http://purl.obolibrary.org/obo/bfo/2020/bfo.owl Giorgio A. Ubbiali SCO is a middle-level ontology, representing the major theoretical challenges to sustainability: 1) The polysemy of the term sustainability. 2) The relationship between sustainability and sustainable development. 3) The complexity underlying sustainability. SCO aims to play a pivotal role in harmonizing and integrating top-level and domain ontologies regarding sustainability. https://creativecommons.org/licenses/by/4.0/ L'ontologia fondazionale della sostenibilità L'ontologie fondationnelle de la durabilité Sustainability Core Ontology (SCO) Ubbiali, G. A., Borghini, A., & Lange, M. C. (2024). Ontologies for Sustainability: Theoretical Challenges. https://doi.org/10.31219/osf.io/z8uqr The SCO Structured Vocabulary (SV) constitutes the prior version of this resources. SCO SV is available on GitHub at the following link: https://github.com/gioUbbiali/Sustainability-Core-Ontology.git 2024-09-17 Version 1.0.0. Currently, this resource includes labels and definitions in the following three natural languages: English, Italian, and French. In the next version of this resource, the creator intends to also encompass Italian and French translations of the remaining pieces of information as well as to cover other natural languages. The current version of SCO does not cover classes and object properties accounting for systems granularity, scales, and levels. A deeper representation of system change and behaviors is equally required. These themes will be topics of inclusion in the next version of this resource. The current version of this resource does not include semi-formal natural language definitions or First Order Logics definitions. In the next version of this resource, the creator intends to also include them. The most recent version of this file is available on GitHub at the following link: https://github.com/gioUbbiali/Sustainability-Core-Ontology.git Discussion with subject matter experts is required to revise this axiom with regard to the “represents” object property. This was the most appropriate object property among those pertaining to OBO-Foundry and compliant ontologies to use in constructing this axiom. Nevertheless, implementations seem necessary to deepen the characterization, for instance with regard to representing and measuring the complex system of interest.. Revisions may regard adapting this object property or even further creating a new ad hoc object property. The CCO object properties “describes” and “is measurement of” appear other interesting options. http://www.ontologyrepository.com/CommonCoreOntologies/describes http://www.ontologyrepository.com/CommonCoreOntologies/is_a_measurement_of To amend this axiom in case worth is associated with some object aggregate that is part of the complex system or complex system environment of interest. To extend this axiom to also cover the "object aggregate" class. http://gioUbbiali.github.io/sco/SCO_0000001 In the original definition, INO developers define this class with respect to interactors involved in the interaction process. INO includes the classes “interactor” and “interactor role” (see SeeAlso note). Here, we generalize this definition, excluding reference to interactors. In the context of SCO, we aim to provide users with an upper-level class that generally points to the involvement of material entities in an interaction process mutually influencing each other. We suggest not using this class directly but, instead, extending SCO-provided subclasses as needed. We wish users to classify interactions according to whether they occur among system components, among system environment components, or between system and system environment components. Original definition: “Interaction is a processual entity that has two or more participants (i.e., interactors) that have an effect upon one another.” http://gioUbbiali.github.io/sco/SCO_0000001 interaction http://gioUbbiali.github.io/sco/SCO_0000001 interaction http://gioUbbiali.github.io/sco/SCO_0000001 interazione http://gioUbbiali.github.io/sco/SCO_0000001 http://purl.obolibrary.org/obo/INO_0000015 http://purl.obolibrary.org/obo/INO_0000016 http://gioUbbiali.github.io/sco/SCO_0000001 A process that has at least two material entities as participants that have an effect upon one another. http://gioUbbiali.github.io/sco/SCO_0000001 Un processo che ha almeno due entità materiali come partecipanti, aventi un effetto l’una sull’altra. http://gioUbbiali.github.io/sco/SCO_0000001 Un processus qui a au moins deux entités matérielles comme participants, ayant un effet l’une sur l’autre. http://gioUbbiali.github.io/sco/SCO_0000001 http://purl.obolibrary.org/obo/INO_0000002 http://gioUbbiali.github.io/sco/SCO_0000002 This class aims to be the starting point for developing a representation of system change. Future SCO implementations will provide additional classes and object properties addressing system behaviors, system processes, system scales and levels, and related themes. Related axioms must be revised accordingly. http://gioUbbiali.github.io/sco/SCO_0000002 développement de système http://gioUbbiali.github.io/sco/SCO_0000002 sviluppo del sistema http://gioUbbiali.github.io/sco/SCO_0000002 system development http://gioUbbiali.github.io/sco/SCO_0000002 A process whose specific outcome is the progression of a system over time from an initial condition to a later condition. http://gioUbbiali.github.io/sco/SCO_0000002 Un processo il cui specifico risultato è la progressione di un sistema nel tempo da una condizione iniziale a una condizione successiva. http://gioUbbiali.github.io/sco/SCO_0000002 Un processus dont le résultat spécifique est la progression d’un système dans le temps, depuis une condition initiale à une condition suivante. http://gioUbbiali.github.io/sco/SCO_0000002 http://purl.obolibrary.org/obo/GO_0032502 http://gioUbbiali.github.io/sco/SCO_0000002 AnnotationVocabulary:Provisional http://gioUbbiali.github.io/sco/SCO_0000003 indicator information http://gioUbbiali.github.io/sco/SCO_0000003 il valore dell'indicatore http://gioUbbiali.github.io/sco/SCO_0000003 indicator value http://gioUbbiali.github.io/sco/SCO_0000003 la valeur de l’indicateur http://gioUbbiali.github.io/sco/SCO_0000003 See the comments under the corresponding "indicator" class. http://gioUbbiali.github.io/sco/SCO_0000003 http://purl.unep.org/sdg/SDGIO_00000000 http://purl.unep.org/sdg/SDGIO_00000001 http://purl.unep.org/sdg/SDGIO_00000003 http://gioUbbiali.github.io/sco/SCO_0000003 A representational information content entity that generically depends on some indicator and is about, providing insights into, the complex system to which the indicator belongs. http://gioUbbiali.github.io/sco/SCO_0000003 Un contenu représentatif d’information qui dépend de façon générique d’un indicateur et qui concerne, fournissant des indications/renseignements, sur le système complexe auquel l’indicateur appartient. http://gioUbbiali.github.io/sco/SCO_0000003 Un contenuto informativo rappresentativo che genericamente dipende da un indicatore e riguarda, fornisce informazioni sul, complesso sistema a cui l'indicatore appartiene. http://gioUbbiali.github.io/sco/SCO_0000003 AnnotationVocabulary:Provisional http://gioUbbiali.github.io/sco/SCO_0000004 contenu informatif de la perspective http://gioUbbiali.github.io/sco/SCO_0000004 contenuto informativo della prospettiva http://gioUbbiali.github.io/sco/SCO_0000004 perspective information content entity http://gioUbbiali.github.io/sco/SCO_0000004 An information content entity that generically depends on some complex system component or complex system environment component and is about the perspective (that concretizes it) of that complex system component or complex system environment component. http://gioUbbiali.github.io/sco/SCO_0000004 Un contenu d’information qui dépend de façon générique d’une composante de système complexe ou d’une composant d’environnement de système complexe et qui concerne la perspective (qui le concrétise) de cette composante de système complexe ou de cette composante environnement de système complexe. http://gioUbbiali.github.io/sco/SCO_0000004 Un contenuto informativo che dipende genericamente da una componente del sistema complesso o da una componente dell'ambiente del sistema complesso e riguarda la prospettiva (che lo concretizza) di tale componente del sistema complesso o dell’ambiente del sistema complesso. http://gioUbbiali.github.io/sco/SCO_0000004 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000005 contenu informatif de la valeur http://gioUbbiali.github.io/sco/SCO_0000005 contenuto informativo del valore http://gioUbbiali.github.io/sco/SCO_0000005 worth information content entity http://gioUbbiali.github.io/sco/SCO_0000005 An information content entity that generically depends on a complex system or a complex system environment (or some part(s) of them) and is about the worth (that concretizes it) that some complex system component or complex system environment component recognizes that that complex system or complex system environment (or some part(s) of them) bearer. http://gioUbbiali.github.io/sco/SCO_0000005 Un contenu d’information qui dépend de façon générique d’un système complexe ou de l’environnement de système complexe (ou une ou plus parties de ceux-ci) et qui concerne la valeur (qui le concrétise) qu’une composante de système complexe ou de son environnement reconnaît d’avoir à ce système complexe-là ou à ce-t-environnement de système complexe-là (ou une ou plus parties de celux-ci). http://gioUbbiali.github.io/sco/SCO_0000005 Un contenuto informativo che dipende genericamente dal sistema complesso o dall'ambiente del sistema complesso (o una o più parti di essi) e riguarda il valore (che lo concretizza) che una componente del sistema complesso del suo ambiente riconosce di avere a quel sistema complesso o ambiente del sistema complesso (o una o più parti di essi). http://gioUbbiali.github.io/sco/SCO_0000005 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000006 system context http://gioUbbiali.github.io/sco/SCO_0000006 See the comment under the "system" class. http://gioUbbiali.github.io/sco/SCO_0000006 ambiente del sistema http://gioUbbiali.github.io/sco/SCO_0000006 environnement de système http://gioUbbiali.github.io/sco/SCO_0000006 system environment http://gioUbbiali.github.io/sco/SCO_0000006 A material entity that surrounds and is distinct and disjoint from a system. http://gioUbbiali.github.io/sco/SCO_0000006 Un'entità materiale che circonda ed è distinta e disgiunta da un sistema. http://gioUbbiali.github.io/sco/SCO_0000006 Une entité matérielle qui entourne et qui est distincte et disjointe d’un système. http://gioUbbiali.github.io/sco/SCO_0000006 AnnotationVocabulary:Provisional http://gioUbbiali.github.io/sco/SCO_0000007 relation among system components, interconnection among system components http://gioUbbiali.github.io/sco/SCO_0000007 Interaction entre les composantes de système http://gioUbbiali.github.io/sco/SCO_0000007 interaction among system components http://gioUbbiali.github.io/sco/SCO_0000007 interazione tra le componenti del sistema http://gioUbbiali.github.io/sco/SCO_0000007 An interaction that occurs among at least two system components. http://gioUbbiali.github.io/sco/SCO_0000007 Une interaction qui se produit entre au moins deux composantes de système. http://gioUbbiali.github.io/sco/SCO_0000007 Un’interazione che avviene tra almeno due componenti del sistema. http://gioUbbiali.github.io/sco/SCO_0000007 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000008 relation among system environment components, interconnection among system environment components http://gioUbbiali.github.io/sco/SCO_0000008 interaction among system environment components http://gioUbbiali.github.io/sco/SCO_0000008 interaction entre les composantes de l’environnement de système http://gioUbbiali.github.io/sco/SCO_0000008 interazione tra le componenti dell’ambiente di sistema http://gioUbbiali.github.io/sco/SCO_0000008 An interaction that occurs among at least two system environment components. http://gioUbbiali.github.io/sco/SCO_0000008 Une interaction qui se produit entre au moins deux composantes de l’environnement d’un système. http://gioUbbiali.github.io/sco/SCO_0000008 Un’interazione che avviene tra almeno due componenti dell’ambiente di un sistema. http://gioUbbiali.github.io/sco/SCO_0000008 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000009 relation between system components and the system environment, interconnection between system components and the system environment http://gioUbbiali.github.io/sco/SCO_0000009 Interaction entre les composantes de système et les composantes de l’environnement de système http://gioUbbiali.github.io/sco/SCO_0000009 interaction between system components and system environment components http://gioUbbiali.github.io/sco/SCO_0000009 interazione tra le componenti del sistema e le componenti de l'ambiente del sistema http://gioUbbiali.github.io/sco/SCO_0000009 An interaction that occurs between at least one system component and one system environment component where the latter belongs to the system environment of the system to which the system component belongs. http://gioUbbiali.github.io/sco/SCO_0000009 Une interaction qui se produit entre au moins une composante d’un système et au moins une composante de l’environnement du système auquel la composante de système appartient. http://gioUbbiali.github.io/sco/SCO_0000009 Un’interazione che avviene tra almeno una componente di un sistema e almeno un componente dell’ ambiente del sistema a cui la componente del sistema appartiene. http://gioUbbiali.github.io/sco/SCO_0000009 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000010 complex system development http://gioUbbiali.github.io/sco/SCO_0000010 développement de système complexe http://gioUbbiali.github.io/sco/SCO_0000010 sviluppo del sistema complesso http://gioUbbiali.github.io/sco/SCO_0000010 Le développement d’un système complexe. http://gioUbbiali.github.io/sco/SCO_0000010 Lo sviluppo di un sistema complesso. http://gioUbbiali.github.io/sco/SCO_0000010 The system development of a complex system. http://gioUbbiali.github.io/sco/SCO_0000010 AnnotationVocabulary:Provisional http://gioUbbiali.github.io/sco/SCO_0000011 historie de système http://gioUbbiali.github.io/sco/SCO_0000011 storia del sistema http://gioUbbiali.github.io/sco/SCO_0000011 system history http://gioUbbiali.github.io/sco/SCO_0000011 La storia di un sistema. http://gioUbbiali.github.io/sco/SCO_0000011 L’histoire d’un système. http://gioUbbiali.github.io/sco/SCO_0000011 The history of a system. http://gioUbbiali.github.io/sco/SCO_0000011 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000012 complex system context http://gioUbbiali.github.io/sco/SCO_0000012 ambiente del sistema complesso http://gioUbbiali.github.io/sco/SCO_0000012 complex system environment http://gioUbbiali.github.io/sco/SCO_0000012 environnement de système complexe http://gioUbbiali.github.io/sco/SCO_0000012 A system environment that surrounds and is distinct and disjoint from a complex system. http://gioUbbiali.github.io/sco/SCO_0000012 Un ambiente del sistema che circonda ed è distinto e disgiunto da un sistema complesso. http://gioUbbiali.github.io/sco/SCO_0000012 Un environnement de système qui entourne et qui est distinct et disjoint d’un système complexe. http://gioUbbiali.github.io/sco/SCO_0000012 AnnotationVocabulary:Provisional http://gioUbbiali.github.io/sco/SCO_0000013 system element http://gioUbbiali.github.io/sco/SCO_0000013 system variable http://gioUbbiali.github.io/sco/SCO_0000013 componente del sistema http://gioUbbiali.github.io/sco/SCO_0000013 conposante de système http://gioUbbiali.github.io/sco/SCO_0000013 system component http://gioUbbiali.github.io/sco/SCO_0000013 A material entity that belongs to a system. http://gioUbbiali.github.io/sco/SCO_0000013 Un'entità materiale che appartiene a un sistema. http://gioUbbiali.github.io/sco/SCO_0000013 Une entité matérielle qui appartient à un système. http://gioUbbiali.github.io/sco/SCO_0000013 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000014 system environment element http://gioUbbiali.github.io/sco/SCO_0000014 system environment variable http://gioUbbiali.github.io/sco/SCO_0000014 componente dell' ambiente del systema http://gioUbbiali.github.io/sco/SCO_0000014 conposante de l'environnement de système http://gioUbbiali.github.io/sco/SCO_0000014 system environment component http://gioUbbiali.github.io/sco/SCO_0000014 A material entity that belongs to a system environment. http://gioUbbiali.github.io/sco/SCO_0000014 Un'entità materiale che appartiene all’ambiente di un sistema. http://gioUbbiali.github.io/sco/SCO_0000014 Une entité matérielle qui appartient à l’environnement d’un système. http://gioUbbiali.github.io/sco/SCO_0000014 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000015 Ubbiali, G. A., Borghini, A., & Lange, M. C. (2024). Ontologies for Sustainability: Theoretical Challenges. https://doi.org/10.31219/osf.io/z8uqr http://gioUbbiali.github.io/sco/SCO_0000015 socio-ecological system, social-ecological system http://gioUbbiali.github.io/sco/SCO_0000015 complex system http://gioUbbiali.github.io/sco/SCO_0000015 sistema complesso http://gioUbbiali.github.io/sco/SCO_0000015 système complexe http://gioUbbiali.github.io/sco/SCO_0000015 IOBC: http://purl.jp/bio/4/id/200906033993517889 IOBC: http://purl.jp/bio/4/id/201406059151625127 EnvThes: http://vocabs.lter-europe.net/EnvThes/21908 I2SV: https://i2insights.org/index/integration-and-implementation-sciences-vocabulary#complex-systems http://gioUbbiali.github.io/sco/SCO_0000015 A system whose system components interact dynamically and nonlinearly, causing the emergence of a collective nontrivial and self-organized behavior. No internal/external centralized controls are required. http://gioUbbiali.github.io/sco/SCO_0000015 Un sistema le cui componenti interagiscono dinamicamente e non linearmente, causando l’emergere di un comportamento collettivo, non banale e auto-organizzato. Non è richiesto nessun controllo centralizzato, né interno né esterno. http://gioUbbiali.github.io/sco/SCO_0000015 Un système dont les composantes interagissent dynamiquement et non linéairement, causant l’émergence d’un comportement collectif, non trivial et auto-organisé. Aucun contrôle interne ou externe centralisé n’est requis. http://gioUbbiali.github.io/sco/SCO_0000015 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000016 SCO currently accounts for perspectives of complex system components and complex system environment components because the focus of this ontology is on complex systems. Future versions of this ontology may explore extending reference more broadly to systems. http://gioUbbiali.github.io/sco/SCO_0000016 perspective http://gioUbbiali.github.io/sco/SCO_0000016 perspective http://gioUbbiali.github.io/sco/SCO_0000016 prospettiva http://gioUbbiali.github.io/sco/SCO_0000016 /SCO_0000039 http://gioUbbiali.github.io/sco/SCO_0000016 A disposition whose realization leads the complex system component or the complex system environment component to (re)position itself within and regarding the complex system or complex system environment it belongs to (or a part of it) and possibly act accordingly. http://gioUbbiali.github.io/sco/SCO_0000016 Una disposizione la cui realizzazione porta la componente del sistema complesso o la componente dell’ambiente del sistema complesso a (ri)posizionarsi nel e rispetto al sistema complesso o all’ ambiente del sistema complesso a cui appartiene (o parte di esso) ed eventualmente ad agire di conseguenza. http://gioUbbiali.github.io/sco/SCO_0000016 Une disposition dont la réalisation conduit la composante de système complexe ou la composante de l’environnement du système complexe à se (re)positionner dans et par rapport au système complexe ou à l’environnement du système complexe auquel elle appartient (ou d’une partie de celui-ci) et, éventuellement, à agir en conséquence. http://gioUbbiali.github.io/sco/SCO_0000016 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000017 To distinguish and account for indicators according to the perspectives of different complex systems (and environment) components, we suggest proceeding following the indications provided under the “according to the perspective” annotation property. In this case, regarding the subclasses to create, we recommend establishing axioms restricting to this class. http://gioUbbiali.github.io/sco/SCO_0000017 indicateur (rôle) http://gioUbbiali.github.io/sco/SCO_0000017 indicator-role http://gioUbbiali.github.io/sco/SCO_0000017 ruolo di indicatore http://gioUbbiali.github.io/sco/SCO_0000017 See the comments under the corresponding "indicator" class. http://gioUbbiali.github.io/sco/SCO_0000017 A role whose realization leads the complex system component to be recognized as a carrier of an indicator value, by some complex system component or complex system environment component according to its/their perspective. http://gioUbbiali.github.io/sco/SCO_0000017 Un rôle dont la réalisation conduit la composante de système complexe à être reconnu comme porteuse d’une valeur de l’indicateur, par quelque composante de système complexe ou de son l’environnement, selon sa/leur propre perspective. http://gioUbbiali.github.io/sco/SCO_0000017 un ruolo la cui realizzazione porta la componente del sistema complesso ad essere riconosciuto come portatore di un valore dell’indicatore, da parte di qualche componente del sistema complesso o del suo ambiente, secondo la propria prospettiva. http://gioUbbiali.github.io/sco/SCO_0000017 AnnotationVocabulary:Provisional http://gioUbbiali.github.io/sco/SCO_0000018 ruolo di parte interessata (stakeholder) http://gioUbbiali.github.io/sco/SCO_0000018 rôle de partie prenante (stakeholder) http://gioUbbiali.github.io/sco/SCO_0000018 stakeholder-role http://gioUbbiali.github.io/sco/SCO_0000018 A role whose realization leads the complex system component to be recognized as a bearer, in the belonging complex system, of at least one role (different from the role of stakeholder) and/or disposition (primarily a disposition to benefit/be damaged as being part of that complex system). http://gioUbbiali.github.io/sco/SCO_0000018 Un ruolo la cui realizzazione porta la componente del sistema complesso ad essere riconosciuta come detentrice, nel sistema complesso a cui appartiene, di almeno un ruolo (diverso dal ruolo di stakeholder) e/o disposizione (in primo luogo una predisposizione a beneficiare/essere danneggiata in quanto parte di tale sistema complesso). http://gioUbbiali.github.io/sco/SCO_0000018 Un rôle dont la réalisation conduit la composante du système complexe à être reconnue, dans le système complexe auquel elle appartient, comme porteuse d’au moins un rôle (différent du rôle de partie prenante) et/ou d’une disposition (principalement une disposition à bénéficier ou à être endommagé parce qu’elle fait partie de ce système complexe). http://gioUbbiali.github.io/sco/SCO_0000018 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000019 value http://gioUbbiali.github.io/sco/SCO_0000019 Due to the SCO focus on complex systems, the worth-role class have been designed referring specifically to complex systems. Nevertheless, future implementations may broaden the space of application to also systems. Implementations may equally deepen this representation, detailing and elucidating the distinction and connection between worth and value(s). http://gioUbbiali.github.io/sco/SCO_0000019 To distinguish and account for what is considered worthy of value for different complex systems (and environment) components according to proper perspectives,we suggest proceeding following the indications provided under the “according to the perspective” annotation property. In this case, regarding the subclasses to create, we recommend establishing axioms restricting to this class. http://gioUbbiali.github.io/sco/SCO_0000019 Valeur (sens donner de la valeur) http://gioUbbiali.github.io/sco/SCO_0000019 valore (senso dare valore) http://gioUbbiali.github.io/sco/SCO_0000019 worth-role http://gioUbbiali.github.io/sco/SCO_0000019 (related) http://humanbehaviourchange.org/ontology/BCIO_006063 http://gioUbbiali.github.io/sco/SCO_0000019 https://bio.scai.fraunhofer.de/ontology/epilepsy#worthiness http://gioUbbiali.github.io/sco/SCO_0000019 A role whose realization leads the complex system or the complex system environment (or some part(s) of them) to be recognized to bearer relevance by some complex system component or complex system environment component according to its/their perspective. http://gioUbbiali.github.io/sco/SCO_0000019 Un ruolo la cui realizzazione porta il sistema complesso o l'ambiente del sistema complesso (o una o più delle parti di essi) ad essere riconosciuto come rilevante da parte di qualche componente del sistema complesso o del suo ambiente, secondo la propria prospettiva. http://gioUbbiali.github.io/sco/SCO_0000019 Un rôle dont la réalisation conduit le système complexe ou l’environnement de système complexe (ou une ou plus parties de ceux-ci) à être reconnu comme significatif par quelque composante de système complexe ou de son l’environnement, selon sa/leur propre perspective. http://gioUbbiali.github.io/sco/SCO_0000019 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000020 relation between complex system components and complex system environment components, interconnection between complex system components and complex system environment components http://gioUbbiali.github.io/sco/SCO_0000020 Interaction entre les composantes de système complexe et les composantes de environnement de système complexe http://gioUbbiali.github.io/sco/SCO_0000020 interaction between complex system components and complex system environment components http://gioUbbiali.github.io/sco/SCO_0000020 interazione tra le componenti del sistema complesso e le componenti dell’ambiente del sistema complesso http://gioUbbiali.github.io/sco/SCO_0000020 An interaction that occurs between at least one complex system component and one complex system environment component where the latter belongs to the complex system environment of the complex system to which the complex system component belongs. http://gioUbbiali.github.io/sco/SCO_0000020 Une interaction qui se produit entre au moins une composante d’un système complexe et au moins une composante de l’environnement du système complexe auquel la composante de système complexe appartient. http://gioUbbiali.github.io/sco/SCO_0000020 Un’interazione che avviene tra almeno una componente di un sistema complesso e almeno una componente dell’ambiente del sistema complesso a cui la componente del sistema complesso appartiene. http://gioUbbiali.github.io/sco/SCO_0000020 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000021 relation among complex system environment components, interconnection among complex system environment components http://gioUbbiali.github.io/sco/SCO_0000021 interaction among complex system environment components http://gioUbbiali.github.io/sco/SCO_0000021 interaction entre les composants de l’environnement de système complexe http://gioUbbiali.github.io/sco/SCO_0000021 interazione tra le componenti dell’ambiente di sistema complesso http://gioUbbiali.github.io/sco/SCO_0000021 An interaction that occurs among at least two complex system environment components. http://gioUbbiali.github.io/sco/SCO_0000021 Une interaction qui se produit entre au moins deux composantes de l’environnement d’un système complexe. http://gioUbbiali.github.io/sco/SCO_0000021 Un’interazione che avviene tra almeno due componenti dell’ambiente di un sistema complesso. http://gioUbbiali.github.io/sco/SCO_0000021 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000022 relation among complex system components, interconnection among complex system components http://gioUbbiali.github.io/sco/SCO_0000022 Interaction entre les composantes de système complexe http://gioUbbiali.github.io/sco/SCO_0000022 interaction among complex system components http://gioUbbiali.github.io/sco/SCO_0000022 interazione tra le componenti del sistema complesso http://gioUbbiali.github.io/sco/SCO_0000022 An interaction that occurs among at least two system components of a complex system. http://gioUbbiali.github.io/sco/SCO_0000022 Une interaction qui se produit entre au moins deux composantes de système d’un système complexe. http://gioUbbiali.github.io/sco/SCO_0000022 Un’interazione che avviene tra almeno due componenti del sistema di un sistema complesso. http://gioUbbiali.github.io/sco/SCO_0000022 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000023 complex system history http://gioUbbiali.github.io/sco/SCO_0000023 historie de système complexe http://gioUbbiali.github.io/sco/SCO_0000023 storia del sistema complesso http://gioUbbiali.github.io/sco/SCO_0000023 La storia del sistema di un sistema complesso. http://gioUbbiali.github.io/sco/SCO_0000023 L’historique de système d’un système complexe. http://gioUbbiali.github.io/sco/SCO_0000023 The system history of a complex system. http://gioUbbiali.github.io/sco/SCO_0000023 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000024 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000024 Future SCO implementations may deal with representing system environment boudaries. http://gioUbbiali.github.io/sco/SCO_0000024 confine del sistema http://gioUbbiali.github.io/sco/SCO_0000024 frontière de système http://gioUbbiali.github.io/sco/SCO_0000024 system boundary http://gioUbbiali.github.io/sco/SCO_0000024 A fiat surface of a system. http://gioUbbiali.github.io/sco/SCO_0000024 Una superficie fiat di un sistema. http://gioUbbiali.github.io/sco/SCO_0000024 Une surface fiat d’un système. http://gioUbbiali.github.io/sco/SCO_0000025 Future SCO implementations may consider including classes also covering spatial region for the system environment. http://gioUbbiali.github.io/sco/SCO_0000025 regione spaziale del sistema http://gioUbbiali.github.io/sco/SCO_0000025 région d’espace de système http://gioUbbiali.github.io/sco/SCO_0000025 system spatial region http://gioUbbiali.github.io/sco/SCO_0000025 A three-dimensional spatial region of a system. http://gioUbbiali.github.io/sco/SCO_0000025 Una regione di spazio tridimensionale di un sistema. http://gioUbbiali.github.io/sco/SCO_0000025 Une région d’espace tridimensionnelle d’un système. http://gioUbbiali.github.io/sco/SCO_0000025 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000026 complex system environment element http://gioUbbiali.github.io/sco/SCO_0000026 complex system environment variable http://gioUbbiali.github.io/sco/SCO_0000026 complex system environment component http://gioUbbiali.github.io/sco/SCO_0000026 componente dell' ambiente del systema complesso http://gioUbbiali.github.io/sco/SCO_0000026 conposante de l'environnement de système complexe http://gioUbbiali.github.io/sco/SCO_0000026 A system evironment component that belongs to the system environment of a complex system. http://gioUbbiali.github.io/sco/SCO_0000026 Una componente dell'ambiente di sistema che appartiene all’ambiente di un sistema complesso. http://gioUbbiali.github.io/sco/SCO_0000026 Une composante de l'environnement de système qui appartient à l’environnement d’un système complexe. http://gioUbbiali.github.io/sco/SCO_0000026 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000027 agent de l’environnement de système http://gioUbbiali.github.io/sco/SCO_0000027 agente dell’ambiente del sistema http://gioUbbiali.github.io/sco/SCO_0000027 system environnement agent http://gioUbbiali.github.io/sco/SCO_0000027 /SCO_0000037 http://gioUbbiali.github.io/sco/SCO_0000027 /SCO_0000038 http://gioUbbiali.github.io/sco/SCO_0000027 See information under the "has agent at t" property. http://gioUbbiali.github.io/sco/SCO_0000027 A system environment component that is an agent in an interaction among system environment components or in an interaction between system components and system environment components. http://gioUbbiali.github.io/sco/SCO_0000027 Una componente dell’ambiente del sistema che è un agente in un'interazione tra le componenti dell'ambiente del sistema o in un'interazione tra componenti del sistema e le componenti dell'ambiente del sistema. http://gioUbbiali.github.io/sco/SCO_0000027 Une composante de l’environnement de système qui est un agent dans une interaction entre les composantes de l’environnement du système ou dans une interaction entre les composantes de système et les composants de l’environnement de système. http://gioUbbiali.github.io/sco/SCO_0000027 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000028 complex system element http://gioUbbiali.github.io/sco/SCO_0000028 complex system variable http://gioUbbiali.github.io/sco/SCO_0000028 complex system component http://gioUbbiali.github.io/sco/SCO_0000028 componente del sistema complesso http://gioUbbiali.github.io/sco/SCO_0000028 conposante de système complexe http://gioUbbiali.github.io/sco/SCO_0000028 A system component that belongs to a complex system. http://gioUbbiali.github.io/sco/SCO_0000028 Una componente del sistema che appartiene a un sistema complesso. http://gioUbbiali.github.io/sco/SCO_0000028 Une composante de système qui appartient à un système complexe. http://gioUbbiali.github.io/sco/SCO_0000028 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000029 agent de système http://gioUbbiali.github.io/sco/SCO_0000029 agente del sistema http://gioUbbiali.github.io/sco/SCO_0000029 system agent http://gioUbbiali.github.io/sco/SCO_0000029 /SCO_0000037 http://gioUbbiali.github.io/sco/SCO_0000029 /SCO_0000038 http://gioUbbiali.github.io/sco/SCO_0000029 See information under the "has agent at t" property. http://gioUbbiali.github.io/sco/SCO_0000029 A system component that is an agent in an interaction among system components or in an interaction between system components and system environment components. http://gioUbbiali.github.io/sco/SCO_0000029 Una componente di sistema che è un agente in un'interazione tra le componenti del sistema o in un'interazione tra le componenti di sistema e le componenti dell'ambiente di sistema. http://gioUbbiali.github.io/sco/SCO_0000029 Une composante de système qui est un agent dans une interaction entre les composantes de l’environnement du système ou dans une interaction entre les composantes de système et les composants de l’environnement de système. http://gioUbbiali.github.io/sco/SCO_0000029 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000030 complex system stakeholder perspective, system stakeholder perspective http://gioUbbiali.github.io/sco/SCO_0000030 Prospettiva di parte interessata (stakeholder) http://gioUbbiali.github.io/sco/SCO_0000030 perspective de partie prenante (stakeholder) http://gioUbbiali.github.io/sco/SCO_0000030 stakeholder perspective http://gioUbbiali.github.io/sco/SCO_0000030 A perspective that is bearered by a stakeholder. http://gioUbbiali.github.io/sco/SCO_0000030 Una prospettiva che è detenuta da una parte interessata (stakeholder). http://gioUbbiali.github.io/sco/SCO_0000030 Une perspective qui est détenue par une partie prenante (stakeholder). http://gioUbbiali.github.io/sco/SCO_0000030 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000031 complex system boundary http://gioUbbiali.github.io/sco/SCO_0000031 confine del sistema complesso http://gioUbbiali.github.io/sco/SCO_0000031 frontière de système complexe http://gioUbbiali.github.io/sco/SCO_0000031 A system boundary of a complex system. http://gioUbbiali.github.io/sco/SCO_0000031 Un confine del sistema di un sistema complesso. http://gioUbbiali.github.io/sco/SCO_0000031 Une frontière de système d’un système complexe. http://gioUbbiali.github.io/sco/SCO_0000031 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000032 complex system spatial region http://gioUbbiali.github.io/sco/SCO_0000032 regione spaziale del sistema complesso http://gioUbbiali.github.io/sco/SCO_0000032 région d’espace de système complexe http://gioUbbiali.github.io/sco/SCO_0000032 A system spatial region of a complex system. http://gioUbbiali.github.io/sco/SCO_0000032 Una regione di spazio del sistema di un sistema complesso. http://gioUbbiali.github.io/sco/SCO_0000032 Une région d’espace de système d’un système complexe. http://gioUbbiali.github.io/sco/SCO_0000032 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000033 agent de l’environnement de système complexe http://gioUbbiali.github.io/sco/SCO_0000033 agente dell’ambiente del sistema complesso http://gioUbbiali.github.io/sco/SCO_0000033 complex system environment agent http://gioUbbiali.github.io/sco/SCO_0000033 /SCO_0000037 http://gioUbbiali.github.io/sco/SCO_0000033 /SCO_0000038 http://gioUbbiali.github.io/sco/SCO_0000033 See information under the "has agent at t" property. http://gioUbbiali.github.io/sco/SCO_0000033 A complex system environment component that is an agent in an interaction among complex system environment components or in an interaction between complex system components and complex system environment components. http://gioUbbiali.github.io/sco/SCO_0000033 Una componente dell’ambiente del sistema complesso che è un agente in un'interazione tra componenti dell’ambiente del sistema complesso o in un'interazione tra le componenti del sistema complesso e le componenti dell’ambiente del sistema complesso. http://gioUbbiali.github.io/sco/SCO_0000033 Une composante de l’environnement de système complexe qui est un agent dans une interaction entre les composantes de l’environnement de système complexe ou dans une interaction entre les composantes de système complexe et les composantes de l’environnement de système complexe. http://gioUbbiali.github.io/sco/SCO_0000033 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000034 agent de système complexe http://gioUbbiali.github.io/sco/SCO_0000034 agente del sistema complesso http://gioUbbiali.github.io/sco/SCO_0000034 complex system agent http://gioUbbiali.github.io/sco/SCO_0000034 /SCO_0000037 http://gioUbbiali.github.io/sco/SCO_0000034 /SCO_0000038 http://gioUbbiali.github.io/sco/SCO_0000034 See information under the "has agent at t" property. http://gioUbbiali.github.io/sco/SCO_0000034 A complex system component that is an agent in an interaction among complex system components or in an interaction between complex system components and complex system environment components. http://gioUbbiali.github.io/sco/SCO_0000034 Una componente del sistema complesso che è un agente in un'interazione tra le componenti del sistema complesso o in un'interazione tra le componenti del sistema complesso e le componenti dell’ambiente del sistema complesso. http://gioUbbiali.github.io/sco/SCO_0000034 Une composante de système complexe qui est un agent dans une interaction entre les composantes de système complexe ou dans une interaction entre les composantes de système complexe et les composantes de l’environnement de système complexe. http://gioUbbiali.github.io/sco/SCO_0000034 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000035 complex system indicator http://gioUbbiali.github.io/sco/SCO_0000035 system indicator http://gioUbbiali.github.io/sco/SCO_0000035 Due to the SCO focus on complex systems, indicator classes have been designed referring specifically to complex systems. Nevertheless, future implementations may broaden the space of application to also systems. http://gioUbbiali.github.io/sco/SCO_0000035 SCO indicator classes have been designed referring to the characterization of sustainable development indicators (SDGs indicators) proposed by SDGIO. we aimed to deepen this characterization and establish upper-level classes for SDGIO ones. http://gioUbbiali.github.io/sco/SCO_0000035 indicateur http://gioUbbiali.github.io/sco/SCO_0000035 indicator http://gioUbbiali.github.io/sco/SCO_0000035 indicatore http://gioUbbiali.github.io/sco/SCO_0000035 http://purl.unep.org/sdg/SDGIO_00000002 http://gioUbbiali.github.io/sco/SCO_0000035 A complex system component with an indicator role. http://gioUbbiali.github.io/sco/SCO_0000035 La componente del sistema complesso con un ruolo d’indicatore. http://gioUbbiali.github.io/sco/SCO_0000035 Une composante de système complexe ayant un rôle d’indicateur. http://gioUbbiali.github.io/sco/SCO_0000035 AnnotationVocabulary:Provisional http://gioUbbiali.github.io/sco/SCO_0000036 complex system stakeholder, system stakeholder http://gioUbbiali.github.io/sco/SCO_0000036 parte interessata (stakeholder) http://gioUbbiali.github.io/sco/SCO_0000036 partie prenante (stakeholder) http://gioUbbiali.github.io/sco/SCO_0000036 stakeholder http://gioUbbiali.github.io/sco/SCO_0000036 A complex system component with a stakeholder role. http://gioUbbiali.github.io/sco/SCO_0000036 Una componente del sistema complesso con un ruolo di stakeholder. http://gioUbbiali.github.io/sco/SCO_0000036 Une composante du système complexe avec un rôle de partie prenante. http://gioUbbiali.github.io/sco/SCO_0000036 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000037 Common Core Ontologies (CC) provide corresponding properties for this and the “agent at time t” relations. See “see also” annotation”. As these relations apply specifically to the CCO “Agent” class and lack reference to time, the SCO creator decided to establish SCO's own versions of these relations, directly referring to the original source. See “adapted from” annotation. http://gioUbbiali.github.io/sco/SCO_0000037 Future implementations may involve the introduction of an “act within the system” class, to deepen the characterization of system agency. Insights to implementation may come from the following CCO classes: http://www.ontologyrepository.com/CommonCoreOntologies/Act http://www.ontologyrepository.com/CommonCoreOntologies/IntentionalAct http://www.ontologyrepository.com/CommonCoreOntologies/Agent http://www.ontologyrepository.com/CommonCoreOntologies/AgentCapability The aim is to align SCO and CCO “agent” classes in order to have a shared theory of agency. http://gioUbbiali.github.io/sco/SCO_0000037 a un agent au temps t http://gioUbbiali.github.io/sco/SCO_0000037 ha un agente al tempo t http://gioUbbiali.github.io/sco/SCO_0000037 has agent at time t http://gioUbbiali.github.io/sco/SCO_0000037 http://www.ontologyrepository.com/CommonCoreOntologies/agent_in http://www.ontologyrepository.com/CommonCoreOntologies/has_agent http://gioUbbiali.github.io/sco/SCO_0000037 A primitive relation between a process x, a continuant y, and a time at which y is causally active in x. http://gioUbbiali.github.io/sco/SCO_0000037 Una relazione primitiva tra un processo x, un continuante y e un tempo t a cui y è causalmente attivo in x. http://gioUbbiali.github.io/sco/SCO_0000037 Une relation primitive entre un processus x, un continuant y et un temps t auquel y est causalement actif en x. http://gioUbbiali.github.io/sco/SCO_0000037 https://doi.org/10.1186/gb-2005-6-5-r46 http://gioUbbiali.github.io/sco/SCO_0000037 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000038 agent en au temps t http://gioUbbiali.github.io/sco/SCO_0000038 agent in at time t http://gioUbbiali.github.io/sco/SCO_0000038 agente in al tempo t http://gioUbbiali.github.io/sco/SCO_0000038 See information under the inverse "has agent at t" property. http://gioUbbiali.github.io/sco/SCO_0000038 A primitive relation between a continuant x, a process y, and a time at which x is causally active in y. http://gioUbbiali.github.io/sco/SCO_0000038 Una relazione primitiva tra un continuante x, un processo y e un tempo t a cui x è causalmente attivo in y. http://gioUbbiali.github.io/sco/SCO_0000038 Une relation primitive entre un continuant x, un processus y et un temps t auquel x est causalement actif en y. http://gioUbbiali.github.io/sco/SCO_0000038 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000039 We envisage using this annotation property to highlight (indirectly) the grounding of certain entities on perspectives and characterize them according to the embraced perspective(s). Here, it is provided an explicative example. Let’s consider that two users, A and B, endorse two different perspectives on sustainability, perspective A and perspective B. These perspectives lead to considering different complex system components as stakeholders of the complex system of interest. (This is an explicative example. It could also be the case that there is just one single user who wants to characterize the same entity according to two perspectives on sustainability, or who wants to provide an additional characterization according to a different perspective than the one previously covered.) We suggest proceeding as follows. First, the class “perspective” can be instantiated with two “perspective” individuals, “perspective A” and “perspective B”. These “perspective” individuals will provide descriptions and other relevant information regarding users’ perspectives. Then, two subclasses, “stakeholder – A” and “stakeholder – B”, can be added to the class “stakeholder”. These classes could be created manually and further populated with further subclasses and/or individuals. Alternatively, they can be created by adding SPARQL query results to the ontology, directly as classes or as classes equivalent to some new classes manually created. Subclasses “stakeholder – A” and “stakeholder – B” will cover stakeholders according to the two different user perspectives. Finally, this annotation property can be used to annotate these two subclasses with the corresponding individual “perspective A” and “perspective B”. In proceeding as such, we can highlight the grounding of the role of stakeholder (entity) on perspective (entity) and provide stakeholder characterizations according to the two user perspectives. This procedure supports establishing indirectly the grounding of certain entities on perspectives. This procedure, however, ensures the possibility to also account for different characterizations of the same entity according to different perspectives, thereby assisting in clarifying and comparing those perspectives. Further, as a user may change perspective over time, this procedure can be performed whenever the perspective changes. New classes, covering time references, can be created and annotated with new perspectives. This will also assist in tracking users’ perspectives evolution over time. We contemplate the possible creation of an object property to directly model grounding on perspectives as part of future implementations of SCO. http://gioUbbiali.github.io/sco/SCO_0000039 according to the perspective http://gioUbbiali.github.io/sco/SCO_0000039 secondo la prospettiva http://gioUbbiali.github.io/sco/SCO_0000039 selon la perspective http://gioUbbiali.github.io/sco/SCO_0000040 contenu informatif de la perspective de partie prenante (stakeholder) http://gioUbbiali.github.io/sco/SCO_0000040 contenuto informativo della prospettiva di parte interessata (stakeholder) http://gioUbbiali.github.io/sco/SCO_0000040 stakeholder perspective information content entity http://gioUbbiali.github.io/sco/SCO_0000040 A perspective information content entity of a stakeholder perspective. http://gioUbbiali.github.io/sco/SCO_0000040 Un contenu informatif de la perspective d’une perspective de partie prenante (stakeholder). http://gioUbbiali.github.io/sco/SCO_0000040 Un contenuto informativo della prospettiva di una prospettiva di parte interessata (stakeholder). http://gioUbbiali.github.io/sco/SCO_0000040 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000041 Do not use this class directly. This class is constructed as a grouping for complex system properties, such as emergence and self-organization, in order to facilitate class retrieval and visualization. http://gioUbbiali.github.io/sco/SCO_0000041 complex system property http://gioUbbiali.github.io/sco/SCO_0000041 proprietà del systema complesso http://gioUbbiali.github.io/sco/SCO_0000041 propriété de système complexe http://gioUbbiali.github.io/sco/SCO_0000041 AnnotationVocabulary:Released http://gioUbbiali.github.io/sco/SCO_0000042 This class should be amended according to SCO implementations regarding system scales, levels, and change. http://gioUbbiali.github.io/sco/SCO_0000042 emergence http://gioUbbiali.github.io/sco/SCO_0000042 emergenza (proprietà emergenti) http://gioUbbiali.github.io/sco/SCO_0000042 émergence (propriété émergentes http://gioUbbiali.github.io/sco/SCO_0000042 A quality that inherits in a complex system by virtue of how the complex system behavior and properties at a macroscopic level are nontrivially envisaged from those at a more microscopic one. http://gioUbbiali.github.io/sco/SCO_0000042 Una qualità che il sistema complesso esibisce in virtù del fatto che il comportamento del sistema complesso e le sue proprietà a un livello macroscopico sono non-trivialmente predicibili da quelli a livello più microscopico. http://gioUbbiali.github.io/sco/SCO_0000042 Une qualité qu’un système complexe exhibe en vertu du fait que le comportement du système complexe et ses propriétés à un niveau macroscopique sont non-trivialement prédictibles à partir de ceux aux niveaux plus microscopiques. http://gioUbbiali.github.io/sco/SCO_0000042 AnnotationVocabulary:Provisional http://gioUbbiali.github.io/sco/SCO_0000043 This class should be amended according to SCO implementations regarding system scales, levels, and change. http://gioUbbiali.github.io/sco/SCO_0000043 auto-organisation http://gioUbbiali.github.io/sco/SCO_0000043 auto-organizzazione http://gioUbbiali.github.io/sco/SCO_0000043 self-organization http://gioUbbiali.github.io/sco/SCO_0000043 A quality that inherits in a complex system by virtue of how the complex system components spontaneously arrange, globally generating macroscopic and microscopic structures and behaviors, without any internal and/or external controls. http://gioUbbiali.github.io/sco/SCO_0000043 Una qualità che il sistema complesso esibisce in virtù del fatto che le componenti del sistema complesso si organizzino spontaneamente, generando globalmente strutture e comportamenti macroscopici e microscopici, senza alcun controllo interno e/o esterno. http://gioUbbiali.github.io/sco/SCO_0000043 Une qualité qu’un système complexe exhibe en vertu du fait que les composantes du système complexe s’organisent spontanément, générant globalement des structures et comportements macroscopiques et microscopiques, sans aucun contrôle interne et/ou externe. http://gioUbbiali.github.io/sco/SCO_0000043 AnnotationVocabulary:Provisional bfo:BFO_0000002 An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. bfo:BFO_0000003 An entity that has temporal parts and that happens, unfolds or develops through time. bfo:BFO_0000004 b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) bfo:BFO_0000015 p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) bfo:BFO_0000017 A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. bfo:BFO_0000020 b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) bfo:BFO_0000023 A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. bfo:BFO_0000031 b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) bfo:BFO_0000040 An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. bfo:BFO_0000050 is part of bfo:BFO_0000050 my brain is part of my body (continuant parthood, two material entities) bfo:BFO_0000050 my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) bfo:BFO_0000050 this day is part of this year (occurrent parthood) bfo:BFO_0000050 a core relation that holds between a part and its whole bfo:BFO_0000050 Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. bfo:BFO_0000050 Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ bfo:BFO_0000050 Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. bfo:BFO_0000050 part_of bfo:BFO_0000051 has part bfo:BFO_0000051 my body has part my brain (continuant parthood, two material entities) bfo:BFO_0000051 my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) bfo:BFO_0000051 this year has part this day (occurrent parthood) bfo:BFO_0000051 a core relation that holds between a whole and its part bfo:BFO_0000051 Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. bfo:BFO_0000051 Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ bfo:BFO_0000051 Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. bfo:BFO_0000051 has_part bfo:BFO_0000054 realized in bfo:BFO_0000054 this disease is realized in this disease course bfo:BFO_0000054 this fragility is realized in this shattering bfo:BFO_0000054 this investigator role is realized in this investigation bfo:BFO_0000054 is realized by bfo:BFO_0000054 realized_in bfo:BFO_0000054 [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) bfo:BFO_0000055 realizes bfo:BFO_0000055 this disease course realizes this disease bfo:BFO_0000055 this investigation realizes this investigator role bfo:BFO_0000055 this shattering realizes this fragility bfo:BFO_0000055 to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) bfo:BFO_0000062 preceded by bfo:BFO_0000062 x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. bfo:BFO_0000062 An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. bfo:BFO_0000062 is preceded by bfo:BFO_0000062 preceded_by bfo:BFO_0000063 precedes bfo:BFO_0000063 x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. bfo:BFO_0000066 occurs in bfo:BFO_0000066 b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t bfo:BFO_0000066 occurs_in bfo:BFO_0000066 unfolds in bfo:BFO_0000066 unfolds_in bfo:BFO_0000067 site of bfo:BFO_0000067 [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t CARO:mah bfo:CL_0000000 A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. bfo:CL_0000000 A material entity that has a plasma membrane and results from cellular division. ISBN:0721662544 bfo:CL_0000101 Any neuron having a sensory function; an afferent neuron conveying sensory impulses. MESH:D009474 http://en.wikipedia.org/wiki/Neuron bfo:CL_0000540 The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. bfo:CL_0000540 nerve cell bfo:COB_0001000 A process during which an organism comes into contact with another entity. DOI:10.1186/2041-1480-4-43 bfo:ENVO_01000254 A system which has the disposition to environ one or more material entities. bfo:ENVO_01000254 environment EnvO:EnvO bfo:ENVO_01000739 An environmental system which can sustain and allow the growth of an ecological population. bfo:ENVO_01003004 A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity. GOC:pdt bfo:GO_0003674 A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. bfo:GO_0003674 molecular function GOC:BioGRID GOC:jh2 PMID:9635407 bfo:GO_0004842 Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. bfo:GO_0004842 E2 bfo:GO_0004842 E3 bfo:GO_0004842 ubiquitin conjugating enzyme activity bfo:GO_0004842 ubiquitin ligase activity bfo:GO_0004842 ubiquitin protein ligase activity bfo:GO_0004842 ubiquitin protein-ligase activity bfo:GO_0004842 ubiquitin-conjugating enzyme activity GOC:go_curators bfo:GO_0005634 A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. bfo:GO_0005634 cell nucleus GOC:al GOC:mah GOC:vw PMID:15030757 bfo:GO_0005634 horsetail nucleus GOC:pdt bfo:GO_0008150 A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. bfo:GO_0008150 A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. bfo:GO_0008150 biological process bfo:GO_0008150 physiological process bfo:GO_0008150 single organism process bfo:GO_0008150 single-organism process ISBN:0198506732 bfo:GO_0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. bfo:GO_0016301 phosphokinase activity GOC:ai bfo:GO_0019107 Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule. bfo:IAO_0000002 example to be eventually removed bfo:IAO_0000027 data item bfo:IAO_0000030 information content entity bfo:IAO_0000078 curation status specification bfo:IAO_0000078 bfo:IAO_0000125 bfo:IAO_0000078 The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. bfo:IAO_0000078 Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) bfo:IAO_0000078 PERSON:Bill Bug bfo:IAO_0000078 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> bfo:IAO_0000078 OBI_0000266 bfo:IAO_0000102 data about an ontology part bfo:IAO_0000102 Data about an ontology part is a data item about a part of an ontology, for example a term bfo:IAO_0000102 Person:Alan Ruttenberg bfo:IAO_0000103 failed exploratory term bfo:IAO_0000103 The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job bfo:IAO_0000103 Person:Alan Ruttenberg bfo:IAO_0000111 editor preferred term bfo:IAO_0000111 bfo:IAO_0000122 bfo:IAO_0000111 The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) bfo:IAO_0000111 PERSON:Daniel Schober bfo:IAO_0000111 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> bfo:IAO_0000111 editor preferred term bfo:IAO_0000112 example of usage bfo:IAO_0000112 bfo:IAO_0000122 bfo:IAO_0000112 A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. bfo:IAO_0000112 PERSON:Daniel Schober bfo:IAO_0000112 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> bfo:IAO_0000112 example of usage bfo:IAO_0000112 example of usage bfo:IAO_0000113 in branch bfo:IAO_0000113 An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. bfo:IAO_0000113 GROUP:OBI bfo:IAO_0000113 OBI_0000277 bfo:IAO_0000114 has curation status bfo:IAO_0000114 PERSON:Alan Ruttenberg bfo:IAO_0000114 PERSON:Bill Bug bfo:IAO_0000114 PERSON:Melanie Courtot bfo:IAO_0000114 has curation status bfo:IAO_0000115 definition bfo:IAO_0000115 bfo:IAO_0000122 bfo:IAO_0000115 The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. bfo:IAO_0000115 The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. bfo:IAO_0000115 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. bfo:IAO_0000115 PERSON:Daniel Schober bfo:IAO_0000115 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> bfo:IAO_0000115 bfo:iao.owl bfo:IAO_0000115 definition bfo:IAO_0000115 definition bfo:IAO_0000115 textual definition bfo:IAO_0000116 editor note bfo:IAO_0000116 bfo:IAO_0000122 bfo:IAO_0000116 An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. bfo:IAO_0000116 PERSON:Daniel Schober bfo:IAO_0000116 GROUP:OBI:<http://purl.obofoundry.org/obo/obi> bfo:IAO_0000116 editor note bfo:IAO_0000117 term editor bfo:IAO_0000117 bfo:IAO_0000122 bfo:IAO_0000117 Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people bfo:IAO_0000117 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. bfo:IAO_0000117 PERSON:Daniel Schober bfo:IAO_0000117 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> bfo:IAO_0000117 term editor bfo:IAO_0000118 alternative label bfo:IAO_0000118 bfo:IAO_0000125 bfo:IAO_0000118 A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. bfo:IAO_0000118 OBO Operations committee bfo:IAO_0000118 PERSON:Daniel Schober bfo:IAO_0000118 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> bfo:IAO_0000118 Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). bfo:IAO_0000118 alternative label bfo:IAO_0000119 definition source bfo:IAO_0000119 bfo:IAO_0000122 bfo:IAO_0000119 Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 bfo:IAO_0000119 PERSON:Daniel Schober bfo:IAO_0000119 Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w bfo:IAO_0000119 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> bfo:IAO_0000119 definition source bfo:IAO_0000120 metadata complete bfo:IAO_0000120 Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. bfo:IAO_0000121 organizational term bfo:IAO_0000121 Term created to ease viewing/sort terms for development purpose, and will not be included in a release bfo:IAO_0000122 ready for release bfo:IAO_0000122 bfo:IAO_0000125 bfo:IAO_0000122 Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." bfo:IAO_0000123 metadata incomplete bfo:IAO_0000123 Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. bfo:IAO_0000124 uncurated bfo:IAO_0000124 Nothing done yet beyond assigning a unique class ID and proposing a preferred term. bfo:IAO_0000125 pending final vetting bfo:IAO_0000125 bfo:IAO_0000125 bfo:IAO_0000125 All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. bfo:IAO_0000224 Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. bfo:IAO_0000224 PERSON: Alan Ruttenberg bfo:IAO_0000224 PERSON: Melanie Courtot bfo:IAO_0000225 obsolescence reason specification bfo:IAO_0000225 bfo:IAO_0000125 bfo:IAO_0000225 The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. bfo:IAO_0000225 The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. bfo:IAO_0000225 PERSON: Alan Ruttenberg bfo:IAO_0000225 PERSON: Melanie Courtot bfo:IAO_0000226 placeholder removed bfo:IAO_0000227 terms merged bfo:IAO_0000227 An editor note should explain what were the merged terms and the reason for the merge. bfo:IAO_0000228 term imported bfo:IAO_0000228 This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. bfo:IAO_0000229 term split bfo:IAO_0000229 This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. bfo:IAO_0000231 has obsolescence reason bfo:IAO_0000231 Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. bfo:IAO_0000231 PERSON:Alan Ruttenberg bfo:IAO_0000231 PERSON:Melanie Courtot bfo:IAO_0000232 curator note bfo:IAO_0000232 bfo:IAO_0000122 bfo:IAO_0000232 An administrative note of use for a curator but of no use for a user bfo:IAO_0000232 PERSON:Alan Ruttenberg bfo:IAO_0000232 bfo:iao.owl bfo:IAO_0000232 curator note bfo:IAO_0000233 term tracker item bfo:IAO_0000233 the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ bfo:IAO_0000233 bfo:IAO_0000125 bfo:IAO_0000233 An IRI or similar locator for a request or discussion of an ontology term. bfo:IAO_0000233 Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg bfo:IAO_0000233 Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg bfo:IAO_0000233 The 'tracker item' can associate a tracker with a specific ontology term. bfo:IAO_0000233 term tracker item bfo:IAO_0000234 ontology term requester bfo:IAO_0000234 bfo:IAO_0000125 bfo:IAO_0000234 The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. bfo:IAO_0000234 Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg bfo:IAO_0000234 Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg bfo:IAO_0000409 denotator type bfo:IAO_0000409 The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. bfo:IAO_0000409 A denotator type indicates how a term should be interpreted from an ontological perspective. bfo:IAO_0000409 Alan Ruttenberg bfo:IAO_0000409 Barry Smith, Werner Ceusters bfo:IAO_0000410 universal bfo:IAO_0000410 Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. bfo:IAO_0000410 Alan Ruttenberg bfo:IAO_0000410 A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf bfo:IAO_0000411 is denotator type bfo:IAO_0000411 Relates an class defined in an ontology, to the type of it's denotator bfo:IAO_0000411 In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') bfo:IAO_0000411 Alan Ruttenberg bfo:IAO_0000412 imported from bfo:IAO_0000412 bfo:IAO_0000125 bfo:IAO_0000412 For external terms/classes, the ontology from which the term was imported bfo:IAO_0000412 PERSON:Alan Ruttenberg bfo:IAO_0000412 PERSON:Melanie Courtot bfo:IAO_0000412 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> bfo:IAO_0000420 defined class bfo:IAO_0000420 A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal bfo:IAO_0000420 "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. bfo:IAO_0000420 Alan Ruttenberg bfo:IAO_0000421 named class expression bfo:IAO_0000421 A named class expression is a logical expression that is given a name. The name can be used in place of the expression. bfo:IAO_0000421 named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions bfo:IAO_0000421 Alan Ruttenberg bfo:IAO_0000423 to be replaced with external ontology term bfo:IAO_0000423 Terms with this status should eventually replaced with a term from another ontology. bfo:IAO_0000423 Alan Ruttenberg bfo:IAO_0000423 group:OBI bfo:IAO_0000424 expand expression to bfo:IAO_0000424 ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" bfo:IAO_0000424 A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones bfo:IAO_0000424 Chris Mungall bfo:IAO_0000424 expand expression to bfo:IAO_0000425 expand assertion to bfo:IAO_0000425 ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" bfo:IAO_0000425 A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. bfo:IAO_0000425 Chris Mungall bfo:IAO_0000426 first order logic expression bfo:IAO_0000426 An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. bfo:IAO_0000426 PERSON:Alan Ruttenberg bfo:IAO_0000427 antisymmetric property bfo:IAO_0000427 part_of antisymmetric property xsd:true bfo:IAO_0000427 Use boolean value xsd:true to indicate that the property is an antisymmetric property bfo:IAO_0000427 Alan Ruttenberg bfo:IAO_0000428 requires discussion bfo:IAO_0000428 bfo:IAO_0000125 bfo:IAO_0000428 A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. bfo:IAO_0000428 Alan Ruttenberg bfo:IAO_0000428 group:OBI bfo:IAO_0000589 OBO foundry unique label bfo:IAO_0000589 bfo:IAO_0000125 bfo:IAO_0000589 An alternative name for a class or property which is unique across the OBO Foundry. bfo:IAO_0000589 The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . bfo:IAO_0000589 PERSON:Alan Ruttenberg bfo:IAO_0000589 PERSON:Bjoern Peters bfo:IAO_0000589 PERSON:Chris Mungall bfo:IAO_0000589 PERSON:Melanie Courtot bfo:IAO_0000589 GROUP:OBO Foundry <http://obofoundry.org/> bfo:IAO_0000596 has ID digit count bfo:IAO_0000596 Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" bfo:IAO_0000596 Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) bfo:IAO_0000596 Person:Alan Ruttenberg bfo:IAO_0000597 has ID range allocated bfo:IAO_0000597 Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300] bfo:IAO_0000597 Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms bfo:IAO_0000597 Person:Alan Ruttenberg bfo:IAO_0000598 has ID policy for bfo:IAO_0000598 Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" bfo:IAO_0000598 Relating an ontology used to record id policy to the ontology namespace whose policy it manages bfo:IAO_0000598 Person:Alan Ruttenberg bfo:IAO_0000599 has ID prefix bfo:IAO_0000599 Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" bfo:IAO_0000599 Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. bfo:IAO_0000599 Person:Alan Ruttenberg bfo:IAO_0000600 elucidation bfo:IAO_0000600 person:Alan Ruttenberg bfo:IAO_0000600 Person:Barry Smith bfo:IAO_0000600 Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms bfo:IAO_0000600 elucidation bfo:IAO_0000601 has associated axiom(nl) bfo:IAO_0000601 Person:Alan Ruttenberg bfo:IAO_0000601 Person:Alan Ruttenberg bfo:IAO_0000601 An axiom associated with a term expressed using natural language bfo:IAO_0000602 has associated axiom(fol) bfo:IAO_0000602 Person:Alan Ruttenberg bfo:IAO_0000602 Person:Alan Ruttenberg bfo:IAO_0000602 An axiom expressed in first order logic using CLIF syntax bfo:IAO_0000603 is allocated id range bfo:IAO_0000603 Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" bfo:IAO_0000603 PERSON:Alan Ruttenberg bfo:IAO_0000700 has ontology root term bfo:IAO_0000700 Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. bfo:IAO_0000700 Nicolas Matentzoglu bfo:IAO_0006011 may be identical to bfo:IAO_0006011 A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. bfo:IAO_0006011 David Osumi-Sutherland bfo:IAO_0006012 scheduled for obsoletion on or after bfo:IAO_0006012 Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. bfo:IAO_0006012 Chris Mungall, Jie Zheng bfo:IAO_0010000 has axiom id bfo:IAO_0010000 Person:Alan Ruttenberg bfo:IAO_0010000 Person:Alan Ruttenberg bfo:IAO_0010000 A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI bfo:IAO_0100001 term replaced by bfo:IAO_0100001 bfo:IAO_0000125 bfo:IAO_0100001 Use on obsolete terms, relating the term to another term that can be used as a substitute bfo:IAO_0100001 Person:Alan Ruttenberg bfo:IAO_0100001 Person:Alan Ruttenberg bfo:IAO_8000000 ontology module bfo:IAO_8000000 I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. bfo:IAO_8000000 ontology file bfo:IAO_8000001 base ontology module bfo:IAO_8000001 An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. bfo:IAO_8000002 editors ontology module bfo:IAO_8000002 An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. bfo:IAO_8000002 source ontology module bfo:IAO_8000003 main release ontology module bfo:IAO_8000003 An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. bfo:IAO_8000003 TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module bfo:IAO_8000004 bridge ontology module bfo:IAO_8000004 An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. bfo:IAO_8000005 import ontology module bfo:IAO_8000005 A subset ontology module that is intended to be imported from another ontology. bfo:IAO_8000005 TODO: add axioms that indicate this is the output of a module extraction process. bfo:IAO_8000005 import file bfo:IAO_8000006 subset ontology module bfo:IAO_8000006 An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. bfo:IAO_8000006 ontology slim bfo:IAO_8000006 subset ontology bfo:IAO_8000007 curation subset ontology module bfo:IAO_8000007 A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. bfo:IAO_8000008 analysis ontology module bfo:IAO_8000008 An ontology module that is intended for usage in analysis or discovery applications. bfo:IAO_8000009 single layer ontology module bfo:IAO_8000009 A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. bfo:IAO_8000009 ribbon subset bfo:IAO_8000010 exclusion subset ontology module bfo:IAO_8000010 A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. bfo:IAO_8000010 antislim bfo:IAO_8000011 external import ontology module bfo:IAO_8000011 An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. bfo:IAO_8000011 external import bfo:IAO_8000012 species subset ontology module bfo:IAO_8000012 A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. bfo:IAO_8000012 taxon subset bfo:IAO_8000013 reasoned ontology module bfo:IAO_8000013 An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. bfo:IAO_8000014 generated ontology module bfo:IAO_8000014 An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. bfo:IAO_8000014 TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process bfo:IAO_8000015 template generated ontology module bfo:IAO_8000015 An ontology module that is automatically generated from a template specification and fillers for slots in that template. bfo:IAO_8000016 taxonomic bridge ontology module bfo:IAO_8000017 ontology module subsetted by expressivity bfo:IAO_8000018 obo basic subset ontology module bfo:IAO_8000018 A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports bfo:IAO_8000019 ontology module subsetted by OWL profile bfo:IAO_8000020 EL++ ontology module bfo:OBI_0000011 planned process bfo:OBI_0000011 planned process bfo:OBI_0000011 Injecting mice with a vaccine in order to test its efficacy bfo:OBI_0000011 bfo:IAO_0000122 bfo:OBI_0000011 A process that realizes a plan which is the concretization of a plan specification. bfo:OBI_0000011 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) bfo:OBI_0000011 We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. bfo:OBI_0000011 Bjoern Peters bfo:OBI_0000011 branch derived bfo:OBI_0000047 processed material bfo:OBI_0000047 Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples bfo:OBI_0000047 bfo:IAO_0000122 bfo:OBI_0000047 Is a material entity that is created or changed during material processing. bfo:OBI_0000047 PERSON: Alan Ruttenberg bfo:OBI_0000070 assay bfo:OBI_0000070 Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. bfo:OBI_0000070 bfo:IAO_0000122 bfo:OBI_0000070 A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. bfo:OBI_0000070 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. bfo:OBI_0000070 PlanAndPlannedProcess Branch bfo:OBI_0000070 measuring bfo:OBI_0000070 scientific observation bfo:OBI_0000070 OBI branch derived bfo:OBI_0000967 container bfo:OBI_0000967 bfo:IAO_0000123 bfo:OBI_0000967 A device that can be used to restrict the location of material entities over time bfo:OBI_0000967 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?) bfo:OBI_0000967 PERSON: Bjoern Peters bfo:OBI_0000968 device bfo:OBI_0000968 A voltmeter is a measurement device which is intended to perform some measure function. bfo:OBI_0000968 An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. bfo:OBI_0000968 bfo:IAO_0000122 bfo:OBI_0000968 A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. bfo:OBI_0000968 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. bfo:OBI_0000968 PERSON: Helen Parkinson bfo:OBI_0000968 instrument bfo:OBI_0000968 OBI development call 2012-12-17. bfo:OBI_0100026 organism bfo:OBI_0100026 animal bfo:OBI_0100026 fungus bfo:OBI_0100026 plant bfo:OBI_0100026 virus bfo:OBI_0100026 bfo:IAO_0000122 bfo:OBI_0100026 A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. bfo:OBI_0100026 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') bfo:OBI_0100026 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. bfo:OBI_0100026 GROUP: OBI Biomaterial Branch bfo:OBI_0100026 WEB: http://en.wikipedia.org/wiki/Organism bfo:OGMS_0000031 A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. bfo:OMO_0001000 The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. bfo:OMO_0001000 This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. bfo:OMO_0001000 http://orcid.org/0000-0001-5208-3432 bfo:OMO_0001001 This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. bfo:OMO_0001001 OBO Operations call bfo:OMO_0002000 'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . } bfo:OMO_0002000 Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. bfo:OMO_0002000 https://github.com/ontodev/robot/issues/963 bfo:OMO_0003000 CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) bfo:OMO_0003000 A synonym type for describing abbreviations or initalisms bfo:OMO_0003001 A synonym type for describing ambiguous synonyms bfo:OMO_0003002 A synonym type for describing dubious synonyms bfo:OMO_0003003 EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) bfo:OMO_0003003 A synonym type for describing layperson or colloquial synonyms bfo:OMO_0003004 CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) bfo:OMO_0003004 A synonym type for describing pluralization synonyms bfo:OMO_0003005 CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) bfo:OMO_0003005 A synonym type for describing UK spelling variants bfo:OMO_0003006 A synonym type for common misspellings bfo:OMO_0003007 A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway bfo:OMO_0003008 MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. bfo:OMO_0003008 A synonym type for names that have been used as primary labels in the past. bfo:OMO_0003009 The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College bfo:OMO_0003009 A synonym type for the legal entity name PATOC:GVG bfo:PATO_0000001 A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities WordNet:WordNet bfo:PATO_0000402 A branchiness quality inhering in a bearer by virtue of the bearer's having branches. bfo:PATO_0000402 ramified bfo:PATO_0000402 ramiform ISBN:0881923214 bfo:PATO_0001199 A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel. PATOC:nw bfo:PATO_0001470 A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity. bfo:PATO_0001470 proportion bfo:PATO_0001470 proportionality bfo:PATO_0001470 quotient bfo:PATO_0001470 ratio bfo:PATO_0001470 rate PATOC:GVG bfo:PATO_0002124 A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. bfo:RO_0000052 inheres in bfo:RO_0000052 this fragility is a characteristic of this vase bfo:RO_0000052 this red color is a characteristic of this apple bfo:RO_0000052 a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. bfo:RO_0000052 inheres_in bfo:RO_0000052 Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. bfo:RO_0000052 characteristic of bfo:RO_0000053 bearer of bfo:RO_0000053 this apple is bearer of this red color bfo:RO_0000053 this vase is bearer of this fragility bfo:RO_0000053 Inverse of characteristic_of bfo:RO_0000053 A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bfo:RO_0000053 bearer_of bfo:RO_0000053 is bearer of bfo:RO_0000053 has characteristic bfo:RO_0000056 participates in bfo:RO_0000056 this blood clot participates in this blood coagulation bfo:RO_0000056 this input material (or this output material) participates in this process bfo:RO_0000056 this investigator participates in this investigation bfo:RO_0000056 a relation between a continuant and a process, in which the continuant is somehow involved in the process bfo:RO_0000056 participates_in bfo:RO_0000057 has participant bfo:RO_0000057 this blood coagulation has participant this blood clot bfo:RO_0000057 this investigation has participant this investigator bfo:RO_0000057 this process has participant this input material (or this output material) bfo:RO_0000057 a relation between a process and a continuant, in which the continuant is somehow involved in the process bfo:RO_0000057 Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. bfo:RO_0000057 has_participant bfo:RO_0000058 A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). bfo:RO_0000058 An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). bfo:RO_0000058 A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. bfo:RO_0000059 A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). bfo:RO_0000059 An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). bfo:RO_0000059 A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. bfo:RO_0000079 this catalysis function is a function of this enzyme bfo:RO_0000079 a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence bfo:RO_0000079 A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. bfo:RO_0000079 function_of bfo:RO_0000079 is function of bfo:RO_0000079 This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. bfo:RO_0000079 function of bfo:RO_0000080 this red color is a quality of this apple bfo:RO_0000080 a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence bfo:RO_0000080 A quality inheres in its bearer at all times for which the quality exists. bfo:RO_0000080 is quality of bfo:RO_0000080 quality_of bfo:RO_0000080 This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. bfo:RO_0000080 quality of bfo:RO_0000081 this investigator role is a role of this person bfo:RO_0000081 a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence bfo:RO_0000081 A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. bfo:RO_0000081 is role of bfo:RO_0000081 role_of bfo:RO_0000081 This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. bfo:RO_0000081 role of bfo:RO_0000085 this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) bfo:RO_0000085 a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence bfo:RO_0000085 A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. bfo:RO_0000085 has_function bfo:RO_0000085 has function bfo:RO_0000086 this apple has quality this red color bfo:RO_0000086 a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence bfo:RO_0000086 A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. bfo:RO_0000086 has_quality bfo:RO_0000086 has quality bfo:RO_0000087 this person has role this investigator role (more colloquially: this person has this role of investigator) bfo:RO_0000087 a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence bfo:RO_0000087 A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. bfo:RO_0000087 has_role bfo:RO_0000087 has role bfo:RO_0000091 a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence bfo:RO_0000091 has disposition bfo:RO_0000092 inverse of has disposition bfo:RO_0000092 bfo:RO_0002259 bfo:RO_0000092 This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. bfo:RO_0000092 disposition of bfo:RO_0000300 bfo:IAO_0000125 bfo:RO_0000300 OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. bfo:RO_0000300 https://orcid.org/0000-0002-7073-9172 bfo:RO_0000301 bfo:IAO_0000125 bfo:RO_0000301 OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first. bfo:RO_0000301 https://orcid.org/0000-0002-7073-9172 bfo:RO_0000302 bfo:IAO_0000125 bfo:RO_0000302 OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first. bfo:RO_0000302 https://orcid.org/0000-0002-7073-9172 bfo:RO_0001000 this cell derives from this parent cell (cell division) bfo:RO_0001000 this nucleus derives from this parent nucleus (nuclear division) bfo:RO_0001000 bfo:IAO_0000125 bfo:RO_0001000 a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity bfo:RO_0001000 This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. bfo:RO_0001000 derives_from bfo:RO_0001001 this parent cell derives into this cell (cell division) bfo:RO_0001001 this parent nucleus derives into this nucleus (nuclear division) bfo:RO_0001001 bfo:IAO_0000125 bfo:RO_0001001 a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity bfo:RO_0001001 This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. bfo:RO_0001001 derives_into bfo:RO_0001015 is location of bfo:RO_0001015 my head is the location of my brain bfo:RO_0001015 this cage is the location of this rat bfo:RO_0001015 a relation between two independent continuants, the location and the target, in which the target is entirely within the location bfo:RO_0001015 Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ bfo:RO_0001015 location_of bfo:RO_0001018 contained in bfo:RO_0001018 Containment is location not involving parthood, and arises only where some immaterial continuant is involved. bfo:RO_0001018 Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): bfo:RO_0001018 contained_in bfo:RO_0001019 contains bfo:RO_0001020 penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) bfo:RO_0001020 A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. bfo:RO_0001021 A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. bfo:RO_0001022 penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) bfo:RO_0001022 A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. bfo:RO_0001023 A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. bfo:RO_0001900 An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. bfo:RO_0001900 temporal interpretation bfo:RO_0001900 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ bfo:RO_0001901 ## Elucidation This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; ## How to interpret (informal) First the &quot;atemporal&quot; FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation bfo:RO_0001902 ## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y) bfo:RO_0002000 the surface of my skin is a 2D boundary of my body bfo:RO_0002000 a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity bfo:RO_0002000 A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. bfo:RO_0002000 Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. bfo:RO_0002000 2D_boundary_of bfo:RO_0002000 boundary of bfo:RO_0002000 is 2D boundary of bfo:RO_0002000 is boundary of bfo:RO_0002000 surface of bfo:RO_0002001 bfo:IAO_0000125 bfo:RO_0002001 May be obsoleted, see https://github.com/oborel/obo-relations/issues/260 bfo:RO_0002001 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002002 my body has 2D boundary the surface of my skin bfo:RO_0002002 a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity bfo:RO_0002002 A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. bfo:RO_0002002 Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. bfo:RO_0002002 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002002 has boundary bfo:RO_0002002 has_2D_boundary bfo:RO_0002003 A relation that holds between two neurons that are electrically coupled via gap junctions. bfo:RO_0002003 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002004 The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). bfo:RO_0002004 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002005 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002006 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002007 X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 bfo:RO_0002007 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002008 A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. bfo:RO_0002008 Note from NCEAS meeting: consider changing primary label bfo:RO_0002008 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002009 A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. bfo:RO_0002009 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002010 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). bfo:RO_0002010 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002010 regulates in other organism bfo:RO_0002011 A relationship that holds between a process that regulates a transport process and the entity transported by that process. bfo:RO_0002011 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002012 A part of relation that applies only between occurrents. bfo:RO_0002013 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. bfo:RO_0002014 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. bfo:RO_0002015 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. bfo:RO_0002018 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. bfo:RO_0002019 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. bfo:RO_0002020 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. bfo:RO_0002021 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. https://orcid.org/0000-0002-7073-9172 bfo:RO_0002023 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. https://orcid.org/0000-0002-7073-9172 bfo:RO_0002024 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. https://orcid.org/0000-0002-7073-9172 bfo:RO_0002025 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. https://orcid.org/0000-0002-7073-9172 bfo:RO_0002026 A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. PMID:24138933 Wikipedia:Infant_mortality bfo:RO_0002029 Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. bfo:RO_0002081 David Osumi-Sutherland bfo:RO_0002081 <= bfo:RO_0002082 x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. bfo:RO_0002082 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002082 David Osumi-Sutherland bfo:RO_0002083 David Osumi-Sutherland bfo:RO_0002084 David Osumi-Sutherland bfo:RO_0002085 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002085 di bfo:RO_0002086 David Osumi-Sutherland bfo:RO_0002087 David Osumi-Sutherland bfo:RO_0002087 starts_at_end_of bfo:RO_0002088 David Osumi-Sutherland bfo:RO_0002089 David Osumi-Sutherland bfo:RO_0002090 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002090 David Osumi-Sutherland bfo:RO_0002090 ends_at_start_of bfo:RO_0002090 meets bfo:RO_0002091 David Osumi-Sutherland bfo:RO_0002091 io bfo:RO_0002092 David Osumi-Sutherland bfo:RO_0002092 d bfo:RO_0002092 during bfo:RO_0002093 David Osumi-Sutherland bfo:RO_0002093 o bfo:RO_0002093 overlaps bfo:RO_0002100 bfo:IAO_0000125 bfo:RO_0002100 Relation between a neuron and a material anatomical entity that its soma is part of. bfo:RO_0002100 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002101 bfo:IAO_0000125 bfo:RO_0002101 relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. bfo:RO_0002101 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002101 fasciculates with bfo:RO_0002102 bfo:IAO_0000125 bfo:RO_0002102 Relation between a neuron and some structure its axon forms (chemical) synapses in. bfo:RO_0002102 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002102 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002103 bfo:IAO_0000125 bfo:RO_0002103 Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. bfo:RO_0002103 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002103 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002104 Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] bfo:RO_0002104 bfo:IAO_0000125 bfo:RO_0002104 Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. bfo:RO_0002104 https://orcid.org/0000-0001-9990-8331 bfo:RO_0002104 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002104 https://orcid.org/0000-0003-1617-8244 bfo:RO_0002104 http://www.ncbi.nlm.nih.gov/pubmed/19243617 bfo:RO_0002105 bfo:IAO_0000125 bfo:RO_0002105 A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. bfo:RO_0002105 https://orcid.org/0000-0001-5948-3092 bfo:RO_0002105 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002106 bfo:IAO_0000125 bfo:RO_0002106 A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. bfo:RO_0002106 https://orcid.org/0000-0001-5948-3092 bfo:RO_0002106 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002107 bfo:IAO_0000125 bfo:RO_0002107 A relation between a motor neuron and a muscle that it synapses to via a type II bouton. bfo:RO_0002107 https://orcid.org/0000-0001-5948-3092 bfo:RO_0002107 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002108 bfo:IAO_0000125 bfo:RO_0002108 Relation between a muscle and a motor neuron that synapses to it via a type II bouton. bfo:RO_0002108 https://orcid.org/0000-0001-5948-3092 bfo:RO_0002108 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002109 bfo:IAO_0000125 bfo:RO_0002109 Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. bfo:RO_0002109 https://orcid.org/0000-0001-5948-3092 bfo:RO_0002109 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002110 bfo:IAO_0000125 bfo:RO_0002110 Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. bfo:RO_0002110 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002110 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002110 synapsed in bfo:RO_0002111 bfo:IAO_0000125 bfo:RO_0002111 has neurotransmitter bfo:RO_0002112 bfo:IAO_0000125 bfo:RO_0002112 Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. bfo:RO_0002112 https://orcid.org/0000-0001-5948-3092 bfo:RO_0002112 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002113 bfo:IAO_0000125 bfo:RO_0002113 Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. bfo:RO_0002113 synapses in bfo:RO_0002114 A relation between a motor neuron and a muscle that it synapses to via a type III bouton. bfo:RO_0002115 Relation between a muscle and a motor neuron that synapses to it via a type III bouton. bfo:RO_0002120 bfo:IAO_0000125 bfo:RO_0002120 Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. bfo:RO_0002120 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002120 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002121 bfo:IAO_0000125 bfo:RO_0002121 Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. bfo:RO_0002121 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002121 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002130 bfo:IAO_0000125 bfo:RO_0002130 A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. bfo:RO_0002130 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002130 has synapse in bfo:RO_0002131 bfo:IAO_0000125 bfo:RO_0002131 x overlaps y if and only if there exists some z such that x has part z and z part of y bfo:RO_0002132 bfo:IAO_0000125 bfo:RO_0002132 The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. bfo:RO_0002132 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002132 has fasciculating component bfo:RO_0002134 bfo:IAO_0000125 bfo:RO_0002134 Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. bfo:RO_0002134 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002150 bfo:IAO_0000125 bfo:RO_0002150 X continuous_with Y if and only if X and Y share a fiat boundary. bfo:RO_0002150 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002150 connected to bfo:RO_0002151 bfo:IAO_0000125 bfo:RO_0002151 x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x bfo:RO_0002151 We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom bfo:RO_0002151 proper overlaps bfo:RO_0002156 bfo:IAO_0000125 bfo:RO_0002156 d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. bfo:RO_0002156 ancestral_stucture_of bfo:RO_0002156 evolutionarily_descended_from bfo:RO_0002157 bfo:IAO_0000125 bfo:RO_0002157 inverse of derived by descent from bfo:RO_0002158 bfo:IAO_0000125 bfo:RO_0002158 two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. bfo:RO_0002159 bfo:IAO_0000125 bfo:RO_0002160 lactation SubClassOf 'only in taxon' some 'Mammalia' bfo:RO_0002160 bfo:IAO_0000125 bfo:RO_0002160 x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. bfo:RO_0002160 The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria bfo:RO_0002160 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002160 http://www.ncbi.nlm.nih.gov/pubmed/17921072 bfo:RO_0002160 http://www.ncbi.nlm.nih.gov/pubmed/20973947 bfo:RO_0002161 tooth SubClassOf 'never in taxon' value 'Aves' bfo:RO_0002161 x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. bfo:RO_0002161 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002161 http://www.ncbi.nlm.nih.gov/pubmed/17921072 bfo:RO_0002161 http://www.ncbi.nlm.nih.gov/pubmed/20973947 bfo:RO_0002162 bfo:IAO_0000125 bfo:RO_0002162 x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. bfo:RO_0002162 https://orcid.org/0000-0001-9227-417X bfo:RO_0002162 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002162 http://www.ncbi.nlm.nih.gov/pubmed/17921072 bfo:RO_0002162 http://www.ncbi.nlm.nih.gov/pubmed/20973947 bfo:RO_0002163 bfo:IAO_0000125 bfo:RO_0002163 A is spatially_disjoint_from B if and only if they have no parts in common bfo:RO_0002163 There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. bfo:RO_0002163 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002163 http://www.ncbi.nlm.nih.gov/pubmed/22293552 bfo:RO_0002163 Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy bfo:RO_0002163 BFO_0000051 exactly 0 (BFO_0000050 some ?Y) bfo:RO_0002163 bfo:RO_0001901 bfo:RO_0002163 http://purl.obolibrary.org/obo/ro/subsets#ro-eco bfo:RO_0002163 spatially disjoint from bfo:RO_0002163 https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern bfo:RO_0002170 a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). bfo:RO_0002170 a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b bfo:RO_0002170 http://www.ncbi.nlm.nih.gov/pubmed/22293552 bfo:RO_0002171 A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. bfo:RO_0002171 non-overlapping with bfo:RO_0002171 shares no parts with bfo:RO_0002171 http://www.ncbi.nlm.nih.gov/pubmed/22293552 bfo:RO_0002172 An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. bfo:RO_0002173 S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg] bfo:RO_0002174 S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. bfo:RO_0002174 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002174 http://www.ncbi.nlm.nih.gov/pubmed/22293552 bfo:RO_0002175 S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S bfo:RO_0002175 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002175 http://www.ncbi.nlm.nih.gov/pubmed/22293552 bfo:RO_0002176 The M8 connects Glasgow and Edinburgh bfo:RO_0002176 a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). bfo:RO_0002176 c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. bfo:RO_0002176 http://www.ncbi.nlm.nih.gov/pubmed/22293552 bfo:RO_0002177 a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. bfo:RO_0002178 Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. bfo:RO_0002178 Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure bfo:RO_0002178 http://www.ncbi.nlm.nih.gov/pubmed/20064205 bfo:RO_0002179 Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. bfo:RO_0002179 Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure bfo:RO_0002179 http://www.ncbi.nlm.nih.gov/pubmed/20064205 bfo:RO_0002180 bfo:IAO_0000125 bfo:RO_0002180 w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. bfo:RO_0002180 The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. bfo:RO_0002200 bfo:IAO_0000125 bfo:RO_0002200 A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). bfo:RO_0002200 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002201 bfo:IAO_0000125 bfo:RO_0002201 inverse of has phenotype bfo:RO_0002201 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002202 bfo:IAO_0000125 bfo:RO_0002202 x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y bfo:RO_0002202 https://orcid.org/0000-0001-9114-8737 bfo:RO_0002202 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002202 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002202 https://orcid.org/0000-0003-1980-3228 bfo:RO_0002203 bfo:IAO_0000125 bfo:RO_0002203 inverse of develops from bfo:RO_0002203 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002203 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002203 https://orcid.org/0000-0003-1980-3228 bfo:RO_0002204 bfo:IAO_0000125 bfo:RO_0002204 definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x" bfo:RO_0002204 We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g. bfo:RO_0002204 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002205 every HOTAIR lncRNA is the gene product of some HOXC gene bfo:RO_0002205 every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene bfo:RO_0002205 bfo:IAO_0000125 bfo:RO_0002205 x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y bfo:RO_0002205 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002206 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' bfo:RO_0002206 bfo:IAO_0000125 bfo:RO_0002206 x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process bfo:RO_0002206 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002207 bfo:IAO_0000125 bfo:RO_0002207 Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. bfo:RO_0002207 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002207 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002207 FBbt bfo:RO_0002207 has developmental precursor bfo:RO_0002208 A parasite that kills or sterilizes its host bfo:RO_0002209 inverse of parasitoid of bfo:RO_0002210 bfo:IAO_0000125 bfo:RO_0002210 inverse of directly develops from bfo:RO_0002210 developmental precursor of bfo:RO_0002211 p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. bfo:RO_0002211 https://orcid.org/0000-0001-7476-6306 bfo:RO_0002211 https://orcid.org/0000-0002-3837-8864 bfo:RO_0002211 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002211 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002211 GO bfo:RO_0002211 false bfo:RO_0002212 p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. bfo:RO_0002212 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002212 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002213 p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. bfo:RO_0002213 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002213 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002214 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) bfo:RO_0002214 heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') bfo:RO_0002214 bfo:IAO_0000125 bfo:RO_0002214 x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. bfo:RO_0002214 Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) bfo:RO_0002214 TODO: add homeomorphy axiom bfo:RO_0002214 This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. bfo:RO_0002214 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002215 mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) bfo:RO_0002215 osteoclast SubClassOf 'capable of' some 'bone resorption' bfo:RO_0002215 A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. bfo:RO_0002215 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002215 has function realized in bfo:RO_0002215 http://www.ncbi.nlm.nih.gov/pubmed/20123131 bfo:RO_0002215 http://www.ncbi.nlm.nih.gov/pubmed/21208450 bfo:RO_0002216 c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. bfo:RO_0002216 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002216 has function in bfo:RO_0002217 OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role bfo:RO_0002217 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002217 agent in bfo:RO_0002218 OBSOLETE x has participant y if and only if x realizes some active role that inheres in y bfo:RO_0002218 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002218 has agent bfo:RO_0002219 bfo:IAO_0000125 bfo:RO_0002219 x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x bfo:RO_0002219 https://orcid.org/0000-0002-6601-2165 https://github.com/jhpoelen/eol-globi-data/issues/225#issuecomment-218584934 bfo:RO_0002220 A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. bfo:RO_0002220 The epidermis layer of a vertebrate is adjacent to the dermis. bfo:RO_0002220 The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. bfo:RO_0002220 The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. bfo:RO_0002220 bfo:IAO_0000125 bfo:RO_0002220 x adjacent to y if and only if x and y share a boundary. bfo:RO_0002220 This relation acts as a join point with BSPO bfo:RO_0002220 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002221 bfo:IAO_0000125 bfo:RO_0002221 inverse of surrounded by bfo:RO_0002221 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002222 bfo:IAO_0000125 bfo:RO_0002222 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002222 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra bfo:RO_0002223 bfo:IAO_0000125 bfo:RO_0002223 inverse of starts with bfo:RO_0002223 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002223 Chris Mungall bfo:RO_0002223 Allen bfo:RO_0002224 Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor bfo:RO_0002224 bfo:IAO_0000125 bfo:RO_0002224 x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. bfo:RO_0002224 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002224 Chris Mungall bfo:RO_0002224 started by bfo:RO_0002225 bfo:IAO_0000125 bfo:RO_0002225 x develops from part of y if and only if there exists some z such that x develops from z and z is part of y bfo:RO_0002225 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002226 bfo:IAO_0000125 bfo:RO_0002226 x develops_in y if x is located in y whilst x is developing bfo:RO_0002226 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002226 EHDAA2 bfo:RO_0002226 Jonathan Bard, EHDAA2 bfo:RO_0002227 A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. bfo:RO_0002228 A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. bfo:RO_0002229 bfo:IAO_0000125 bfo:RO_0002229 inverse of ends with bfo:RO_0002229 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002229 Chris Mungall bfo:RO_0002230 bfo:IAO_0000125 bfo:RO_0002230 x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. bfo:RO_0002230 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002230 Chris Mungall bfo:RO_0002230 finished by bfo:RO_0002231 bfo:IAO_0000125 bfo:RO_0002231 x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y bfo:RO_0002231 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002231 starts with process that occurs in bfo:RO_0002232 bfo:IAO_0000125 bfo:RO_0002232 x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y bfo:RO_0002232 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002232 ends with process that occurs in bfo:RO_0002233 bfo:IAO_0000125 bfo:RO_0002233 p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. bfo:RO_0002233 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002233 consumes bfo:RO_0002234 bfo:IAO_0000125 bfo:RO_0002234 p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. bfo:RO_0002234 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002234 produces bfo:RO_0002235 A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) bfo:RO_0002236 A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) bfo:RO_0002237 A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well. bfo:RO_0002238 X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. bfo:RO_0002240 A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event. bfo:RO_0002240 ExO:0000001 bfo:RO_0002241 A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event. bfo:RO_0002241 ExO:0000000 bfo:RO_0002242 A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor bfo:RO_0002242 ExO:0000055 bfo:RO_0002243 A broad relationship between an exposure event or process and the course takes from the source to the target. bfo:RO_0002243 http://purl.obolibrary.org/obo/ExO_0000004 bfo:RO_0002244 Any relationship between an exposure event or process and any other entity. bfo:RO_0002245 g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background. bfo:RO_0002246 g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background. bfo:RO_0002248 Any portion of roundup 'has active ingredient' some glyphosate bfo:RO_0002248 A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance. bfo:RO_0002248 has active substance bfo:RO_0002248 has active pharmaceutical ingredient bfo:RO_0002249 inverse of has active ingredient bfo:RO_0002252 In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1. bfo:RO_0002252 b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. bfo:RO_0002253 inverse of connecting branch of bfo:RO_0002254 Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] bfo:RO_0002254 bfo:IAO_0000125 bfo:RO_0002254 x has developmental contribution from y iff x has some part z such that z develops from y bfo:RO_0002254 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002255 bfo:IAO_0000125 bfo:RO_0002255 inverse of has developmental contribution from bfo:RO_0002255 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002256 bfo:IAO_0000125 bfo:RO_0002256 t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T bfo:RO_0002256 https://orcid.org/0000-0001-9114-8737 bfo:RO_0002256 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002256 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002256 induced by bfo:RO_0002256 http://www.ncbi.nlm.nih.gov/pubmed/20064205 bfo:RO_0002256 Developmental Biology, Gilbert, 8th edition, figure 6.5(F) bfo:RO_0002256 GO:0001759 bfo:RO_0002257 bfo:IAO_0000125 bfo:RO_0002257 Inverse of developmentally induced by bfo:RO_0002257 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002258 bfo:IAO_0000125 bfo:RO_0002258 Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p bfo:RO_0002258 false bfo:RO_0002258 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002260 c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) bfo:RO_0002261 c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) bfo:RO_0002262 c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) bfo:RO_0002263 A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. bfo:RO_0002263 c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. bfo:RO_0002264 A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. bfo:RO_0002264 c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. bfo:RO_0002264 affects bfo:RO_0002285 bfo:IAO_0000125 bfo:RO_0002285 x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else bfo:RO_0002285 This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage bfo:RO_0002285 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002285 replaces bfo:RO_0002286 bfo:IAO_0000125 bfo:RO_0002286 Inverse of developmentally preceded by bfo:RO_0002286 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002287 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue bfo:RO_0002287 bfo:IAO_0000125 bfo:RO_0002287 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002291 bfo:IAO_0000125 bfo:RO_0002291 x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x bfo:RO_0002291 Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part. bfo:RO_0002291 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002292 bfo:IAO_0000125 bfo:RO_0002292 y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. bfo:RO_0002292 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002293 bfo:IAO_0000125 bfo:RO_0002293 inverse of ubiquiotously expressed in bfo:RO_0002293 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002295 bfo:IAO_0000125 bfo:RO_0002295 p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). bfo:RO_0002295 This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. bfo:RO_0002295 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002296 every flower development (GO:0009908) results in development of some flower (PO:0009046) bfo:RO_0002296 bfo:IAO_0000125 bfo:RO_0002296 p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. bfo:RO_0002296 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002296 http://www.geneontology.org/GO.doc.development.shtml bfo:RO_0002297 an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. bfo:RO_0002297 every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) bfo:RO_0002297 bfo:IAO_0000125 bfo:RO_0002297 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002297 GOC:mtg_berkeley_2013 bfo:RO_0002298 an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. bfo:RO_0002298 tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) bfo:RO_0002298 bfo:IAO_0000125 bfo:RO_0002298 The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. bfo:RO_0002298 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002298 GOC:mtg_berkeley_2013 bfo:RO_0002299 an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bfo:RO_0002299 bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) bfo:RO_0002299 bfo:IAO_0000125 bfo:RO_0002299 The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. bfo:RO_0002299 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002299 GOC:mtg_berkeley_2013 bfo:RO_0002300 foramen ovale closure SubClassOf results in disappearance of foramen ovale bfo:RO_0002300 bfo:IAO_0000125 bfo:RO_0002300 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002301 every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) bfo:RO_0002301 bfo:IAO_0000125 bfo:RO_0002301 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002302 Inverse of 'is substance that treats' bfo:RO_0002303 Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview bfo:RO_0002303 bfo:IAO_0000428 bfo:RO_0002303 x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. bfo:RO_0002303 https://orcid.org/0000-0002-4366-3088 bfo:RO_0002303 adapted for living in bfo:RO_0002304 p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. bfo:RO_0002305 p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. bfo:RO_0002309 A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. bfo:RO_0002310 An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human, bfo:RO_0002310 An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes. bfo:RO_0002310 OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. bfo:RO_0002310 This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions. bfo:RO_0002312 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002313 Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. bfo:RO_0002313 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002313 regulates localization of bfo:RO_0002314 q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. bfo:RO_0002314 Because part_of is transitive, inheres in is a sub-relation of characteristic of part of bfo:RO_0002314 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002314 inheres in part of bfo:RO_0002314 http://www.ncbi.nlm.nih.gov/pubmed/20064205 bfo:RO_0002314 characteristic of part of bfo:RO_0002314 http://purl.obolibrary.org/obo/ro/docs/reflexivity/ bfo:RO_0002315 an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. bfo:RO_0002315 The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity bfo:RO_0002315 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002315 GOC:mtg_berkeley_2013 bfo:RO_0002320 A relationship that holds via some environmental process bfo:RO_0002320 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002321 A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) bfo:RO_0002321 Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 bfo:RO_0002321 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002322 An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. bfo:RO_0002322 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002322 adapted for bfo:RO_0002323 A mereological relationship or a topological relationship bfo:RO_0002323 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002323 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships bfo:RO_0002323 bfo:RO_0001901 bfo:RO_0002323 mereotopologically related to bfo:RO_0002324 A relationship that holds between entities participating in some developmental process (GO:0032502) bfo:RO_0002324 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002325 Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) bfo:RO_0002325 a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. bfo:RO_0002325 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002326 ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. bfo:RO_0002326 Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. bfo:RO_0002326 eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex bfo:RO_0002326 We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. bfo:RO_0002326 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002327 a particular instances of akt-2 enables some instance of protein kinase activity bfo:RO_0002327 c enables p iff c is capable of p and c acts to execute p. bfo:RO_0002327 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002327 catalyzes bfo:RO_0002327 executes bfo:RO_0002327 has bfo:RO_0002327 is catalyzing bfo:RO_0002327 is executing bfo:RO_0002328 A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. bfo:RO_0002328 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002329 this relation holds between c and p when c is part of some c', and c' is capable of p. bfo:RO_0002329 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002329 false bfo:RO_0002330 holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. bfo:RO_0002330 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002331 c involved_in p if and only if c enables some process p', and p' is part of p bfo:RO_0002331 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002331 actively involved in bfo:RO_0002331 enables part of bfo:RO_0002332 every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid bfo:RO_0002332 p regulates levels of c if p regulates some amount (PATO:0000070) of c bfo:RO_0002332 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002332 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002333 inverse of enables bfo:RO_0002333 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002334 inverse of regulates bfo:RO_0002334 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002335 inverse of negatively regulates bfo:RO_0002335 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002336 inverse of positively regulates bfo:RO_0002336 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002337 A relationship that holds via some process of localization bfo:RO_0002337 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002338 This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. bfo:RO_0002338 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002339 This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. bfo:RO_0002339 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002340 Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. bfo:RO_0002340 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002341 Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l bfo:RO_0002341 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002342 Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. bfo:RO_0002342 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002343 'pollen tube growth' results_in growth_of some 'pollen tube' bfo:RO_0002343 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002344 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) bfo:RO_0002344 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002345 Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. bfo:RO_0002345 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002348 an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. bfo:RO_0002348 p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. bfo:RO_0002348 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002349 p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. bfo:RO_0002349 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002350 An organism that is a member of a population of organisms bfo:RO_0002350 is member of is a mereological relation between a item and a collection. bfo:RO_0002350 is member of bfo:RO_0002350 member part of bfo:RO_0002350 SIO bfo:RO_0002351 has member is a mereological relation between a collection and an item. bfo:RO_0002351 SIO bfo:RO_0002352 inverse of has input bfo:RO_0002352 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002353 inverse of has output bfo:RO_0002353 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002354 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002355 A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. bfo:RO_0002355 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002356 The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. bfo:RO_0002356 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002357 p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. bfo:RO_0002357 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002360 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002371 a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a bfo:RO_0002371 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002372 m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. bfo:RO_0002372 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002372 Wikipedia:Insertion_(anatomy) bfo:RO_0002373 m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. bfo:RO_0002373 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002373 Wikipedia:Insertion_(anatomy) bfo:RO_0002374 false bfo:RO_0002374 bfo:IAO_0000428 bfo:RO_0002374 x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat bfo:RO_0002374 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002374 http://www.ncbi.nlm.nih.gov/pubmed/22293552 bfo:RO_0002374 has fused element bfo:RO_0002375 bfo:IAO_0000428 bfo:RO_0002375 A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. bfo:RO_0002375 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002376 Deschutes River tributary_of Columbia River bfo:RO_0002376 inferior epigastric vein tributary_of external iliac vein bfo:RO_0002376 bfo:IAO_0000428 bfo:RO_0002376 x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. bfo:RO_0002376 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002376 drains into bfo:RO_0002376 drains to bfo:RO_0002376 tributary channel of bfo:RO_0002376 http://en.wikipedia.org/wiki/Tributary bfo:RO_0002376 http://www.medindia.net/glossary/venous_tributary.htm bfo:RO_0002377 Deschutes River distributary_of Little Lava Lake bfo:RO_0002377 bfo:IAO_0000428 bfo:RO_0002377 x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x bfo:RO_0002377 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002377 branch of bfo:RO_0002377 distributary channel of bfo:RO_0002377 http://en.wikipedia.org/wiki/Distributary bfo:RO_0002378 bfo:IAO_0000428 bfo:RO_0002378 x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. bfo:RO_0002378 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002378 anastomoses with bfo:RO_0002379 A lump of clay and a statue bfo:RO_0002379 x spatially_coextensive_with y if and inly if x and y have the same location bfo:RO_0002379 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002380 In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S bfo:RO_0002380 x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y bfo:RO_0002380 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002381 In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. bfo:RO_0002381 bfo:IAO_0000428 bfo:RO_0002381 x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. bfo:RO_0002381 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002382 bfo:IAO_0000428 bfo:RO_0002382 x proper_distributary_of y iff x distributary_of y and x does not flow back into y bfo:RO_0002382 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002383 bfo:IAO_0000428 bfo:RO_0002383 x proper_tributary_of y iff x tributary_of y and x does not originate from y bfo:RO_0002383 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002384 bfo:IAO_0000428 bfo:RO_0002384 x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). bfo:RO_0002384 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002385 bfo:IAO_0000428 bfo:RO_0002385 x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y bfo:RO_0002385 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002386 bfo:IAO_0000428 bfo:RO_0002386 x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y bfo:RO_0002386 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002387 bfo:IAO_0000428 bfo:RO_0002387 x has the potential to develop into y iff x develops into y or if x is capable of developing into y bfo:RO_0002387 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002388 bfo:IAO_0000428 bfo:RO_0002388 x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y bfo:RO_0002388 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002400 'protein catabolic process' SubClassOf has_direct_input some protein bfo:RO_0002400 bfo:IAO_0000428 bfo:RO_0002400 p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. bfo:RO_0002400 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002400 directly consumes bfo:RO_0002401 bfo:IAO_0000428 bfo:RO_0002401 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002402 translation SubClassOf has_direct_output some protein bfo:RO_0002402 bfo:IAO_0000428 bfo:RO_0002402 p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. bfo:RO_0002402 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002402 directly produces bfo:RO_0002403 bfo:IAO_0000428 bfo:RO_0002403 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002404 bfo:IAO_0000428 bfo:RO_0002404 inverse of upstream of bfo:RO_0002404 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002405 bfo:IAO_0000428 bfo:RO_0002405 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002407 p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. bfo:RO_0002407 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002407 indirectly activates bfo:RO_0002409 p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. bfo:RO_0002409 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002409 indirectly inhibits https://en.wikipedia.org/wiki/Causality bfo:RO_0002410 relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. bfo:RO_0002410 This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. bfo:RO_0002410 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002411 p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. bfo:RO_0002411 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002412 p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. bfo:RO_0002412 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002413 p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. bfo:RO_0002413 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002413 directly provides input for bfo:RO_0002413 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002414 bfo:IAO_0000428 bfo:RO_0002414 transitive form of directly_provides_input_for bfo:RO_0002414 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002416 An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. bfo:RO_0002416 logical macro assertion bfo:RO_0002416 http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/ bfo:RO_0002418 p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. bfo:RO_0002418 We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 bfo:RO_0002418 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002418 influences (processual) bfo:RO_0002418 affects bfo:RO_0002419 An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N. bfo:RO_0002420 A logical macro assertion whose domain is an IRI for a class bfo:RO_0002420 The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL bfo:RO_0002421 A logical macro assertion whose domain is an IRI for a property bfo:RO_0002421 logical macro assertion on a property bfo:RO_0002422 Used to annotate object properties to describe a logical meta-property or characteristic of the object property. bfo:RO_0002422 logical macro assertion on an object property bfo:RO_0002424 false bfo:RO_0002424 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002425 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002426 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002427 inverse of causally upstream of or within bfo:RO_0002427 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002427 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002428 c involved in regulation of p if c is involved in some p' and p' regulates some p bfo:RO_0002428 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002429 c involved in regulation of p if c is involved in some p' and p' positively regulates some p bfo:RO_0002429 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002430 c involved in regulation of p if c is involved in some p' and p' negatively regulates some p bfo:RO_0002430 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002431 c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p bfo:RO_0002431 OWL does not allow defining object properties via a Union bfo:RO_0002431 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002431 involved in or reguates bfo:RO_0002432 A protein that enables activity in a cytosol. https://orcid.org/0000-0002-6601-2165 https://orcid.org/0000-0002-7073-9172 bfo:RO_0002432 c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. bfo:RO_0002432 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002432 executes activity in bfo:RO_0002432 enables activity in bfo:RO_0002433 p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. bfo:RO_0002433 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002434 A relationship that holds between two entities in which the processes executed by the two entities are causally connected. bfo:RO_0002434 This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. bfo:RO_0002434 Considering relabeling as 'pairwise interacts with' bfo:RO_0002434 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002434 in pairwise interaction with bfo:RO_0002435 An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) bfo:RO_0002435 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002436 An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. bfo:RO_0002436 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002436 binds bfo:RO_0002436 molecularly binds with bfo:RO_0002437 An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. bfo:RO_0002437 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002437 interacts with on organism level bfo:RO_0002438 An interaction relationship in which the partners are related via a feeding relationship. bfo:RO_0002438 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002439 A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] bfo:RO_0002439 Baleen whale preys on krill bfo:RO_0002439 An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members bfo:RO_0002439 https://orcid.org/0000-0001-7134-3324 bfo:RO_0002439 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002439 https://orcid.org/0000-0003-3138-4118 bfo:RO_0002439 is subject of predation interaction with bfo:RO_0002439 preys upon bfo:RO_0002440 A biotic interaction in which the two organisms live together in more or less intimate association. bfo:RO_0002440 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002440 http://www.ncbi.nlm.nih.gov/pubmed/19278549 bfo:RO_0002441 An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). bfo:RO_0002441 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002441 http://www.ncbi.nlm.nih.gov/pubmed/19278549 bfo:RO_0002442 An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). bfo:RO_0002442 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002442 http://www.ncbi.nlm.nih.gov/pubmed/19278549 bfo:RO_0002443 An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). bfo:RO_0002443 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002443 http://www.ncbi.nlm.nih.gov/pubmed/19278549 bfo:RO_0002444 Pediculus humanus capitis parasite of human bfo:RO_0002444 A parasite-host relationship where an organism benefits at the expense of another. bfo:RO_0002444 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002444 parasitizes bfo:RO_0002444 direct parasite of bfo:RO_0002445 Inverse of parasite of bfo:RO_0002445 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002445 has parasite bfo:RO_0002445 parasitised by bfo:RO_0002445 directly parasitized by bfo:RO_0002446 Porifiera attaches to substrate bfo:RO_0002446 A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. bfo:RO_0002446 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002446 semibiotically interacts with bfo:RO_0002447 Axiomatization to GO to be added later bfo:RO_0002447 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002447 An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. bfo:RO_0002448 The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. bfo:RO_0002448 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002448 https://orcid.org/0000-0003-4639-4431 bfo:RO_0002448 molecularly controls bfo:RO_0002449 The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. bfo:RO_0002449 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002449 https://orcid.org/0000-0003-4639-4431 bfo:RO_0002449 directly inhibits bfo:RO_0002449 molecularly decreases activity of bfo:RO_0002450 The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. bfo:RO_0002450 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002450 https://orcid.org/0000-0003-4639-4431 bfo:RO_0002450 directly activates bfo:RO_0002450 molecularly increases activity of bfo:RO_0002451 all dengue disease transmitted by some mosquito bfo:RO_0002451 A relationship that holds between a disease and organism bfo:RO_0002451 Add domain and range constraints bfo:RO_0002451 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002452 A relation that holds between a disease or an organism and a phenotype bfo:RO_0002452 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002453 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002454 X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y bfo:RO_0002454 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002455 Bees pollinate Flowers bfo:RO_0002455 This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. bfo:RO_0002455 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002455 is subject of pollination interaction with bfo:RO_0002456 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002456 has polinator bfo:RO_0002456 is target of pollination interaction with bfo:RO_0002457 Inverse of provides nutrients for bfo:RO_0002457 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002458 inverse of preys on bfo:RO_0002458 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002458 has predator bfo:RO_0002458 is target of predation interaction with bfo:RO_0002459 Anopheles is a vector for Plasmodium bfo:RO_0002459 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002459 a is a vector for b if a carries and transmits an infectious pathogen b into another living organism bfo:RO_0002460 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002461 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002462 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002463 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002464 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002465 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002466 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002467 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002468 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002469 A biotic interaction where a material entity provides nutrition for an organism. bfo:RO_0002469 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002470 A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. bfo:RO_0002470 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002470 is subject of eating interaction with bfo:RO_0002471 Inverse of eats bfo:RO_0002471 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002471 eaten by bfo:RO_0002471 is target of eating interaction with bfo:RO_0002472 A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and the a supports either the existence of b, or the truth value of b. bfo:RO_0002472 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002473 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' bfo:RO_0002473 x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. bfo:RO_0002473 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002473 http://www.ncbi.nlm.nih.gov/pubmed/22293552 bfo:RO_0002474 An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one. bfo:RO_0002475 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton' bfo:RO_0002475 A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. bfo:RO_0002475 shares no connection with bfo:RO_0002476 ABal nucleus child nucleus of ABa nucleus (in C elegans) bfo:RO_0002476 c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d bfo:RO_0002476 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002477 A child nucleus relationship in which the cells are part of a hermaphroditic organism bfo:RO_0002477 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002478 A child nucleus relationship in which the cells are part of a male organism bfo:RO_0002478 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002479 p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. bfo:RO_0002479 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002480 An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y bfo:RO_0002480 Axiomatization to GO to be added later bfo:RO_0002480 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002481 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002482 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002484 Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of) bfo:RO_0002485 See notes for inverse relation bfo:RO_0002485 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002486 This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. bfo:RO_0002486 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002487 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002488 x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). bfo:RO_0002488 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002489 x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). bfo:RO_0002489 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002490 x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) bfo:RO_0002490 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002491 x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) bfo:RO_0002491 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002491 exists during bfo:RO_0002492 x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). bfo:RO_0002492 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002493 x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). bfo:RO_0002493 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002494 x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships bfo:RO_0002494 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002495 x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t bfo:RO_0002495 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002496 x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). bfo:RO_0002496 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002497 x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. bfo:RO_0002497 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002500 A relationship between a material entity and a process where the material entity has some causal role that influences the process bfo:RO_0002500 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002501 p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. bfo:RO_0002501 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002501 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002502 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002502 depends on bfo:RO_0002502 bfo:BFO_0000169 bfo:RO_0002503 q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 bfo:RO_0002503 This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. bfo:RO_0002503 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002503 http://www.ncbi.nlm.nih.gov/pubmed/20064205 bfo:RO_0002504 brain always_present_in_taxon 'Vertebrata' bfo:RO_0002504 forelimb always_present_in_taxon Euarchontoglires bfo:RO_0002504 S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S bfo:RO_0002504 This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. bfo:RO_0002504 never lost in bfo:RO_0002505 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate bfo:RO_0002505 p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c bfo:RO_0002505 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002505 has intermediate product bfo:RO_0002506 The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch bfo:RO_0002506 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002506 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002507 A coral reef environment is determined by a particular coral reef bfo:RO_0002507 s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. bfo:RO_0002507 The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future bfo:RO_0002507 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002507 http://www.ncbi.nlm.nih.gov/pubmed/24330602 bfo:RO_0002508 inverse of determined by bfo:RO_0002508 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002509 s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. bfo:RO_0002509 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002510 x is transcribed from y if and only if x is synthesized from template y bfo:RO_0002510 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002510 http://www.ncbi.nlm.nih.gov/pubmed/20226267 bfo:RO_0002511 inverse of transcribed from bfo:RO_0002511 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002511 http://www.ncbi.nlm.nih.gov/pubmed/20226267 bfo:RO_0002512 x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y bfo:RO_0002512 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002512 http://www.ncbi.nlm.nih.gov/pubmed/20226267 bfo:RO_0002513 inverse of ribosomal translation of bfo:RO_0002513 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002513 http://www.ncbi.nlm.nih.gov/pubmed/20226267 bfo:RO_0002514 A relation that holds between two entities that have the property of being sequences or having sequences. bfo:RO_0002514 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002514 http://www.ncbi.nlm.nih.gov/pubmed/20226267 bfo:RO_0002515 Every UTR is adjacent to a CDS of the same transcript bfo:RO_0002515 Two consecutive DNA residues are sequentially adjacent bfo:RO_0002515 Two exons on a processed transcript that were previously connected by an intron are adjacent bfo:RO_0002515 x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y bfo:RO_0002515 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002515 http://www.ncbi.nlm.nih.gov/pubmed/20226267 bfo:RO_0002516 Every CDS has as a start sequence the start codon for that transcript bfo:RO_0002516 x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence bfo:RO_0002516 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002516 started by bfo:RO_0002516 http://www.ncbi.nlm.nih.gov/pubmed/20226267 bfo:RO_0002517 inverse of has start sequence bfo:RO_0002517 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002517 starts bfo:RO_0002517 http://www.ncbi.nlm.nih.gov/pubmed/20226267 bfo:RO_0002518 Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) bfo:RO_0002518 x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence bfo:RO_0002518 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002518 ended by bfo:RO_0002518 http://www.ncbi.nlm.nih.gov/pubmed/20226267 bfo:RO_0002519 inverse of has end sequence bfo:RO_0002519 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002519 ends bfo:RO_0002519 http://www.ncbi.nlm.nih.gov/pubmed/20226267 bfo:RO_0002520 x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. bfo:RO_0002520 In the SO paper, this was defined as an instance-type relation bfo:RO_0002520 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002520 http://www.ncbi.nlm.nih.gov/pubmed/20226267 bfo:RO_0002521 Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. bfo:RO_0002521 x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering bfo:RO_0002521 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002522 The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) bfo:RO_0002522 x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y bfo:RO_0002522 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002523 inverse of bounds sequence of bfo:RO_0002523 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002524 x has subsequence y iff all of the sequence parts of y are sequence parts of x bfo:RO_0002524 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002524 contains bfo:RO_0002524 http://www.ncbi.nlm.nih.gov/pubmed/20226267 bfo:RO_0002525 inverse of has subsequence bfo:RO_0002525 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002525 contained by bfo:RO_0002526 x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. bfo:RO_0002526 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002527 x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. bfo:RO_0002527 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002527 disconnected from bfo:RO_0002528 inverse of downstream of sequence of bfo:RO_0002528 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002529 x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. bfo:RO_0002529 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002530 A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript bfo:RO_0002530 x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y bfo:RO_0002530 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002531 A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript bfo:RO_0002531 inverse of immediately downstream of bfo:RO_0002531 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002532 Any entity that is ordered in discrete units along a linear axis. bfo:RO_0002532 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002533 Any individual unit of a collection of like units arranged in a linear order bfo:RO_0002533 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002534 Any entity that can be divided into parts such that each part is an atomical unit of a sequence bfo:RO_0002534 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002539 Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property. bfo:RO_0002540 Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property. bfo:RO_0002541 Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1. bfo:RO_0002542 Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2 bfo:RO_0002543 Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1. bfo:RO_0002544 Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2 bfo:RO_0002545 Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in. bfo:RO_0002546 A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process bfo:RO_0002547 Count of number of days intervening between the start of the stage and the time of coitum. bfo:RO_0002548 Count of number of days intervening between the end of the stage and the time of coitum. bfo:RO_0002551 Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' bfo:RO_0002551 A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. bfo:RO_0002551 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002551 has supporting framework bfo:RO_0002552 p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. bfo:RO_0002552 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002553 x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y bfo:RO_0002553 Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism bfo:RO_0002553 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002553 http://eol.org/schema/terms/hyperparasitoidOf bfo:RO_0002553 https://en.wikipedia.org/wiki/Hyperparasite bfo:RO_0002553 hyperparasitoid of bfo:RO_0002553 epiparasite of bfo:RO_0002554 inverse of hyperparasite of bfo:RO_0002554 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002554 has epiparasite bfo:RO_0002554 has hyperparasite bfo:RO_0002554 hyperparasitoidized by bfo:RO_0002555 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002555 http://en.wikipedia.org/wiki/Allelopathy bfo:RO_0002556 Inverse of has pathogen bfo:RO_0002556 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002557 A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member bfo:RO_0002557 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002558 inverse of is evidence for bfo:RO_0002558 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002558 http://www.ncbi.nlm.nih.gov/pubmed/25052702 bfo:RO_0002559 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002559 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002560 If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p bfo:RO_0002561 If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p bfo:RO_0002562 R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process bfo:RO_0002563 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002564 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002565 Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c bfo:RO_0002565 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002566 The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). bfo:RO_0002566 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002566 https://orcid.org/0000-0003-4639-4431 bfo:RO_0002566 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002567 A relation that holds between elements of a musculoskeletal system or its analogs. bfo:RO_0002567 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002568 m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. bfo:RO_0002568 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002568 Wikipedia:Antagonist_(muscle) bfo:RO_0002569 inverse of branching part of bfo:RO_0002569 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002570 x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. bfo:RO_0002570 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002570 UBERON:cjm bfo:RO_0002571 x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. bfo:RO_0002571 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002571 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002572 s is luminal space of x iff s is lumen_of x and s is an immaterial entity bfo:RO_0002572 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002573 A relation that holds between an attribute or a qualifier and another attribute. bfo:RO_0002573 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002573 http://www.ncbi.nlm.nih.gov/pubmed/20064205 bfo:RO_0002574 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002575 relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y bfo:RO_0002575 The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P" bfo:RO_0002576 inverse of has skeleton bfo:RO_0002576 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002577 A material entity consisting of multiple components that are causally integrated. bfo:RO_0002577 May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 bfo:RO_0002577 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002577 http://www.jbiomedsem.com/content/4/1/43 bfo:RO_0002577 SCO cretor comment: RO defines the class “system” as a subclass of the “material entity” class. Nevertheless, a system is a fiat object, e.g. an object that is “delimited” according to the perspective of the stakeholder (Landgrebe and Smith 2022, p. 117,118). System delimitation determines the boundaries of the systems, but the stakeholder, however, does not create the system through this delimitation process (Landgrebe and Smith 2022, p. 117,118). As this class is extensively reused among ontologies within the OBO-Foundry context, we maintain its current hierarchical position. However, we recommend a revision of this class. There are two possible strategies to consider: 1) to reclassify this class as a subclass of “fiat object part” one or 2) to create a dedicated “fiat object” class that will be a subclass of “material entity” and the superclass for the “system” one (and related subclasses). We leave the discussion open with the intention of engaging with subject matter experts, planning that these modifications may be included in the next release of this resource. As the environment of a system corresponds to what has not been delimited as part of such a system, these considerations correspondingly also apply to the class “system environment” (at least regarding the system-system environment boundaries). bfo:RO_0002577 system bfo:RO_0002577 SCO creator cited reference: Landgrebe, Jobst, and Barry Smith. 2022. Why Machines Will Never Rule the World: Artificial Intelligence without Fear. Taylor & Francis. 10.4324/9781003310105 bfo:RO_0002578 p directly regulates q iff p is immediately causally upstream of q and p regulates q. bfo:RO_0002578 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002578 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002579 relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y bfo:RO_0002581 If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL bfo:RO_0002582 If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. bfo:RO_0002583 holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y). bfo:RO_0002584 gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' bfo:RO_0002584 s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p bfo:RO_0002584 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002585 p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. bfo:RO_0002586 p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p bfo:RO_0002589 p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released. bfo:RO_0002592 p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c bfo:RO_0002593 holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y). bfo:RO_0002594 An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis. bfo:RO_0002595 A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. bfo:RO_0002595 Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. bfo:RO_0002595 https://orcid.org/0000-0002-6601-2165 bfo:RO_0002595 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002596 pyrethroid -> growth bfo:RO_0002596 Holds between c and p if and only if c is capable of some activity a, and a regulates p. bfo:RO_0002596 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002597 Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. bfo:RO_0002597 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002598 renin -> arteriolar smooth muscle contraction bfo:RO_0002598 Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. bfo:RO_0002598 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002599 pazopanib -> pathological angiogenesis bfo:RO_0002599 Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p. Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship bfo:RO_0002599 treats bfo:RO_0002599 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002600 benzene -> cancer [CHEBI] bfo:RO_0002600 Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p. bfo:RO_0002600 causes disease bfo:RO_0002600 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002601 A shortcut relationship that holds between two entities based on their identity criteria bfo:RO_0002602 A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds. bfo:RO_0002603 x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y bfo:RO_0002604 'anterior end of organism' is-opposite-of 'posterior end of organism' bfo:RO_0002604 'increase in temperature' is-opposite-of 'decrease in temperature' bfo:RO_0002604 x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). bfo:RO_0002605 x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). bfo:RO_0002606 c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d. bfo:RO_0002606 treats bfo:RO_0002606 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002607 c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. bfo:RO_0002607 May be ceded to OBI bfo:RO_0002608 Inverse of 'causal agent in process' bfo:RO_0002608 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002609 A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. bfo:RO_0002610 A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. bfo:RO_0002612 A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom bfo:RO_0002613 A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom bfo:RO_0002614 An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support. bfo:RO_0002614 A relationship between a piece of evidence and an entity that plays a role in supporting that evidence. bfo:RO_0002615 Inverse of is-model-of bfo:RO_0002617 In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context. bfo:RO_0002617 this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent. bfo:RO_0002626 https://github.com/jhpoelen/eol-globi-data/issues/143 bfo:RO_0002629 p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. bfo:RO_0002629 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002630 p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. bfo:RO_0002630 http://purl.obolibrary.org/obo/ro/docs/causal-relations bfo:RO_0002632 A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host bfo:RO_0002632 https://en.wikipedia.org/wiki/Parasitism#Types bfo:RO_0002633 inverse of ectoparasite of bfo:RO_0002634 https://en.wikipedia.org/wiki/Parasitism#Types bfo:RO_0002634 A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system bfo:RO_0002634 lives inside of bfo:RO_0002636 A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite bfo:RO_0002637 inverse of mesoparasite of bfo:RO_0002638 A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells. bfo:RO_0002638 https://en.wikipedia.org/wiki/Parasitism#Types bfo:RO_0002639 inverse of intercellular endoparasite of bfo:RO_0002640 A sub-relation of endoparasite-of in which the parasite inhabits host cells. bfo:RO_0002640 https://en.wikipedia.org/wiki/Parasitism#Types bfo:RO_0002641 inverse of intracellular endoparasite of bfo:RO_0002801 Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. bfo:RO_0002801 https://en.wikipedia.org/wiki/Communal_roosting bfo:RO_0002802 An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. bfo:RO_0002802 A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. bfo:RO_0002802 https://doi.org/10.3390/v13071356 bfo:RO_0002803 An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. bfo:RO_0002803 inverse of reservoir host of bfo:RO_0003000 bfo:IAO_0000125 bfo:RO_0003000 a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. bfo:RO_0003000 https://orcid.org/0000-0001-9114-8737 bfo:RO_0003001 bfo:IAO_0000125 bfo:RO_0003001 a produced_by b iff some process that occurs_in b has_output a. bfo:RO_0003001 https://orcid.org/0000-0001-9114-8737 bfo:RO_0003002 Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. bfo:RO_0003002 https://orcid.org/0000-0003-4639-4431 bfo:RO_0003003 Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. bfo:RO_0003003 https://orcid.org/0000-0003-4639-4431 bfo:RO_0003301 A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. bfo:RO_0003301 https://orcid.org/0000-0002-1048-5019 bfo:RO_0003301 is used to study bfo:RO_0003302 The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. bfo:RO_0003302 A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition. bfo:RO_0003302 Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. bfo:RO_0003303 A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition. bfo:RO_0003304 A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition. bfo:RO_0003305 A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual. bfo:RO_0003305 contributes to expressivity of condition bfo:RO_0003306 A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population. bfo:RO_0003306 contributes to penetrance of condition bfo:RO_0003307 A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition. bfo:RO_0003307 is preventative for condition bfo:RO_0003308 A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. bfo:RO_0003309 A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition. bfo:RO_0003310 A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity. bfo:RO_0003311 A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity. bfo:RO_0004007 p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. https://orcid.org/0000-0002-6601-2165 GOC:dph GOC:kva GOC:pt PMID:27812932 bfo:RO_0004008 p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. https://orcid.org/0000-0002-6601-2165 GOC:dph GOC:kva GOC:pt PMID:27812932 bfo:RO_0004009 p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. bfo:RO_0004011 Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. bfo:RO_0004012 Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. bfo:RO_0004013 Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. bfo:RO_0004014 Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. bfo:RO_0004015 Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. bfo:RO_0004016 Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. bfo:RO_0004020 A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. bfo:RO_0004021 A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. bfo:RO_0004022 A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. bfo:RO_0004024 A relationship between a disease and a process where the disease process disrupts the execution of the process. bfo:RO_0004026 A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. bfo:RO_0004026 TODO: complete range axiom once more of CARO has been mireoted in to this ontology bfo:RO_0004027 A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity bfo:RO_0004028 A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. bfo:RO_0004029 A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. bfo:RO_0004030 A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. bfo:RO_0004031 Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. bfo:RO_0004034 c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive bfo:RO_0004035 c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative bfo:RO_0004036 true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation. bfo:RO_0004048 Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" bfo:RO_0007000 A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity. bfo:RO_0007001 A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes. bfo:RO_0008501 An interaction relationship wherein a plant or algae is living on the outside surface of another plant. bfo:RO_0008501 https://en.wikipedia.org/wiki/Epiphyte bfo:RO_0008502 inverse of epiphyte of bfo:RO_0008503 A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material bfo:RO_0008503 https://en.wikipedia.org/wiki/Kleptoparasitism bfo:RO_0008504 inverse of kleptoparasite of bfo:RO_0008505 An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. bfo:RO_0008506 An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. bfo:RO_0008507 An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. bfo:RO_0008508 inverse of lays eggs on bfo:RO_0008509 Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) bfo:RO_0008509 x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. bfo:RO_0009001 muffin 'has substance added' some 'baking soda' bfo:RO_0009001 bfo:IAO_0000428 bfo:RO_0009001 "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. bfo:RO_0009001 The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. bfo:RO_0009001 https://orcid.org/0000-0002-8844-9165 bfo:RO_0009002 'egg white' 'has substance removed' some 'egg yolk' bfo:RO_0009002 bfo:IAO_0000428 bfo:RO_0009002 "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. bfo:RO_0009002 https://orcid.org/0000-0002-8844-9165 bfo:RO_0009003 sardines 'immersed in' some 'oil and mustard' bfo:RO_0009003 bfo:IAO_0000428 bfo:RO_0009003 "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. bfo:RO_0009003 https://orcid.org/0000-0002-8844-9165 bfo:RO_0009004 sardine has consumer some homo sapiens bfo:RO_0009004 bfo:IAO_0000428 bfo:RO_0009004 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. bfo:RO_0009004 https://orcid.org/0000-0002-8844-9165 bfo:RO_0009005 bread 'has primary substance added' some 'flour' bfo:RO_0009005 bfo:IAO_0000428 bfo:RO_0009005 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance. bfo:RO_0009005 https://orcid.org/0000-0002-8844-9165 bfo:RO_0009006 A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material. bfo:RO_0009006 A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic. bfo:RO_0009007 Inverse of 'assay measures characteristic' bfo:RO_0009501 A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. bfo:RO_0009501 An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) bfo:RO_0009501 Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. bfo:RO_0009501 r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. https://orcid.org/0000-0002-6601-2165 bfo:RO_0009501 triggered by process bfo:RO_0010001 Genetic information generically depend on molecules of DNA. bfo:RO_0010001 The novel *War and Peace* generically depends on this copy of the novel. bfo:RO_0010001 The pattern shared by chess boards generically depends on any chess board. bfo:RO_0010001 The score of a symphony g-depends on a copy of the score. bfo:RO_0010001 This pdf file generically depends on this server. bfo:RO_0010001 A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. bfo:RO_0010001 [072-ISO] bfo:RO_0010001 g-depends on bfo:RO_0010002 Molecules of DNA are carriers of genetic information. bfo:RO_0010002 This copy of *War and Peace* is carrier of the novel written by Tolstoy. bfo:RO_0010002 This hard drive is carrier of these data items. bfo:RO_0010002 *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* bfo:RO_0010002 [072-ISO] bfo:RO_0011002 The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. bfo:RO_0011002 https://orcid.org/0000-0003-4639-4431 bfo:RO_0011003 The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. bfo:RO_0011003 https://orcid.org/0000-0003-4639-4431 bfo:RO_0011004 The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. bfo:RO_0011004 https://orcid.org/0000-0003-4639-4431 bfo:RO_0011007 The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. bfo:RO_0011007 https://orcid.org/0000-0003-4639-4431 bfo:RO_0011008 The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. bfo:RO_0011008 https://orcid.org/0000-0003-4639-4431 bfo:RO_0011009 The entity A has an activity that directly positively regulates the quantity of B. bfo:RO_0011009 https://orcid.org/0000-0003-4639-4431 bfo:RO_0011010 The entity A has an activity that directly negatively regulates the quantity of B. bfo:RO_0011010 https://orcid.org/0000-0003-4639-4431 bfo:RO_0011013 The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. bfo:RO_0011013 https://orcid.org/0000-0003-4639-4431 bfo:RO_0011013 indirectly activates bfo:RO_0011014 AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) bfo:RO_0011014 An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. bfo:RO_0011014 https://orcid.org/0000-0003-4639-4431 bfo:RO_0011015 AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) bfo:RO_0011015 An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. bfo:RO_0011015 https://orcid.org/0000-0003-4639-4431 bfo:RO_0011016 The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. bfo:RO_0011016 https://orcid.org/0000-0003-4639-4431 bfo:RO_0011016 indirectly inhibits bfo:RO_0011021 The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. bfo:RO_0011021 https://orcid.org/0000-0003-4639-4431 bfo:RO_0011022 The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. bfo:RO_0011022 https://orcid.org/0000-0003-4639-4431 bfo:RO_0011023 The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. bfo:RO_0011023 https://orcid.org/0000-0003-4639-4431 bfo:RO_0011024 The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. bfo:RO_0011024 https://orcid.org/0000-0003-4639-4431 bfo:RO_0012000 a relation between a process and a continuant, in which the process is regulated by the small molecule continuant bfo:RO_0012001 a relation between a process and a continuant, in which the process is activated by the small molecule continuant bfo:RO_0012002 a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant bfo:RO_0012003 p acts on population of c iff c' is a collection, has members of type c, and p has participant c bfo:RO_0012004 a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process bfo:RO_0012005 a relation between a continuant and a process, in which the continuant is a small molecule that activates the process bfo:RO_0012006 a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process bfo:RO_0012007 The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. bfo:RO_0012009 p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. bfo:RO_0012010 p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. bfo:RO_0012011 p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. bfo:RO_0012012 p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. bfo:RO_0012013 x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). bfo:RO_0012013 positively regulates in other organism bfo:RO_0012014 x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). bfo:RO_0012014 negatively regulates in other organism bfo:RO_0013001 A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. bfo:RO_0013001 has synaptic input or output in bfo:RO_0013002 A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. bfo:RO_0013003 A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. bfo:RO_0013004 A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). bfo:RO_0013005 A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). bfo:RO_0013006 A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). bfo:RO_0013007 Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. bfo:RO_0013007 has sensory dendrite location bfo:RO_0013007 has sensory terminal in bfo:RO_0013007 has sensory terminal location bfo:RO_0013008 A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. bfo:RO_0013009 A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. bfo:RO_0014001 A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. bfo:RO_0015001 transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data]) bfo:RO_0015001 A relation between a material entity and some data in which the data is taken as exemplifying the material entity. bfo:RO_0015001 C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C. bfo:RO_0015001 https://orcid.org/0000-0002-5260-9315 bfo:RO_0015002 https://orcid.org/0000-0002-5260-9315 bfo:RO_0015003 A relation between a group and another group it is part of but does not fully constitute. bfo:RO_0015003 X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. bfo:RO_0015003 https://orcid.org/0000-0001-7258-9596 bfo:RO_0015004 'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1'). bfo:RO_0015004 transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3. bfo:RO_0015004 A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. bfo:RO_0015004 C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types. bfo:RO_0015004 has marker gene combination bfo:RO_0015004 has marker signature set https://orcid.org/0000-0002-6601-2165 bfo:RO_0015006 q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. https://orcid.org/0000-0002-6601-2165 bfo:RO_0015007 q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. https://orcid.org/0000-0002-6601-2165 bfo:RO_0015008 q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. https://orcid.org/0000-0002-6601-2165 bfo:RO_0015009 q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. https://orcid.org/0000-0002-6601-2165 bfo:RO_0015011 s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. https://orcid.org/0000-0002-6601-2165 bfo:RO_0015012 q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. bfo:RO_0015015 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') PMID:19243617 bfo:RO_0015015 A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. bfo:RO_0015016 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') PMID:19243617 bfo:RO_0015016 A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. bfo:RO_0016002 A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. bfo:RO_0016004 X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. bfo:RO_0016004 ExO:0000083 bfo:RO_0017001 A diagnostic testing device utilizes a specimen. bfo:RO_0017001 X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. bfo:RO_0017001 utilizes bfo:RO_0017003 A relation between entities in which one increases or decreases as the other does the same. bfo:RO_0017003 directly correlated with bfo:RO_0017004 A relation between entities in which one increases as the other decreases. bfo:RO_0017004 inversely correlated with bfo:RO_0017005 anticoagulant-containing test tube contains measured amount 5 ml of blood specimen. bfo:RO_0017005 A relation between a container and measurement datum that specifies the actual amount of material in the container. bfo:RO_0017006 anticoagulant-containing test tube has maximum capacity 10 ml. bfo:RO_0017006 A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume. bfo:RO_0017008 biobank organization owns a specimen bfo:RO_0017008 hospital owns a laboratory facility bfo:RO_0017008 A primitive relation that holds between entities x and y in which y is at x's full disposal. bfo:RO_0017009 freezer is owned by a biobank organization bfo:RO_0017009 Inverse of the owns relation. bfo:RO_0018001 Helper relation for OWL definition of RO:0018002 myristoylates bfo:RO_0018002 A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input bfo:RO_0018003 inverse of myristoylates bfo:RO_0018027 mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) bfo:RO_0018027 a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor bfo:RO_0018028 pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) bfo:RO_0018028 a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level bfo:RO_0018029 tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) bfo:RO_0018029 a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level bfo:RO_0018031 pyruvate anion (CHEBI:15361) is the conjugate base of the neutral pyruvic acid (CHEBI:32816) bfo:RO_0018031 A is a direct conjugate base of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by receiving a particular proton transforms it into B. bfo:RO_0018032 neutral pyruvic acid (CHEBI:32816) is the conjugate acid of the pyruvate anion (CHEBI:15361) bfo:RO_0018032 A is a direct conjugate acid of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing a particular proton transforms it into B. bfo:RO_0018033 (E)-cinnamoyl-CoA(4-) (CHEBI:57252) is a deprotonated form (E)-cinnamoyl-CoA (CHEBI:10956), which involves removing four protons. bfo:RO_0018033 A is a deprotonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by adding some nonzero number of protons transforms it into B. This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations. bfo:RO_0018034 (E)-cinnamoyl-CoA (CHEBI:10956) is a protonated form of (E)-cinnamoyl-CoA(4-) (CHEBI:57252), which involves adding four protons. bfo:RO_0018034 A is a protonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing some nonzero number of protons transforms it into B. This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations. bfo:RO_0018035 phenol (CHEBI:15882) and aniline (CHEBI:17296) are matched molecular pairs because they differ by one chemical transformation i.e., the replacement of aryl primary amine with aryl primary alcohol. https://doi.org/10.1002/ddr.21045 https://doi.org/10.1021/jm200452d https://en.wikipedia.org/wiki/Matched_molecular_pair_analysis bfo:RO_0018035 A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C. bfo:RO_0018035 is MMP with bfo:RO_0018035 is matched molecular pair with bfo:CHEBI_38707 bfo:CHEBI_38709 bfo:RO_0018036 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol. bfo:RO_0018036 Two chemicals are tautomers if they can be readily interconverted. This commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms. bfo:RO_0018036 is desmotrope of bfo:CHEBI_30795 bfo:CHEBI_58957 bfo:RO_0018037 carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795) bfo:RO_0018037 Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization. bfo:CHEBI_50851 bfo:CHEBI_50854 bfo:RO_0018038 hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851) bfo:RO_0018038 Chemical A has functional parent Chemical B if there is chemical transformation through which chemical B can be produced from chemical A. For example, the relationship between a salt and a freebased compound is a "has functional parent" relationship. bfo:CHEBI_48557 bfo:CHEBI_31472 bfo:RO_0018039 dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped. bfo:RO_0018039 Chemicals A and B are enantiomers if they share the same molecular graph except the change of the configuration of substituents around exactly one chiral center. A chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers). bfo:RO_0018039 is optical isomer of bfo:CHEBI_39106 bfo:CHEBI_52083 bfo:RO_0018040 pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates. bfo:RO_0018040 Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B. bfo:RO_0019000 A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. bfo:RO_0019001 A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. bfo:RO_0019002 A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. bfo:RO_0019501 Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. bfo:RO_0020101 brachial artery vessel supplies blood to brachialis muscle bfo:RO_0020101 x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. bfo:RO_0020102 cystic vein vessel drains blood from gallbladder bfo:RO_0020102 x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. bfo:RO_0020103 alveolar capillary directly supplies and drains some alveolus bfo:RO_0020103 x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. bfo:RO_0020202 A relationship between a ratio or proportion and its dividend. bfo:RO_0020202 has dividend bfo:RO_0020203 A relationship between a ratio or proportion and its divisor. bfo:RO_0020203 has divisor bfo:RO_0040035 This relation groups relations between diseases and any other kind of entity. bfo:RO_0040036 p has anatomical participant c iff p has participant c, and c is an anatomical entity bfo:RO_0040042 part-of is homeomorphic for independent continuants. bfo:RO_0040042 R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. bfo:HOM_0000000 BGEE:curator bfo:RO_HOM0000000 Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. bfo:RO_HOM0000000 TODO: Add homeomorphy axiom bfo:RO_HOM0000000 sameness bfo:RO_HOM0000000 similar to http://dx.doi.org/10.1007/BF02814479 bfo:RO_HOM0000000 correspondence bfo:RO_HOM0000000 resemblance http://dx.doi.org/10.1002/bies.950180611 http://dx.doi.org/10.1002/jmor.1051730307 http://dx.doi.org/10.1007/BF02814480 bfo:HOM_0000001 bfo:RO_HOM0000001 Similarity that results from common evolutionary origin. bfo:RO_HOM0000001 homologous to http://dx.doi.org/10.1016/j.jhevol.2006.11.010 bfo:HOM_0000002 bfo:RO_HOM0000002 Similarity that results from independent evolution. bfo:RO_HOM0000002 homoplasous to bfo:RO_HOM0000002 analogy http://dx.doi.org/10.1007/BF02814484 http://dx.doi.org/10.1007/s00427-003-0301-4 http://dx.doi.org/10.1186/1742-9994-2-15 bfo:HOM_0000003 bfo:RO_HOM0000003 Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. bfo:RO_HOM0000003 homocracous to http://dx.doi.org/10.1016/j.jhevol.2006.11.010 bfo:HOM_0000004 bfo:RO_HOM0000004 Homoplasy that involves different underlying mechanisms or structures. bfo:RO_HOM0000004 analogy http://dx.doi.org/10.1016/j.jhevol.2006.11.010 bfo:HOM_0000005 bfo:RO_HOM0000005 Homoplasy that involves homologous underlying mechanisms or structures. bfo:RO_HOM0000005 parallel evolution http://dx.doi.org/10.1016/j.jhevol.2006.11.014 http://dx.doi.org/10.1146/annurev.es.20.110189.000411 bfo:HOM_0000006 ISBN:0123195837 bfo:RO_HOM0000006 Homology that is defined by similarity with regard to selected structural parameters. bfo:RO_HOM0000006 structural homologous to bfo:RO_HOM0000006 idealistic homology http://dx.doi.org/10.1016/S0169-5347(97)01125-7 bfo:HOM_0000007 ISBN:0123195837 bfo:RO_HOM0000007 Homology that is defined by common descent. bfo:RO_HOM0000007 homology bfo:RO_HOM0000007 cladistic homology bfo:RO_HOM0000007 historical homologous to bfo:RO_HOM0000007 phylogenetic homology bfo:RO_HOM0000007 taxic homology bfo:RO_HOM0000007 true homology http://dx.doi.org/10.1016/S0169-5347(97)01125-7 http://dx.doi.org/10.1146/annurev.es.20.110189.000411 bfo:HOM_0000008 bfo:RO_HOM0000008 Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. bfo:RO_HOM0000008 biological homologous to bfo:RO_HOM0000008 transformational homology http://dx.doi.org/10.1016/j.jhevol.2006.11.010 bfo:HOM_0000009 bfo:RO_HOM0000009 Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. bfo:RO_HOM0000009 atavism bfo:RO_HOM0000009 rudiment bfo:RO_HOM0000009 reversion bfo:HOM_0000010 MeSH:Synteny bfo:RO_HOM0000010 Structural homology that is detected by similarity in content and organization between chromosomes. bfo:RO_HOM0000010 syntenic homologous to bfo:RO_HOM0000010 synteny http://dx.doi.org/10.1016/S0168-9525(00)02005-9 http://dx.doi.org/10.1146/annurev.genet.39.073003.114725 bfo:HOM_0000011 http://www.ncbi.nlm.nih.gov/pubmed/5449325 bfo:RO_HOM0000011 Historical homology that involves genes that diverged after a duplication event. bfo:RO_HOM0000011 paralogous to http://dx.doi.org/10.1186/1471-213X-7-100 bfo:HOM_0000012 DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y bfo:RO_HOM0000012 Paralogy that involves sets of syntenic blocks. bfo:RO_HOM0000012 syntenic paralogous to bfo:RO_HOM0000012 duplicon bfo:RO_HOM0000012 paralogon http://dx.doi.org/10.1101/gr.6380007 bfo:HOM_0000013 bfo:RO_HOM0000013 Syntenic homology that involves chromosomes of different species. bfo:RO_HOM0000013 syntenic orthologous to bfo:HOM_0000014 ISBN:0123195837 ISBN:978-0471984931 bfo:RO_HOM0000014 Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. bfo:RO_HOM0000014 fractional homology bfo:RO_HOM0000014 partial homologous to bfo:RO_HOM0000014 segmental homology bfo:RO_HOM0000014 mixed homology bfo:RO_HOM0000014 modular homology bfo:RO_HOM0000014 partial correspondence bfo:RO_HOM0000014 percent homology http://dx.doi.org/10.1016/0022-2836(76)90195-9 bfo:HOM_0000015 bfo:RO_HOM0000015 Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. bfo:RO_HOM0000015 protein structural homologous to bfo:HOM_0000016 SO:non_functional_homolog_of bfo:RO_HOM0000016 Structural homology that involves a pseudogenic feature and its functional ancestor. bfo:RO_HOM0000016 pseudogene bfo:RO_HOM0000016 non functional homologous to http://dx.doi.org/10.1007/BF02814484 http://dx.doi.org/10.1016/S0168-9525(00)02005-9 http://dx.doi.org/10.1146/annurev.genet.39.073003.114725 bfo:HOM_0000017 http://www.ncbi.nlm.nih.gov/pubmed/5449325 bfo:RO_HOM0000017 Historical homology that involves genes that diverged after a speciation event. bfo:RO_HOM0000017 orthologous to http://dx.doi.org/10.1016/S0168-9525(00)02005-9 http://dx.doi.org/10.1146/annurev.genet.39.073003.114725 bfo:HOM_0000018 bfo:RO_HOM0000018 Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. bfo:RO_HOM0000018 xenologous to bfo:HOM_0000019 BGEE:curator bfo:RO_HOM0000019 Historical homology that involves two members sharing no other homologs in the lineages considered. bfo:RO_HOM0000019 1 to 1 homologous to bfo:RO_HOM0000019 1:1 homology bfo:RO_HOM0000019 one-to-one homology http://dx.doi.org/10.1007/BF02814484 bfo:HOM_0000020 http://www.ensembl.org/info/docs/compara/homology_method.html bfo:RO_HOM0000020 Orthology that involves two genes that did not experience any duplication after the speciation event that created them. bfo:RO_HOM0000020 1 to 1 orthologous to bfo:RO_HOM0000020 1:1 orthology bfo:RO_HOM0000020 one-to-one orthology http://dx.doi.org/10.1038/75560 bfo:HOM_0000022 bfo:RO_HOM0000022 Paralogy that results from a whole genome duplication event. bfo:RO_HOM0000022 ohnologous to bfo:RO_HOM0000022 homoeology http://dx.doi.org/10.1146/annurev.genet.39.073003.114725 bfo:HOM_0000023 bfo:RO_HOM0000023 Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. bfo:RO_HOM0000023 in-paralogous to bfo:RO_HOM0000023 inparalogy bfo:RO_HOM0000023 symparalogy http://dx.doi.org/10.1146/annurev.genet.39.073003.114725 bfo:HOM_0000024 bfo:RO_HOM0000024 Paralogy that results from a duplication preceding a given speciation event. bfo:RO_HOM0000024 alloparalogy bfo:RO_HOM0000024 out-paralogous to bfo:RO_HOM0000024 outparalogy http://dx.doi.org/10.1006/scdb.1999.0338 http://dx.doi.org/10.1038/nrg2099 bfo:HOM_0000025 bfo:RO_HOM0000025 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. bfo:RO_HOM0000025 pro-orthologous to http://dx.doi.org/10.1006/scdb.1999.0338 http://dx.doi.org/10.1038/nrg2099 bfo:HOM_0000026 bfo:RO_HOM0000026 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. bfo:RO_HOM0000026 semi-orthologous to http://dx.doi.org/10.1146/annurev.es.20.110189.000411 bfo:HOM_0000027 bfo:RO_HOM0000027 Iterative homology that involves structures arranged along the main body axis. bfo:RO_HOM0000027 serial homologous to bfo:RO_HOM0000027 homonomy bfo:HOM_0000028 ISBN:978-0674639416 bfo:RO_HOM0000028 Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. bfo:RO_HOM0000028 heterochronous homologous to bfo:RO_HOM0000028 heterochrony http://en.wikipedia.org/wiki/Pedomorphosis bfo:HOM_0000029 ISBN:978-0674639416 bfo:RO_HOM0000029 Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. bfo:RO_HOM0000029 juvenification bfo:RO_HOM0000029 pedomorphosis http://en.wikipedia.org/wiki/Peramorphosis bfo:HOM_0000030 bfo:RO_HOM0000030 Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. http://en.wikipedia.org/wiki/Progenesis bfo:HOM_0000031 ISBN:978-0674639416 bfo:RO_HOM0000031 Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. http://en.wikipedia.org/wiki/Neoteny bfo:HOM_0000032 ISBN:978-0674639416 bfo:RO_HOM0000032 Paedomorphosis that is produced by a retardation of somatic development. bfo:RO_HOM0000032 juvenilization bfo:RO_HOM0000032 neotenous to http://en.wikipedia.org/wiki/Mimicry bfo:HOM_0000033 bfo:RO_HOM0000033 Convergence that results from co-evolution usually involving an evolutionary arms race. bfo:RO_HOM0000033 mimicrous to http://dx.doi.org/10.1038/415741a bfo:HOM_0000034 http://www.ensembl.org/info/docs/compara/homology_method.html bfo:RO_HOM0000034 Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. bfo:RO_HOM0000034 1 to many orthologous to bfo:RO_HOM0000034 1:many orthology bfo:RO_HOM0000034 one-to-many orthology bfo:RO_HOM0000034 co-orthology bfo:RO_HOM0000034 many to 1 orthology http://dx.doi.org/10.1093/molbev/msp002 bfo:HOM_0000036 bfo:RO_HOM0000036 Historical homology that involves two members of a larger set of homologs. bfo:RO_HOM0000036 many to many homologous to bfo:RO_HOM0000036 many-to-many homology bfo:RO_HOM0000036 many:many homology bfo:HOM_0000037 BGEE:curator bfo:RO_HOM0000037 Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. bfo:RO_HOM0000037 1 to many homologous to bfo:RO_HOM0000037 one-to-many homology bfo:RO_HOM0000037 1:many homology bfo:HOM_0000042 ISBN:978-0252068140 bfo:RO_HOM0000042 Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. bfo:RO_HOM0000042 apomorphous to bfo:RO_HOM0000042 synapomorphy bfo:HOM_0000043 ISBN:978-0252068140 bfo:RO_HOM0000043 Historical homology that is based on distant shared ancestry. bfo:RO_HOM0000043 plesiomorphous to bfo:RO_HOM0000043 symplesiomorphy http://dx.doi.org/10.1007/BF02814485 http://dx.doi.org/10.1038/nature07891 bfo:HOM_0000044 bfo:RO_HOM0000044 Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. bfo:RO_HOM0000044 deep genetic homology bfo:RO_HOM0000044 deep homologous to bfo:RO_HOM0000044 generative homology bfo:RO_HOM0000044 homoiology http://dx.doi.org/10.1073/pnas.0807433105 bfo:HOM_0000045 bfo:RO_HOM0000045 Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. bfo:RO_HOM0000045 hemiplasous to bfo:HOM_0000046 http://www.ncbi.nlm.nih.gov/pubmed/11110898 bfo:RO_HOM0000046 Historical homology that involves not recombining and subsequently differentiated sex chromosomes. bfo:RO_HOM0000046 gametologous to bfo:HOM_0000047 ISBN:0195307615 bfo:RO_HOM0000047 Historical homology that involves the chromosomes able to pair (synapse) during meiosis. bfo:RO_HOM0000047 chromosomal homologous to http://dx.doi.org/10.1038/415741a bfo:HOM_0000048 http://www.ensembl.org/info/docs/compara/homology_method.html bfo:RO_HOM0000048 Orthology that involves two genes that experienced duplications more recent than the species split that created them. bfo:RO_HOM0000048 many to many orthologous to bfo:RO_HOM0000048 many-to-many orthology bfo:RO_HOM0000048 many:many orthology bfo:RO_HOM0000048 trans-orthology bfo:RO_HOM0000048 co-orthology bfo:RO_HOM0000048 trans-homology bfo:HOM_0000049 http://www.ensembl.org/info/docs/compara/homology_method.html bfo:RO_HOM0000049 Paralogy that involves genes from the same species. bfo:RO_HOM0000049 within-species paralogous to bfo:HOM_0000050 http://www.ensembl.org/info/docs/compara/homology_method.html bfo:RO_HOM0000050 Paralogy that involves genes from different species. bfo:RO_HOM0000050 between-species paralogous to http://en.wikipedia.org/wiki/Pedomorphosis bfo:HOM_0000051 bfo:RO_HOM0000051 Paedomorphosis that is produced by delayed growth of immature structures into the adult form. bfo:RO_HOM0000051 post-displacement http://en.wikipedia.org/wiki/Peramorphosis bfo:HOM_0000052 ISBN:978-0674639416 bfo:RO_HOM0000052 Peramorphosis that is produced by a delay in the offset of development. http://dx.doi.org/10.1007/BF00173425 http://dx.doi.org/10.1016/S0168-9525(00)02005-9 bfo:HOM_0000053 bfo:RO_HOM0000053 Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. bfo:RO_HOM0000053 synologous to http://dx.doi.org/10.1016/S0168-9525(00)02005-9 bfo:HOM_0000054 bfo:RO_HOM0000054 Orthology that involves functional equivalent genes with retention of the ancestral function. bfo:RO_HOM0000054 isoorthologous to http://dx.doi.org/10.1016/S0168-9525(00)02005-9 bfo:HOM_0000055 ISBN:978-0878932665 bfo:RO_HOM0000055 Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. bfo:RO_HOM0000055 tandem paralogous to bfo:RO_HOM0000055 iterative paralogy bfo:RO_HOM0000055 serial paralogy http://dx.doi.org/10.1007/BF02814485 http://dx.doi.org/10.1016/j.jhevol.2006.11.010 http://dx.doi.org/10.1186/1742-9994-2-15 bfo:HOM_0000057 ISBN:0199141118 bfo:RO_HOM0000057 Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). bfo:RO_HOM0000057 apomorphic tendency bfo:RO_HOM0000057 cryptic homology bfo:RO_HOM0000057 latent homologous to bfo:RO_HOM0000057 underlying synapomorphy bfo:RO_HOM0000057 homoiology bfo:RO_HOM0000057 homoplastic tendency bfo:RO_HOM0000057 re-awakening http://dx.doi.org/10.1186/1742-9994-2-15 bfo:HOM_0000058 DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R bfo:RO_HOM0000058 Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. bfo:RO_HOM0000058 generative homology bfo:RO_HOM0000058 syngenous to http://dx.doi.org/10.1146/annurev.genet.39.073003.114725 bfo:HOM_0000060 http://www.ensembl.org/info/docs/compara/homology_method.html bfo:RO_HOM0000060 Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. bfo:RO_HOM0000060 1:1 paralogy bfo:RO_HOM0000060 apparent 1:1 orthology bfo:RO_HOM0000060 apparent orthologous to bfo:RO_HOM0000060 pseudoorthology http://dx.doi.org/10.1146/annurev.genet.39.073003.114725 bfo:HOM_0000061 bfo:RO_HOM0000061 Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. bfo:RO_HOM0000061 pseudoparalogous to http://dx.doi.org/10.1093/nar/gkl1043 bfo:HOM_0000062 bfo:RO_HOM0000062 Historical homology that involves functional equivalent genes with retention of the ancestral function. bfo:RO_HOM0000062 equivalogous to http://dx.doi.org/10.1101/gr.1774904 http://dx.doi.org/10.1126/science.287.5450.116 bfo:HOM_0000063 bfo:RO_HOM0000063 Historical homology that involves orthologous pairs of interacting molecules in different organisms. bfo:RO_HOM0000063 interologous to http://dx.doi.org/10.1007/BF02814484 http://dx.doi.org/10.1038/415741a bfo:HOM_0000065 bfo:RO_HOM0000065 Similarity that is characterized by interchangeability in function. bfo:RO_HOM0000065 functional similarity http://dx.doi.org/10.1146/annurev.es.20.110189.000411 bfo:HOM_0000066 bfo:RO_HOM0000066 Biological homology that involves parts of the same organism. bfo:RO_HOM0000066 iterative homologous to bfo:HOM_0000068 http://www.ncbi.nlm.nih.gov/pubmed/3065587 bfo:RO_HOM0000068 Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. bfo:RO_HOM0000068 duplicate xenology bfo:RO_HOM0000068 multiple xenology bfo:RO_HOM0000068 paraxenologous to bfo:HOM_0000069 http://www.ncbi.nlm.nih.gov/pubmed/3065587 bfo:RO_HOM0000069 Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. bfo:RO_HOM0000069 plerologous to http://dx.doi.org/10.1007/BF02814484 http://dx.doi.org/10.1007/BF02814485 bfo:HOM_0000071 ISBN:0123195837 bfo:RO_HOM0000071 Structural homology that involves structures with the same or similar relative positions. bfo:RO_HOM0000071 homotopous to http://dx.doi.org/10.1007/BF02814485 http://dx.doi.org/10.1016/j.cell.2008.06.030 bfo:HOM_0000072 bfo:RO_HOM0000072 Biological homology that involves an ectopic structure and the normally positioned structure. bfo:RO_HOM0000072 heterotopy http://dx.doi.org/10.1073/pnas.0505156102 bfo:HOM_0000073 bfo:RO_HOM0000073 Synology that results from allopolyploidy. bfo:RO_HOM0000073 homoeologous to http://dx.doi.org/10.1007/s10441-007-9023-8 http://dx.doi.org/10.1046/j.1525-142x.2000.00054.x bfo:HOM_0000074 bfo:RO_HOM0000074 Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. bfo:RO_HOM0000074 axis paramorphism http://dx.doi.org/10.1101/gr.1774904 bfo:HOM_0000075 bfo:RO_HOM0000075 Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. bfo:RO_HOM0000075 regulogous to CARO:0001001 FBC:DOS FBbt:00005099 bfo:UBERON_0000122 A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. bfo:UBERON_0000122 funiculus FBbt:00005099 bfo:UBERON_0000122 nerve fiber bundle bfo:UBERON_0000122 neural fiber bundle http://orcid.org/0000-0001-9114-8737 bfo:UBERON_0000466 Anatomical entity that has no mass. FMA:67112 bfo:UBERON_0000466 immaterial physical anatomical entity FMA:62955 http://orcid.org/0000-0001-9114-8737 bfo:UBERON_0001062 Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. BTO:0001102 Wikipedia:Blood_vessel bfo:UBERON_0001981 A vessel through which blood circulates in the body. bfo:UBERON_0001981 consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus EMAPA:35993 bfo:UBERON_0001981 vascular element FMA:50722 bfo:UBERON_0001981 region of vascular tree organ FMA:50722 bfo:UBERON_0001981 vascular tree organ region ISBN:0073040584 Wikipedia:Capillary https://github.com/obophenotype/uberon/issues/137 bfo:UBERON_0001982 Any of the smallest blood vessels connecting arterioles with venules. bfo:UBERON_0001982 not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element bfo:UBERON_0001982 blood capillary bfo:UBERON_0001982 capillary vessel CARO:0010000 bfo:UBERON_0010000 An anatomical structure that has more than one cell as a part. FBbt:00100313 bfo:UBERON_0010000 multicellular structure terms:contributor terms:contributor terms:contributor contributor terms:contributor entity responsible for making contributions to the resource terms:creator terms:creator terms:creator creator terms:creator entity responsible for making the resource terms:source terms:source terms:source source terms:source related resource from which the described resource is derived terms:source The intent is to provide a user with a reference as to how the thing being annotated was derived or arrived at. - The source can be a URL to a standard, common dictionary (e.g. Oxford), or similar reference. Or it can be a short description of where the entity being annotated was derived from. - The 'Source' annotation would most likely be used as an annotation on an annotation. For instance annotating a Natural Language definition annotation. oboInOwl:hasBroadSynonym An alternative label for a class or property which has a more general meaning than the preferred name/primary label. oboInOwl:hasBroadSynonym http://orcid.org/0000-0001-5208-3432 oboInOwl:hasBroadSynonym https://github.com/information-artifact-ontology/ontology-metadata/issues/18 oboInOwl:hasBroadSynonym has broad synonym oboInOwl:hasBroadSynonym has_broad_synonym oboInOwl:hasBroadSynonym https://github.com/information-artifact-ontology/ontology-metadata/issues/18 oboInOwl:hasExactSynonym An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. oboInOwl:hasExactSynonym http://orcid.org/0000-0001-5208-3432 oboInOwl:hasExactSynonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 oboInOwl:hasExactSynonym has exact synonym oboInOwl:hasExactSynonym has_exact_synonym oboInOwl:hasExactSynonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 oboInOwl:hasNarrowSynonym An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. oboInOwl:hasNarrowSynonym http://orcid.org/0000-0001-5208-3432 oboInOwl:hasNarrowSynonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 oboInOwl:hasNarrowSynonym has narrow synonym oboInOwl:hasNarrowSynonym has_narrow_synonym oboInOwl:hasNarrowSynonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 oboInOwl:hasRelatedSynonym An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. oboInOwl:hasRelatedSynonym http://orcid.org/0000-0001-5208-3432 oboInOwl:hasRelatedSynonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 oboInOwl:hasRelatedSynonym has related synonym oboInOwl:hasRelatedSynonym has_related_synonym oboInOwl:hasRelatedSynonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 CommonCoreOntologies:InformationContentEntity ICE CommonCoreOntologies:InformationContentEntity A Generically Dependent Continuant that generically depends on some Information Bearing Entity and stands in relation of aboutness to some Entity. CommonCoreOntologies:InformationContentEntity http://purl.obolibrary.org/obo/IAO_0000030 CommonCoreOntologies:InformationContentEntity Information Content Entity is here intended to be a class of Entities whose instances are the informational content of Information Bearing Entities. For example, three instances of information bearers -- such as a bar chart, color-coded map, and a written report -- each of which lists the GDP of Countries for the year 2010 are each different carriers of the same information content. It is this content that is generically dependent upon its carrier. This treatment of Informational Content Entity (cf. the Information Artifact Ontology) leads to a principle of subtyping based upon the relationship that ICE's have with the Entity they are about rather than characteristics such as format, language, measurement scale, or media. The latter are treated here as being Qualities of bearers. CommonCoreOntologies:InformationContentEntity http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology CommonCoreOntologies:InformationContentEntity Information Content Entity CommonCoreOntologies:RepresentationalInformationContentEntity An Information Content Entity that represents some Entity. CommonCoreOntologies:RepresentationalInformationContentEntity the content of a court transcript represents a courtroom proceeding CommonCoreOntologies:RepresentationalInformationContentEntity the content of a photograph of the Statue of Liberty represents the Statue of Liberty CommonCoreOntologies:RepresentationalInformationContentEntity the content of a video of a sporting event represents that sporting event CommonCoreOntologies:RepresentationalInformationContentEntity http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology CommonCoreOntologies:RepresentationalInformationContentEntity Representational Information Content Entity CommonCoreOntologies:is_about A primitive relationship between an Information Content Entity and some Entity. CommonCoreOntologies:is_about http://purl.obolibrary.org/obo/IAO_0000136 CommonCoreOntologies:is_about http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology CommonCoreOntologies:is_about is about CommonCoreOntologies:is_subject_of A primitive relationship between an instance of an Entity and an instance of an Information Content Entity. CommonCoreOntologies:is_subject_of http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology CommonCoreOntologies:is_subject_of is subject of CommonCoreOntologies:represented_by y represented_by x iff x is an instance of Information Content Entity, and y is an instance of Entity, and z is carrier of x, such that x is about y in virtue of there existing an isomorphism between characteristics of z and y. CommonCoreOntologies:represented_by http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology CommonCoreOntologies:represented_by See notes for inverse property. CommonCoreOntologies:represented_by represented by CommonCoreOntologies:represents x represents y iff x is an instance of Information Content Entity, y is an instance of Entity, and z is carrier of x, such that x is about y in virtue of there existing an isomorphism between characteristics of z and y. CommonCoreOntologies:represents The relationship that is being defined here is that between the content of a photographic image and its object, between the content of a video and its objects and events, between the content of an audio recording and the sounds or events generating those sounds, or between the content of a written transcript and the verbal event that it transcribes. CommonCoreOntologies:represents http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology CommonCoreOntologies:represents Isomorphism between the carrier of x and the represented entity can be via a direct similarity relation, e.g., grooves in a vinyl record corresponding to sound waves, or linguistic convention, e.g., a court stenographer's transcription of spoken words, as well as others, such as encoding processes for images. CommonCoreOntologies:represents represents CommonCoreOntologies:represents Given a stronger temporal interpretation, this property may be functional. For more info please refer to https://github.com/BFO-ontology/BFO-2020/tree/master/src/owl/temporal%20extensions. AnnotationVocabulary:MaturityLevel maturity level AnnotationVocabulary:MaturityLevel classifier used to specify the state of a resource in its development process AnnotationVocabulary:Provisional provisional AnnotationVocabulary:Provisional construct or ontology development state in which content is subject to change and may change considerably AnnotationVocabulary:Provisional IOF users should be aware that the resource is not dependable, but can be used for reference and for further work. AnnotationVocabulary:Released released AnnotationVocabulary:Released construct or ontology development state in which the resource is stable, usable, and has been made available to external users AnnotationVocabulary:Released Release notes will be provided for any changes concerning released content, and any revisions will be backward compatible with the prior version to the degree possible. AnnotationVocabulary:adaptedFrom AnnotationVocabulary: AnnotationVocabulary:adaptedFrom adapted from AnnotationVocabulary:adaptedFrom source for the resource that was modified to create the subject resource AnnotationVocabulary:directSource AnnotationVocabulary: AnnotationVocabulary:directSource direct source AnnotationVocabulary:directSource definitive source of the subject resource AnnotationVocabulary:excerptedFrom AnnotationVocabulary: AnnotationVocabulary:excerptedFrom excerpted from AnnotationVocabulary:excerptedFrom source of a resource that was imported unmodified from an external ontology AnnotationVocabulary:excerptedFrom This annotation is to be used when an element from a non-IOF ontology is used in an IOF ontology (and the source ontology is not imported in its entirety). AnnotationVocabulary:explanatoryNote explanatory note AnnotationVocabulary:explanatoryNote note that provides additional explanatory information about a given notion or resource AnnotationVocabulary:firstOrderLogicAxiom first-order logic axiom AnnotationVocabulary:firstOrderLogicAxiom logic axiom annotation written in first order logic AnnotationVocabulary:firstOrderLogicAxiom First-order logic axioms MAY be provided if the term is primitive ('is primitive' is true ) or non-primitive. A construct MAY include more than one first-order logic axiom annotation. AnnotationVocabulary:firstOrderLogicDefinition first order logic definition AnnotationVocabulary:firstOrderLogicDefinition logic definition that expresses the axioms of a class or an object property in first order logic AnnotationVocabulary:firstOrderLogicDefinition An example of a First Order Logic definition for 'Product' might be (again bearing in mind the natural language terms appearing should be regarded as symbols in the IOF signature): - Continuant(x) ∧ ¬(SpecificallyDependentContinuant(x) ∨ Person(x) ∨ Organization(x)) ∧ ∃r (ProductRole(r) ∧ hasRole(x, r)) AnnotationVocabulary:firstOrderLogicDefinition The First Order Logic Definition annotation is comprised of the (complete) necessary and sufficient conditions. - This annotation is Required for each non-primitive (aka non-axiomatic) class (i.e. unary relation) of a published IOF OWL ontology. This is the most authoritative and comprehensive definition of an IOF element. - IOF Common Logic ontologies do not require this annotation, but if included it must be logically equivalent to the Common Logic definition. - A primitive (aka axiomatic) term will not have a First Order Logic definition in either an OWL or Common Logic IOF ontology. - There should be at most one First Order Logic definition. - The specific symbols to be used for existential and universal quantification along with those for conjunction, disjunction, negation, conditional (i.e. if-then), and equivalence will be those commonly used in the mathematical formulas and statement. - Conjunction - ∧; Disjunction - ∨; Negation - ¬; Existential Quantification - ∃; Universal Quantification - ∀; Conditional - →; Equivalence - ↔; Left/Right Parentheses - (,); Left/Right Brackets - {,}. AnnotationVocabulary:isPrimitive is primitive AnnotationVocabulary:isPrimitive boolean flag indicating that necessary and sufficient conditions are not provided AnnotationVocabulary:isPrimitive 'is primitive' must be present if the term does not have necessary and sufficient conditions and the value of the annotation must be set to true. When 'is primitive' is set to true, a value for a 'primitive rationale' annotation must also be provided. AnnotationVocabulary:logicAxiom logic axiom AnnotationVocabulary:logicAxiom logical statements constraining the interpretation of the notion represented by the construct that do not provide necessary and sufficient conditions AnnotationVocabulary:logicAxiom This annotation property is an abstraction of the more specialized logic axiom annotations used in IOF. However, this annotation property can also be used to group together the logic axiom annotation values of different forms (such as FOL and natural language) that express the same meaning for a particular construct. AnnotationVocabulary:logicAxiom A first order logic axiom expression and a semi-formal natural language axiom expression should be added as Property values for each logic axiom annotation using 1 of each of the corresponding logic axiom annotation subproperties. AnnotationVocabulary:logicDefinition logic definition AnnotationVocabulary:logicDefinition definition in the form of a logical expression AnnotationVocabulary:maturity maturity AnnotationVocabulary:maturity annotation property used to indicate the development status of a resource AnnotationVocabulary:maturity Any value for maturity MUST be an instance of MaturityLevel. All IOF ontologies MUST include exactly one maturity annotation. IOF constructs may include a maturity annotation. AnnotationVocabulary:naturalLanguageDefinition natural language definition AnnotationVocabulary:naturalLanguageDefinition definition written in plain text for human understanding AnnotationVocabulary:naturalLanguageDefinition This annotation is Required for each non-primitive or non-axiomatic class of an IOF (OWL or Common Logic) ontology. - It is optional for primitive (aka axiomatic) classes since such the Elucidation annotation is required and will satisfy the role of a natural language definition. - It is optional, but recommended, for relations when the intent of a relation may be misunderstood. - There should be at most one. - This natural language definition should be subject matter expert friendly and consistent with any formal definition or elucidation. - Natural language definitions should use class and relation names with following caveats: a) Relations – For those relations whose label (i.e. local identifier) consist of multiple terms hyphenate the terms of the label: e.g. 'hasPlan' would be written as 'has-plan' b) Classes – For classes whose label has multiple distinct terms, e.g, ManufacturingOperationSpecification, separate the terms but bound them with apostrophe marks: 'Manufacturing Operation Specification'. AnnotationVocabulary:primitiveRationale primitive rationale AnnotationVocabulary:primitiveRationale reason why necessary and sufficient conditions could not be provided AnnotationVocabulary:primitiveRationale When 'is primitive' is set to true, a value for 'primitive rationale' must be provided. The rationale should indicate what is missing if additional work is required to define necessary and sufficient conditions. AnnotationVocabulary:semiFormalNaturalLanguageAxiom semi-formal natural language axiom AnnotationVocabulary:semiFormalNaturalLanguageAxiom logic axiom expressed in natural language AnnotationVocabulary:semiFormalNaturalLanguageAxiom Semi-formal natural language axioms MAY be provided if the term is primitive (is primitive is true). A construct MAY include more than one semi-formal natural language axiom annotation. AnnotationVocabulary:semiFormalNaturalLanguageDefinition semi-formal natural language definition AnnotationVocabulary:semiFormalNaturalLanguageDefinition logic definition that expresses a first order logic definition or common logic definition in natural language AnnotationVocabulary:semiFormalNaturalLanguageDefinition This annotation is required if an element in an IOF OWL ontology has a First Order Logic definition or in a IOF Common Logic (where the element is defined using Common Logic). - The intent of this annotation to provide a transition or bridge from the First Order Logic definition of a notion to the natural language definition. This definition is intended to help a user understand the intended interpretation of the notion. - As example using the First Order Logic definition of 'Product' above, a semi-formal translation of that might be: - Product =def. Continuant that is not a Person and not an Organization and not a Specifically Dependent Continuant and there is a Product Role that the thing has or bears. AnnotationVocabulary:subjectMatterExpertExplanation subject matter expert explanation AnnotationVocabulary:subjectMatterExpertExplanation definition of the term expressed in natural language that has the minimal usage of ontological terms and is intended to be a self-standing explanation AnnotationVocabulary:subjectMatterExpertExplanation Usage of this annotation is optional but is recommended in cases where: - the natural language definition or elucidation rely heavily on the terms defined in the ontology - there exists an explanation of the term that is more familiar to SMEs that does not coincide with the definition present in the ontology AnnotationVocabulary:usageNote usage note AnnotationVocabulary:usageNote note that provides information about how a given notion or resource is used in the ontology's context /SCO_0000016