diff --git a/imports/chebi_import.obo b/imports/chebi_import.obo index 4620704..f7e1c25 100644 --- a/imports/chebi_import.obo +++ b/imports/chebi_import.obo @@ -568,7 +568,6 @@ synonym: "L-Amino acid" RELATED [KEGG_COMPOUND] is_a: CHEBI:33704 ! alpha-amino acid relationship: is_conjugate_acid_of CHEBI:59814 ! L-alpha-amino acid anion relationship: is_tautomer_of CHEBI:59869 ! L-alpha-amino acid zwitterion -relationship: RO:0000087 CHEBI:75771 ! mouse metabolite [Term] id: CHEBI:15734 @@ -5842,7 +5841,7 @@ name: HPODE def: "Hydroperoxy-octadecadienoic acids, formed in mammalian cells by peroxidation of linoleic acid." [] synonym: "HPODEs" RELATED [ChEBI] is_a: CHEBI:36326 ! octadecanoid -is_a: CHEBI:61051 ! lipid hydroperoxide +is_a: CHEBI:64009 ! hydroperoxy fatty acid relationship: has_functional_parent CHEBI:17351 ! linoleic acid relationship: is_conjugate_acid_of CHEBI:131862 ! HPODE(1-) @@ -6908,12 +6907,18 @@ is_a: CHEBI:48354 ! polar solvent [Term] id: CHEBI:48359 name: protophilic solvent +def: "Solvent that is capable of acting as a hydron (proton) acceptor." [] +synonym: "HBA solvent" RELATED [ChEBI] +synonym: "hydrogen bond acceptor solvent" RELATED [ChEBI] +synonym: "protophilic solvent" EXACT IUPAC_NAME [IUPAC] is_a: CHEBI:39142 ! Bronsted base is_a: CHEBI:48354 ! polar solvent [Term] id: CHEBI:48360 name: amphiprotic solvent +def: "Self-ionizing solvent possessing both characteristics of Bronsted acids and bases." [] +synonym: "amphiprotic solvent" EXACT IUPAC_NAME [IUPAC] is_a: CHEBI:48356 ! protic solvent is_a: CHEBI:48359 ! protophilic solvent @@ -7692,9 +7697,10 @@ relationship: RO:0000087 CHEBI:26115 ! phytoalexin [Term] id: CHEBI:61051 name: lipid hydroperoxide -def: "A peroxol that is the primary oxygenated product of a polyunsaturated fatty acid." [] -synonym: "a hydroperoxy-polyunsaturated fatty acid" RELATED [UniProt] +def: "Any lipid carrying one or more hydroperoxy substituents." [] +synonym: "a lipid hydroperoxide" RELATED [UniProt] synonym: "lipid hydroperoxides" RELATED [ChEBI] +is_a: CHEBI:18059 ! lipid is_a: CHEBI:35924 ! peroxol [Term] @@ -7879,6 +7885,23 @@ synonym: "neuroprotectants" RELATED [ChEBI] synonym: "neuroprotective agents" RELATED [ChEBI] is_a: CHEBI:50267 ! protective agent +[Term] +id: CHEBI:64009 +name: hydroperoxy fatty acid +def: "Any fatty acid carrying one or more hydroperoxy substituents." [] +synonym: "hydroperoxy fatty acids" RELATED [ChEBI] +is_a: CHEBI:35366 ! fatty acid +is_a: CHEBI:61051 ! lipid hydroperoxide +relationship: is_conjugate_acid_of CHEBI:64012 ! hydroperoxy fatty acid anion + +[Term] +id: CHEBI:64012 +name: hydroperoxy fatty acid anion +def: "A fatty acid anion that is the conjugate base of any hydroperoxy fatty acid, formed by deprotonation of the carboxylic acid moiety." [] +synonym: "hydroperoxy fatty acid anions" RELATED [ChEBI] +is_a: CHEBI:28868 ! fatty acid anion +relationship: is_conjugate_base_of CHEBI:64009 ! hydroperoxy fatty acid + [Term] id: CHEBI:64047 name: food additive @@ -8712,7 +8735,7 @@ is_a: CHEBI:58953 ! saturated fatty acid anion [Term] id: CHEBI:78295 name: food component -def: "Any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants." [] +def: "A physiological role played by any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants." [] synonym: "dietary component" RELATED [ChEBI] synonym: "dietary components" RELATED [ChEBI] synonym: "food components" RELATED [ChEBI] diff --git a/imports/chebi_import.owl b/imports/chebi_import.owl index e7be3cb..56f7233 100644 --- a/imports/chebi_import.owl +++ b/imports/chebi_import.owl @@ -2521,12 +2521,6 @@ - - - - - - @@ -8416,12 +8410,6 @@ grupos group - - - - grupo - IUPAC - @@ -8453,6 +8441,12 @@ groupe IUPAC + + + + grupo + IUPAC + @@ -23411,7 +23405,7 @@ - + @@ -27137,8 +27131,31 @@ + Solvent that is capable of acting as a hydron (proton) acceptor. + protophilic solvent + HBA solvent + hydrogen bond acceptor solvent protophilic solvent + + + + protophilic solvent + IUPAC + + + + + + HBA solvent + ChEBI + + + + + hydrogen bond acceptor solvent + ChEBI + @@ -27147,8 +27164,17 @@ + Self-ionizing solvent possessing both characteristics of Bronsted acids and bases. + amphiprotic solvent amphiprotic solvent + + + + amphiprotic solvent + IUPAC + + @@ -29651,16 +29677,17 @@ + - A peroxol that is the primary oxygenated product of a polyunsaturated fatty acid. - a hydroperoxy-polyunsaturated fatty acid + Any lipid carrying one or more hydroperoxy substituents. + a lipid hydroperoxide lipid hydroperoxides lipid hydroperoxide - a hydroperoxy-polyunsaturated fatty acid + a lipid hydroperoxide UniProt @@ -30283,6 +30310,53 @@ + + + + + + + + + + + + Any fatty acid carrying one or more hydroperoxy substituents. + hydroperoxy fatty acids + hydroperoxy fatty acid + + + + + hydroperoxy fatty acids + ChEBI + + + + + + + + + + + + + + + A fatty acid anion that is the conjugate base of any hydroperoxy fatty acid, formed by deprotonation of the carboxylic acid moiety. + hydroperoxy fatty acid anions + hydroperoxy fatty acid anion + + + + + hydroperoxy fatty acid anions + ChEBI + + + + @@ -33495,7 +33569,7 @@ - Any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants. + A physiological role played by any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants. dietary component dietary components food components diff --git a/imports/go_import.obo b/imports/go_import.obo index d1f0ece..d598b9a 100644 --- a/imports/go_import.obo +++ b/imports/go_import.obo @@ -53,14 +53,14 @@ is_a: GO:0003674 ! molecular_function id: GO:0003993 name: acid phosphatase activity def: "Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an acid pH optimum." [EC:3.1.3.2] -synonym: "acid monophosphatase activity" EXACT [EC:3.1.3.2] -synonym: "acid nucleoside diphosphate phosphatase activity" EXACT [EC:3.1.3.2] -synonym: "acid phosphohydrolase activity" EXACT [EC:3.1.3.2] -synonym: "acid phosphomonoester hydrolase activity" EXACT [EC:3.1.3.2] -synonym: "acid phosphomonoesterase activity" EXACT [EC:3.1.3.2] +synonym: "acid monophosphatase activity" RELATED [EC:3.1.3.2] +synonym: "acid nucleoside diphosphate phosphatase activity" RELATED [EC:3.1.3.2] +synonym: "acid phosphohydrolase activity" RELATED [EC:3.1.3.2] +synonym: "acid phosphomonoester hydrolase activity" RELATED [EC:3.1.3.2] +synonym: "acid phosphomonoesterase activity" RELATED [EC:3.1.3.2] synonym: "glycerophosphatase activity" BROAD [EC:3.1.3.2] -synonym: "orthophosphoric-monoester phosphohydrolase (acid optimum)" EXACT [EC:3.1.3.2] -synonym: "phosphate-monoester phosphohydrolase (acid optimum)" EXACT [EC:3.1.3.2] +synonym: "orthophosphoric-monoester phosphohydrolase (acid optimum)" RELATED [EC:3.1.3.2] +synonym: "phosphate-monoester phosphohydrolase (acid optimum)" RELATED [EC:3.1.3.2] synonym: "phosphomonoesterase activity" BROAD [EC:3.1.3.2] synonym: "uteroferrin" RELATED [EC:3.1.3.2] is_a: GO:0016791 ! phosphatase activity @@ -76,9 +76,9 @@ is_a: GO:0016798 ! hydrolase activity, acting on glycosyl bonds id: GO:0004556 name: alpha-amylase activity def: "Catalysis of the endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more alpha-(1->4)-linked D-glucose units." [EC:3.2.1.1] -synonym: "1,4-alpha-D-glucan glucanohydrolase activity" EXACT [EC:3.2.1.1] -synonym: "alpha amylase activity" EXACT [EC:3.2.1.1] -synonym: "endoamylase activity" EXACT [EC:3.2.1.1] +synonym: "1,4-alpha-D-glucan glucanohydrolase activity" RELATED [EC:3.2.1.1] +synonym: "alpha amylase activity" RELATED [EC:3.2.1.1] +synonym: "endoamylase activity" RELATED [EC:3.2.1.1] synonym: "glycogenase activity" BROAD [EC:3.2.1.1] synonym: "taka-amylase A" RELATED [EC:3.2.1.1] is_a: GO:0016160 ! amylase activity @@ -134,20 +134,21 @@ synonym: "subcellular entity" RELATED [NIF_Subcellular:nlx_subcell_100315] [Term] id: GO:0005622 -name: intracellular -def: "The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm." [ISBN:0198506732] +name: intracellular anatomical structure +def: "A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm." [ISBN:0198506732] synonym: "internal to cell" EXACT [] +synonym: "intracellular" EXACT [] synonym: "nucleocytoplasm" RELATED [GOC:mah] synonym: "protoplasm" EXACT [] synonym: "protoplast" RELATED [GOC:mah] -is_a: GO:0005575 ! cellular_component +is_a: GO:0110165 ! cellular anatomical entity [Term] id: GO:0005737 name: cytoplasm def: "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN:0198547684] is_a: GO:0110165 ! cellular anatomical entity -relationship: BFO:0000050 GO:0005622 ! intracellular +relationship: BFO:0000050 GO:0005622 ! intracellular anatomical structure [Term] id: GO:0005886 @@ -347,19 +348,19 @@ is_a: GO:0016757 ! transferase activity, transferring glycosyl groups id: GO:0008878 name: glucose-1-phosphate adenylyltransferase activity def: "Catalysis of the reaction: alpha-D-glucose 1-phosphate + ATP = ADP-glucose + diphosphate." [EC:2.7.7.27, RHEA:12120] -synonym: "adenosine diphosphate glucose pyrophosphorylase activity" EXACT [EC:2.7.7.27] -synonym: "adenosine diphosphoglucose pyrophosphorylase activity" EXACT [EC:2.7.7.27] +synonym: "adenosine diphosphate glucose pyrophosphorylase activity" RELATED [EC:2.7.7.27] +synonym: "adenosine diphosphoglucose pyrophosphorylase activity" RELATED [EC:2.7.7.27] synonym: "ADGase activity" EXACT [] -synonym: "ADP glucose pyrophosphorylase activity" EXACT [EC:2.7.7.27] -synonym: "ADP-glucose diphosphorylase activity" EXACT [EC:2.7.7.27] -synonym: "ADP-glucose pyrophosphorylase activity" EXACT [EC:2.7.7.27] -synonym: "ADP-glucose synthase activity" EXACT [EC:2.7.7.27] -synonym: "ADP-glucose synthetase activity" EXACT [EC:2.7.7.27] -synonym: "ADP:alpha-D-glucose-1-phosphate adenylyltransferase activity" EXACT [EC:2.7.7.27] +synonym: "ADP glucose pyrophosphorylase activity" RELATED [EC:2.7.7.27] +synonym: "ADP-glucose diphosphorylase activity" RELATED [EC:2.7.7.27] +synonym: "ADP-glucose pyrophosphorylase activity" RELATED [EC:2.7.7.27] +synonym: "ADP-glucose synthase activity" RELATED [EC:2.7.7.27] +synonym: "ADP-glucose synthetase activity" RELATED [EC:2.7.7.27] +synonym: "ADP:alpha-D-glucose-1-phosphate adenylyltransferase activity" RELATED [EC:2.7.7.27] synonym: "ADPG pyrophosphorylase activity" EXACT [] -synonym: "ATP:alpha-D-glucose-1-phosphate adenylyltransferase activity" EXACT [EC:2.7.7.27] +synonym: "ATP:alpha-D-glucose-1-phosphate adenylyltransferase activity" RELATED [EC:2.7.7.27] synonym: "ATP:alpha-glucose-1-phosphate adenylyl transferase activity" EXACT [] -synonym: "glucose 1-phosphate adenylyltransferase activity" EXACT [EC:2.7.7.27] +synonym: "glucose 1-phosphate adenylyltransferase activity" RELATED [EC:2.7.7.27] is_a: GO:0070566 ! adenylyltransferase activity [Term] @@ -579,6 +580,9 @@ relationship: RO:0002211 GO:0016791 ! phosphatase activity id: GO:0016020 name: membrane def: "A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it." [GOC:dos, GOC:mah, ISBN:0815316194] +synonym: "membrane region" NARROW [] +synonym: "region of membrane" NARROW [] +synonym: "whole membrane" NARROW [] is_a: GO:0110165 ! cellular anatomical entity [Term] @@ -597,13 +601,13 @@ is_a: GO:0071840 ! cellular component organization or biogenesis id: GO:0016157 name: sucrose synthase activity def: "Catalysis of the reaction: UDP-glucose + D-fructose = UDP + sucrose." [EC:2.4.1.13] -synonym: "NDP-glucose:D-fructose 2-alpha-D-glucosyltransferase activity" EXACT [EC:2.4.1.13] -synonym: "sucrose synthetase activity" EXACT [EC:2.4.1.13] -synonym: "sucrose-UDP glucosyltransferase activity" EXACT [EC:2.4.1.13] -synonym: "sucrose-uridine diphosphate glucosyltransferase activity" EXACT [EC:2.4.1.13] -synonym: "UDP-glucose-fructose glucosyltransferase activity" EXACT [EC:2.4.1.13] -synonym: "UDPglucose-fructose glucosyltransferase activity" EXACT [EC:2.4.1.13] -synonym: "uridine diphosphoglucose-fructose glucosyltransferase activity" EXACT [EC:2.4.1.13] +synonym: "NDP-glucose:D-fructose 2-alpha-D-glucosyltransferase activity" RELATED [EC:2.4.1.13] +synonym: "sucrose synthetase activity" RELATED [EC:2.4.1.13] +synonym: "sucrose-UDP glucosyltransferase activity" RELATED [EC:2.4.1.13] +synonym: "sucrose-uridine diphosphate glucosyltransferase activity" RELATED [EC:2.4.1.13] +synonym: "UDP-glucose-fructose glucosyltransferase activity" RELATED [EC:2.4.1.13] +synonym: "UDPglucose-fructose glucosyltransferase activity" RELATED [EC:2.4.1.13] +synonym: "uridine diphosphoglucose-fructose glucosyltransferase activity" RELATED [EC:2.4.1.13] is_a: GO:0035251 ! UDP-glucosyltransferase activity [Term] @@ -616,10 +620,10 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds id: GO:0016161 name: beta-amylase activity def: "Catalysis of the reaction: (1,4-alpha-D-glucosyl)(n+1) + H2O = (1,4-alpha-D-glucosyl)(n-1) + alpha-maltose. This reaction is the hydrolysis of 1,4-alpha-glucosidic linkages in polysaccharides so as to remove successive maltose units from the non-reducing ends of the chains." [EC:3.2.1.2] -synonym: "1,4-alpha-D-glucan maltohydrolase activity" EXACT [EC:3.2.1.2] -synonym: "beta amylase activity" EXACT [EC:3.2.1.2] +synonym: "1,4-alpha-D-glucan maltohydrolase activity" RELATED [EC:3.2.1.2] +synonym: "beta amylase activity" RELATED [EC:3.2.1.2] synonym: "glycogenase activity" BROAD [EC:3.2.1.2] -synonym: "saccharogen amylase activity" EXACT [EC:3.2.1.2] +synonym: "saccharogen amylase activity" RELATED [EC:3.2.1.2] is_a: GO:0016160 ! amylase activity [Term] @@ -967,8 +971,8 @@ name: intracellular organelle def: "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:go_curators] is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle -intersection_of: BFO:0000050 GO:0005622 ! intracellular -relationship: BFO:0000050 GO:0005622 ! intracellular +intersection_of: BFO:0000050 GO:0005622 ! intracellular anatomical structure +relationship: BFO:0000050 GO:0005622 ! intracellular anatomical structure [Term] id: GO:0043231 @@ -1048,15 +1052,15 @@ id: GO:0046524 name: sucrose-phosphate synthase activity def: "Catalysis of the reaction: UDP-glucose + D-fructose 6-phosphate = UDP + sucrose 6-phosphate." [EC:2.4.1.14] synonym: "SPS" RELATED [EC:2.4.1.14] -synonym: "sucrose 6-phosphate synthase activity" EXACT [EC:2.4.1.14] -synonym: "sucrose phosphate synthetase activity" EXACT [EC:2.4.1.14] -synonym: "sucrose phosphate-uridine diphosphate glucosyltransferase activity" EXACT [EC:2.4.1.14] -synonym: "sucrosephosphate-UDP glucosyltransferase activity" EXACT [EC:2.4.1.14] -synonym: "UDP-glucose-fructose-phosphate glucosyltransferase activity" EXACT [EC:2.4.1.14] -synonym: "UDP-glucose:D-fructose-6-phosphate 2-alpha-D-glucosyltransferase activity" EXACT [EC:2.4.1.14] -synonym: "UDPglucose-fructose-phosphate glucosyltransferase activity" EXACT [EC:2.4.1.14] -synonym: "UDPglucose:D-fructose-6-phosphate 2-alpha-D-glucosyltransferase activity" EXACT [EC:2.4.1.14] -synonym: "uridine diphosphoglucose-fructose phosphate glucosyltransferase activity" EXACT [EC:2.4.1.14] +synonym: "sucrose 6-phosphate synthase activity" RELATED [EC:2.4.1.14] +synonym: "sucrose phosphate synthetase activity" RELATED [EC:2.4.1.14] +synonym: "sucrose phosphate-uridine diphosphate glucosyltransferase activity" RELATED [EC:2.4.1.14] +synonym: "sucrosephosphate-UDP glucosyltransferase activity" RELATED [EC:2.4.1.14] +synonym: "UDP-glucose-fructose-phosphate glucosyltransferase activity" RELATED [EC:2.4.1.14] +synonym: "UDP-glucose:D-fructose-6-phosphate 2-alpha-D-glucosyltransferase activity" RELATED [EC:2.4.1.14] +synonym: "UDPglucose-fructose-phosphate glucosyltransferase activity" RELATED [EC:2.4.1.14] +synonym: "UDPglucose:D-fructose-6-phosphate 2-alpha-D-glucosyltransferase activity" RELATED [EC:2.4.1.14] +synonym: "uridine diphosphoglucose-fructose phosphate glucosyltransferase activity" RELATED [EC:2.4.1.14] is_a: GO:0035251 ! UDP-glucosyltransferase activity [Term] @@ -1181,7 +1185,7 @@ id: GO:0048831 name: regulation of shoot system development def: "Any process that modulates the frequency, rate or extent of shoot development." [GOC:tb, PMID:16361392] synonym: "regulation of shoot development" EXACT [] -is_a: GO:2000026 ! regulation of multicellular organismal development +is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0008150 ! biological_process intersection_of: RO:0002211 GO:0048367 ! shoot system development relationship: RO:0002211 GO:0048367 ! shoot system development @@ -1552,6 +1556,7 @@ relationship: BFO:0000051 GO:0098590 ! plasma membrane region id: GO:0140013 name: meiotic nuclear division def: "One of the two nuclear divisions that occur as part of the meiotic cell cycle." [PMID:9334324] +synonym: "meiosis" EXACT [] is_a: GO:0000280 ! nuclear division is_a: GO:1903046 ! meiotic cell cycle process intersection_of: GO:0000280 ! nuclear division @@ -1561,6 +1566,7 @@ intersection_of: BFO:0000050 GO:0051321 ! meiotic cell cycle id: GO:0140014 name: mitotic nuclear division def: "A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell." [ISBN:0198547684] +synonym: "mitosis" EXACT [] is_a: GO:0000280 ! nuclear division is_a: GO:1903047 ! mitotic cell cycle process intersection_of: GO:0000280 ! nuclear division @@ -1570,7 +1576,7 @@ intersection_of: BFO:0000050 GO:0000278 ! mitotic cell cycle id: GO:1900055 name: regulation of leaf senescence def: "Any process that modulates the frequency, rate or extent of leaf senescence." [GOC:TermGenie] -is_a: GO:2000024 ! regulation of leaf development +is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0008150 ! biological_process intersection_of: RO:0002211 GO:0010150 ! leaf senescence relationship: RO:0002211 GO:0010150 ! leaf senescence @@ -1669,7 +1675,7 @@ relationship: BFO:0000050 GO:0000278 ! mitotic cell cycle id: GO:2000024 name: regulation of leaf development def: "Any process that modulates the frequency, rate or extent of leaf development." [GOC:obol] -is_a: GO:0048831 ! regulation of shoot system development +is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0008150 ! biological_process intersection_of: RO:0002211 GO:0048366 ! leaf development relationship: RO:0002211 GO:0048366 ! leaf development @@ -1697,7 +1703,7 @@ relationship: RO:0002211 GO:0022414 ! reproductive process id: GO:2000280 name: regulation of root development def: "Any process that modulates the frequency, rate or extent of root development." [GOC:obol] -is_a: GO:2000026 ! regulation of multicellular organismal development +is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0008150 ! biological_process intersection_of: RO:0002211 GO:0048364 ! root development relationship: RO:0002211 GO:0048364 ! root development diff --git a/imports/go_import.owl b/imports/go_import.owl index 82b3c2d..c71aa03 100644 --- a/imports/go_import.owl +++ b/imports/go_import.owl @@ -271,13 +271,13 @@ Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an acid pH optimum. glycerophosphatase activity phosphomonoesterase activity - acid monophosphatase activity - acid nucleoside diphosphate phosphatase activity - acid phosphohydrolase activity - acid phosphomonoester hydrolase activity - acid phosphomonoesterase activity - orthophosphoric-monoester phosphohydrolase (acid optimum) - phosphate-monoester phosphohydrolase (acid optimum) + acid monophosphatase activity + acid nucleoside diphosphate phosphatase activity + acid phosphohydrolase activity + acid phosphomonoester hydrolase activity + acid phosphomonoesterase activity + orthophosphoric-monoester phosphohydrolase (acid optimum) + phosphate-monoester phosphohydrolase (acid optimum) uteroferrin acid phosphatase activity @@ -301,43 +301,43 @@ - + acid monophosphatase activity EC:3.1.3.2 - + acid nucleoside diphosphate phosphatase activity EC:3.1.3.2 - + acid phosphohydrolase activity EC:3.1.3.2 - + acid phosphomonoester hydrolase activity EC:3.1.3.2 - + acid phosphomonoesterase activity EC:3.1.3.2 - + orthophosphoric-monoester phosphohydrolase (acid optimum) EC:3.1.3.2 - + phosphate-monoester phosphohydrolase (acid optimum) EC:3.1.3.2 @@ -373,9 +373,9 @@ Catalysis of the endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more alpha-(1->4)-linked D-glucose units. glycogenase activity - 1,4-alpha-D-glucan glucanohydrolase activity - alpha amylase activity - endoamylase activity + 1,4-alpha-D-glucan glucanohydrolase activity + alpha amylase activity + endoamylase activity taka-amylase A alpha-amylase activity @@ -393,19 +393,19 @@ - + 1,4-alpha-D-glucan glucanohydrolase activity EC:3.2.1.1 - + alpha amylase activity EC:3.2.1.1 - + endoamylase activity EC:3.2.1.1 @@ -532,18 +532,19 @@ - - The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. + + A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm. internal to cell + intracellular protoplasm nucleocytoplasm protoplast - intracellular + intracellular anatomical structure - The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. + A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm. ISBN:0198506732 @@ -1108,23 +1109,23 @@ Catalysis of the reaction: alpha-D-glucose 1-phosphate + ATP = ADP-glucose + diphosphate. ADGase activity - ADP glucose pyrophosphorylase activity - ADP-glucose diphosphorylase activity - ADP-glucose pyrophosphorylase activity - ADP-glucose synthase activity - ADP-glucose synthetase activity - ADP:alpha-D-glucose-1-phosphate adenylyltransferase activity ADPG pyrophosphorylase activity - ATP:alpha-D-glucose-1-phosphate adenylyltransferase activity ATP:alpha-glucose-1-phosphate adenylyl transferase activity - adenosine diphosphate glucose pyrophosphorylase activity - adenosine diphosphoglucose pyrophosphorylase activity - glucose 1-phosphate adenylyltransferase activity + ADP glucose pyrophosphorylase activity + ADP-glucose diphosphorylase activity + ADP-glucose pyrophosphorylase activity + ADP-glucose synthase activity + ADP-glucose synthetase activity + ADP:alpha-D-glucose-1-phosphate adenylyltransferase activity + ATP:alpha-D-glucose-1-phosphate adenylyltransferase activity + adenosine diphosphate glucose pyrophosphorylase activity + adenosine diphosphoglucose pyrophosphorylase activity + glucose 1-phosphate adenylyltransferase activity glucose-1-phosphate adenylyltransferase activity - + glucose 1-phosphate adenylyltransferase activity EC:2.7.7.27 @@ -1137,55 +1138,55 @@ - + ADP glucose pyrophosphorylase activity EC:2.7.7.27 - + ADP-glucose diphosphorylase activity EC:2.7.7.27 - + ADP-glucose pyrophosphorylase activity EC:2.7.7.27 - + ADP-glucose synthase activity EC:2.7.7.27 - + ADP-glucose synthetase activity EC:2.7.7.27 - + ADP:alpha-D-glucose-1-phosphate adenylyltransferase activity EC:2.7.7.27 - + ATP:alpha-D-glucose-1-phosphate adenylyltransferase activity EC:2.7.7.27 - + adenosine diphosphate glucose pyrophosphorylase activity EC:2.7.7.27 - + adenosine diphosphoglucose pyrophosphorylase activity EC:2.7.7.27 @@ -1797,6 +1798,9 @@ A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. + membrane region + region of membrane + whole membrane membrane @@ -1857,13 +1861,13 @@ Catalysis of the reaction: UDP-glucose + D-fructose = UDP + sucrose. - NDP-glucose:D-fructose 2-alpha-D-glucosyltransferase activity - UDP-glucose-fructose glucosyltransferase activity - UDPglucose-fructose glucosyltransferase activity - sucrose synthetase activity - sucrose-UDP glucosyltransferase activity - sucrose-uridine diphosphate glucosyltransferase activity - uridine diphosphoglucose-fructose glucosyltransferase activity + NDP-glucose:D-fructose 2-alpha-D-glucosyltransferase activity + UDP-glucose-fructose glucosyltransferase activity + UDPglucose-fructose glucosyltransferase activity + sucrose synthetase activity + sucrose-UDP glucosyltransferase activity + sucrose-uridine diphosphate glucosyltransferase activity + uridine diphosphoglucose-fructose glucosyltransferase activity sucrose synthase activity @@ -1874,43 +1878,43 @@ - + NDP-glucose:D-fructose 2-alpha-D-glucosyltransferase activity EC:2.4.1.13 - + UDP-glucose-fructose glucosyltransferase activity EC:2.4.1.13 - + UDPglucose-fructose glucosyltransferase activity EC:2.4.1.13 - + sucrose synthetase activity EC:2.4.1.13 - + sucrose-UDP glucosyltransferase activity EC:2.4.1.13 - + sucrose-uridine diphosphate glucosyltransferase activity EC:2.4.1.13 - + uridine diphosphoglucose-fructose glucosyltransferase activity EC:2.4.1.13 @@ -1939,9 +1943,9 @@ Catalysis of the reaction: (1,4-alpha-D-glucosyl)(n+1) + H2O = (1,4-alpha-D-glucosyl)(n-1) + alpha-maltose. This reaction is the hydrolysis of 1,4-alpha-glucosidic linkages in polysaccharides so as to remove successive maltose units from the non-reducing ends of the chains. glycogenase activity - 1,4-alpha-D-glucan maltohydrolase activity - beta amylase activity - saccharogen amylase activity + 1,4-alpha-D-glucan maltohydrolase activity + beta amylase activity + saccharogen amylase activity beta-amylase activity @@ -1958,19 +1962,19 @@ - + 1,4-alpha-D-glucan maltohydrolase activity EC:3.2.1.2 - + beta amylase activity EC:3.2.1.2 - + saccharogen amylase activity EC:3.2.1.2 @@ -3190,16 +3194,16 @@ Catalysis of the reaction: UDP-glucose + D-fructose 6-phosphate = UDP + sucrose 6-phosphate. - UDP-glucose-fructose-phosphate glucosyltransferase activity - UDP-glucose:D-fructose-6-phosphate 2-alpha-D-glucosyltransferase activity - UDPglucose-fructose-phosphate glucosyltransferase activity - UDPglucose:D-fructose-6-phosphate 2-alpha-D-glucosyltransferase activity - sucrose 6-phosphate synthase activity - sucrose phosphate synthetase activity - sucrose phosphate-uridine diphosphate glucosyltransferase activity - sucrosephosphate-UDP glucosyltransferase activity - uridine diphosphoglucose-fructose phosphate glucosyltransferase activity SPS + UDP-glucose-fructose-phosphate glucosyltransferase activity + UDP-glucose:D-fructose-6-phosphate 2-alpha-D-glucosyltransferase activity + UDPglucose-fructose-phosphate glucosyltransferase activity + UDPglucose:D-fructose-6-phosphate 2-alpha-D-glucosyltransferase activity + sucrose 6-phosphate synthase activity + sucrose phosphate synthetase activity + sucrose phosphate-uridine diphosphate glucosyltransferase activity + sucrosephosphate-UDP glucosyltransferase activity + uridine diphosphoglucose-fructose phosphate glucosyltransferase activity sucrose-phosphate synthase activity @@ -3210,62 +3214,62 @@ - + + SPS + EC:2.4.1.14 + + + + UDP-glucose-fructose-phosphate glucosyltransferase activity EC:2.4.1.14 - + UDP-glucose:D-fructose-6-phosphate 2-alpha-D-glucosyltransferase activity EC:2.4.1.14 - + UDPglucose-fructose-phosphate glucosyltransferase activity EC:2.4.1.14 - + UDPglucose:D-fructose-6-phosphate 2-alpha-D-glucosyltransferase activity EC:2.4.1.14 - + sucrose 6-phosphate synthase activity EC:2.4.1.14 - + sucrose phosphate synthetase activity EC:2.4.1.14 - + sucrose phosphate-uridine diphosphate glucosyltransferase activity EC:2.4.1.14 - + sucrosephosphate-UDP glucosyltransferase activity EC:2.4.1.14 - - - - uridine diphosphoglucose-fructose phosphate glucosyltransferase activity - EC:2.4.1.14 - - SPS + uridine diphosphoglucose-fructose phosphate glucosyltransferase activity EC:2.4.1.14 @@ -3657,7 +3661,7 @@ - + @@ -4846,6 +4850,7 @@ One of the two nuclear divisions that occur as part of the meiotic cell cycle. + meiosis meiotic nuclear division @@ -4874,6 +4879,7 @@ A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. + mitosis mitotic nuclear division @@ -4899,7 +4905,7 @@ - + @@ -5269,7 +5275,7 @@ - + @@ -5369,7 +5375,7 @@ - + diff --git a/imports/peco_import.obo b/imports/peco_import.obo index e967b84..6986c95 100644 --- a/imports/peco_import.obo +++ b/imports/peco_import.obo @@ -1,6 +1,6 @@ format-version: 1.2 ontology: to/imports/peco_import -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: ()\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (antibiotic exposure)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))\n\n# Class: (cytokinin exposure)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))\n\n# Class: (auxin exposure)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))\n\n# Class: (fertilizer exposure)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))\n\n# Class: (growth hormone exposure)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))\n\n# Class: (pesticide exposure)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))\n\n# Class: (herbicide exposure)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))\n\n# Class: (micronutrient exposure)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))\n\n# Class: (insecticide exposure)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"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\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"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\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"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.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: ()\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (antimicrobial agent exposure)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))\n\n# Class: (cytokinin exposure)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))\n\n# Class: (auxin exposure)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))\n\n# Class: (fertilizer exposure)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))\n\n# Class: (growth hormone exposure)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))\n\n# Class: (pesticide exposure)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))\n\n# Class: (herbicide exposure)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))\n\n# Class: (micronutrient exposure)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))\n\n# Class: (insecticide exposure)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"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\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"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\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"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.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\n) [Term] id: BFO:0000001 @@ -3637,7 +3637,7 @@ def: "An inorganic chemical exposure (PECO:0001004) involving the application of synonym: "inorganic anion treatment (narrow)" NARROW [] is_a: PECO:0001004 ! inorganic chemical exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 CHEBI:24834 ! inorganic anion +intersection_of: RO:0002309 CHEBI:24834 ! inorganic anion [Term] id: PECO:0001019 @@ -3663,7 +3663,9 @@ is_a: PECO:0001036 ! chemical stress exposure [Term] id: PECO:0007041 name: antibiotic exposure +name: antimicrobial agent exposure def: "A chemical exposure (PECO:0007189) involving the use of antibiotic for selection purposes." [Gramene:pankaj_jaiswal, TO:moorel] +def: "An exposure to a chemical that has the role of antimicrobial agent" [] synonym: "antibiotic treatment (narrow)" NARROW [] is_a: PECO:0007189 ! chemical exposure @@ -3743,6 +3745,7 @@ is_a: PECO:0001001 ! plant exposure id: PECO:0007066 name: cytokinin exposure def: "A growth hormone exposure (PECO:0007165) involving the use of cytokinin (or its homolog) growth hormone." [Gramene:pankaj_jaiswal] +def: "An exposure to a chemical that has the role of cytokinin" [] synonym: "6-benzylaminopurine (related)" RELATED [] synonym: "cytokinin treatment (narrow)" NARROW [] synonym: "N-benzyl-adenine (related)" RELATED [] @@ -3757,12 +3760,13 @@ synonym: "ethylene treatment (narrow)" NARROW [] is_a: PECO:0001019 ! organic gas exposure is_a: PECO:0007165 ! growth hormone exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 CHEBI:29362 ! ethylene group +intersection_of: RO:0002309 CHEBI:29362 ! ethylene group [Term] id: PECO:0007074 name: auxin exposure def: "A growth hormone exposure (PECO:0007165) involving the use of auxin (or its homolog)." [Gramene:pankaj_jaiswal] +def: "An exposure to a chemical that has the role of auxin" [] synonym: "auxin treatment (narrow)" NARROW [] is_a: PECO:0007165 ! growth hormone exposure @@ -3774,12 +3778,13 @@ synonym: "JA regimen (related)" RELATED [] synonym: "jasmonic acid treatment (narrow)" NARROW [] is_a: PECO:0007165 ! growth hormone exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 CHEBI:18292 ! jasmonic acid +intersection_of: RO:0002309 CHEBI:18292 ! jasmonic acid [Term] id: PECO:0007085 name: fertilizer exposure def: "A plant nutrient exposure (PECO:0007241) involving the use of a fertilizer, a combination of plant nutrients." [Gramene:pankaj_jaiswal] +def: "An exposure to a chemical that has the role of fertilizer" [] synonym: "fertilizer treatment (narrow)" NARROW [] is_a: PECO:0007241 ! plant nutrient exposure @@ -3805,7 +3810,7 @@ synonym: "ABA regimen (related)" RELATED [] synonym: "abscisic acid treatment (narrow)" NARROW [] is_a: PECO:0007165 ! growth hormone exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 CHEBI:22152 ! 2-cis-abscisic acid +intersection_of: RO:0002309 CHEBI:22152 ! 2-cis-abscisic acid [Term] id: PECO:0007107 @@ -3815,7 +3820,7 @@ synonym: "ascomycetes (related)" RELATED [] synonym: "Ascomycota treatment (narrow)" NARROW [] is_a: PECO:0007233 ! fungal plant exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 NCBITaxon:4890 ! Ascomycota +intersection_of: RO:0002309 NCBITaxon:4890 ! Ascomycota [Term] id: PECO:0007109 @@ -3832,7 +3837,7 @@ synonym: "dsRNA nonenveloped viruses (related)" RELATED [] synonym: "dsRNA virus treatment (narrow)" NARROW [] is_a: PECO:0007210 ! virus plant exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 NCBITaxon:35325 ! dsRNA viruses +intersection_of: RO:0002309 NCBITaxon:35325 ! dsRNA viruses [Term] id: PECO:0007114 @@ -3920,7 +3925,7 @@ synonym: "light regimen (related)" RELATED [] synonym: "radiation treatment (narrow)" NARROW [] is_a: PECO:0007316 ! physical plant exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 CHEBI:30212 ! photon +intersection_of: RO:0002309 CHEBI:30212 ! photon [Term] id: PECO:0007154 @@ -3933,6 +3938,7 @@ is_a: PECO:0007151 ! radiation exposure id: PECO:0007165 name: growth hormone exposure def: "A chemical exposure (PECO:0007189) involving the application of one or more plant growth hormones." [Gramene:pankaj_jaiswal] +def: "An exposure to a chemical that has the role of growth hormone" [] synonym: "growth hormone treatment (narrow)" NARROW [] is_a: PECO:0007189 ! chemical exposure @@ -3940,6 +3946,7 @@ is_a: PECO:0007189 ! chemical exposure id: PECO:0007167 name: pesticide exposure def: "A chemical exposure (PECO:0007189) involving the application of a pesticide; a chemical entity or mixture of chemical entities." [Gramene:pankaj_jaiswal] +def: "An exposure to a chemical that has the role of pesticide" [] synonym: "pesticide treatment (narrow)" NARROW [] is_a: PECO:0007189 ! chemical exposure @@ -3989,12 +3996,13 @@ synonym: "Weedone-2,4-DP (related)" RELATED [CAS:94-75-7] is_a: PECO:0007074 ! auxin exposure is_a: PECO:0007183 ! herbicide exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 CHEBI:19351 ! (2,4-dichlorophenoxy)acetate +intersection_of: RO:0002309 CHEBI:19351 ! (2,4-dichlorophenoxy)acetate [Term] id: PECO:0007183 name: herbicide exposure def: "A pesticide exposure (PECO:0007167) involving the application of a herbicide; a chemical entity or mixture of chemical entities." [Gramene:pankaj_jaiswal] +def: "An exposure to a chemical that has the role of herbicide" [] synonym: "herbicide treatment (narrow)" NARROW [] is_a: PECO:0007167 ! pesticide exposure @@ -4005,7 +4013,7 @@ def: "A chemical exposure (PECO:0007189) involving use of salts as supplement to synonym: "salt treatment (narrow)" NARROW [] is_a: PECO:0007189 ! chemical exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 CHEBI:24866 ! salt +intersection_of: RO:0002309 CHEBI:24866 ! salt [Term] id: PECO:0007189 @@ -4076,7 +4084,7 @@ synonym: "Dreschlera oryzae (related)" RELATED [] synonym: "Helminthosporium oryzae (related)" RELATED [] is_a: PECO:0007055 ! Cochliobolus spp. exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 NCBITaxon:101162 ! Bipolaris oryzae +intersection_of: RO:0002309 NCBITaxon:101162 ! Bipolaris oryzae [Term] id: PECO:0007212 @@ -4124,7 +4132,7 @@ synonym: "Pyricularia oryzae (related)" RELATED [] synonym: "rice blast fungus (related)" RELATED [] is_a: PECO:0007135 ! Magnaporthe spp. exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 NCBITaxon:148305 ! Magnaporthe grisea +intersection_of: RO:0002309 NCBITaxon:148305 ! Magnaporthe grisea [Term] id: PECO:0007228 @@ -4142,7 +4150,7 @@ synonym: "Fusarium moniliforme (related)" RELATED [] synonym: "Gibberella fujikuroi treatment (narrow)" NARROW [] is_a: PECO:0007341 ! Fusarium exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 NCBITaxon:117187 ! Fusarium verticillioides +intersection_of: RO:0002309 NCBITaxon:117187 ! Fusarium verticillioides [Term] id: PECO:0007230 @@ -4175,6 +4183,7 @@ is_a: PECO:0007047 ! other nutrient exposure [Term] id: PECO:0007239 name: micronutrient exposure +def: "An exposure to a chemical that has the role of micronutrient" [] def: "The treatment involving exposure of plant to elements that are required in tiny quantities for growth, as supplement to study various types of responses." [Gramene:pankaj_jaiswal] synonym: "micronutrient treatment (narrow)" NARROW [] synonym: "trace element regimen (related)" RELATED [] @@ -4244,7 +4253,7 @@ def: "The treatment involving exposure of plant to oxygen to study various types synonym: "oxygen treatment (narrow)" NARROW [] is_a: PECO:0007043 ! non-mineral nutrient exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 CHEBI:25805 ! oxygen atom +intersection_of: RO:0002309 CHEBI:25805 ! oxygen atom [Term] id: PECO:0007284 @@ -4360,7 +4369,7 @@ synonym: "rice yellow mottle virus treatment (narrow)" NARROW [] synonym: "RYMV (related)" RELATED [] is_a: PECO:0007109 ! ssRNA positive-strand virus with no DNA stage exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 NCBITaxon:31744 ! Rice yellow mottle virus +intersection_of: RO:0002309 NCBITaxon:31744 ! Rice yellow mottle virus [Term] id: PECO:0007333 @@ -4371,7 +4380,7 @@ synonym: "insect plant treatment (narrow)" NARROW [] synonym: "true insects (related)" RELATED [] is_a: PECO:0007349 ! metazoan plant exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 NCBITaxon:50557 ! Insecta +intersection_of: RO:0002309 NCBITaxon:50557 ! Insecta [Term] id: PECO:0007337 @@ -4382,7 +4391,7 @@ synonym: "round worm (related)" RELATED [] synonym: "roundworm (related)" RELATED [] is_a: PECO:0007349 ! metazoan plant exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 NCBITaxon:6231 ! Nematoda +intersection_of: RO:0002309 NCBITaxon:6231 ! Nematoda [Term] id: PECO:0007341 @@ -4392,7 +4401,7 @@ synonym: "Fusarium spp. (related)" RELATED [] synonym: "Fusarium treatment (narrow)" NARROW [] is_a: PECO:0007118 ! Gibberella spp. exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 NCBITaxon:5506 ! Fusarium +intersection_of: RO:0002309 NCBITaxon:5506 ! Fusarium [Term] id: PECO:0007349 @@ -4402,7 +4411,7 @@ synonym: "Animalia (related)" RELATED [] synonym: "metazoan plant treatment (narrow)" NARROW [] is_a: PECO:0007357 ! biotic plant exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 NCBITaxon:33208 ! Metazoa +intersection_of: RO:0002309 NCBITaxon:33208 ! Metazoa [Term] id: PECO:0007357 @@ -4439,7 +4448,7 @@ synonym: "Nakataea sigmoidae (related)" RELATED [] synonym: "Sclerotium oryzae (related)" RELATED [] is_a: PECO:0007135 ! Magnaporthe spp. exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 NCBITaxon:165778 ! Nakataea oryzae +intersection_of: RO:0002309 NCBITaxon:165778 ! Nakataea oryzae [Term] id: PECO:0007371 @@ -4449,7 +4458,7 @@ synonym: "Meloidogyne javanica treatment (narrow)" NARROW [] synonym: "root-knot nematode (related)" RELATED [] is_a: PECO:0007127 ! Meloidogyne spp. exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 NCBITaxon:6303 ! Meloidogyne javanica +intersection_of: RO:0002309 NCBITaxon:6303 ! Meloidogyne javanica [Term] id: PECO:0007372 @@ -4459,7 +4468,7 @@ synonym: "Meloidogyne incognita treatment (narrow)" NARROW [] synonym: "southern root-knot nematode (related)" RELATED [] is_a: PECO:0007127 ! Meloidogyne spp. exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 NCBITaxon:6306 ! Meloidogyne incognita +intersection_of: RO:0002309 NCBITaxon:6306 ! Meloidogyne incognita [Term] id: PECO:0007387 @@ -4477,7 +4486,7 @@ synonym: "flood prone region treatment (narrow)" NARROW [] synonym: "flooding (related)" RELATED [] is_a: PECO:0007064 ! ecological environment exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 ENVO:02500002 ! flooding +intersection_of: RO:0002309 ENVO:02500002 ! flooding [Term] id: PECO:0007397 @@ -4499,7 +4508,7 @@ synonym: "nitrate treatment (narrow)" NARROW [] is_a: PECO:0001009 ! inorganic anion exposure is_a: PECO:0007102 ! nitrogen fertilizer exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 CHEBI:17632 ! nitrate +intersection_of: RO:0002309 CHEBI:17632 ! nitrate [Term] id: PECO:0007409 @@ -4508,7 +4517,7 @@ def: "A growth hormone exposure (PECO:0007165) involving the use of brassinoster synonym: "brassinosteroid treatment (narrow)" NARROW [] is_a: PECO:0007165 ! growth hormone exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 CHEBI:22921 ! brassinosteroid +intersection_of: RO:0002309 CHEBI:22921 ! brassinosteroid [Term] id: PECO:0007629 @@ -4517,12 +4526,13 @@ def: "An exposure involving exposure of plant to molecular or ionic forms of hyd synonym: "hydrogen treatment (narrow)" NARROW [] is_a: PECO:0007043 ! non-mineral nutrient exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 CHEBI:49637 ! hydrogen atom +intersection_of: RO:0002309 CHEBI:49637 ! hydrogen atom [Term] id: PECO:0007632 name: insecticide exposure def: "A pesticide exposure (PECO:0007167) involving the application of an insecticide; a chemical entity or mixture of chemical entities." [Gramene:pankaj_jaiswal] +def: "An exposure to a chemical that has the role of insecticide" [] synonym: "insecticide treatment (narrow)" NARROW [] is_a: PECO:0007167 ! pesticide exposure @@ -4533,7 +4543,7 @@ def: "An herbicide exposure (PECO:0007183) involving the use of an imidazolinone synonym: "imidazolinone treatment (narrow)" NARROW [] is_a: PECO:0007183 ! herbicide exposure intersection_of: PECO:0001001 ! plant exposure -intersection_of: RO:0002244 CHEBI:24781 ! imidazolinone +intersection_of: RO:0002309 CHEBI:24781 ! imidazolinone [Term] id: RO:0002577 diff --git a/imports/peco_import.owl b/imports/peco_import.owl index f6f3ff7..5f27d1b 100644 --- a/imports/peco_import.owl +++ b/imports/peco_import.owl @@ -632,6 +632,12 @@ + + + + + + @@ -13688,7 +13694,7 @@ - + @@ -13786,8 +13792,10 @@ A chemical exposure (PECO:0007189) involving the use of antibiotic for selection purposes. + An exposure to a chemical that has the role of antimicrobial agent antibiotic treatment (narrow) antibiotic exposure + antimicrobial agent exposure @@ -14000,6 +14008,7 @@ A growth hormone exposure (PECO:0007165) involving the use of cytokinin (or its homolog) growth hormone. + An exposure to a chemical that has the role of cytokinin cytokinin treatment (narrow) 6-benzylaminopurine (related) N-benzyl-adenine (related) @@ -14023,7 +14032,7 @@ - + @@ -14070,6 +14079,7 @@ A growth hormone exposure (PECO:0007165) involving the use of auxin (or its homolog). + An exposure to a chemical that has the role of auxin auxin treatment (narrow) auxin exposure @@ -14090,7 +14100,7 @@ - + @@ -14137,6 +14147,7 @@ A plant nutrient exposure (PECO:0007241) involving the use of a fertilizer, a combination of plant nutrients. + An exposure to a chemical that has the role of fertilizer fertilizer treatment (narrow) fertilizer exposure @@ -14191,7 +14202,7 @@ - + @@ -14220,7 +14231,7 @@ - + @@ -14267,7 +14278,7 @@ - + @@ -14484,7 +14495,7 @@ - + @@ -14549,6 +14560,7 @@ A chemical exposure (PECO:0007189) involving the application of one or more plant growth hormones. + An exposure to a chemical that has the role of growth hormone growth hormone treatment (narrow) growth hormone exposure @@ -14587,6 +14599,7 @@ A chemical exposure (PECO:0007189) involving the application of a pesticide; a chemical entity or mixture of chemical entities. + An exposure to a chemical that has the role of pesticide pesticide treatment (narrow) pesticide exposure @@ -14675,7 +14688,7 @@ - + @@ -14787,6 +14800,7 @@ A pesticide exposure (PECO:0007167) involving the application of a herbicide; a chemical entity or mixture of chemical entities. + An exposure to a chemical that has the role of herbicide herbicide treatment (narrow) herbicide exposure @@ -14807,7 +14821,7 @@ - + @@ -14970,7 +14984,7 @@ - + @@ -15088,7 +15102,7 @@ - + @@ -15138,7 +15152,7 @@ - + @@ -15255,6 +15269,7 @@ + An exposure to a chemical that has the role of micronutrient The treatment involving exposure of plant to elements that are required in tiny quantities for growth, as supplement to study various types of responses. micronutrient treatment (narrow) trace element regimen (related) @@ -15416,7 +15431,7 @@ - + @@ -15693,7 +15708,7 @@ - + @@ -15723,7 +15738,7 @@ - + @@ -15755,7 +15770,7 @@ - + @@ -15786,7 +15801,7 @@ - + @@ -15816,7 +15831,7 @@ - + @@ -15903,7 +15918,7 @@ - + @@ -15937,7 +15952,7 @@ - + @@ -15967,7 +15982,7 @@ - + @@ -16014,7 +16029,7 @@ - + @@ -16071,7 +16086,7 @@ - + @@ -16093,7 +16108,7 @@ - + @@ -16121,7 +16136,7 @@ - + @@ -16167,6 +16182,7 @@ A pesticide exposure (PECO:0007167) involving the application of an insecticide; a chemical entity or mixture of chemical entities. + An exposure to a chemical that has the role of insecticide insecticide treatment (narrow) insecticide exposure @@ -16187,7 +16203,7 @@ - + diff --git a/subsets/to-basic.obo b/subsets/to-basic.obo index e2367b5..adabf18 100644 --- a/subsets/to-basic.obo +++ b/subsets/to-basic.obo @@ -13187,6 +13187,24 @@ synonym: "shooCFt Zn content (related)" RELATED [] xref: TO_GIT:412 is_a: TO:0020090 ! zinc content trait +[Term] +id: TO:1000074 +name: linolenic acid content +def: "An essential fatty acid (TO:0000604) content which is the amount of a polyunsaturated, 18 carbon long fatty acid, with three double bonds." [CHEBI:25048, TO:cooperl] +comment: There are two forms of linolenic acid, alpha and gamma, depending upon where the double bonds occur. +is_a: TO:0000604 ! fat and essential oil content +created_by: Laurel_Cooper +creation_date: 2020-09-16 + +[Term] +id: TO:1000075 +name: palmitic acid content +def: "A fatty acid content (TO:0000604) which is the amount of a straight-chain, sixteen-carbon, saturated long-chain fatty acid in a plant structure." [CHEBI:15756, TO:cooperl] +synonym: "hexadecanoic acid (exact)" EXACT [] +is_a: TO:0000604 ! fat and essential oil content +created_by: Laurel_Cooper +creation_date: 2020-09-16 + [Typedef] id: part_of name: part of diff --git a/to.obo b/to.obo index 1743249..292b357 100644 --- a/to.obo +++ b/to.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2020-08-20 +data-version: releases/2020-10-13 saved-by: cooperl subsetdef: Allium_porrum "Terms_used_for_leek" subsetdef: Cucurbita "Terms_used_for_squash" @@ -2546,7 +2546,7 @@ is_a: CHEBI:27208 [Term] id: CHEBI:36329 is_a: CHEBI:36326 -is_a: CHEBI:61051 +is_a: CHEBI:64009 [Term] id: CHEBI:36338 @@ -3504,6 +3504,7 @@ is_a: CHEBI:23849 [Term] id: CHEBI:61051 +is_a: CHEBI:18059 is_a: CHEBI:35924 [Term] @@ -3588,6 +3589,15 @@ is_a: CHEBI:51086 id: CHEBI:63726 is_a: CHEBI:50267 +[Term] +id: CHEBI:64009 +is_a: CHEBI:35366 +is_a: CHEBI:61051 + +[Term] +id: CHEBI:64012 +is_a: CHEBI:28868 + [Term] id: CHEBI:64047 is_a: CHEBI:33232 @@ -4345,7 +4355,7 @@ is_a: GO:0005488 [Term] id: GO:0005622 -is_a: GO:0005575 +is_a: GO:0110165 [Term] id: GO:0005737 @@ -4849,7 +4859,7 @@ is_a: GO:0099402 [Term] id: GO:0048831 -is_a: GO:2000026 +is_a: GO:0050793 [Term] id: GO:0048856 @@ -5029,7 +5039,7 @@ is_a: GO:1903047 [Term] id: GO:1900055 -is_a: GO:2000024 +is_a: GO:0050793 [Term] id: GO:1900120 @@ -5071,7 +5081,7 @@ is_a: GO:0022402 [Term] id: GO:2000024 -is_a: GO:0048831 +is_a: GO:0050793 [Term] id: GO:2000026 @@ -5084,7 +5094,7 @@ is_a: GO:0050789 [Term] id: GO:2000280 -is_a: GO:2000026 +is_a: GO:0050793 [Term] id: GO:2000762 @@ -26908,6 +26918,24 @@ synonym: "shooCFt Zn content (related)" RELATED [] xref: TO_GIT:412 is_a: TO:0020090 ! zinc content trait +[Term] +id: TO:1000074 +name: linolenic acid content +def: "An essential fatty acid (TO:0000604) content which is the amount of a polyunsaturated, 18 carbon long fatty acid, with three double bonds." [CHEBI:25048, TO:cooperl] +comment: There are two forms of linolenic acid, alpha and gamma, depending upon where the double bonds occur. +is_a: TO:0000604 ! fat and essential oil content +created_by: Laurel_Cooper +creation_date: 2020-09-16 + +[Term] +id: TO:1000075 +name: palmitic acid content +def: "A fatty acid content (TO:0000604) which is the amount of a straight-chain, sixteen-carbon, saturated long-chain fatty acid in a plant structure." [CHEBI:15756, TO:cooperl] +synonym: "hexadecanoic acid (exact)" EXACT [] +is_a: TO:0000604 ! fat and essential oil content +created_by: Laurel_Cooper +creation_date: 2020-09-16 + [Typedef] id: evaluation_location name: evaluation location diff --git a/to.owl b/to.owl index 45b9025..d628006 100644 --- a/to.owl +++ b/to.owl @@ -14,7 +14,7 @@ xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:po="http://purl.obolibrary.org/obo/po#"> - + @@ -5278,7 +5278,7 @@ - + @@ -7124,6 +7124,7 @@ + @@ -7287,6 +7288,23 @@ + + + + + + + + + + + + + + + + + @@ -8785,7 +8803,7 @@ - + @@ -9761,7 +9779,7 @@ - + @@ -10113,7 +10131,7 @@ - + @@ -10191,7 +10209,7 @@ - + @@ -10216,7 +10234,7 @@ - + @@ -63369,6 +63387,50 @@ also holes etc). + + + + + An essential fatty acid (TO:0000604) content which is the amount of a polyunsaturated, 18 carbon long fatty acid, with three double bonds. + Laurel_Cooper + 2020-09-16 + plant_trait_ontology + TO:1000074 + There are two forms of linolenic acid, alpha and gamma, depending upon where the double bonds occur. + linolenic acid content + + + + + An essential fatty acid (TO:0000604) content which is the amount of a polyunsaturated, 18 carbon long fatty acid, with three double bonds. + CHEBI:25048 + TO:cooperl + + + + + + + + + A fatty acid content (TO:0000604) which is the amount of a straight-chain, sixteen-carbon, saturated long-chain fatty acid in a plant structure. + Laurel_Cooper + 2020-09-16 + hexadecanoic acid (exact) + plant_trait_ontology + TO:1000075 + palmitic acid content + + + + + A fatty acid content (TO:0000604) which is the amount of a straight-chain, sixteen-carbon, saturated long-chain fatty acid in a plant structure. + CHEBI:15756 + TO:cooperl + + + +