From e514adf10d77dd3616edfacce94a1bc42a50a69c Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Wed, 12 Jul 2023 15:11:32 +0100 Subject: [PATCH] update relationship labels and ro_import --- src/imports/ro_import.owl | 490 +++++++++++++++++++++++-------- src/imports/ro_terms.txt | 1 + src/template_generation_tools.py | 12 +- 3 files changed, 381 insertions(+), 122 deletions(-) diff --git a/src/imports/ro_import.owl b/src/imports/ro_import.owl index d2898a637..ab7625161 100644 --- a/src/imports/ro_import.owl +++ b/src/imports/ro_import.owl @@ -55,7 +55,14 @@ - + + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> + editor note + @@ -107,6 +114,12 @@ + + + + + + @@ -233,6 +246,12 @@ + + + + + + @@ -295,6 +314,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An http://www.obofoundry.org/ro/#OBO_REL:part_of + https://wiki.geneontology.org/Part_of @@ -654,6 +674,7 @@ range: spatial region or site (immaterial continuant) http://www.obofoundry.org/ro/#OBO_REL:located_in located in + https://wiki.geneontology.org/Located_in @@ -676,7 +697,7 @@ range: spatial region or site (immaterial continuant) A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + 2017-05-24T09:30:46Z has regulatory component activity @@ -689,7 +710,7 @@ range: spatial region or site (immaterial continuant) A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity @@ -703,7 +724,7 @@ range: spatial region or site (immaterial continuant) A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity @@ -715,7 +736,7 @@ range: spatial region or site (immaterial continuant) - dos + 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity @@ -730,7 +751,7 @@ range: spatial region or site (immaterial continuant) w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + 2017-05-24T09:49:21Z has component process @@ -742,7 +763,7 @@ range: spatial region or site (immaterial continuant) - dos + 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by @@ -751,7 +772,7 @@ range: spatial region or site (immaterial continuant) Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + @@ -762,7 +783,7 @@ range: spatial region or site (immaterial continuant) Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + 2017-09-17T13:52:38Z directly negatively regulated by @@ -770,7 +791,7 @@ range: spatial region or site (immaterial continuant) Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + @@ -781,7 +802,7 @@ range: spatial region or site (immaterial continuant) Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + 2017-09-17T13:52:47Z directly positively regulated by @@ -789,7 +810,7 @@ range: spatial region or site (immaterial continuant) Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + @@ -800,7 +821,7 @@ range: spatial region or site (immaterial continuant) A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity @@ -809,7 +830,7 @@ range: spatial region or site (immaterial continuant) A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + @@ -898,6 +919,25 @@ range: spatial region or site (immaterial continuant) + + + + + + + + + X continuous_with Y if and only if X and Y share a fiat boundary. + + connected to + The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) + + continuous with + FMA:85972 + + + + @@ -1133,6 +1173,7 @@ range: spatial region or site (immaterial continuant) has input + https://wiki.geneontology.org/Has_input @@ -1142,8 +1183,8 @@ range: spatial region or site (immaterial continuant) - - + + @@ -1223,7 +1264,7 @@ range: spatial region or site (immaterial continuant) affects acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -1252,6 +1293,7 @@ range: spatial region or site (immaterial continuant) holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect + @@ -1267,6 +1309,7 @@ range: spatial region or site (immaterial continuant) causally upstream of, negative effect + @@ -1351,6 +1394,7 @@ range: spatial region or site (immaterial continuant) This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables + https://wiki.geneontology.org/Enables @@ -1409,7 +1453,7 @@ range: spatial region or site (immaterial continuant) actively involved in enables part of involved in - + https://wiki.geneontology.org/Involved_in @@ -1423,6 +1467,7 @@ range: spatial region or site (immaterial continuant) enabled by + https://wiki.geneontology.org/Enabled_by @@ -1504,8 +1549,8 @@ range: spatial region or site (immaterial continuant) - - + + 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). @@ -1604,6 +1649,7 @@ range: spatial region or site (immaterial continuant) indirectly activates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -1631,6 +1677,7 @@ range: spatial region or site (immaterial continuant) indirectly inhibits indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -2156,6 +2203,16 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + 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. + Groups both positive and negative correlation + correlated with + + + + @@ -2169,6 +2226,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -2186,6 +2244,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -2219,7 +2278,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:49:30Z acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -2237,6 +2296,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:49:51Z acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -2256,7 +2316,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:53:14Z acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -2276,7 +2336,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:53:22Z acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -2289,6 +2349,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-03-13T23:55:05Z causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -2301,6 +2362,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-03-13T23:55:19Z causally upstream of or within, positive effect + @@ -2323,7 +2385,7 @@ For example, A and B may be gene products and binding of B by A positively regul p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z indirectly causally upstream of @@ -2336,7 +2398,7 @@ For example, A and B may be gene products and binding of B by A positively regul p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z indirectly regulates @@ -2363,6 +2425,20 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + A relation between entities in which one increases or decreases as the other does the same. + directly correlated with + + positively correlated with + + + + @@ -2479,7 +2555,8 @@ For example, A and B may be gene products and binding of B by A positively regul - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + 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]) + 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 @@ -2498,7 +2575,8 @@ For example, A and B may be gene products and binding of B by A positively regul - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process @@ -2556,7 +2634,8 @@ For example, A and B may be gene products and binding of B by A positively regul - 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. + 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]) + 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 @@ -2613,28 +2692,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. - CARO:0000000 - Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure. - anatomical entity - - - - - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. - CAROC:Brownsville2014 - - - - - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + 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. molecular function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. @@ -2643,7 +2704,7 @@ For example, A and B may be gene products and binding of B by A positively regul - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + 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. GOC:pdt @@ -2652,7 +2713,7 @@ For example, A and B may be gene products and binding of B by A positively regul - A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + 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. jl 2012-09-19T15:05:24Z Wikipedia:Biological_process @@ -2667,7 +2728,7 @@ For example, A and B may be gene products and binding of B by A positively regul - A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + 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. GOC:pdt @@ -2712,6 +2773,36 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + curation status specification + + The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) + PERSON:Bill Bug + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + OBI_0000266 + curation status specification + + + + @@ -2742,6 +2833,160 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + + + AAO:0010841 + AEO:0000000 + BILA:0000000 + BIRNLEX:6 + CARO:0000000 + EHDAA2:0002229 + FBbt:10000000 + FMA:62955 + HAO:0000000 + MA:0000001 + NCIT:C12219 + TAO:0100000 + TGMA:0001822 + UMLS:C1515976 + WBbt:0000100 + XAO:0000000 + ZFA:0100000 + UBERON:0001062 + + + anatomical entity + + + + + 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. + FMA:62955 + http://orcid.org/0000-0001-9114-8737 + + + + + UMLS:C1515976 + ncithesaurus:Anatomic_Structure_System_or_Substance + + + + + + + + + + + + + example to be eventually removed + example to be eventually removed + + + + + + + + metadata complete + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + organizational term + Term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + ready for release + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + metadata incomplete + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + uncurated + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + pending final vetting + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + to be replaced with external ontology term + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + + requires discussion + + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + +