diff --git a/imports/go_terms.txt b/imports/go_terms.txt index b10e3cc..f4777f1 100644 --- a/imports/go_terms.txt +++ b/imports/go_terms.txt @@ -1,3 +1,4 @@ http://purl.obolibrary.org/obo/GO_0051704 #multi-organism process http://purl.obolibrary.org/obo/GO_0044419 #interspecies interaction between organisms http://purl.obolibrary.org/obo/GO_0051703 #intraspecies interaction between organisms +http://purl.obolibrary.org/obo/GO_0035176 #social behavior diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index cdb129c..2576818 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -1,18 +1,18 @@ - - - - - - - - - - - - - + + + + + + + + + + + + + diff --git a/src/ontology/imports/envo_import.owl b/src/ontology/imports/envo_import.owl index 1541d04..0f48b7b 100644 --- a/src/ontology/imports/envo_import.owl +++ b/src/ontology/imports/envo_import.owl @@ -1,6 +1,6 @@ - + + + + + @@ -107,6 +113,23 @@ + + + + + + + + + + + + + + + + + @@ -130,6 +153,24 @@ + + + + + + + + + + + + + + + + + + @@ -252,6 +293,31 @@ + + + + + + + + + + + + + + + + + + + + + true + + + + @@ -363,6 +429,12 @@ + + + + + + @@ -516,6 +588,7 @@ + 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]) independent continuant @@ -546,6 +619,44 @@ + + + + + quality + + + + + + + + + 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 relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) + 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]) + specifically dependent continuant + + + + + 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 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]) + generically dependent continuant + + + + @@ -921,6 +1032,7 @@ resulting from the influence of human beings on nature. + @@ -1112,6 +1224,53 @@ resulting from the influence of human beings on nature. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An environmental system which is determined by materials bearing roughly homogeneous qualities. + environmental system determined by a quality + + + + @@ -1153,7 +1312,7 @@ resulting from the influence of human beings on nature. - + @@ -1223,6 +1382,114 @@ resulting from the influence of human beings on nature. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An environmental system determined by part of a living or dead plant, or a whole small plant. + environment associated with a plant part or small plant + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An environmental system which includes both living and non-living components. + ecosystem + + + + + An environmental system which includes both living and non-living components. + https://en.wikipedia.org/wiki/Ecosystem + + + + @@ -1241,6 +1508,7 @@ resulting from the influence of human beings on nature. + A process in which includes the components of an environmental system as participants. environmental system process @@ -1675,6 +1943,112 @@ resulting from the influence of human beings on nature. + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + trait + quality + + + + + + + + + + A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. + morphology + + + + + + + + + qualitative + + + + + + + + + A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. + deviation(from_normal) + + + + + + + + + A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. + size + + + + + + + + + + A size quality which is relatively low. + hypoplasia + underdeveloped + reduced + small + tiny + decreased size + + + + + + + + + A quality which inheres in a continuant. + monadic quality of a continuant + multiply inhering quality of a physical entity + quality of a continuant + quality of a single physical entity + quality of an object + quality of continuant + monadic quality of an object + monadic quality of continuant + physical object quality + + + + + + + + + A quality that has a value that is decreased compared to normal or average. + decreased quality + + + + + + + + + + A quality of an object that has a value that is decreased compared to normal or average. + decreased object quality + + + + @@ -1684,6 +2058,63 @@ resulting from the influence of human beings on nature. + + + + + A plant structure (PO:0005679) which is a whole organism. + genet (broad) + ramet (broad) + planta entera (Spanish, exact) + 植物体全体 (Japanese, exact) + bush (narrow) + frutex (narrow) + frutices (narrow) + gametophyte (narrow) + herb (narrow) + liana (narrow) + prothalli (narrow) + prothallium (narrow) + prothallus (narrow) + seedling (narrow) + shrub (narrow) + sporophyte (narrow) + suffrutex (narrow) + suffrutices (narrow) + tree (narrow) + vine (narrow) + woody clump (narrow) + clonal colony (related) + colony (related) + whole plant + + + + + + + + + An anatomical structure that is or was part of a plant, or was derived from a part of a plant. + estructura vegetal (Spanish, exact) + 植物 構造 (Japanese, exact) + plant structure + + + + + + + + + An anatomical entity that is or was part of a plant. + entidad anat&#243mica vegetal (Spanish, exact) + 植物 解剖学（形態）的実体 (Japanese, exact) + plant anatomical entity + + + + @@ -1694,6 +2125,16 @@ resulting from the influence of human beings on nature. + + + + + 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. + anatomical entity + + + + + diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index 4264c20..f22a95b 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -291,6 +291,95 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -358,6 +447,14 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + + @@ -450,6 +547,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + @@ -506,20 +605,19 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - - + + + + + + + + @@ -744,6 +842,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + @@ -823,6 +922,32 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -1037,6 +1162,24 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + + + + + + + + + + + + + + + receptor activity + + + + @@ -1127,6 +1278,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + - + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' @@ -1207,10 +1388,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + @@ -1219,9 +1399,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -1229,9 +1409,10 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + + @@ -1266,10 +1447,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + @@ -1288,9 +1468,10 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + + @@ -1316,7 +1497,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" + From ligand activity to has_ligand @@ -1325,8 +1506,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -1335,12 +1516,24 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + @@ -1351,9 +1544,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -1361,6 +1554,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" @@ -1368,7 +1562,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -1379,7 +1573,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -1395,7 +1589,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -1405,6 +1599,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction @@ -1412,9 +1608,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -1423,12 +1619,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -1439,9 +1648,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -1449,18 +1658,17 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - true - MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z - infer input from direct reg + inferring direct neg reg edge from input to regulatory subfunction - - - + + + + @@ -1468,9 +1676,10 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + + @@ -1479,25 +1688,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - - - - - - - - - - - - - - + @@ -1510,9 +1706,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -1520,9 +1716,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - true - GP(X) part_of complex(Y) enables MF(Z) -> X contributes_to Z - contrib to MF + inferring direct positive reg edge from input to regulatory subfunction @@ -1530,9 +1724,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -1541,9 +1735,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -1551,9 +1745,10 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + + @@ -1569,7 +1764,448 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + + + + + + + + + + + From has_ligand to ligand activity + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + effector input is compound function input + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Input of effector is input of its parent MF + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly regulates X, its parent MF directly regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly positively regulates X, its parent MF directly positively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly negatively regulates X, its parent MF directly negatively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/pco-edit.owl b/src/ontology/pco-edit.owl index d11d9ae..1a8101c 100644 --- a/src/ontology/pco-edit.owl +++ b/src/ontology/pco-edit.owl @@ -513,6 +513,64 @@ obo:PCO_0000032 rdf:type owl:Class ; rdfs:label "biological family"@en . +### http://purl.obolibrary.org/obo/PCO_0000033 +obo:PCO_0000033 rdf:type owl:Class ; + rdfs:subClassOf obo:GO_0035176 , + [ rdf:type owl:Restriction ; + owl:onProperty obo:RO_0000057 ; + owl:someValuesFrom obo:PCO_0000027 + ] ; + obo:IAO_0000115 "A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially."@en ; + obo:IAO_0000116 "Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029"@en ; + obo:IAO_0000119 "GenEpiO curators"@en ; + rdfs:label "human social gathering activity"@en . + + +### http://purl.obolibrary.org/obo/PCO_0000034 +obo:PCO_0000034 rdf:type owl:Class ; + rdfs:subClassOf obo:PCO_0000033 ; + obo:IAO_0000115 "A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area."@en ; + obo:IAO_0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034"@en ; + obo:IAO_0000119 "GenEpio curators"@en ; + rdfs:label "human community event"@en . + + +### http://purl.obolibrary.org/obo/PCO_0000035 +obo:PCO_0000035 rdf:type owl:Class ; + rdfs:subClassOf obo:PCO_0000033 ; + obo:IAO_0000115 "A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose."@en ; + obo:IAO_0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030"@en ; + obo:IAO_0000119 "GenEpiO curators"@en ; + rdfs:label "party"@en . + + +### http://purl.obolibrary.org/obo/PCO_0000037 +obo:PCO_0000037 rdf:type owl:Class ; + rdfs:subClassOf obo:PCO_0000033 ; + obo:IAO_0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033"@en ; + obo:IAO_0000119 "A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering."@en , + "GenEpio curators"@en ; + rdfs:label "potluck"@en . + + +### http://purl.obolibrary.org/obo/PCO_0000038 +obo:PCO_0000038 rdf:type owl:Class ; + rdfs:subClassOf obo:PCO_0000033 ; + obo:IAO_0000115 "A human social gathering at which two people are married. May include a legal or social ceremony."@en ; + obo:IAO_0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031"@en ; + obo:IAO_0000119 "GenEpio curators"@en ; + rdfs:label "wedding"@en . + + +### http://purl.obolibrary.org/obo/PCO_0000039 +obo:PCO_0000039 rdf:type owl:Class ; + rdfs:subClassOf obo:PCO_0000033 ; + obo:IAO_0000115 "A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby."@en ; + obo:IAO_0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032"@en ; + obo:IAO_0000119 "GenEpiO curators"@en ; + rdfs:label "baby shower"@en . + + ### http://purl.obolibrary.org/obo/PCO_0001000 obo:PCO_0001000 rdf:type owl:Class ; rdfs:subClassOf obo:BFO_0000040 , diff --git a/src/ontology/pco.owl b/src/ontology/pco.owl index 66ac742..b1e28bd 100644 --- a/src/ontology/pco.owl +++ b/src/ontology/pco.owl @@ -17,7 +17,7 @@ xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"> - + @@ -2238,6 +2238,43 @@ AND t has_input y + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -3903,6 +3940,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + @@ -4684,6 +4723,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + + + @@ -5793,6 +5836,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6116,6 +6160,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b. Chris Mungall inhibits @@ -6133,6 +6182,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + Holds between molecules a and b if and only if a executes a process that directly activates a process executed by b. Chris Mungall activates @@ -10161,8 +10215,16 @@ Environmental exposures include those imposed by natural environments, experimen 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 relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) + 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]) specifically dependent continuant + + + + 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]) + + @@ -10199,6 +10261,7 @@ Environmental exposures include those imposed by natural environments, experimen 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]) generically dependent continuant @@ -10741,6 +10804,7 @@ resulting from the influence of human beings on nature. + @@ -10932,6 +10996,53 @@ resulting from the influence of human beings on nature. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An environmental system which is determined by materials bearing roughly homogeneous qualities. + environmental system determined by a quality + + + + @@ -10974,6 +11085,7 @@ resulting from the influence of human beings on nature. + @@ -11043,6 +11155,114 @@ resulting from the influence of human beings on nature. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An environmental system determined by part of a living or dead plant, or a whole small plant. + environment associated with a plant part or small plant + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An environmental system which includes both living and non-living components. + ecosystem + + + + + An environmental system which includes both living and non-living components. + https://en.wikipedia.org/wiki/Ecosystem + + + + @@ -11061,6 +11281,7 @@ resulting from the influence of human beings on nature. + A process in which includes the components of an environmental system as participants. environmental system process @@ -11131,6 +11352,7 @@ resulting from the influence of human beings on nature. + receptor activity @@ -11148,9 +11370,24 @@ resulting from the influence of human beings on nature. + + The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. + behavioral response to stimulus + behaviour + behavioural response to stimulus + single-organism behavior behavior + + + + The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. + GOC:ems + GOC:jl + ISBN:0395448956 + PMID:20160973 + @@ -11283,6 +11520,27 @@ resulting from the influence of human beings on nature. + + + + + + Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. + social behaviour + cooperative behavior + social behavior + + + + + Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. + GOC:jh2 + PMID:12848939 + Wikipedia:Social_behavior + + + + @@ -11397,6 +11655,12 @@ resulting from the influence of human beings on nature. + + + + + + @@ -11456,8 +11720,27 @@ resulting from the influence of human beings on nature. + Any process in which an organism has a behavioral effect on another organism of the same or different species. + behavioral interaction between organisms + behavioral interaction with other organism + behavioural interaction between organisms + behavioural interaction with other organism + behavioral signaling + behavioral signalling multi-organism behavior + + + + Any process in which an organism has a behavioral effect on another organism of the same or different species. + GOC:ai + + + + + behavioral signalling + GOC:mah + @@ -12823,6 +13106,7 @@ resulting from the influence of human beings on nature. + A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. morphology @@ -12837,6 +13121,35 @@ resulting from the influence of human beings on nature. + + + + + qualitative + + + + + + + + + A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. + deviation(from_normal) + + + + + + + + + A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. + size + + + + @@ -12887,6 +13200,22 @@ resulting from the influence of human beings on nature. + + + + + + A size quality which is relatively low. + hypoplasia + underdeveloped + reduced + small + tiny + decreased size + + + + @@ -13080,6 +13409,27 @@ resulting from the influence of human beings on nature. + + + + + A quality that has a value that is decreased compared to normal or average. + decreased quality + + + + + + + + + + A quality of an object that has a value that is decreased compared to normal or average. + decreased object quality + + + + @@ -13099,7 +13449,6 @@ resulting from the influence of human beings on nature. - @@ -13117,12 +13466,6 @@ resulting from the influence of human beings on nature. collection of organisms collection of organisms - - - - - Consider moving to "object aggregate" - @@ -13309,12 +13652,13 @@ Classes for population already exist in IDO ('organism population', I - - + The maximum number of individuals that can be supported in a population that is growing according to logistic growth. - Might be better to add this as a data property. + Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE. ISBN:0878932739 - carrying capacity + + obsolete carrying capacity + true @@ -13608,7 +13952,7 @@ Classes for population already exist in IDO ('organism population', I - A collection of organisms connected by social or biological relations (biotic interactions). + A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other. Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete. These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). community @@ -13660,6 +14004,18 @@ Classes for population already exist in IDO ('organism population', I + + + + + A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other. + genealogical family + Matthew Brush, as part of http://datamodel.clinicalgenome.org/interpretation/ + biological family + + + + @@ -13790,6 +14146,63 @@ Classes for population already exist in IDO ('organism population', I + + + + + A plant structure (PO:0005679) which is a whole organism. + genet (broad) + ramet (broad) + planta entera (Spanish, exact) + 植物体全体 (Japanese, exact) + bush (narrow) + frutex (narrow) + frutices (narrow) + gametophyte (narrow) + herb (narrow) + liana (narrow) + prothalli (narrow) + prothallium (narrow) + prothallus (narrow) + seedling (narrow) + shrub (narrow) + sporophyte (narrow) + suffrutex (narrow) + suffrutices (narrow) + tree (narrow) + vine (narrow) + woody clump (narrow) + clonal colony (related) + colony (related) + whole plant + + + + + + + + + An anatomical structure that is or was part of a plant, or was derived from a part of a plant. + estructura vegetal (Spanish, exact) + 植物 構造 (Japanese, exact) + plant structure + + + + + + + + + An anatomical entity that is or was part of a plant. + entidad anat&#243mica vegetal (Spanish, exact) + 植物 解剖学（形態）的実体 (Japanese, exact) + plant anatomical entity + + + + @@ -13861,6 +14274,16 @@ Classes for population already exist in IDO ('organism population', I + + + + + 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. + anatomical entity + + + + @@ -14245,6 +14668,14 @@ binary, and takes no temporal argument. + + + + + + + + @@ -14296,16 +14727,40 @@ binary, and takes no temporal argument. - - true - MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z - infer input from direct reg - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + true + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg + + + + + + @@ -14544,6 +14999,63 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + From ligand activity to has_ligand + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" @@ -14589,6 +15101,463 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct neg reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct positive reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From has_ligand to ligand activity + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + effector input is compound function input + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Input of effector is input of its parent MF + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly regulates X, its parent MF directly regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly positively regulates X, its parent MF directly positively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly negatively regulates X, its parent MF directly negatively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +