diff --git a/aeon-base.owl b/aeon-base.owl index 79d18cd..b2be1ec 100644 --- a/aeon-base.owl +++ b/aeon-base.owl @@ -13,7 +13,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + Christian Hauschke Christoph Lange Michael Conlon @@ -23,7 +23,7 @@ Academic Event Ontology AEON is being developed as a part of the ConfIDent project (https://projects.tib.eu/confident). - 2022-11-25 + 2023-01-11 @@ -618,8 +618,8 @@ - - + + A relation obtaining between an academic event and another academic event. A collocated event is an event that takes place at the same location and time as another academic event. https://orcid.org/0000-0002-1595-3213 @@ -633,8 +633,8 @@ - - + + A relation obtaining between an academic event and another academic event. A joint event is an event that shares some of the planning and organizing logistics with another academic event, but is otherwise independent from it. https://orcid.org/0000-0002-1595-3213 @@ -648,8 +648,8 @@ - - + + A relation obtaining between an academic event and another academic event or event series. An umbrelle event is a superordinate event that combines several smaller academic events at the same time. To say p 'has umbrella event' d =def. there exists an academic event d that is a superordinate event of p and that there must be other academic events that have the same relation. https://orcid.org/0000-0002-1595-3213 has umbrella event @@ -743,6 +743,12 @@ + + + + + + @@ -779,6 +785,12 @@ + + + + + + @@ -1486,6 +1498,12 @@ cancled → withdrawn + + + + + + @@ -3379,6 +3397,7 @@ see also: https://github.com/OBOFoundry/COB/issues/138 wrt the problem of OBO cl + A plan specification that defines an organized sociocultural event by providing its topic or purpose, as well as implicit and explicit details on who is suppose to attend and how this event is planned to be carried out by its participants, in terms of achieving particular objectives, fulfilling particular conditions and performing particular actions. When we speak of implicit details in the definition of this class, we mean the fact that, apart from explicitly providing information about e.g. the location and participation conditions of such an event in its announcement, details regarding its sociocultural format often remains tacit and are implied by the use of commonly known event type labels. Saying for example, "We're happy to announce the 11th international conference on sociolinguistics.", implies this 'conference' to be planned and executed by legitimate organizers, to have a certain formal code of conduct expected to be adhered to by the participants, or that is intended for a rather large and diverse audience. Similarly denoting an organized sociocultural event as a "birthday party", implies that one has to be invited to attend, or that one would be considered rude if one were to 'steel the show' from the person being celebrated. @@ -3395,17 +3414,50 @@ see also: https://github.com/OBOFoundry/COB/issues/138 wrt the problem of OBO cl - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - A planned process that is a gathering of people organized by one or more people for a particular purpose, often with a particular theme and to be realized within a particular sociocultural format. It may be one-time, occasional or sporadic, or recurring/periodic. + A process that is a planned gathering of people organized by one or more people for a particular purpose, often with a particular theme and to be realized within a particular sociocultural format. It may be one-time, occasional or sporadic, or recurring/periodic. There are certain children of this “organized sociocultural event” class, that are most likely unproblematic to define using an Aristotelian approach, such as "party", "online event", "business event", "networking event" or "academic event". All of these are organised sociocultural events (OSCEs) with a rather clear theme, purpose and shared implied event format. A party, for example, will in most cultures be an OSCE that serves the purpose to celebrate something and its format will in most cases be rightly expected to be informal. Similarly, a business event will in most cultures be considered an OSCE with the primary goal of doing some form of business and thus its participants are expected to adhere to certain conventions on how to behave according to the sociocultural context of the particular OSCE. However, as soon as we try to get more specific in the definition of possible OSCE subclasses, we run into the problem of finding appropriate differentia criteria and that there is a multitude of possible combinations of such very general concepts. For example, we would need to define an "online business networking party" class, if we needed to represent an OSCE that entails all of these aspects as central part of its theme and context dependent sociocultural event format. Thus, the children of OSCEs should not be understood as universal classes but rather always as defined classes, if we need to take into account that the labels, used to denote the concepts representing the various types of OSCEs, differ depending on the social and cultural context in which they are used. In other words these concepts might better be understood as sociocultural constructs or prototypes. The dimensions in which OSCEs are to be defined by their sociocultural event format are the obvious "what", "when", "who", "where", and "how" questions. As planned processes they are determined by a plan to facilitate a gathering of people according to some kind of purpose or theme and sociocultural format. Yet, such a plan is not something we can easily make assertions about, since it resides in the brains of the participants of an OSCEs. What we can make assertions about is the communicated information from which the specification of an OSCE plan can be derived. What the organizers of an OSCE have stated about their plan, makes up the sociocultural format that defines the characteristics of an OSCE. Hence, we narrow the OBI pattern of defining a planned process via its plan specification, by introducing a special type of plan specification, called sociocultural event format, to define this class and its children, well knowing that this adds a layer of complexity usually not needed in human communication, but needed to enable machine reasoning. This class is only defined as a placeholder in AEON and should actually better be defined in a more general OBO based or BFO aligned ontology. Its current inclusion in AEON is thus meant only as a demonstration of the proposed organized sociocultural event pattern. @@ -3418,7 +3470,7 @@ This class is only defined as a placeholder in AEON and should actually better b - A planned process that is a gathering of people organized by one or more people for a particular purpose, often with a particular theme and to be realized within a particular sociocultural format. It may be one-time, occasional or sporadic, or recurring/periodic. + A process that is a planned gathering of people organized by one or more people for a particular purpose, often with a particular theme and to be realized within a particular sociocultural format. It may be one-time, occasional or sporadic, or recurring/periodic. https://en.wikipedia.org/wiki/Category:Organized_events @@ -3458,6 +3510,7 @@ This class is only defined as a placeholder in AEON and should actually better b + An organized sociocultural event that is the set of all recurring organized sociocultural events of a destinct identity. This destinct identity is usually demarked by a shared name that only differs with regard to some ordnial symbol, such as 1st or the year of the organized sociocultural event. @@ -3530,6 +3583,7 @@ This class is only defined as a placeholder in AEON and should actually better b + A sociocultural event format that states that the primary purpose (objective) of an organised sociocultural event is to facilitate a busines communication and actions between its participants and which specifies the formal mode of this communication process. business event format @@ -3542,7 +3596,8 @@ This class is only defined as a placeholder in AEON and should actually better b - An objective specifiaction that describes one of the main goals of a planned process to be the facilitation of an excahnge of knowledge between the participants of this planned process. + + An objective specifiaction that describes one of the main goals of a planned process to be the facilitation of an exchange of knowledge between the participants of this planned process. knowledge exchange objective @@ -3576,6 +3631,7 @@ This class is only defined as a placeholder in AEON and should actually better b + An objective specifiaction that describes one of the main goals of a planned process to be the facilitation of business related comminucation and actions between the participants of this planned process. @@ -3638,7 +3694,6 @@ This class is only defined as a placeholder in AEON and should actually better b - A session format that has as part some demonstration format. demo session format @@ -3774,7 +3829,6 @@ This class is only defined as a placeholder in AEON and should actually better b - An academic event track that has the goal to allow exemplary demonstrations of of work that has been implemented in a particular context and that fits into the topic (theme) of the academic event of which this track is a part of. @@ -3933,6 +3987,12 @@ This class is only defined as a placeholder in AEON and should actually better b + + + + + + diff --git a/aeon-full.owl b/aeon-full.owl index 7a59921..3e98c62 100644 --- a/aeon-full.owl +++ b/aeon-full.owl @@ -16,7 +16,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + Christian Hauschke Christoph Lange Michael Conlon @@ -25,7 +25,7 @@ Academic Event Ontology AEON is being developed as a part of the ConfIDent project (https://projects.tib.eu/confident). - 2022-11-25 + 2023-01-11 @@ -978,8 +978,8 @@ We also have the outstanding issue of how to aim different definitions to differ - - + + A relation obtaining between an academic event and another academic event. A collocated event is an event that takes place at the same location and time as another academic event. https://orcid.org/0000-0002-1595-3213 @@ -993,8 +993,8 @@ We also have the outstanding issue of how to aim different definitions to differ - - + + A relation obtaining between an academic event and another academic event. A joint event is an event that shares some of the planning and organizing logistics with another academic event, but is otherwise independent from it. https://orcid.org/0000-0002-1595-3213 @@ -1008,8 +1008,8 @@ We also have the outstanding issue of how to aim different definitions to differ - - + + A relation obtaining between an academic event and another academic event or event series. An umbrelle event is a superordinate event that combines several smaller academic events at the same time. To say p 'has umbrella event' d =def. there exists an academic event d that is a superordinate event of p and that there must be other academic events that have the same relation. https://orcid.org/0000-0002-1595-3213 has umbrella event @@ -1110,7 +1110,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - + @@ -1140,7 +1140,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part - + @@ -1163,7 +1163,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - + Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in @@ -1182,8 +1182,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - - + + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes @@ -1211,7 +1211,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. unfolds in unfolds_in - + @@ -1362,7 +1362,7 @@ every c that is a concretization of g specifically denotes r Person:Alan Ruttenberg Person:Helen Parkinson 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - + is member of organization @@ -1380,7 +1380,7 @@ every c that is a concretization of g specifically denotes r inheres_in - + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of @@ -1401,7 +1401,7 @@ every c that is a concretization of g specifically denotes r is bearer of - + has characteristic @@ -1420,7 +1420,7 @@ every c that is a concretization of g specifically denotes r a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in - + participates in @@ -1448,13 +1448,28 @@ every c that is a concretization of g specifically denotes r Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - + http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant + + + + + + + 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). + 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). + 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. + + is concretized as + + + + @@ -1463,7 +1478,9 @@ every c that is a concretization of g specifically denotes r 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). 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). 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. - + + + concretizes @@ -1515,7 +1532,7 @@ every c that is a concretization of g specifically denotes r is role of role_of - + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of @@ -1564,7 +1581,7 @@ every c that is a concretization of g specifically denotes r A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role - + has role @@ -1602,7 +1619,7 @@ every c that is a concretization of g specifically denotes r A part of relation that applies only between occurrents. - + occurrent part of @@ -1617,7 +1634,7 @@ every c that is a concretization of g specifically denotes r Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. @@ -1636,7 +1653,7 @@ every c that is a concretization of g specifically denotes r inverse of starts with Chris Mungall Allen - + starts @@ -1654,7 +1671,7 @@ every c that is a concretization of g specifically denotes r x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall started by - + starts with @@ -1670,7 +1687,7 @@ every c that is a concretization of g specifically denotes r inverse of ends with Chris Mungall - + ends @@ -1687,7 +1704,7 @@ every c that is a concretization of g specifically denotes r 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. Chris Mungall finished by - + ends with @@ -1707,7 +1724,7 @@ every c that is a concretization of g specifically denotes r p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. Chris Mungall produces - + @@ -1730,7 +1747,7 @@ every c that is a concretization of g specifically denotes r Chris Mungall actively involved in enables part of - + involved in @@ -1749,7 +1766,7 @@ every c that is a concretization of g specifically denotes r SIO - + member of @@ -1764,7 +1781,7 @@ every c that is a concretization of g specifically denotes r SIO - + has member @@ -1776,7 +1793,7 @@ every c that is a concretization of g specifically denotes r inverse of has output Chris Mungall - + output of @@ -1791,7 +1808,7 @@ every c that is a concretization of g specifically denotes r c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall - + involved in regulation of @@ -1805,7 +1822,7 @@ every c that is a concretization of g specifically denotes r OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates - + involved in or involved in regulation of @@ -1816,7 +1833,7 @@ every c that is a concretization of g specifically denotes r A relationship between a material entity and a process where the material entity has some causal role that influences the process - + causal agent in process @@ -1827,7 +1844,7 @@ every c that is a concretization of g specifically denotes r "has ocurrent part" is a relation that holds between a whole occurrent (process) and its part. - + has occurrent part @@ -2367,7 +2384,7 @@ cancled → withdrawn Damion Dooley Mark Miller 2019-07-14T07:05:50Z - + has representation @@ -2526,6 +2543,12 @@ cancled → withdrawn + + + + + + @@ -4629,6 +4652,7 @@ see also: https://github.com/OBOFoundry/COB/issues/138 wrt the problem of OBO cl + A plan specification that defines an organized sociocultural event by providing its topic or purpose, as well as implicit and explicit details on who is suppose to attend and how this event is planned to be carried out by its participants, in terms of achieving particular objectives, fulfilling particular conditions and performing particular actions. When we speak of implicit details in the definition of this class, we mean the fact that, apart from explicitly providing information about e.g. the location and participation conditions of such an event in its announcement, details regarding its sociocultural format often remains tacit and are implied by the use of commonly known event type labels. Saying for example, "We're happy to announce the 11th international conference on sociolinguistics.", implies this 'conference' to be planned and executed by legitimate organizers, to have a certain formal code of conduct expected to be adhered to by the participants, or that is intended for a rather large and diverse audience. Similarly denoting an organized sociocultural event as a "birthday party", implies that one has to be invited to attend, or that one would be considered rude if one were to 'steel the show' from the person being celebrated. @@ -4645,10 +4669,43 @@ see also: https://github.com/OBOFoundry/COB/issues/138 wrt the problem of OBO cl - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -4656,12 +4713,50 @@ see also: https://github.com/OBOFoundry/COB/issues/138 wrt the problem of OBO cl - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - A planned process that is a gathering of people organized by one or more people for a particular purpose, often with a particular theme and to be realized within a particular sociocultural format. It may be one-time, occasional or sporadic, or recurring/periodic. + A process that is a planned gathering of people organized by one or more people for a particular purpose, often with a particular theme and to be realized within a particular sociocultural format. It may be one-time, occasional or sporadic, or recurring/periodic. There are certain children of this “organized sociocultural event” class, that are most likely unproblematic to define using an Aristotelian approach, such as "party", "online event", "business event", "networking event" or "academic event". All of these are organised sociocultural events (OSCEs) with a rather clear theme, purpose and shared implied event format. A party, for example, will in most cultures be an OSCE that serves the purpose to celebrate something and its format will in most cases be rightly expected to be informal. Similarly, a business event will in most cultures be considered an OSCE with the primary goal of doing some form of business and thus its participants are expected to adhere to certain conventions on how to behave according to the sociocultural context of the particular OSCE. However, as soon as we try to get more specific in the definition of possible OSCE subclasses, we run into the problem of finding appropriate differentia criteria and that there is a multitude of possible combinations of such very general concepts. For example, we would need to define an "online business networking party" class, if we needed to represent an OSCE that entails all of these aspects as central part of its theme and context dependent sociocultural event format. Thus, the children of OSCEs should not be understood as universal classes but rather always as defined classes, if we need to take into account that the labels, used to denote the concepts representing the various types of OSCEs, differ depending on the social and cultural context in which they are used. In other words these concepts might better be understood as sociocultural constructs or prototypes. The dimensions in which OSCEs are to be defined by their sociocultural event format are the obvious "what", "when", "who", "where", and "how" questions. As planned processes they are determined by a plan to facilitate a gathering of people according to some kind of purpose or theme and sociocultural format. Yet, such a plan is not something we can easily make assertions about, since it resides in the brains of the participants of an OSCEs. What we can make assertions about is the communicated information from which the specification of an OSCE plan can be derived. What the organizers of an OSCE have stated about their plan, makes up the sociocultural format that defines the characteristics of an OSCE. Hence, we narrow the OBI pattern of defining a planned process via its plan specification, by introducing a special type of plan specification, called sociocultural event format, to define this class and its children, well knowing that this adds a layer of complexity usually not needed in human communication, but needed to enable machine reasoning. This class is only defined as a placeholder in AEON and should actually better be defined in a more general OBO based or BFO aligned ontology. Its current inclusion in AEON is thus meant only as a demonstration of the proposed organized sociocultural event pattern. @@ -4674,7 +4769,7 @@ This class is only defined as a placeholder in AEON and should actually better b - A planned process that is a gathering of people organized by one or more people for a particular purpose, often with a particular theme and to be realized within a particular sociocultural format. It may be one-time, occasional or sporadic, or recurring/periodic. + A process that is a planned gathering of people organized by one or more people for a particular purpose, often with a particular theme and to be realized within a particular sociocultural format. It may be one-time, occasional or sporadic, or recurring/periodic. https://en.wikipedia.org/wiki/Category:Organized_events @@ -4739,6 +4834,7 @@ This class is only defined as a placeholder in AEON and should actually better b + An organized sociocultural event that is the set of all recurring organized sociocultural events of a destinct identity. This destinct identity is usually demarked by a shared name that only differs with regard to some ordnial symbol, such as 1st or the year of the organized sociocultural event. @@ -4823,6 +4919,7 @@ This class is only defined as a placeholder in AEON and should actually better b + A sociocultural event format that states that the primary purpose (objective) of an organised sociocultural event is to facilitate a busines communication and actions between its participants and which specifies the formal mode of this communication process. business event format @@ -4835,7 +4932,8 @@ This class is only defined as a placeholder in AEON and should actually better b - An objective specifiaction that describes one of the main goals of a planned process to be the facilitation of an excahnge of knowledge between the participants of this planned process. + + An objective specifiaction that describes one of the main goals of a planned process to be the facilitation of an exchange of knowledge between the participants of this planned process. knowledge exchange objective @@ -4875,6 +4973,7 @@ This class is only defined as a placeholder in AEON and should actually better b + An objective specifiaction that describes one of the main goals of a planned process to be the facilitation of business related comminucation and actions between the participants of this planned process. @@ -5356,7 +5455,7 @@ This class is only defined as a placeholder in AEON and should actually better b (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - + continuant @@ -5447,7 +5546,7 @@ This class is only defined as a placeholder in AEON and should actually better b (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - + occurrent @@ -5530,7 +5629,7 @@ This class is only defined as a placeholder in AEON and should actually better b (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - + independent continuant @@ -5827,7 +5926,7 @@ This class is only defined as a placeholder in AEON and should actually better b (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - + process @@ -5919,7 +6018,7 @@ This class is only defined as a placeholder in AEON and should actually better b (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - + realizable entity @@ -6056,7 +6155,7 @@ This class is only defined as a placeholder in AEON and should actually better b (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - + specifically dependent continuant @@ -6101,7 +6200,7 @@ This class is only defined as a placeholder in AEON and should actually better b (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - + role @@ -6357,15 +6456,23 @@ This class is only defined as a placeholder in AEON and should actually better b + + + + + + gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. 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]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + generically dependent continuant @@ -7008,7 +7115,7 @@ This class is only defined as a placeholder in AEON and should actually better b A primary administrative division of a country, such as a state in the United States. - Geonames:http://www.geonames.org/export/codes.html + Geonames:http://www.geonames.org/export/codes.html @@ -7312,6 +7419,41 @@ This class is only defined as a placeholder in AEON and should actually better b + + + + + + + + + + + + + + + + + + + + + + information carrier + In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. + + A quality of an information bearer that imparts the information content + 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. + 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. + PERSON: Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + + information carrier + + + + @@ -7507,7 +7649,7 @@ Previous. An information content entity is a non-realizable information entity t OBI Plan and Planned Process branch OBI_0000344 - + 2/3/2009 Comment from OBI review. Action specification not well enough specified. @@ -7950,10 +8092,18 @@ When there is no such string, it is almost always because the entities take the + + + + + + + + - + @@ -7981,9 +8131,8 @@ When there is no such string, it is almost always because the entities take the Homo sapiens human human being - man - + Homo sapiens @@ -8042,7 +8191,7 @@ objectives is a planned process. This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - + planned process @@ -8088,7 +8237,7 @@ for now. PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI - + organization @@ -8111,7 +8260,7 @@ OBI doesn't take position as to when an organism starts or ends being an o This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism - + organism diff --git a/aeon.owl b/aeon.owl index 88856c4..3ab08ed 100644 --- a/aeon.owl +++ b/aeon.owl @@ -16,7 +16,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + Christian Hauschke Christoph Lange Michael Conlon @@ -25,7 +25,7 @@ Academic Event Ontology AEON is being developed as a part of the ConfIDent project (https://projects.tib.eu/confident). - 2022-11-25 + 2023-01-11 @@ -978,8 +978,8 @@ We also have the outstanding issue of how to aim different definitions to differ - - + + A relation obtaining between an academic event and another academic event. A collocated event is an event that takes place at the same location and time as another academic event. https://orcid.org/0000-0002-1595-3213 @@ -993,8 +993,8 @@ We also have the outstanding issue of how to aim different definitions to differ - - + + A relation obtaining between an academic event and another academic event. A joint event is an event that shares some of the planning and organizing logistics with another academic event, but is otherwise independent from it. https://orcid.org/0000-0002-1595-3213 @@ -1008,8 +1008,8 @@ We also have the outstanding issue of how to aim different definitions to differ - - + + A relation obtaining between an academic event and another academic event or event series. An umbrelle event is a superordinate event that combines several smaller academic events at the same time. To say p 'has umbrella event' d =def. there exists an academic event d that is a superordinate event of p and that there must be other academic events that have the same relation. https://orcid.org/0000-0002-1595-3213 has umbrella event @@ -1110,7 +1110,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - + @@ -1140,7 +1140,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part - + @@ -1163,7 +1163,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - + Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in @@ -1182,8 +1182,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - - + + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes @@ -1211,7 +1211,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. unfolds in unfolds_in - + @@ -1362,7 +1362,7 @@ every c that is a concretization of g specifically denotes r Person:Alan Ruttenberg Person:Helen Parkinson 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - + is member of organization @@ -1380,7 +1380,7 @@ every c that is a concretization of g specifically denotes r inheres_in - + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of @@ -1401,7 +1401,7 @@ every c that is a concretization of g specifically denotes r is bearer of - + has characteristic @@ -1420,7 +1420,7 @@ every c that is a concretization of g specifically denotes r a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in - + participates in @@ -1448,13 +1448,28 @@ every c that is a concretization of g specifically denotes r Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - + http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant + + + + + + + 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). + 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). + 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. + + is concretized as + + + + @@ -1463,7 +1478,9 @@ every c that is a concretization of g specifically denotes r 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). 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). 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. - + + + concretizes @@ -1515,7 +1532,7 @@ every c that is a concretization of g specifically denotes r is role of role_of - + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of @@ -1564,7 +1581,7 @@ every c that is a concretization of g specifically denotes r A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role - + has role @@ -1602,7 +1619,7 @@ every c that is a concretization of g specifically denotes r A part of relation that applies only between occurrents. - + occurrent part of @@ -1617,7 +1634,7 @@ every c that is a concretization of g specifically denotes r Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. @@ -1636,7 +1653,7 @@ every c that is a concretization of g specifically denotes r inverse of starts with Chris Mungall Allen - + starts @@ -1654,7 +1671,7 @@ every c that is a concretization of g specifically denotes r x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall started by - + starts with @@ -1670,7 +1687,7 @@ every c that is a concretization of g specifically denotes r inverse of ends with Chris Mungall - + ends @@ -1687,7 +1704,7 @@ every c that is a concretization of g specifically denotes r 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. Chris Mungall finished by - + ends with @@ -1707,7 +1724,7 @@ every c that is a concretization of g specifically denotes r p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. Chris Mungall produces - + @@ -1730,7 +1747,7 @@ every c that is a concretization of g specifically denotes r Chris Mungall actively involved in enables part of - + involved in @@ -1749,7 +1766,7 @@ every c that is a concretization of g specifically denotes r SIO - + member of @@ -1764,7 +1781,7 @@ every c that is a concretization of g specifically denotes r SIO - + has member @@ -1776,7 +1793,7 @@ every c that is a concretization of g specifically denotes r inverse of has output Chris Mungall - + output of @@ -1791,7 +1808,7 @@ every c that is a concretization of g specifically denotes r c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall - + involved in regulation of @@ -1805,7 +1822,7 @@ every c that is a concretization of g specifically denotes r OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates - + involved in or involved in regulation of @@ -1816,7 +1833,7 @@ every c that is a concretization of g specifically denotes r A relationship between a material entity and a process where the material entity has some causal role that influences the process - + causal agent in process @@ -1827,7 +1844,7 @@ every c that is a concretization of g specifically denotes r "has ocurrent part" is a relation that holds between a whole occurrent (process) and its part. - + has occurrent part @@ -2367,7 +2384,7 @@ cancled → withdrawn Damion Dooley Mark Miller 2019-07-14T07:05:50Z - + has representation @@ -2526,6 +2543,12 @@ cancled → withdrawn + + + + + + @@ -4629,6 +4652,7 @@ see also: https://github.com/OBOFoundry/COB/issues/138 wrt the problem of OBO cl + A plan specification that defines an organized sociocultural event by providing its topic or purpose, as well as implicit and explicit details on who is suppose to attend and how this event is planned to be carried out by its participants, in terms of achieving particular objectives, fulfilling particular conditions and performing particular actions. When we speak of implicit details in the definition of this class, we mean the fact that, apart from explicitly providing information about e.g. the location and participation conditions of such an event in its announcement, details regarding its sociocultural format often remains tacit and are implied by the use of commonly known event type labels. Saying for example, "We're happy to announce the 11th international conference on sociolinguistics.", implies this 'conference' to be planned and executed by legitimate organizers, to have a certain formal code of conduct expected to be adhered to by the participants, or that is intended for a rather large and diverse audience. Similarly denoting an organized sociocultural event as a "birthday party", implies that one has to be invited to attend, or that one would be considered rude if one were to 'steel the show' from the person being celebrated. @@ -4645,10 +4669,43 @@ see also: https://github.com/OBOFoundry/COB/issues/138 wrt the problem of OBO cl - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -4656,12 +4713,50 @@ see also: https://github.com/OBOFoundry/COB/issues/138 wrt the problem of OBO cl - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - A planned process that is a gathering of people organized by one or more people for a particular purpose, often with a particular theme and to be realized within a particular sociocultural format. It may be one-time, occasional or sporadic, or recurring/periodic. + A process that is a planned gathering of people organized by one or more people for a particular purpose, often with a particular theme and to be realized within a particular sociocultural format. It may be one-time, occasional or sporadic, or recurring/periodic. There are certain children of this “organized sociocultural event” class, that are most likely unproblematic to define using an Aristotelian approach, such as "party", "online event", "business event", "networking event" or "academic event". All of these are organised sociocultural events (OSCEs) with a rather clear theme, purpose and shared implied event format. A party, for example, will in most cultures be an OSCE that serves the purpose to celebrate something and its format will in most cases be rightly expected to be informal. Similarly, a business event will in most cultures be considered an OSCE with the primary goal of doing some form of business and thus its participants are expected to adhere to certain conventions on how to behave according to the sociocultural context of the particular OSCE. However, as soon as we try to get more specific in the definition of possible OSCE subclasses, we run into the problem of finding appropriate differentia criteria and that there is a multitude of possible combinations of such very general concepts. For example, we would need to define an "online business networking party" class, if we needed to represent an OSCE that entails all of these aspects as central part of its theme and context dependent sociocultural event format. Thus, the children of OSCEs should not be understood as universal classes but rather always as defined classes, if we need to take into account that the labels, used to denote the concepts representing the various types of OSCEs, differ depending on the social and cultural context in which they are used. In other words these concepts might better be understood as sociocultural constructs or prototypes. The dimensions in which OSCEs are to be defined by their sociocultural event format are the obvious "what", "when", "who", "where", and "how" questions. As planned processes they are determined by a plan to facilitate a gathering of people according to some kind of purpose or theme and sociocultural format. Yet, such a plan is not something we can easily make assertions about, since it resides in the brains of the participants of an OSCEs. What we can make assertions about is the communicated information from which the specification of an OSCE plan can be derived. What the organizers of an OSCE have stated about their plan, makes up the sociocultural format that defines the characteristics of an OSCE. Hence, we narrow the OBI pattern of defining a planned process via its plan specification, by introducing a special type of plan specification, called sociocultural event format, to define this class and its children, well knowing that this adds a layer of complexity usually not needed in human communication, but needed to enable machine reasoning. This class is only defined as a placeholder in AEON and should actually better be defined in a more general OBO based or BFO aligned ontology. Its current inclusion in AEON is thus meant only as a demonstration of the proposed organized sociocultural event pattern. @@ -4674,7 +4769,7 @@ This class is only defined as a placeholder in AEON and should actually better b - A planned process that is a gathering of people organized by one or more people for a particular purpose, often with a particular theme and to be realized within a particular sociocultural format. It may be one-time, occasional or sporadic, or recurring/periodic. + A process that is a planned gathering of people organized by one or more people for a particular purpose, often with a particular theme and to be realized within a particular sociocultural format. It may be one-time, occasional or sporadic, or recurring/periodic. https://en.wikipedia.org/wiki/Category:Organized_events @@ -4739,6 +4834,7 @@ This class is only defined as a placeholder in AEON and should actually better b + An organized sociocultural event that is the set of all recurring organized sociocultural events of a destinct identity. This destinct identity is usually demarked by a shared name that only differs with regard to some ordnial symbol, such as 1st or the year of the organized sociocultural event. @@ -4823,6 +4919,7 @@ This class is only defined as a placeholder in AEON and should actually better b + A sociocultural event format that states that the primary purpose (objective) of an organised sociocultural event is to facilitate a busines communication and actions between its participants and which specifies the formal mode of this communication process. business event format @@ -4835,7 +4932,8 @@ This class is only defined as a placeholder in AEON and should actually better b - An objective specifiaction that describes one of the main goals of a planned process to be the facilitation of an excahnge of knowledge between the participants of this planned process. + + An objective specifiaction that describes one of the main goals of a planned process to be the facilitation of an exchange of knowledge between the participants of this planned process. knowledge exchange objective @@ -4875,6 +4973,7 @@ This class is only defined as a placeholder in AEON and should actually better b + An objective specifiaction that describes one of the main goals of a planned process to be the facilitation of business related comminucation and actions between the participants of this planned process. @@ -5356,7 +5455,7 @@ This class is only defined as a placeholder in AEON and should actually better b (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - + continuant @@ -5447,7 +5546,7 @@ This class is only defined as a placeholder in AEON and should actually better b (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - + occurrent @@ -5530,7 +5629,7 @@ This class is only defined as a placeholder in AEON and should actually better b (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - + independent continuant @@ -5827,7 +5926,7 @@ This class is only defined as a placeholder in AEON and should actually better b (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - + process @@ -5919,7 +6018,7 @@ This class is only defined as a placeholder in AEON and should actually better b (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - + realizable entity @@ -6056,7 +6155,7 @@ This class is only defined as a placeholder in AEON and should actually better b (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - + specifically dependent continuant @@ -6101,7 +6200,7 @@ This class is only defined as a placeholder in AEON and should actually better b (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - + role @@ -6357,15 +6456,23 @@ This class is only defined as a placeholder in AEON and should actually better b + + + + + + gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. 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]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + generically dependent continuant @@ -7008,7 +7115,7 @@ This class is only defined as a placeholder in AEON and should actually better b A primary administrative division of a country, such as a state in the United States. - Geonames:http://www.geonames.org/export/codes.html + Geonames:http://www.geonames.org/export/codes.html @@ -7312,6 +7419,41 @@ This class is only defined as a placeholder in AEON and should actually better b + + + + + + + + + + + + + + + + + + + + + + information carrier + In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. + + A quality of an information bearer that imparts the information content + 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. + 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. + PERSON: Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + + information carrier + + + + @@ -7507,7 +7649,7 @@ Previous. An information content entity is a non-realizable information entity t OBI Plan and Planned Process branch OBI_0000344 - + 2/3/2009 Comment from OBI review. Action specification not well enough specified. @@ -7950,10 +8092,18 @@ When there is no such string, it is almost always because the entities take the + + + + + + + + - + @@ -7981,9 +8131,8 @@ When there is no such string, it is almost always because the entities take the Homo sapiens human human being - man - + Homo sapiens @@ -8042,7 +8191,7 @@ objectives is a planned process. This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - + planned process @@ -8088,7 +8237,7 @@ for now. PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI - + organization @@ -8111,7 +8260,7 @@ OBI doesn't take position as to when an organism starts or ends being an o This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism - + organism diff --git a/src/ontology/imports/bfo_import.owl b/src/ontology/imports/bfo_import.owl index a2ed810..9a28ef5 100644 --- a/src/ontology/imports/bfo_import.owl +++ b/src/ontology/imports/bfo_import.owl @@ -12,8 +12,8 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:terms="http://purl.org/dc/terms/"> - - 2022-11-25 + + 2023-01-11 diff --git a/src/ontology/imports/envo_import.owl b/src/ontology/imports/envo_import.owl index daef99e..f8cc26f 100644 --- a/src/ontology/imports/envo_import.owl +++ b/src/ontology/imports/envo_import.owl @@ -11,8 +11,8 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - 2022-11-25 + + 2023-01-11 @@ -314,7 +314,7 @@ A primary administrative division of a country, such as a state in the United States. - Geonames:http://www.geonames.org/export/codes.html + Geonames:http://www.geonames.org/export/codes.html diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl index eaca512..43c7c5d 100644 --- a/src/ontology/imports/iao_import.owl +++ b/src/ontology/imports/iao_import.owl @@ -13,8 +13,8 @@ xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/"> - - 2022-11-25 + + 2023-01-11 @@ -625,6 +625,35 @@ every c that is a concretization of g specifically denotes r + + + + + + + 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). + 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). + 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. + + is concretized as + + + + + + + + + + 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). + 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). + 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. + + concretizes + + + + @@ -1506,6 +1535,35 @@ every c that is a concretization of g specifically denotes r + + + + + + + + + + + + + + + + information carrier + In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. + + A quality of an information bearer that imparts the information content + 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. + 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. + PERSON: Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + + information carrier + + + + diff --git a/src/ontology/imports/ico_import.owl b/src/ontology/imports/ico_import.owl index afd3ea7..f79936e 100644 --- a/src/ontology/imports/ico_import.owl +++ b/src/ontology/imports/ico_import.owl @@ -8,8 +8,8 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"> - - 2022-11-25 + + 2023-01-11 diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl index 8a8e38f..a0539bf 100644 --- a/src/ontology/imports/obi_import.owl +++ b/src/ontology/imports/obi_import.owl @@ -10,9 +10,9 @@ xmlns:prov="http://www.w3.org/ns/prov#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"> - - 2022-11-25 - + + 2023-01-11 + @@ -127,7 +127,7 @@ this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes @@ -157,7 +157,7 @@ Person:Alan Ruttenberg Person:Helen Parkinson 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - + is member of organization @@ -171,7 +171,7 @@ 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). 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). 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. - + concretizes @@ -201,7 +201,7 @@ Damion Dooley Mark Miller 2019-07-14T07:05:50Z - + has representation @@ -324,7 +324,7 @@ Alan Ruttenberg OBI Plan and Planned Process branch OBI_0000344 - + 2/3/2009 Comment from OBI review. Action specification not well enough specified. @@ -385,10 +385,18 @@ Request that IAO either clarify these or change definitions not to use them + + + + + + + - + @@ -417,9 +425,8 @@ Request that IAO either clarify these or change definitions not to use themHomo sapiens human human being - man - + Homo sapiens @@ -453,7 +460,7 @@ objectives is a planned process. 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - + planned process @@ -499,7 +506,7 @@ for now. PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI - + organization @@ -522,7 +529,7 @@ OBI doesn't take position as to when an organism starts or ends being an o This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism - + organism diff --git a/src/ontology/imports/obib_import.owl b/src/ontology/imports/obib_import.owl index 8f7aa23..0b5bb05 100644 --- a/src/ontology/imports/obib_import.owl +++ b/src/ontology/imports/obib_import.owl @@ -10,8 +10,8 @@ xmlns:prov="http://www.w3.org/ns/prov#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"> - - 2022-11-25 + + 2023-01-11 diff --git a/src/ontology/imports/omo_import.owl b/src/ontology/imports/omo_import.owl index 3f8658c..072f643 100644 --- a/src/ontology/imports/omo_import.owl +++ b/src/ontology/imports/omo_import.owl @@ -11,8 +11,8 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - 2022-11-25 + + 2023-01-11 diff --git a/src/ontology/imports/oostt_import.owl b/src/ontology/imports/oostt_import.owl index fb6c5d3..e10c4f6 100644 --- a/src/ontology/imports/oostt_import.owl +++ b/src/ontology/imports/oostt_import.owl @@ -10,8 +10,8 @@ xmlns:prov="http://www.w3.org/ns/prov#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"> - - 2022-11-25 + + 2023-01-11 diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index 3986047..c958e39 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -15,9 +15,9 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - 2022-11-25 - + + 2023-01-11 + @@ -205,7 +205,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - + @@ -234,7 +234,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part - + @@ -256,7 +256,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - + Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in @@ -274,7 +274,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes @@ -300,7 +300,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. occurs_in unfolds in unfolds_in - + @@ -322,7 +322,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in - + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of @@ -342,7 +342,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. bearer_of is bearer of - + has characteristic @@ -360,7 +360,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in - + participates in @@ -387,13 +387,27 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - + http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant + + + + + + 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). + 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). + 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. + + concretizes + + + + @@ -404,7 +418,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of - + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of @@ -421,7 +435,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role - + has role @@ -434,7 +448,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. A part of relation that applies only between occurrents. - + occurrent part of @@ -449,7 +463,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. @@ -468,7 +482,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. inverse of starts with Chris Mungall Allen - + starts @@ -486,7 +500,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall started by - + starts with @@ -502,7 +516,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. inverse of ends with Chris Mungall - + ends @@ -519,7 +533,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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. Chris Mungall finished by - + ends with @@ -539,7 +553,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. Chris Mungall produces - + @@ -562,7 +576,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Chris Mungall actively involved in enables part of - + involved in @@ -580,7 +594,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. member part of SIO - + member of @@ -594,7 +608,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has member is a mereological relation between a collection and an item. SIO - + has member @@ -606,7 +620,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. inverse of has output Chris Mungall - + output of @@ -621,7 +635,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall - + involved in regulation of @@ -635,7 +649,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates - + involved in or involved in regulation of @@ -646,7 +660,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. A relationship between a material entity and a process where the material entity has some causal role that influences the process - + causal agent in process @@ -680,7 +694,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - + continuant @@ -702,7 +716,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An entity that has temporal parts and that happens, unfolds or develops through time. - + occurrent @@ -719,8 +733,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - + independent continuant @@ -731,7 +746,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - + process @@ -748,7 +763,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - + realizable entity @@ -764,8 +779,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - + specifically dependent continuant @@ -776,12 +792,29 @@ A continuant cannot have an occurrent as part: use 'participates in'. A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - + role + + + + + + + + + + + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. + + generically dependent continuant + + + +