cacb148 :arc9cacb149 :arc9cacb146 :arc9cacb147 :arc9cacb144 :arc9cacb145 :arc9cacb142 :arc9cacb143 :arc9cacb140 :arc9cacb141 :arc9cacb159 :arc9cacb157 :arc9cacb158 :arc9cacb155 :arc9cacb156 :arc9cacb153 :arc9cacb154 :arc9cacb151 :arc9cacb152 :arc9cacb150 :arc9cacb168 :arc9cacb169 :arc9cacb166 :arc9cacb167 :arc9cacb164 :arc9cacb165 :arc9cacb162 :arc9cacb163 :arc9cacb160 :arc9cacb161 :arc9cacb91 :arc9cacb90 :arc9cacb97 :arc9cacb96 :arc9cacb99 :arc9cacb98 :arc9cacb93 :arc9cacb92 :arc9cacb95 :arc9cacb94 :arc9cacb80 :arc9cacb89 :arc9cacb86 :arc9cacb85 :arc9cacb88 :arc9cacb87 :arc9cacb82 :arc9cacb81 :arc9cacb84 :arc9cacb83 fear of death psychomotor retardation persistent sadness compulsive behavior separation anxiety obsessive compulsive disorder anxiety disorder generalized anxiety disorder intrusive thoughts fear of being left alone No more specific mapping in SNOMED exists to symptom "worry about future" pessimistic anxiety about behaviour or performance fear of appearing ridiculous fear of public speaking self-depreciation altered appetite social phobia anhedonia depressive disorder major depressive disorder panic disorder More appropriate SNOMED mapping does not exist to cover abdominal discomfort/nausea as caused by anxiety abdominal discomfort psychomotor agitation disturbance in sleep behavior incoherent thinking No more specific mapping to symptom "worry about future panic attacks" in SNOMED No more specific mapping to symptom "worry about sleep/reluctance to sleep" in SNOMED worry panic fatigue Kelsey Rook The Psychometric Ontology of Experience and Measures provides an ontology of domain concepts for the measurement of symptoms and syndromes related to psychiatric conditions. 2023-11-20 Psychometric Ontology of Experience and Measures http://purl.org/ontology/POEM Psychometric Ontology of Experience and Measures (POEM) en Contributors are those that engage in discussions in the context of SIO (in alphabetical order): sivaram arabandi christopher baker joachim baran jerven bolleman matthew brush alison callahan leonid chepelev kevin cohen melanie courtot geraint duck laura furlong elisa kendall tatsuya kushida luke mccarthy jim mccusker jose miguel cruz-toledo chris mungall robert hoehndorf simon jupp jin-dong kim dana klassen thomas luetteke james malone chris mungall david osumi-sutherland tazro ohta nuria queralt stephen reed alexandre riazanov matthias samwald robert stevens mark wilkinson karin verspoor natalia villanueva-rosales Michel Dumontier sio.owl http://orcid.org/0000-0003-4727-9435 The semanticscience integrated ontology (SIO) provides a simple, integrated ontology (types, relations) for objects, processes and their attributes. This project provides foundational support for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects. website: http://semanticscience.org email: sio-ontology@googlegroups.com mailing list: http://groups.google.com/group/sio-ontology 2010-03-29 2024-03-25 free to use,share,modify. modify with attribution [http://creativecommons.org/licenses/by/4.0/]. Semanticscience Integrated Ontology (SIO) http://www.jbiomedsem.com/content/5/1/14 sio http://semanticscience.org/resource/ general class inclusion axioms: 'is part of' some 'physical entity' subClassOf 'is located in' some 'physical entity' role chains: 'has capability' o 'is realized in' -> 'is participant in' http://sio.semanticscience.org 1.59 :arc9cacb982 :arc9cacb986 :arc9cacb992 :arc9cacb996 :arc9cacb1001 :arc9cacb1005 :arc9cacb1014 :arc9cacb1019 :arc9cacb1027 :arc9cacb1031 :arc9cacb1035 :arc9cacb1039 :arc9cacb1046 :arc9cacb1053 :arc9cacb1058 :arc9cacb1063 :arc9cacb1069 :arc9cacb1073