From 31efb0c9a397458c75cf6b80ead859332827a07b Mon Sep 17 00:00:00 2001 From: Ramona Walls Date: Sat, 12 Mar 2022 16:54:48 -0700 Subject: [PATCH] update imports for release --- src/ontology/imports/bco_import.owl | 53 +- src/ontology/imports/envo_import.owl | 2416 ++++++- src/ontology/imports/exo_import.owl | 31 +- src/ontology/imports/iao_import.owl | 322 +- src/ontology/imports/omrse_import.owl | 207 +- src/ontology/imports/pato_import.owl | 5833 ++++++++++++++--- src/ontology/imports/pco_import.owl | 31 +- src/ontology/imports/po_import.owl | 22 +- src/ontology/imports/ro_import.owl | 24 +- src/ontology/imports/stato_import.owl | 122 +- src/ontology/imports/uo_import.owl | 22 +- .../reports/srpdio-edit.owl-obo-report.tsv | 836 +++ src/ontology/srpdio-edit.owl | 1 + .../data/default/chemical_concentration.txt | 385 ++ src/patterns/data/default/data_item_about.txt | 61 + .../data/default/entity_attribute.txt | 18 + .../data/default/plant_part_concentration.txt | 530 ++ 17 files changed, 9864 insertions(+), 1050 deletions(-) create mode 100644 src/patterns/data/default/chemical_concentration.txt create mode 100644 src/patterns/data/default/data_item_about.txt create mode 100644 src/patterns/data/default/entity_attribute.txt create mode 100644 src/patterns/data/default/plant_part_concentration.txt diff --git a/src/ontology/imports/bco_import.owl b/src/ontology/imports/bco_import.owl index 5b73ecf..885a3c3 100644 --- a/src/ontology/imports/bco_import.owl +++ b/src/ontology/imports/bco_import.owl @@ -78,7 +78,40 @@ - + + definition + definition + textual definition + + The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition + definition + textual definition + @@ -232,18 +265,36 @@ + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/imports/envo_import.owl b/src/ontology/imports/envo_import.owl index 3dd8c68..fa60d5b 100644 --- a/src/ontology/imports/envo_import.owl +++ b/src/ontology/imports/envo_import.owl @@ -54,7 +54,9 @@ - + + definition + @@ -172,6 +174,70 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -208,18 +274,36 @@ + + + + + + + + + + + + + + + + + + @@ -264,7 +348,9 @@ - + + has_exact_synonym + @@ -582,6 +668,31 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + + + + + + + + + x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y + Chris Mungall + David Osumi-Sutherland + Melissa Haendel + Terry Meehan + This is the transitive form of the develops from relation + develops from + + + + @@ -672,6 +783,21 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p + false + Chris Mungall + In general you should not use this relation to make assertions - use one of the more specific relations below this one + This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from + developmentally preceded by + + + + @@ -1147,6 +1273,38 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + halide anion + + + + + + + + + + + sulfate + + + + + + + + + + + nitrite + + + + @@ -1158,6 +1316,27 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + fluoride + + + + + + + + + + + nitrate + + + + @@ -1167,6 +1346,16 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + chloride + + + + @@ -1178,6 +1367,25 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + phosphate(3-) + + + + + + + + + anion + + + + @@ -1216,6 +1424,25 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + copper molecular entity + + + + + + + + + + monoatomic anion + + + + @@ -1254,6 +1481,16 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + inorganic anion + + + + @@ -1263,6 +1500,16 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + inorganic oxide + + + + @@ -1282,6 +1529,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + monoatomic ion + + + + + + + + + ion + + + + + + + + + iron molecular entity + + + + @@ -1330,6 +1605,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + phosphorus molecular entity + + + + @@ -1359,6 +1643,44 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + sulfur molecular entity + + + + + + + + + vanadium molecular entity + + + + + + + + + + + ammonium + + + + + + + + + monoatomic entity + + + + @@ -1426,6 +1748,16 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + polyatomic anion + + + + @@ -1453,6 +1785,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + alkaline earth molecular entity + + + + @@ -1471,119 +1812,327 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - - - - elemental pnictogen + + + + monoatomic monoanion - + - - - metal atom + + + + elemental chlorine - + - - - main group molecular entity + + + + monoatomic chlorine - + - - - carbon group molecular entity + + + monoatomic halogen - + - - - noble gas molecular entity + + + elemental halogen - + - - - hydrogen molecular entity + + + + nitrogen oxoanion - + - - - s-block molecular entity + + + + pnictogen oxoanion - + - - - p-block molecular entity + + + + + phosphorus oxoanion - + - - - - helium molecular entity + + + + + elemental pnictogen - + - - - - hydrides + + + + sulfur oxoanion - + - - - oxygen hydride + + + chalcogen oxoanion - + - - + + + transition element molecular entity + + + + + + + + + actinoid molecular entity + + + + + + + + + uranium molecular entity + + + + + + + + + metal atom + + + + + + + + + main group molecular entity + + + + + + + + + boron group molecular entity + + + + + + + + + carbon group molecular entity + + + + + + + + + noble gas molecular entity + + + + + + + + + lead molecular entity + + + + + + + + + hydrogen molecular entity + + + + + + + + + aluminium molecular entity + + + + + + + + + + + elemental aluminium + + + + + + + + + s-block molecular entity + + + + + + + + + p-block molecular entity + + + + + + + + + d-block molecular entity + + + + + + + + + f-block molecular entity + + + + + + + + + + helium molecular entity + + + + + + + + + + hydrides + + + + + + + + + oxygen hydride + + + + + + + + biomacromolecule + + + + + iron group molecular entity + + + + + + + + + copper group molecular entity + + + + + + + + + vanadium group molecular entity + + + + @@ -1603,6 +2152,53 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + gold molecular entity + + + + + + + + + elemental gold + + + + + + + + + + nitrogen hydride + + + + + + + + + elemental vanadium + + + + + + + + + + oxoanion + + + + @@ -1613,6 +2209,25 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + phosphate ion + + + + + + + + + + pnictogen hydride + + + + @@ -1641,6 +2256,43 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + polyatomic ion + + + + + + + + + monoanion + + + + + + + + + elemental fluorine + + + + + + + + + monoatomic fluorine + + + + @@ -1660,6 +2312,35 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + inorganic ion + + + + + + + + + + inorganic cation + + + + + + + + + cation + + + + @@ -1680,6 +2361,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + barium molecular entity + + + + + + + + + elemental barium + + + + @@ -1689,6 +2388,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + elemental lead + + + + + + + + + elemental copper + + + + @@ -1727,6 +2444,43 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + sulfur oxide + + + + + + + + + onium compound + + + + + + + + + onium cation + + + + + + + + + elemental uranium + + + + @@ -1790,6 +2544,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + monovalent inorganic cation + + + + + + + + + reactive nitrogen species + + + + @@ -1828,6 +2600,43 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + trivalent inorganic anion + + + + + + + + + divalent inorganic anion + + + + + + + + + monovalent inorganic anion + + + + + + + + + + elemental iron + + + + @@ -2153,7 +2962,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Geonames:T.TAL SWEETRealm:Talus TGN:21508 - https://en.wikipedia.org/wiki/Scree + https://en.wikipedia.org/wiki/Scree ENVO TALUS talus slope @@ -2164,7 +2973,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Broken rock that appears at the bottom of crags, mountain cliffs or valley shoulders. - https://en.wikipedia.org/wiki/Scree + https://en.wikipedia.org/wiki/Scree @@ -2694,6 +3503,18 @@ The lower boundary that separates soil from the nonsoil underneath is most diffi + + + + + https://en.wikipedia.org/wiki/Tap_water + ENVO + ENVO:00003096 + tap water + + + + @@ -3543,6 +4364,33 @@ In nature ice is formed either by: (a) the freezing of water, (b) the condensati + + + + + + + + + + + + + + + + + + + + + + An alkaline environment is an environment in which entities are exposed to high pH, typically greater than a pH of 9. + alkaline environment + + + + @@ -3686,6 +4534,34 @@ In nature ice is formed either by: (a) the freezing of water, (b) the condensati + + + + + + + + + + + + + + + + + + + + + + A portion of alkaline water is a portion of water with a pH greater than 7. + Here, we commit to a threshold of pH as this is almost universally accepted. + alkaline water + + + + @@ -8225,6 +9101,26 @@ Some definitions include additional discussion of the the physics involved which + + + + + + + + + + + + + The concentration of nitrate and nitrite when measured in liquid water. + http://orcid.org/0000-0002-3410-4655 + liquid water nitrate and nitrite concentration + concentration of nitrate and nitrite in liquid water + + + + @@ -8438,6 +9334,54 @@ Some definitions include additional discussion of the the physics involved which + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of a chloride when measured in water. + water chloride concentration + concentration of chloride in water + + + + @@ -8517,6 +9461,102 @@ Some definitions include additional discussion of the the physics involved which + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of a ammonium when measured in soil. + soil ammonium concentration + concentration of ammonium in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of a nitrate when measured in soil. + soil nitrate concentration + concentration of nitrate in soil + + + + @@ -8797,9 +9837,9 @@ Some definitions include additional discussion of the the physics involved which - + - + @@ -8809,7 +9849,7 @@ Some definitions include additional discussion of the the physics involved which - + @@ -8828,7 +9868,7 @@ Some definitions include additional discussion of the the physics involved which - + @@ -8838,29 +9878,173 @@ Some definitions include additional discussion of the the physics involved which - The concentration of dioxygen when measured in liquid water. - liquid water dioxygen concentration - concentration of dioxygen in liquid water + The concentration of ammonium when measured in liquid water. + liquid water ammonium concentration + concentration of ammonium in liquid water - + - + - + - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of dioxygen when measured in liquid water. + liquid water dioxygen concentration + concentration of dioxygen in liquid water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of nitrate when measured in liquid water. + liquid water nitrate concentration + concentration of nitrate in liquid water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of nitrite when measured in liquid water. + liquid water nitrite concentration + concentration of nitrite in liquid water + + + + + + + + + + + + + + + + + + + + @@ -8873,6 +10057,36 @@ Some definitions include additional discussion of the the physics involved which + + + + + An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + data item + + + + + + + + + A generically dependent continuant that is about some thing. + information content entity + + + + + + + + + A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. + measurement datum + + + + @@ -9382,6 +10596,16 @@ Some definitions include additional discussion of the the physics involved which + + + + + A time quality inhering in a bearer by virtue of how long the bearer has existed. + age + + + + @@ -9503,6 +10727,16 @@ Some definitions include additional discussion of the the physics involved which + + + + + A quality in which events occur in sequence. + time + + + + @@ -9689,6 +10923,26 @@ Some definitions include additional discussion of the the physics involved which + + + + + A concentration quality inhering in a medium by virtue of the bearer's tendency to hydronate a specific reference base. + medium acidity + + + + + + + + + An medium acidity quality inhering in a solution by virtue of the bearer's a low concentration of H+ ions. + alkaline + + + + @@ -10077,7 +11331,7 @@ Some definitions include additional discussion of the the physics involved which 植物体全体 (Japanese, exact) - NIG:Yukiko_Yamazaki + NIG:Yukiko_Yamazaki @@ -10128,109 +11382,997 @@ Some definitions include additional discussion of the the physics involved which - + - - - A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant. - PO_GIT:57 - estructura vegetal (Spanish, exact) - 植物 構造 (Japanese, exact) + + + A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall. + CL:0000034 + PO_GIT:272 + c&#233lula meristem&#225tica (Spanish, exact) + stem cell (exact) + 分裂組織細胞 (Japanese, exact) plant_anatomy - PO:0009011 - - 'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome. - plant structure + PO:0004010 + + meristematic cell - + - A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant. - CARO:0000003 - POC:curators + A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall. + ISBN:0471245208 + POC:Laurel_Cooper - + - estructura vegetal (Spanish, exact) + c&#233lula meristem&#225tica (Spanish, exact) POC:Maria_Alejandra_Gandolfo - + - 植物 構造 (Japanese, exact) - NIG:Yukiko_Yamazaki + 分裂組織細胞 (Japanese, exact) + NIG:Yukiko_Yamazaki - - - - 'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome. - PO:cooperl - - + - - + + - - + + - An anatomical entity that is or was part of a plant. - rwalls - 2010-11-15T11:41:38Z - PO_GIT:224 - entidad anat&#243mica vegetal (Spanish, exact) - 植物 解剖学（形態）的実体 (Japanese, exact) + A primordium (PO:0025127) that develops from a root anlagen (PO:0025433) and is committed to the development of a root (PO:0009005). + PO_GIT:467 + portion of root primordium tissue (exact) + primordio de ra&#237z (Spanish, exact) + root primordia (exact, plural) + 根原基（可視的） (Japanese, exact) plant_anatomy - PO:0025131 - Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. - plant anatomical entity + PO:0005029 + A root primordium may arise from cells of a pericycle (PO:0006203) in a root in most seed plant (pericyclic lateral root primordium; PO:0025492), from cells of an endodermis (PO:0000252) in ferns and some seed plants (non-pericyclic lateral root primordium: PO:0025493), or from cells of a shoot axis (PO:0025029), in the case of a basal root primordium (PO:0025479) or shoot-borne root primordium (PO:0025480). Transition from root primordium to root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147). + root primordium - - - - - - - - - cjm - - - + - An anatomical entity that is or was part of a plant. - BFO:0000004 - CARO:0000000 + A primordium (PO:0025127) that develops from a root anlagen (PO:0025433) and is committed to the development of a root (PO:0009005). + ISBN:0521288959 POC:curators - + - entidad anat&#243mica vegetal (Spanish, exact) + primordio de ra&#237z (Spanish, exact) POC:Maria_Alejandra_Gandolfo - + - 植物 解剖学（形態）的実体 (Japanese, exact) - NIG:Yukiko_Yamazaki + 根原基（可視的） (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + + + + + + + + + + + A plant structure development stage (PO:0009012) that has as primary participant a whole plant (PO:0000003). + PO_GIT:390 + plant_structure_development_stage + Solanaceae whole plant growth stages (SGN:0000001) (related) + cereal plant growth stage ontology (GRO:0007199) (related) + maize growth stage (GRO:0007002) (related) + plant growth stages in Arabidopsis (TAIR:0000021) (related) + rice growth stage (GRO:0007040) (related) + sorghum growth stage (GRO:0007124) (related) + wheat, barley and oat growth stage (GRO:0007156) (related) + PO:0007033 + + whole plant development stage + - - - Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. - CAROC:Brownsville2014 + + + A plant structure development stage (PO:0009012) that has as primary participant a whole plant (PO:0000003). + POC:curators + + + + + + + + + + + + A cell which is a plant structure (PO:0009011). + cell (broad) + GO:0005623 + PO_GIT:56 + c&#233lula vegetal (Spanish, exact) + 植物細胞 (Japanese, exact) + plant_anatomy + PO:0009002 + + + + Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid) and includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". GO:0009505. Definition of plant-type cell wall (GO:0009505): A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances, synonym; exact: cellulose and pectin-containing cell wall. + plant cell + + + + + A cell which is a plant structure (PO:0009011). + GO:0005623 + POC:curators + + + + + c&#233lula vegetal (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + 植物細胞 (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + + + + + + + + + + + + + + + + + + A plant axis (PO:0025004) that lacks shoot axis nodes (PO:0005004) and usually grows indeterminately. + PO:0003006 + PO_GIT:578 + ra&#237z (Spanish, exact) + radices (exact, plural) + radix (exact) + 根 (Japanese, exact) + aerial root (narrow) + climbing root (narrow) + plant_anatomy + PO:0009005 + + + + + + + + + + Roots function in the absorption of water and inorganic nutrients, anchoring the plant body to the substrate and supporting it, storage of food and nutrients, and vegetative reproduction. The roots of most vascular plant species enter into symbiosis with soil-borne microorganisms. Roots are usually positively geotropic and found underground, although there are many exceptions such as the aerial roots of orchids. Roots often form secondary thickening from the root lateral meristem (PO:0006308). Commonly thought of as one of the three basic parts of the plant body, along with the shoot axis (PO:0025029) and leaves (PO:0025034). + root + + + + + A plant axis (PO:0025004) that lacks shoot axis nodes (PO:0005004) and usually grows indeterminately. + ISBN:978-0879015329 + ISBN:9780964022157 + NYBG:Brandon_Sinn + NYBG:Dario_Cavaliere + POC:Laurel_Cooper + POC:curators + + + + + ra&#237z (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + radices (exact, plural) + FNA:3c46e84c-23e4-416b-91cd-2f7c42e4b13d + + + + + radix (exact) + FNA:e6315684-fc99-4976-b39d-b356c4b7e7fd + + + + + 根 (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + + climbing root (narrow) + FNA:bf0ce902-e91c-401a-92a8-26b20142ce5f + + + + + + + + + + A collective plant organ structure (PO:0025007) that produces shoot-borne portions of meristem tissue (PO:0009013) and the plant structures (PO:0009011) that arise from them. + PO_GIT:135 + sistema de epiblasto (epiblastema) (Spanish, exact) + シュート系、苗条系 (Japanese, exact) + tree crown (narrow) + plant_anatomy + Poaceae crown (related) + shoot (related) + thalli (related) + thallus (related) + PO:0009006 + + + The shoot system is generally used to refer to the above-ground plant parts, although some plants have parts of their shoot system underground. For example, a rhizome (PO:0004542), bulb (PO:0025356), a corm (PO:0025355) or a subterranean tuber (PO:0004547), as in Solanum tuberosum (potato) or yam, are all part of the shoot system. + shoot system + + + + + A collective plant organ structure (PO:0025007) that produces shoot-borne portions of meristem tissue (PO:0009013) and the plant structures (PO:0009011) that arise from them. + POC:Laurel_Cooper + POC:curators + + + + + sistema de epiblasto (epiblastema) (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + シュート系、苗条系 (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + + thalli (related) + FNA:d1431b5c-7b86-46a0-8d3c-bd426fe12c85 + + + + + + thallus (related) + FNA:02756ad4-a09c-48d7-8754-903254e557a9 + + + + + + + + + + + A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types. + portion of tissue (broad) + tissue (broad) + PO_GIT:59 + porci&#243n de un tejido vegetal (Spanish, exact) + 植物組織の一部 (Japanese, exact) + plant_anatomy + plant tissue (related) + PO:0009007 + + + A portion of plant tissue may contain one or several types of cells that are organized in a specific spatial arrangement into a structural unit (which includes a mass of callus) and may include an intercellular matrix. May include other types of isolated cells, such as idioblasts. + portion of plant tissue + + + + + A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types. + POC:curators + TAIR_curator:Leonore_Reiser + + + + + porci&#243n de un tejido vegetal (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + 植物組織の一部 (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + + + + + + A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path. + organ (broad) + PO_GIT:55 + &#243rgano vegetal (Spanish, exact) + 植物 器官 (Japanese, exact) + plant_anatomy + compound plant organ (related) + simple plant organ (related) + PO:0009008 + + Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual plant cells (PO:0009002) that are not part of a portion of plant tissue (e.g., idioblasts, PO:0000283). A plant organ may have one or more different plant organs as parts, such as a sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel (PO:0009030) that may have as part a plant ovule (PO:0020003). + plant organ + + + + + A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path. + POC:curators + + + + + &#243rgano vegetal (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + 植物 器官 (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + + simple plant organ (related) + PATO:01503 + + + + + + + + + A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant. + PO_GIT:57 + estructura vegetal (Spanish, exact) + 植物 構造 (Japanese, exact) + plant_anatomy + PO:0009011 + + 'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome. + plant structure + + + + + A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant. + CARO:0000003 + POC:curators + + + + + estructura vegetal (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + 植物 構造 (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + + 'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome. + PO:cooperl + + + + + + + + A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes. + PO:0007021 + PO_GIT:185 + etapa de desarrollo de estructura vegetal (Spanish, exact) + plant growth and development stage (exact) + plant_structure_development_stage + Arabidopsis growth (related) + PO:0009012 + + Refers to GO:0032502 'developmental process', which includes growth, differentiation, and senescence, and BFO:0000003 'ocurrent'. + plant structure development stage + + + + + A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes. + BFO:0000003 + GO:0032502 + POC:curators + + + + + etapa de desarrollo de estructura vegetal (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + Arabidopsis growth (related) + TAIR:0000205 + + + + + + + + + + + + + + + A portion of plant tissue (PO:0009007) in which plant cells (PO:0009002) have retained their embryonic characteristics, or have reverted to them secondarily, and that divide to produce new cells that can undergo differentiation to form mature tissues, i.e. they have a capacity for morphogenesis and growth. + PO_GIT:472 + meristem (exact) + meristema (Spanish, exact) + meristematic tissue (exact) + 分裂組織 (Japanese, exact) + plant_anatomy + PO:0009013 + + portion of meristem tissue + + + + + A portion of plant tissue (PO:0009007) in which plant cells (PO:0009002) have retained their embryonic characteristics, or have reverted to them secondarily, and that divide to produce new cells that can undergo differentiation to form mature tissues, i.e. they have a capacity for morphogenesis and growth. + APweb:Glossary + Gramene:Pankaj_Jaiswal + + + + + meristema (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + 分裂組織 (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + + + + + + An axial plant organ (PO:0009008). + rwalls + 2010-07-01T03:44:41Z + eje de la planta (Spanish, exact) + plant axes (exact, plural) + 植物軸（軸柱） (Japanese, exact) + plant_anatomy + PO:0025004 + + Includes roots and shoots. + plant axis + + + + + An axial plant organ (PO:0009008). + POC:curators + + + + + eje de la planta (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + plant axes (exact, plural) + FNA:2355281f-ab10-4ae2-a3d8-672cace068a8 + + + + + 植物軸（軸柱） (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + + + + + + + + + + + + A collective plant structure (PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007). + rwalls + 2010-02-09T04:12:11Z + PO_GIT:63 + estructura vegetal colectiva de &#243rgano (Spanish, exact) + 集合植物器官構造 (Japanese, exact) + plant_anatomy + PO:0025007 + + Organs can be of the same type or different types. Examples include flower (PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs, but no complete plant organs. This was formerly named collective plant structure. + collective plant organ structure + + + + + A collective plant structure (PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007). + POC:curators + + + + + estructura vegetal colectiva de &#243rgano (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + 集合植物器官構造 (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + + + + + + + + + + + + A collective plant organ structure (PO:0025007) that produces root meristems (PO:0006085), the plant structures (PO:0009011) that arise from them and the parts thereof. + rwalls + 2010-07-01T02:11:26Z + root (broad) + PO_GIT:136 + sistema de ra&#237z (Spanish, exact) + 根系 (Japanese, exact) + plant_anatomy + PO:0025025 + + Generally the below ground portion of a vascular plant. + root system + + + + + A collective plant organ structure (PO:0025007) that produces root meristems (PO:0006085), the plant structures (PO:0009011) that arise from them and the parts thereof. + POC:Laurel_Cooper + POC:curators + + + + + root (broad) + FNA:b7ce680b-c6ed-4d2e-81e6-66970f7deff9 + + + + + sistema de ra&#237z (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + 根系 (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + + + + + + A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO:0006210) and sub-epidermal meristematic tissue and is committed to the development of a particular plant structure (PO:0009011). + rwalls + 2010-11-15T09:10:22Z + PO_GIT:186 + portion of primordial tissue (exact) + portion of primordium tissue (exact) + primordia (exact, plural) + primordio (Spanish, exact) + 原基（可視的） (Japanese, exact) + plant_anatomy + PO:0025127 + A primordium appears as a protrusion and is the first distinct form of a plant organ (PO:0009008), cardinal organ part (PO:0025001), or collective plant organ structure (PO:0025007). The transition from a primordium to the plant structure it develops into is marked by the development of non-meristematic cells, although meristematic cells may be present after the transition. + primordium + + + + + A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO:0006210) and sub-epidermal meristematic tissue and is committed to the development of a particular plant structure (PO:0009011). + POC:curators + + + + + primordio (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + 原基（可視的） (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + + + + + + + + + + + + An anatomical entity that is or was part of a plant. + rwalls + 2010-11-15T11:41:38Z + PO_GIT:224 + entidad anat&#243mica vegetal (Spanish, exact) + 植物 解剖学（形態）的実体 (Japanese, exact) + plant_anatomy + PO:0025131 + Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. + plant anatomical entity + + + + + + + + + + + cjm + + + + + An anatomical entity that is or was part of a plant. + BFO:0000004 + CARO:0000000 + POC:curators + + + + + entidad anat&#243mica vegetal (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + 植物 解剖学（形態）的実体 (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + + Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. + CAROC:Brownsville2014 + + + + + + + + + A maximal whole plant development stage. + rwalls + 2011-10-19T10:54:37Z + PO_GIT:230 + vida de la planta entera (Spanish, exact) + 植物体の一生 (Japanese, exact) + plant_structure_development_stage + PO:0025337 + There are only two types of life of whole plant. Every life of a whole plant is either a maximal gametophyte stage or a maximal sporophyte stage. + life of whole plant stage + + + + + A maximal whole plant development stage. + POC:curators + + + + + vida de la planta entera (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + 植物体の一生 (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + + + + + + A portion of meristem tissue (PO:0009013) that is committed to the development of a root primordium (PO:0005029). + Laurel_Cooper + 2012-02-08T01:00:56Z + PO_GIT:427 + precursor de ra&#237 (Spanish, exact) + 根原基 (Japanese, exact) + plant_anatomy + PO:0025433 + Only detectable by gene expression, not morphology. May arise in a pericycle (PO:0006203), as for lateral roots in most seed plants, an endodermis (PO:0000252), as for lateral roots in ferns, or from parenchyma cells (PO:0000074) that are part a shoot axis (PO:0025029), in the case of a basal root (PO:0025002) or shoot-borne root (PO:0000042). + root anlagen + + + + + A portion of meristem tissue (PO:0009013) that is committed to the development of a root primordium (PO:0005029). + POC:curators + + + + + precursor de ra&#237 (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + 根原基 (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + + + + + + A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single structural unit demarcated by primarily bona-fide boundaries from other structural units of different types. + Laurel_Cooper + 2012-06-11T14:57:00Z + PO_GIT:480 + estructura vegetal con m&#250ltiples tejidos (Spanish, exact) + 複数の組織からなる植物構造 (Japanese, exact) + plant_anatomy + PO:0025496 + Most multi-tissue plant structures have at least a small connection to other plant structures via a fiat boundary, such as where a leaf (PO:0025034) connects to a shoot axis (PO:0025029), a petal (PO:0009032) connects to a receptacle (PO:0009064), or a branch (PO:0025073) connects to a stem (PO:0009047). Refers to CARO:0000055 multi-tissue structure, def'n: Anatomical structure that has as parts two or more portions of tissue of at least two different types, and which through specific morphogenetic processes, form a single distinct structural unit demarcated by bona-fide boundries from other structural units of differnt types. + multi-tissue plant structure + + + + + A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single structural unit demarcated by primarily bona-fide boundaries from other structural units of different types. + CARO:0000055 + POC:curators + + + + + estructura vegetal con m&#250ltiples tejidos (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + 複数の組織からなる植物構造 (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + + + + + + A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and includes two or more adjacent plant organs (PO:0009008) or adjacent cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007). + Laurel_Cooper + 2012-06-11T15:09:20Z + PO_GIT:479 + estructura vegetal colectiva (Spanish, exact) + 集合的植物構造 (Japanese, exact) + plant_anatomy + PO:0025497 + This is a parent term to describe both collective organ part structure (PO:0025269) (e.g. septum), as well as collective plant organ structure (PO:0025007) (which was formerly named collective plant structure), for example shoot system (PO:0009006). + collective plant structure + + + + + A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and includes two or more adjacent plant organs (PO:0009008) or adjacent cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007). + POC:curators + + + + + estructura vegetal colectiva (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + 集合的植物構造 (Japanese, exact) + NIG:Yukiko_Yamazaki + + + + + + + + + + A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment). + Laurel_Cooper + 2014-05-13T16:51:47Z + PO_GIT:586 + plant_anatomy + PO:0025606 + A native plant cell is one that is not grown or maintained in vitro, nor part of an in vitro plant structure (PO:0000004). + native plant cell + + + + + A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment). + POC:Laurel_Cooper + + + + + + + + + + + + + + + A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between fertilization (or apogamy) and death. + rwalls + 2010-07-15T02:56:11Z + PO_GIT:139 + PO_GIT:68 + fase esporof&#237tica (Spanish, exact) + sporophytic development stage (exact) + sporophytic phase (exact) + sporphyte phase (exact) + 胞子体発生過程 (Japanese, exact) + plant_structure_development_stage + PO:0028002 + + A whole plant (PO:0000003) in the sporophyte development stage usually has twice the chromosome complement of a plant in the gametophytic phase, but may not in the case of apogamy. Examples of apogamy include both naturally occurring instances (such as sporophytes arising form haploid cells as in bryophytes or ferns) as well as in vitro instances (such as haploid embryo culture or in vitro fusion of non-gamete cells or protoplasts). During the sporophyte development stage, a plant may produce meiospores by meiosis. + sporophyte development stage + + + + + A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between fertilization (or apogamy) and death. + POC:curators + + + + + fase esporof&#237tica (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + + + + + 胞子体発生過程 (Japanese, exact) + NIG:Yukiko_Yamazaki + diff --git a/src/ontology/imports/exo_import.owl b/src/ontology/imports/exo_import.owl index 1a7b6da..8a2fd32 100644 --- a/src/ontology/imports/exo_import.owl +++ b/src/ontology/imports/exo_import.owl @@ -8,11 +8,12 @@ xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + - 2022-01-01 + 2022-03-12 @@ -30,7 +31,9 @@ - + + definition + @@ -40,6 +43,24 @@ + + + + + + + + + + + + + + + + + + @@ -66,7 +87,9 @@ - + + has_exact_synonym + diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl index 36cac8d..40c7495 100644 --- a/src/ontology/imports/iao_import.owl +++ b/src/ontology/imports/iao_import.owl @@ -7,11 +7,12 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"> + xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:terms="http://purl.org/dc/terms/"> - + - 2022-01-01 + 2022-03-12 @@ -59,7 +60,35 @@ - + + definition + + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition + @@ -111,6 +140,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + + part of + http://www.obofoundry.org/ro/#OBO_REL:part_of + + + + + + + + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + + has part + + + + @@ -141,6 +238,39 @@ Some currently missing phenomena that should be considered "about" are + + + + + inheres in + this fragility inheres in this vase + this red color inheres in this apple + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + A dependent inheres in its bearer at all times for which the dependent exists. + inheres_in + + inheres in + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + bearer of + + + + + + + + + + ic + IndependentContinuant + a chair + a heart + a leg + a molecule + a spatial region + an atom + an orchestra. + an organism + the bottom right portion of a human torso + the interior of your mouth + 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]) + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + independent continuant + + + + + 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]) + + + + + + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + + + + + + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + + + + + + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + + + + + + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + + + + + + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + + + + + + + + + + sdc + SpecificallyDependentContinuant + Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key + of one-sided specifically dependent continuants: the mass of this tomato + of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. + the disposition of this fish to decay + the function of this heart: to pump blood + the mutual dependence of proton donors and acceptors in chemical reactions [79 + the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction + the pink color of a medium rare piece of grilled filet mignon at its center + the role of being a doctor + the shape of this hole. + the smell of this portion of mozzarella + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + specifically dependent continuant + + + + + 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 doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + per discussion with Barry Smith + + + + + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + + + + @@ -291,6 +535,76 @@ Some currently missing phenomena that should be considered "about" are + + + + + material + MaterialEntity + a flame + a forest fire + a human being + a hurricane + a photon + a puff of smoke + a sea wave + a tornado + an aggregate of human beings. + an energy wave + an epidemic + the undetached arm of a human being + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 + BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. + BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + material entity + + + + + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + + + + + + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + + + + + + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + + + + + + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + + + + diff --git a/src/ontology/imports/omrse_import.owl b/src/ontology/imports/omrse_import.owl index aa2ff02..1d08899 100644 --- a/src/ontology/imports/omrse_import.owl +++ b/src/ontology/imports/omrse_import.owl @@ -16,9 +16,9 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + - 2022-01-01 + 2022-03-12 @@ -66,7 +66,37 @@ - + + definition + + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition + definition + textual definition + @@ -238,18 +268,36 @@ + + + + + + + + + + + + + + + + + + @@ -515,6 +563,41 @@ Some currently missing phenomena that should be considered "about" are + + + + + + inheres in + this fragility inheres in this vase + this red color inheres in this apple + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + A dependent inheres in its bearer at all times for which the dependent exists. + inheres_in + + inheres in + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + bearer of + bearer_of + + + + @@ -1024,6 +1107,38 @@ Some currently missing phenomena that should be considered "about" are + + + + + + + + + + + + + q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of inheres in part of + Chris Mungall + + + inheres in part of + + + + + + + + + + true + + + + @@ -1603,6 +1718,16 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + Chris Mungall + depends on + + + + + @@ -2175,6 +2300,7 @@ For example, A and B may be gene products and binding of B by A positively regul + ic IndependentContinuant @@ -2274,6 +2400,64 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + sdc + SpecificallyDependentContinuant + specifically dependent continuant + Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key + of one-sided specifically dependent continuants: the mass of this tomato + of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. + the disposition of this fish to decay + the function of this heart: to pump blood + the mutual dependence of proton donors and acceptors in chemical reactions [79 + the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction + the pink color of a medium rare piece of grilled filet mignon at its center + the role of being a doctor + the shape of this hole. + the smell of this portion of mozzarella + 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 &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; 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 doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + + + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + specifically dependent continuant + + + + + 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 doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + per discussion with Barry Smith + + + + + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + + + + @@ -2548,6 +2732,23 @@ Previous. An information content entity is a non-realizable information entity t + + + + + measurement datum + Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. + + A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. + 2/2/2009 is_specified_output of some assay? + person:Chris Stoeckert + OBI_0000305 + group:OBI + measurement datum + + + + diff --git a/src/ontology/imports/pato_import.owl b/src/ontology/imports/pato_import.owl index ca77416..5a18c0b 100644 --- a/src/ontology/imports/pato_import.owl +++ b/src/ontology/imports/pato_import.owl @@ -21,9 +21,9 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + - 2022-01-01 + 2022-03-12 @@ -59,7 +59,9 @@ - + + definition + @@ -501,7 +503,9 @@ - + + has_exact_synonym + @@ -2808,790 +2812,2532 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - - A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity. - CHEBI:14202 - CHEBI:4697 - KEGG:C01351 - Donor + + + Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa). + Wikipedia:https://en.wikipedia.org/wiki/Gas chebi_ontology - Donator - donneur - CHEBI:17891 + gas molecular entities + gaseous molecular entities + gaseous molecular entity + CHEBI:138675 - donor + gas molecular entity - - - Donor - KEGG_COMPOUND + + + gas molecular entities + ChEBI - + - Donator + gaseous molecular entities ChEBI - + - donneur + gaseous molecular entity ChEBI - + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - A phosphate ion that is the conjugate base of hydrogenphosphate. - -3 - O4P - InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3 - NBIIXXVUZAFLBC-UHFFFAOYSA-K - 94.97136 - 94.95507 - [O-]P([O-])([O-])=O - CHEBI:14791 - CHEBI:45024 - CHEBI:7793 - Beilstein:3903772 - CAS:14265-44-2 - Gmelin:1997 - KEGG:C00009 - PDBeChem:PO4 - Reaxys:3903772 - phosphate - tetraoxidophosphate(3-) - tetraoxophosphate(3-) - tetraoxophosphate(V) + An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. + 0 + H3N + InChI=1S/H3N/h1H3 + QGZKDVFQNNGYKY-UHFFFAOYSA-N + 17.03056 + 17.02655 + [H]N([H])[H] + CHEBI:13405 + CHEBI:13406 + CHEBI:13407 + CHEBI:13771 + CHEBI:22533 + CHEBI:44269 + CHEBI:44284 + CHEBI:44404 + CHEBI:7434 + Beilstein:3587154 + CAS:7664-41-7 + Drug_Central:4625 + Gmelin:79 + HMDB:HMDB0000051 + KEGG:C00014 + KEGG:D02916 + KNApSAcK:C00007267 + MetaCyc:AMMONIA + MolBase:930 + PDBeChem:NH3 + PMID:110589 + PMID:11139349 + PMID:11540049 + PMID:11746427 + PMID:11783653 + PMID:13753780 + PMID:14663195 + PMID:15092448 + PMID:15094021 + PMID:15554424 + PMID:15969015 + PMID:16008360 + PMID:16050680 + PMID:16348008 + PMID:16349403 + PMID:16614889 + PMID:16664306 + PMID:16842901 + PMID:17025297 + PMID:17439666 + PMID:17569513 + PMID:17737668 + PMID:18670398 + PMID:22002069 + PMID:22081570 + PMID:22088435 + PMID:22100291 + PMID:22130175 + PMID:22150211 + PMID:22240068 + PMID:22290316 + PMID:22342082 + PMID:22385337 + PMID:22443779 + PMID:22560242 + Reaxys:3587154 + Wikipedia:Ammonia + AMMONIA + Ammonia + ammonia + azane chebi_ontology - Orthophosphate - PHOSPHATE ION - PO4(3-) - Phosphate - [PO4](3-) - CHEBI:18367 + Ammoniak + NH3 + R-717 + [NH3] + ammoniac + amoniaco + spirit of hartshorn + CHEBI:16134 - phosphate(3-) + ammonia - + - Beilstein:3903772 + Beilstein:3587154 Beilstein - + - CAS:14265-44-2 + CAS:7664-41-7 ChemIDplus - + - CAS:14265-44-2 + CAS:7664-41-7 KEGG COMPOUND - + - Gmelin:1997 + CAS:7664-41-7 + NIST Chemistry WebBook + + + + + Drug_Central:4625 + DrugCentral + + + + + Gmelin:79 Gmelin - + - PDBeChem:PO4 - ChEBI + PMID:110589 + Europe PMC - + - Reaxys:3903772 - Reaxys + PMID:11139349 + Europe PMC - - - phosphate - IUPAC - + + + PMID:11540049 + Europe PMC - - - tetraoxidophosphate(3-) - IUPAC - + + + PMID:11746427 + Europe PMC - - - tetraoxophosphate(3-) - IUPAC - + + + PMID:11783653 + Europe PMC - - - tetraoxophosphate(V) - IUPAC - + + + PMID:13753780 + Europe PMC - - - Orthophosphate - KEGG_COMPOUND + + + PMID:14663195 + Europe PMC - - - PHOSPHATE ION - PDBeChem + + + PMID:15092448 + Europe PMC - - - PO4(3-) - IUPAC + + + PMID:15094021 + Europe PMC - - - Phosphate - KEGG_COMPOUND + + + PMID:15554424 + Europe PMC - - - [PO4](3-) - IUPAC + + + PMID:15969015 + Europe PMC - - - - - - - - A monoatomic or polyatomic species having one or more elementary charges of the electron. - Anion - anion - chebi_ontology - Anionen - aniones - anions - CHEBI:22563 - - anion - - - - Anion - ChEBI + + + PMID:16008360 + Europe PMC - - - anion - ChEBI + + + PMID:16050680 + Europe PMC - - - anion - IUPAC - + + + PMID:16348008 + Europe PMC - - - Anionen - ChEBI + + + PMID:16349403 + Europe PMC - - - aniones - ChEBI + + + PMID:16614889 + Europe PMC - - - anions - IUPAC + + + PMID:16664306 + Europe PMC - - - - - - - - An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group). - Wikipedia:Cofactor_(biochemistry) - cofactor - cofactors - chebi_ontology - CHEBI:23357 - - cofactor - - - - cofactor - IUPAC + + + PMID:16842901 + Europe PMC - - - cofactors - IUPAC - + + + PMID:17025297 + Europe PMC - - - - - - - - Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. - molecular entity - chebi_ontology - entidad molecular - entidades moleculares - entite moleculaire - molecular entities - molekulare Entitaet - CHEBI:23367 - - molecular entity - - - - molecular entity - IUPAC - + + + PMID:17439666 + Europe PMC - - - entidad molecular - IUPAC + + + PMID:17569513 + Europe PMC - - - entidades moleculares - IUPAC + + + PMID:17737668 + Europe PMC - - - entite moleculaire - IUPAC + + + PMID:18670398 + Europe PMC - - - molecular entities - IUPAC + + + PMID:22002069 + Europe PMC - - - molekulare Entitaet - ChEBI + + + PMID:22081570 + Europe PMC - - - - - - - - A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. - chemical entity - chebi_ontology - CHEBI:24431 - - chemical entity - - - - chemical entity - UniProt + + + PMID:22088435 + Europe PMC - - - - - - - - - A role played by the molecular entity or part thereof within a biological context. - chebi_ontology - biological function - CHEBI:24432 - - biological role - - - - biological function - ChEBI + + + PMID:22100291 + Europe PMC - - - - - - - - - - - - - - A defined linked collection of atoms or a single atom within a molecular entity. - group - chebi_ontology - Gruppe - Rest - groupe - grupo - grupos - CHEBI:24433 - - group - - - - group - IUPAC - + + + PMID:22130175 + Europe PMC - - - Gruppe - ChEBI + + + PMID:22150211 + Europe PMC - - - Rest - ChEBI + + + PMID:22240068 + Europe PMC - - - groupe - IUPAC + + + PMID:22290316 + Europe PMC - - - grupo - IUPAC + + + PMID:22342082 + Europe PMC - - - grupos - IUPAC + + + PMID:22385337 + Europe PMC - - - - - - - - - - - - - - - - Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). - chebi_ontology - CHEBI:24651 - - hydroxides - - - - - - - - - - - - - - - A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). - oxoacid - oxoacids - chebi_ontology - oxacids - oxiacids - oxo acid - oxy-acids - oxyacids - CHEBI:24833 - - oxoacid - - + + + PMID:22443779 + Europe PMC + + + + + PMID:22560242 + Europe PMC + + + + + Reaxys:3587154 + Reaxys + + + - oxoacid + AMMONIA + PDBeChem + + + + + Ammonia + KEGG_COMPOUND + + + + + ammonia IUPAC - + - oxoacids + azane IUPAC - + - oxacids - ChEBI + Ammoniak + ChemIDplus - + - oxiacids - ChEBI + NH3 + IUPAC - + - oxo acid + NH3 + KEGG_COMPOUND + + + + + NH3 + UniProt + + + + + R-717 ChEBI - + - oxy-acids + [NH3] + MolBase + + + + + ammoniac ChEBI - + - oxyacids + amoniaco + ChEBI + + + + + spirit of hartshorn + ChemIDplus + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A sulfur oxoanion obtained by deprotonation of both OH groups of sulfuric acid. + -2 + O4S + InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2 + QAOWNCQODCNURD-UHFFFAOYSA-L + 96.06360 + 95.95283 + [O-]S([O-])(=O)=O + CHEBI:15135 + CHEBI:45687 + CHEBI:9335 + Beilstein:3648446 + CAS:14808-79-8 + Gmelin:2120 + HMDB:HMDB0001448 + KEGG:C00059 + KEGG:D05963 + MetaCyc:SULFATE + PDBeChem:SO4 + PMID:11200094 + PMID:11452993 + PMID:11581495 + PMID:11798107 + PMID:12166931 + PMID:12668033 + PMID:14597181 + PMID:15093386 + PMID:15984785 + PMID:16186560 + PMID:16345535 + PMID:16347366 + PMID:16348007 + PMID:16483812 + PMID:16534979 + PMID:16656509 + PMID:16742508 + PMID:16742518 + PMID:17120760 + PMID:17420092 + PMID:17439666 + PMID:17709180 + PMID:18398178 + PMID:18815700 + PMID:18846414 + PMID:19047345 + PMID:19244483 + PMID:19544990 + PMID:19628332 + PMID:19812358 + PMID:30398859 + Reaxys:3648446 + Wikipedia:Sulfate + Sulfate + sulfate + tetraoxidosulfate(2-) + tetraoxosulfate(2-) + tetraoxosulfate(VI) + chebi_ontology + SO4(2-) + SULFATE ION + Sulfate anion(2-) + Sulfate dianion + Sulfate(2-) + Sulfuric acid ion(2-) + [SO4](2-) + sulphate + sulphate ion + CHEBI:16189 + + sulfate + + + + + Beilstein:3648446 + Beilstein + + + + + CAS:14808-79-8 + ChemIDplus + + + + + CAS:14808-79-8 + NIST Chemistry WebBook + + + + + Gmelin:2120 + Gmelin + + + + + PMID:11200094 + Europe PMC + + + + + PMID:11452993 + Europe PMC + + + + + PMID:11581495 + Europe PMC + + + + + PMID:11798107 + Europe PMC + + + + + PMID:12166931 + Europe PMC + + + + + PMID:12668033 + Europe PMC + + + + + PMID:14597181 + Europe PMC + + + + + PMID:15093386 + Europe PMC + + + + + PMID:15984785 + Europe PMC + + + + + PMID:16186560 + Europe PMC + + + + + PMID:16345535 + Europe PMC + + + + + PMID:16347366 + Europe PMC + + + + + PMID:16348007 + Europe PMC + + + + + PMID:16483812 + Europe PMC + + + + + PMID:16534979 + Europe PMC + + + + + PMID:16656509 + Europe PMC + + + + + PMID:16742508 + Europe PMC + + + + + PMID:16742518 + Europe PMC + + + + + PMID:17120760 + Europe PMC + + + + + PMID:17420092 + Europe PMC + + + + + PMID:17439666 + Europe PMC + + + + + PMID:17709180 + Europe PMC + + + + + PMID:18398178 + Europe PMC + + + + + PMID:18815700 + Europe PMC + + + + + PMID:18846414 + Europe PMC + + + + + PMID:19047345 + Europe PMC + + + + + PMID:19244483 + Europe PMC + + + + + PMID:19544990 + Europe PMC + + + + + PMID:19628332 + Europe PMC + + + + + PMID:19812358 + Europe PMC + + + + + PMID:30398859 + Europe PMC + + + + + Reaxys:3648446 + Reaxys + + + + + Sulfate + KEGG_COMPOUND + + + + + sulfate + IUPAC + + + + + + sulfate + UniProt + + + + + tetraoxidosulfate(2-) + IUPAC + + + + + + tetraoxosulfate(2-) + IUPAC + + + + + + tetraoxosulfate(VI) + IUPAC + + + + + + SO4(2-) + IUPAC + + + + + SULFATE ION + PDBeChem + + + + + Sulfate anion(2-) + HMDB + + + + + Sulfate dianion + HMDB + + + + + Sulfate(2-) + HMDB + + + + + Sulfuric acid ion(2-) + HMDB + + + + + [SO4](2-) + IUPAC + + + + + sulphate + ChEBI + + + + + sulphate ion + ChEBI + + + + + + + + + A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity. + CHEBI:14202 + CHEBI:4697 + KEGG:C01351 + Donor + chebi_ontology + Donator + donneur + CHEBI:17891 + + donor + + + + + Donor + KEGG_COMPOUND + + + + + Donator + ChEBI + + + + + donneur + ChEBI + + + + + + + + + + + + + + + + + + + + + An iron group element atom that has atomic number 26. + 0 + Fe + InChI=1S/Fe + XEEYBQQBJWHFJM-UHFFFAOYSA-N + 55.84500 + 55.93494 + [Fe] + CHEBI:13322 + CHEBI:24872 + CHEBI:5974 + CAS:7439-89-6 + DrugBank:DB01592 + HMDB:HMDB0015531 + KEGG:C00023 + Reaxys:4122945 + WebElements:Fe + iron + chebi_ontology + 26Fe + Eisen + Fe + Iron + fer + ferrum + hierro + iron + CHEBI:18248 + + iron atom + + + + + CAS:7439-89-6 + ChemIDplus + + + + + CAS:7439-89-6 + KEGG COMPOUND + + + + + CAS:7439-89-6 + NIST Chemistry WebBook + + + + + Reaxys:4122945 + Reaxys + + + + + iron + IUPAC + + + + + + 26Fe + IUPAC + + + + + Eisen + ChEBI + + + + + Fe + IUPAC + + + + + Iron + KEGG_COMPOUND + + + + + fer + ChEBI + + + + + ferrum + IUPAC + + + + + hierro + ChEBI + + + + + iron + ChEBI + + + + + + + + + + + + + + + + A phosphate ion that is the conjugate base of hydrogenphosphate. + -3 + O4P + InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3 + NBIIXXVUZAFLBC-UHFFFAOYSA-K + 94.97136 + 94.95507 + [O-]P([O-])([O-])=O + CHEBI:14791 + CHEBI:45024 + CHEBI:7793 + Beilstein:3903772 + CAS:14265-44-2 + Gmelin:1997 + KEGG:C00009 + PDBeChem:PO4 + Reaxys:3903772 + phosphate + tetraoxidophosphate(3-) + tetraoxophosphate(3-) + tetraoxophosphate(V) + chebi_ontology + Orthophosphate + PHOSPHATE ION + PO4(3-) + Phosphate + [PO4](3-) + CHEBI:18367 + + phosphate(3-) + + + + + Beilstein:3903772 + Beilstein + + + + + CAS:14265-44-2 + ChemIDplus + + + + + CAS:14265-44-2 + KEGG COMPOUND + + + + + Gmelin:1997 + Gmelin + + + + + PDBeChem:PO4 + ChEBI + + + + + Reaxys:3903772 + Reaxys + + + + + phosphate + IUPAC + + + + + + tetraoxidophosphate(3-) + IUPAC + + + + + + tetraoxophosphate(3-) + IUPAC + + + + + + tetraoxophosphate(V) + IUPAC + + + + + + Orthophosphate + KEGG_COMPOUND + + + + + PHOSPHATE ION + PDBeChem + + + + + PO4(3-) + IUPAC + + + + + Phosphate + KEGG_COMPOUND + + + + + [PO4](3-) + IUPAC + + + + + + + + + A monoatomic or polyatomic species having one or more elementary charges of the electron. + Anion + anion + chebi_ontology + Anionen + aniones + anions + CHEBI:22563 + + anion + + + + + Anion + ChEBI + + + + + anion + ChEBI + + + + + anion + IUPAC + + + + + + Anionen + ChEBI + + + + + aniones + ChEBI + + + + + anions + IUPAC + + + + + + + + + A molecular entity having an available pair of electrons capable of forming a covalent bond with a hydron (Bronsted base) or with the vacant orbital of some other molecular entity (Lewis base). + KEGG:C00701 + Base + base + chebi_ontology + Base1 + Base2 + Basen + Nucleobase + bases + CHEBI:22695 + + base + + + + + Base + ChEBI + + + + + base + ChEBI + + + + + base + IUPAC + + + + + + Base1 + KEGG_COMPOUND + + + + + Base2 + KEGG_COMPOUND + + + + + Basen + ChEBI + + + + + Nucleobase + KEGG_COMPOUND + + + + + bases + ChEBI + + + + + + + + + An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group). + Wikipedia:Cofactor_(biochemistry) + cofactor + cofactors + chebi_ontology + CHEBI:23357 + + cofactor + + + + + cofactor + IUPAC + + + + + cofactors + IUPAC + + + + + + + + + + Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. + molecular entity + chebi_ontology + entidad molecular + entidades moleculares + entite moleculaire + molecular entities + molekulare Entitaet + CHEBI:23367 + + molecular entity + + + + + molecular entity + IUPAC + + + + + + entidad molecular + IUPAC + + + + + entidades moleculares + IUPAC + + + + + entite moleculaire + IUPAC + + + + + molecular entities + IUPAC + + + + + molekulare Entitaet + ChEBI + + + + + + + + + + A compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction. + enzyme inhibitor + chebi_ontology + enzyme inhibitors + inhibidor enzimatico + inhibidores enzimaticos + inhibiteur enzymatique + inhibiteurs enzymatiques + CHEBI:23924 + + enzyme inhibitor + + + + + enzyme inhibitor + IUPAC + + + + + + enzyme inhibitors + ChEBI + + + + + inhibidor enzimatico + ChEBI + + + + + inhibidores enzimaticos + ChEBI + + + + + inhibiteur enzymatique + ChEBI + + + + + inhibiteurs enzymatiques + ChEBI + + + + + + + + + A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. + chemical entity + chebi_ontology + CHEBI:24431 + + chemical entity + + + + + chemical entity + UniProt + + + + + + + + + + A role played by the molecular entity or part thereof within a biological context. + chebi_ontology + biological function + CHEBI:24432 + + biological role + + + + + biological function + ChEBI + + + + + + + + + + + + + + + A defined linked collection of atoms or a single atom within a molecular entity. + group + chebi_ontology + Gruppe + Rest + groupe + grupo + grupos + CHEBI:24433 + + group + + + + + group + IUPAC + + + + + + Gruppe + ChEBI + + + + + Rest + ChEBI + + + + + groupe + IUPAC + + + + + grupo + IUPAC + + + + + grupos + IUPAC + + + + + + + + + + + + + + + + + Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). + chebi_ontology + CHEBI:24651 + + hydroxides + + + + + + + + + + + + + + + A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). + oxoacid + oxoacids + chebi_ontology + oxacids + oxiacids + oxo acid + oxy-acids + oxyacids + CHEBI:24833 + + oxoacid + + + + + oxoacid + IUPAC + + + + + + oxoacids + IUPAC + + + + + + oxacids + ChEBI + + + + + oxiacids + ChEBI + + + + + oxo acid + ChEBI + + + + + oxy-acids + ChEBI + + + + + oxyacids + ChEBI + + + + + + + + + + chebi_ontology + inorganic anions + CHEBI:24834 + + inorganic anion + + + + + inorganic anions + ChEBI + + + + + + + + + A molecular entity that contains no carbon. + chebi_ontology + anorganische Verbindungen + inorganic compounds + inorganic entity + inorganic molecular entities + inorganics + CHEBI:24835 + + inorganic molecular entity + + + + + anorganische Verbindungen + ChEBI + + + + + inorganic compounds + ChEBI + + + + + inorganic entity + ChEBI + + + + + inorganic molecular entities + ChEBI + + + + + inorganics + ChEBI + + + + + + + + + + chebi_ontology + inorganic oxides + CHEBI:24836 + + inorganic oxide + + + + + inorganic oxides + ChEBI + + + + + + + + + A molecular entity having a net electric charge. + Ion + ion + chebi_ontology + Ionen + iones + ions + CHEBI:24870 + + ion + + + + + Ion + ChEBI + + + + + ion + ChEBI + + + + + ion + IUPAC + + + + + + Ionen + ChEBI + + + + + iones + ChEBI + + + + + ions + ChEBI + + + + + + + + + + + + + + + iron molecular entity + chebi_ontology + iron compounds + iron molecular entities + CHEBI:24873 + + iron molecular entity + + + + + iron molecular entity + ChEBI + + + + + iron compounds + ChEBI + + + + + iron molecular entities ChEBI - + - - - + + + Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites. + CHEBI:26619 + CHEBI:35220 + metabolite chebi_ontology - inorganic anions - CHEBI:24834 + metabolites + primary metabolites + secondary metabolites + CHEBI:25212 - inorganic anion + metabolite + + + + + metabolite + IUPAC + + + + + + metabolites + ChEBI + + + + + primary metabolites + ChEBI + + + + + secondary metabolites + ChEBI + + + + + + + + + + + + + + + + 0 + N + 14.007 + 14.00307 + WebElements:N + nitrogen + chebi_ontology + 7N + N + Stickstoff + azote + nitrogen + nitrogeno + CHEBI:25555 + + nitrogen atom + + + + + nitrogen + IUPAC + + + + + + 7N + IUPAC + + + + + N + IUPAC + + + + + Stickstoff + ChEBI + + + + + azote + IUPAC + + + + + nitrogen + ChEBI + + + + + nitrogeno + ChEBI + + + + + + + + + nonmetal + chebi_ontology + Nichtmetall + Nichtmetalle + no metal + no metales + non-metal + non-metaux + nonmetal + nonmetals + CHEBI:25585 + + nonmetal atom + + + + + nonmetal + IUPAC + + + + + + Nichtmetall + ChEBI + + + + + Nichtmetalle + ChEBI + + + + + no metal + ChEBI + + + + + no metales + ChEBI + + + + + non-metal + ChEBI + + + + + non-metaux + ChEBI + + + + + nonmetal + ChEBI + + + + + nonmetals + ChEBI + + + + + + + + + + An oxide is a chemical compound of oxygen with other chemical elements. + oxide + chebi_ontology + oxides + CHEBI:25741 + + oxide + + + + + oxide + ChEBI + + + + + oxides + ChEBI + + + + + + + + + + + + + + + + 0 + O + InChI=1S/O + QVGXLLKOCUKJST-UHFFFAOYSA-N + 15.99940 + 15.99491 + [O] + KEGG:C00007 + WebElements:O + oxygen + chebi_ontology + 8O + O + Sauerstoff + oxigeno + oxygen + oxygene + CHEBI:25805 + + oxygen atom - + + + oxygen + IUPAC + + + + + + 8O + IUPAC + + + - inorganic anions - ChEBI + O + IUPAC - - - - - - - - A molecular entity that contains no carbon. - chebi_ontology - anorganische Verbindungen - inorganic compounds - inorganic entity - inorganic molecular entities - inorganics - CHEBI:24835 - - inorganic molecular entity - - + - anorganische Verbindungen + Sauerstoff ChEBI - + - inorganic compounds + oxigeno ChEBI - + - inorganic entity + oxygen ChEBI - + - inorganic molecular entities + oxygene ChEBI + + + + + + + + + + + + + + oxygen molecular entity + chebi_ontology + oxygen molecular entities + CHEBI:25806 + + oxygen molecular entity + - + + + oxygen molecular entity + ChEBI + + + - inorganics + oxygen molecular entities ChEBI - + - - - A molecular entity having a net electric charge. - Ion - ion + + + Salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues. In inorganic chemistry, the term is also used to describe anionic coordination entities with phosphorus as central atom. + phosphates chebi_ontology - Ionen - iones - ions - CHEBI:24870 + phosphates + CHEBI:26020 - ion + phosphate - + - Ion + phosphates + IUPAC + + + + + + phosphates ChEBI + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A phosphorus oxoacid that consists of one oxo and three hydroxy groups joined covalently to a central phosphorus atom. + 0 + H3O4P + InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) + NBIIXXVUZAFLBC-UHFFFAOYSA-N + 97.99520 + 97.97690 + [H]OP(=O)(O[H])O[H] + Beilstein:1921286 + CAS:7664-38-2 + Drug_Central:4478 + Gmelin:2000 + HMDB:HMDB0002142 + KEGG:C00009 + KEGG:D05467 + KNApSAcK:C00007408 + PMID:11455380 + PMID:15630224 + PMID:17439666 + PMID:17518491 + PMID:22282755 + PMID:22333268 + PMID:22381614 + PMID:22401268 + Reaxys:1921286 + Wikipedia:Phosphoric_Acid + Phosphoric acid + phosphoric acid + tetraoxophosphoric acid + trihydrogen tetraoxophosphate(3-) + trihydroxidooxidophosphorus + chebi_ontology + H3PO4 + Orthophosphoric acid + Phosphate + Phosphorsaeure + Phosphorsaeureloesungen + [PO(OH)3] + acide phosphorique + acidum phosphoricum + orthophosphoric acid + CHEBI:26078 + + phosphoric acid + + + + + Beilstein:1921286 + Beilstein + + + + + CAS:7664-38-2 + ChemIDplus + + + + + CAS:7664-38-2 + KEGG COMPOUND + + + + + CAS:7664-38-2 + NIST Chemistry WebBook + + + + + Drug_Central:4478 + DrugCentral + + + + + Gmelin:2000 + Gmelin + + + + + PMID:11455380 + Europe PMC + + + + + PMID:15630224 + Europe PMC + + + + + PMID:17439666 + Europe PMC + + + + + PMID:17518491 + Europe PMC + + + + + PMID:22282755 + Europe PMC + + + + + PMID:22333268 + Europe PMC + - - - ion - ChEBI + + + PMID:22381614 + Europe PMC - - - ion - IUPAC - + + + PMID:22401268 + Europe PMC - - - Ionen - ChEBI + + + Reaxys:1921286 + Reaxys - - - iones - ChEBI + + + Phosphoric acid + KEGG_COMPOUND - - - ions - ChEBI + + + phosphoric acid + IUPAC - - - - - - - - Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites. - CHEBI:26619 - CHEBI:35220 - metabolite - chebi_ontology - metabolites - primary metabolites - secondary metabolites - CHEBI:25212 - - metabolite - - + - metabolite + tetraoxophosphoric acid IUPAC - - - metabolites - ChEBI + + + trihydrogen tetraoxophosphate(3-) + IUPAC + - - - primary metabolites - ChEBI + + + trihydroxidooxidophosphorus + IUPAC + - + - secondary metabolites - ChEBI - - - - - - - - - nonmetal - chebi_ontology - Nichtmetall - Nichtmetalle - no metal - no metales - non-metal - non-metaux - nonmetal - nonmetals - CHEBI:25585 - - nonmetal atom - - - - - nonmetal + H3PO4 IUPAC - - + - Nichtmetall - ChEBI + Orthophosphoric acid + KEGG_COMPOUND - + - Nichtmetalle - ChEBI + Phosphate + KEGG_COMPOUND - + - no metal + Phosphorsaeure ChEBI - + - no metales + Phosphorsaeureloesungen ChEBI - + - non-metal - ChEBI + [PO(OH)3] + IUPAC - + - non-metaux + acide phosphorique ChEBI - + - nonmetal + acidum phosphoricum ChEBI - + - nonmetals - ChEBI + orthophosphoric acid + NIST_Chemistry_WebBook - + - - - - An oxide is a chemical compound of oxygen with other chemical elements. - oxide + + + + + + + + chebi_ontology - oxides - CHEBI:25741 + CHEBI:26079 + + phosphoric acid derivative + + + + + + + + + + + + + + + chebi_ontology + phosphorus molecular entities + CHEBI:26082 - oxide + phosphorus molecular entity - - - oxide - ChEBI - - - + - oxides + phosphorus molecular entities ChEBI - + - + @@ -3601,429 +5347,524 @@ For example, A and B may be gene products and binding of B by A positively regul 0 - O - InChI=1S/O - QVGXLLKOCUKJST-UHFFFAOYSA-N - 15.99940 - 15.99491 - [O] - KEGG:C00007 - WebElements:O - oxygen + S + InChI=1S/S + NINIDFKCEFEMDL-UHFFFAOYSA-N + 32.06600 + 31.97207 + [S] + CAS:7704-34-9 + KEGG:C00087 + KEGG:D06527 + PPDB:605 + WebElements:S + sulfur chebi_ontology - 8O - O - Sauerstoff - oxigeno - oxygen - oxygene - CHEBI:25805 + 16S + Elemental sulfur + S + Schwefel + azufre + soufre + sulfur + sulphur + theion + CHEBI:26833 - oxygen atom + sulfur atom - + + + CAS:7704-34-9 + ChemIDplus + + + + + CAS:7704-34-9 + NIST Chemistry WebBook + + + - oxygen + sulfur IUPAC - + - 8O + 16S IUPAC - + - O + Elemental sulfur + KEGG_COMPOUND + + + + + S IUPAC - + + + S + KEGG_COMPOUND + + + + + Schwefel + ChEBI + + + + + azufre + ChEBI + + + + + soufre + ChEBI + + + - Sauerstoff + sulfur ChEBI - + - oxigeno - ChEBI + sulfur + UniProt - + - oxygen + sulphur ChEBI - + - oxygene - ChEBI + theion + IUPAC - + - + - + - oxygen molecular entity + sulfur molecular entity chebi_ontology - oxygen molecular entities - CHEBI:25806 + sulfur molecular entities + CHEBI:26835 - oxygen molecular entity + sulfur molecular entity - + - oxygen molecular entity - ChEBI - - - - - oxygen molecular entities + sulfur molecular entity ChEBI - - - - - - - - Salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues. In inorganic chemistry, the term is also used to describe anionic coordination entities with phosphorus as central atom. - phosphates - chebi_ontology - phosphates - CHEBI:26020 - - phosphate - - - - - phosphates - IUPAC - - - + - phosphates + sulfur molecular entities ChEBI - + - - - - - - - - - - - - - - - - - - - - + + - + - + - A phosphorus oxoacid that consists of one oxo and three hydroxy groups joined covalently to a central phosphorus atom. + A sulfur oxoacid that consists of two oxo and two hydroxy groups joined covalently to a central sulfur atom. 0 - H3O4P - InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) - NBIIXXVUZAFLBC-UHFFFAOYSA-N - 97.99520 - 97.97690 - [H]OP(=O)(O[H])O[H] - Beilstein:1921286 - CAS:7664-38-2 - Drug_Central:4478 - Gmelin:2000 - HMDB:HMDB0002142 - KEGG:C00009 - KEGG:D05467 - KNApSAcK:C00007408 - PMID:11455380 - PMID:15630224 - PMID:17439666 - PMID:17518491 - PMID:22282755 - PMID:22333268 - PMID:22381614 - PMID:22401268 - Reaxys:1921286 - Wikipedia:Phosphoric_Acid - Phosphoric acid - phosphoric acid - tetraoxophosphoric acid - trihydrogen tetraoxophosphate(3-) - trihydroxidooxidophosphorus + H2O4S + InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4) + QAOWNCQODCNURD-UHFFFAOYSA-N + 98.07948 + 97.96738 + [H]OS(=O)(=O)O[H] + CAS:7664-93-9 + Gmelin:2122 + KEGG:C00059 + KEGG:D05963 + KNApSAcK:C00007530 + MolBase:4 + PMID:13568755 + PMID:16122922 + PMID:19397353 + PMID:22047659 + PMID:22136045 + PMID:22204399 + PMID:22267186 + PMID:22296037 + PMID:22364556 + PMID:22435616 + PPDB:606 + Reaxys:2037554 + Wikipedia:Sulfuric_acid + Sulfuric acid + dihydrogen tetraoxosulfate + dihydroxidodioxidosulfur + hydrogen tetraoxosulfate(2-) + hydrogen tetraoxosulfate(VI) + sulfuric acid + tetraoxosulfuric acid chebi_ontology - H3PO4 - Orthophosphoric acid - Phosphate - Phosphorsaeure - Phosphorsaeureloesungen - [PO(OH)3] - acide phosphorique - acidum phosphoricum - orthophosphoric acid - CHEBI:26078 + Acide sulfurique + Acido sulfurico + Acidum sulfuricum + H2SO4 + Schwefelsaeureloesungen + [S(OH)2O2] + [SO2(OH)2] + sulphuric acid + CHEBI:26836 - phosphoric acid + sulfuric acid - - - Beilstein:1921286 - Beilstein - - - + - CAS:7664-38-2 + CAS:7664-93-9 ChemIDplus - + - CAS:7664-38-2 + CAS:7664-93-9 KEGG COMPOUND - + - CAS:7664-38-2 + CAS:7664-93-9 NIST Chemistry WebBook - + - Drug_Central:4478 - DrugCentral + Gmelin:2122 + Gmelin - + - Gmelin:2000 - Gmelin + PMID:13568755 + Europe PMC - + - PMID:11455380 + PMID:16122922 Europe PMC - + - PMID:15630224 + PMID:19397353 Europe PMC - + - PMID:17439666 + PMID:22047659 Europe PMC - + - PMID:17518491 + PMID:22136045 Europe PMC - + - PMID:22282755 + PMID:22204399 Europe PMC - + - PMID:22333268 + PMID:22267186 Europe PMC - + - PMID:22381614 + PMID:22296037 Europe PMC - + - PMID:22401268 + PMID:22364556 Europe PMC - + - Reaxys:1921286 + PMID:22435616 + Europe PMC + + + + + Reaxys:2037554 Reaxys - + - Phosphoric acid + Sulfuric acid KEGG_COMPOUND - + - phosphoric acid + dihydrogen tetraoxosulfate IUPAC + - + - tetraoxophosphoric acid + dihydroxidodioxidosulfur IUPAC - + - trihydrogen tetraoxophosphate(3-) + hydrogen tetraoxosulfate(2-) IUPAC - + - trihydroxidooxidophosphorus + hydrogen tetraoxosulfate(VI) IUPAC - - - H3PO4 + + + sulfuric acid + ChEBI + + + + + sulfuric acid IUPAC + - - - Orthophosphoric acid - KEGG_COMPOUND + + + tetraoxosulfuric acid + IUPAC + - + - Phosphate - KEGG_COMPOUND + Acide sulfurique + ChemIDplus - + - Phosphorsaeure - ChEBI + Acido sulfurico + ChemIDplus - + - Phosphorsaeureloesungen - ChEBI + Acidum sulfuricum + ChemIDplus - + - [PO(OH)3] + H2SO4 IUPAC - + - acide phosphorique - ChEBI + Schwefelsaeureloesungen + ChemIDplus - + - acidum phosphoricum - ChEBI + [S(OH)2O2] + MolBase - + - orthophosphoric acid - NIST_Chemistry_WebBook + [SO2(OH)2] + IUPAC + + + + + sulphuric acid + MolBase - + - - - - - - - - + + + Any nutrient required in small quantities by organisms throughout their life in order to orchestrate a range of physiological functions. + Wikipedia:Micronutrient chebi_ontology - CHEBI:26079 - - phosphoric acid derivative + micronutrients + trace elements + CHEBI:27027 + + micronutrient + + + + micronutrients + ChEBI + + + + + trace elements + ChEBI + - + - - - - - - - - + + + An element whose atom has an incomplete d sub-shell, or which can give rise to cations with an incomplete d sub-shell. + transition element chebi_ontology - phosphorus molecular entities - CHEBI:26082 + Uebergangselement + Uebergangsmetalle + metal de transicion + metal de transition + metales de transicion + metaux de transition + transition element + transition elements + transition metal + transition metals + CHEBI:27081 - phosphorus molecular entity + transition element atom - + + + transition element + IUPAC + + + + + + Uebergangselement + ChEBI + + + + + Uebergangsmetalle + ChEBI + + + - phosphorus molecular entities + metal de transicion + ChEBI + + + + + metal de transition + ChEBI + + + + + metales de transicion + ChEBI + + + + + metaux de transition + ChEBI + + + + + transition element + ChEBI + + + + + transition elements + ChEBI + + + + + transition metal + ChEBI + + + + + transition metals ChEBI @@ -4223,34 +6064,437 @@ For example, A and B may be gene products and binding of B by A positively regul KEGG_COMPOUND - + + + Phosphor + ChEBI + + + + + Phosphorus + KEGG_COMPOUND + + + + + fosforo + ChEBI + + + + + phosphore + ChEBI + + + + + phosphorus + ChEBI + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An onium cation obtained by protonation of ammonia. + +1 + H4N + InChI=1S/H3N/h1H3/p+1 + QGZKDVFQNNGYKY-UHFFFAOYSA-O + 18.03850 + 18.03383 + [H][N+]([H])([H])[H] + CHEBI:22534 + CHEBI:49783 + CHEBI:7435 + CAS:14798-03-9 + Gmelin:84 + KEGG:C01342 + MetaCyc:AMMONIUM + MolBase:929 + PDBeChem:NH4 + PMID:11319011 + PMID:11341317 + PMID:12096804 + PMID:14512268 + PMID:14879753 + PMID:16345391 + PMID:16903292 + PMID:17392693 + PMID:18515490 + PMID:19199063 + PMID:19596600 + PMID:19682559 + PMID:19716251 + PMID:21993530 + PMID:22265469 + PMID:22524020 + PMID:22562341 + PMID:22631217 + Reaxys:16093784 + Wikipedia:Ammonium + ammonium + azanium + chebi_ontology + Ammonium(1+) + NH4(+) + NH4+ + [NH4](+) + ammonium cation + ammonium ion + CHEBI:28938 + + ammonium + + + + + CAS:14798-03-9 + ChemIDplus + + + + + CAS:14798-03-9 + NIST Chemistry WebBook + + + + + Gmelin:84 + Gmelin + + + + + PMID:11319011 + Europe PMC + + + + + PMID:11341317 + Europe PMC + + + + + PMID:12096804 + Europe PMC + + + + + PMID:14512268 + Europe PMC + + + + + PMID:14879753 + Europe PMC + + + + + PMID:16345391 + Europe PMC + + + + + PMID:16903292 + Europe PMC + + + + + PMID:17392693 + Europe PMC + + + + + PMID:18515490 + Europe PMC + + + + + PMID:19199063 + Europe PMC + + + + + PMID:19596600 + Europe PMC + + + + + PMID:19682559 + Europe PMC + + + + + PMID:19716251 + Europe PMC + + + + + PMID:21993530 + Europe PMC + + + + + PMID:22265469 + Europe PMC + + + + + PMID:22524020 + Europe PMC + + + + + PMID:22562341 + Europe PMC + + + + + PMID:22631217 + Europe PMC + + + + + Reaxys:16093784 + Reaxys + + + + + ammonium + ChEBI + + + + + ammonium + IUPAC + + + + + + azanium + IUPAC + + + + + + Ammonium(1+) + ChemIDplus + + + + + NH4(+) + IUPAC + + + + + NH4(+) + UniProt + + + + + NH4+ + KEGG_COMPOUND + + + + + [NH4](+) + MolBase + + + + + ammonium cation + ChemIDplus + + + + + ammonium ion + PDBeChem + + + + + + + + + + + + + + + + + + + + + + -1 + H2N + InChI=1S/H2N/h1H2/q-1 + HYGWNUKOUCZBND-UHFFFAOYSA-N + 16.02262 + 16.01927 + [H][N-][H] + amide + azanide + dihydridonitrate(1-) + chebi_ontology + NH2(-) + CHEBI:29337 + + azanide + + + + + amide + IUPAC + + + + + + azanide + IUPAC + + + + + + dihydridonitrate(1-) + IUPAC + + + + - Phosphor - ChEBI + NH2(-) + IUPAC + + + + + + + + + + + + + + + A divalent inorganic anion resulting from the removal of two protons from ammonia. + -2 + HN + InChI=1S/HN/h1H/q-2 + DZQYTNGKSBCIOE-UHFFFAOYSA-N + 15.01468 + 15.01200 + [N--][H] + azanediide + hydridonitrate(2-) + chebi_ontology + NH(2-) + imide + CHEBI:29340 + + hydridonitrate(2-) + - - - Phosphorus - KEGG_COMPOUND + + + azanediide + IUPAC + - - - fosforo - ChEBI + + + hydridonitrate(2-) + IUPAC + - + - phosphore - ChEBI + NH(2-) + IUPAC - + - phosphorus - ChEBI + imide + IUPAC @@ -4322,6 +6566,26 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + chebi_ontology + inorganic hydrides + CHEBI:33242 + + inorganic hydride + + + + + inorganic hydrides + ChEBI + + + + @@ -4551,6 +6815,40 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + A molecular entity all atoms of which have the same atomic number. + chebi_ontology + homoatomic entity + homoatomic molecular entities + homoatomic molecular entity + CHEBI:33259 + + elemental molecular entity + + + + + homoatomic entity + ChEBI + + + + + homoatomic molecular entities + ChEBI + + + + + homoatomic molecular entity + ChEBI + + + + @@ -5007,6 +7305,67 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + group 8 elements + chebi_ontology + iron group element + iron group elements + CHEBI:33356 + + iron group element atom + + + + + group 8 elements + IUPAC + + + + + + iron group element + ChEBI + + + + + iron group elements + ChEBI + + + + + + + + + + chebi_ontology + oxoacids of sulfur + sulfur oxoacids + CHEBI:33402 + + sulfur oxoacid + + + + + oxoacids of sulfur + ChEBI + + + + + sulfur oxoacids + ChEBI + + + + @@ -5025,113 +7384,297 @@ For example, A and B may be gene products and binding of B by A positively regul pnictogen oxoacid - + + + pnictogen oxoacids + ChEBI + + + + + + + + + + A pnictogen oxoacid which contains phosphorus and oxygen, at least one hydrogen atom bound to oxygen, and forms an ion by the loss of one or more protons. + phosphorus oxoacid + chebi_ontology + Oxosaeure des Phosphors + oxoacids of phosphorus + phosphorus oxoacids + CHEBI:33457 + + phosphorus oxoacid + + + + + phosphorus oxoacid + ChEBI + + + + + Oxosaeure des Phosphors + ChEBI + + + + + oxoacids of phosphorus + ChEBI + + + + + phosphorus oxoacids + ChEBI + + + + + + + + + + pnictogen oxoanion + chebi_ontology + pnictogen oxoanions + CHEBI:33459 + + pnictogen oxoanion + + + + + pnictogen oxoanion + ChEBI + + + + + pnictogen oxoanions + ChEBI + + + + + + + + + + + phosphorus oxoanion + chebi_ontology + oxoanions of phosphorus + phosphorus oxoanions + CHEBI:33461 + + phosphorus oxoanion + + + + + phosphorus oxoanion + ChEBI + + + + + oxoanions of phosphorus + ChEBI + + + + + phosphorus oxoanions + ChEBI + + + + + + + + + + sulfur oxoanion + chebi_ontology + oxoanions of sulfur + sulfur oxoanions + CHEBI:33482 + + sulfur oxoanion + + + + + sulfur oxoanion + ChEBI + + + + + oxoanions of sulfur + ChEBI + + + + + sulfur oxoanions + ChEBI + + + + + + + + + + + + + + + chalcogen oxoacid + chebi_ontology + chalcogen oxoacids + CHEBI:33484 + + chalcogen oxoacid + + + + + chalcogen oxoacid + ChEBI + + + - pnictogen oxoacids + chalcogen oxoacids ChEBI - + - - - - A pnictogen oxoacid which contains phosphorus and oxygen, at least one hydrogen atom bound to oxygen, and forms an ion by the loss of one or more protons. - phosphorus oxoacid + + + chalcogen oxoanion chebi_ontology - Oxosaeure des Phosphors - oxoacids of phosphorus - phosphorus oxoacids - CHEBI:33457 + chalcogen oxoanions + CHEBI:33485 - phosphorus oxoacid + chalcogen oxoanion - + - phosphorus oxoacid + chalcogen oxoanion ChEBI - + - Oxosaeure des Phosphors + chalcogen oxoanions ChEBI + + + + + + + + + + + + + + A molecular entity containing one or more atoms of a transition element. + chebi_ontology + transition element molecular entities + transition metal molecular entity + CHEBI:33497 + + transition element molecular entity + - + - oxoacids of phosphorus + transition element molecular entities ChEBI - + - phosphorus oxoacids + transition metal molecular entity ChEBI - + - - - - pnictogen oxoanion + + + An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity. + CHEBI:25217 + CHEBI:6788 + KEGG:C00050 + PMID:21784043 + Wikipedia:Metal chebi_ontology - pnictogen oxoanions - CHEBI:33459 + elemental metal + elemental metals + metal element + metal elements + metals + CHEBI:33521 - pnictogen oxoanion + metal atom - - - pnictogen oxoanion + + + PMID:21784043 + Europe PMC + + + + + elemental metal ChEBI - + - pnictogen oxoanions + elemental metals ChEBI - - - - - - - - - - phosphorus oxoanion - chebi_ontology - oxoanions of phosphorus - phosphorus oxoanions - CHEBI:33461 - - phosphorus oxoanion - - - - phosphorus oxoanion + + + metal element ChEBI - + - oxoanions of phosphorus + metal elements ChEBI - + - phosphorus oxoanions + metals ChEBI @@ -5190,6 +7733,32 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + chebi_ontology + d-block element + d-block elements + CHEBI:33561 + + d-block element atom + + + + + d-block element + ChEBI + + + + + d-block elements + ChEBI + + + + @@ -5367,6 +7936,134 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + A d-block molecular entity is a molecular entity containing one or more atoms of a d-block element. + d-block molecular entity + chebi_ontology + d-block compounds + d-block molecular entities + CHEBI:33676 + + d-block molecular entity + + + + + d-block molecular entity + ChEBI + + + + + d-block compounds + ChEBI + + + + + d-block molecular entities + ChEBI + + + + + + + + + + Hydrides are chemical compounds of hydrogen with other chemical elements. + chebi_ontology + CHEBI:33692 + + hydrides + + + + + + + + + + + + + + + iron group molecular entity + chebi_ontology + iron group molecular entities + CHEBI:33744 + + iron group molecular entity + + + + + iron group molecular entity + ChEBI + + + + + iron group molecular entities + ChEBI + + + + + + + + + A substance used in a chemical reaction to detect, measure, examine, or produce other substances. + reagent + chebi_ontology + reactif + reactivo + reagents + CHEBI:33893 + + reagent + + + + + reagent + IUPAC + + + + + + reactif + IUPAC + + + + + reactivo + IUPAC + + + + + reagents + ChEBI + + + + @@ -5387,6 +8084,130 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + chebi_ontology + nitrogen hydrides + CHEBI:35106 + + nitrogen hydride + + + + + nitrogen hydrides + ChEBI + + + + + + + + + Saturated acyclic nitrogen hydrides having the general formula NnHn+2. + chebi_ontology + azanes + CHEBI:35107 + + azane + + + + + azanes + ChEBI + + + + + + + + + A substance that diminishes the rate of a chemical reaction. + inhibitor + chebi_ontology + inhibidor + inhibiteur + inhibitors + CHEBI:35222 + + inhibitor + + + + + inhibitor + IUPAC + + + + + + inhibidor + ChEBI + + + + + inhibiteur + ChEBI + + + + + inhibitors + ChEBI + + + + + + + + + A substance that increases the rate of a reaction without modifying the overall standard Gibbs energy change in the reaction. + catalyst + chebi_ontology + Katalysator + catalizador + catalyseur + CHEBI:35223 + + catalyst + + + + + catalyst + IUPAC + + + + + + Katalysator + ChEBI + + + + + catalizador + ChEBI + + + + + catalyseur + ChEBI + + + + @@ -5456,15 +8277,42 @@ For example, A and B may be gene products and binding of B by A positively regul ChEBI - - - phosphate + + + phosphate + ChEBI + + + + + phosphate ions + ChEBI + + + + + + + + + + pnictogen hydride + chebi_ontology + pnictogen hydrides + CHEBI:35881 + + pnictogen hydride + + + + + pnictogen hydride ChEBI - + - phosphate ions + pnictogen hydrides ChEBI @@ -5726,6 +8574,125 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + chebi_ontology + inorganic cations + CHEBI:36915 + + inorganic cation + + + + + inorganic cations + ChEBI + + + + + + + + + A monoatomic or polyatomic species having one or more elementary charges of the proton. + CHEBI:23058 + CHEBI:3473 + KEGG:C01373 + Cation + cation + chebi_ontology + Kation + Kationen + cationes + cations + CHEBI:36916 + + cation + + + + + Cation + KEGG_COMPOUND + + + + + cation + ChEBI + + + + + cation + IUPAC + + + + + + Kation + ChEBI + + + + + Kationen + ChEBI + + + + + cationes + ChEBI + + + + + cations + ChEBI + + + + + + + + + mononuclear parent hydrides + chebi_ontology + mononuclear hydride + mononuclear hydrides + CHEBI:37176 + + mononuclear parent hydride + + + + + mononuclear parent hydrides + IUPAC + + + + + + mononuclear hydride + ChEBI + + + + + mononuclear hydrides + IUPAC + + + + @@ -5871,6 +8838,56 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + A molecular entity able to provide a pair of electrons and thus capable of forming a covalent bond with an electron-pair acceptor (Lewis acid), thereby producing a Lewis adduct. + Lewis base + chebi_ontology + Lewis-Base + base de Lewis + donneur d'une paire d'electrons + electron donor + CHEBI:39144 + + Lewis base + + + + + Lewis base + IUPAC + + + + + + Lewis-Base + ChEBI + + + + + base de Lewis + IUPAC + + + + + donneur d'une paire d'electrons + ChEBI + + + + + electron donor + ChEBI + + + + @@ -6179,6 +9196,114 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + -1 + HO4S + InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-1 + QAOWNCQODCNURD-UHFFFAOYSA-M + 97.07154 + 96.96010 + [H]OS([O-])(=O)=O + CHEBI:29199 + CHEBI:45693 + Gmelin:2121 + hydrogen(tetraoxidosulfate)(1-) + hydrogensulfate + hydrogensulfate(1-) + hydrogentetraoxosulfate(1-) + hydrogentetraoxosulfate(VI) + hydroxidotrioxidosulfate(1-) + chebi_ontology + HSO4(-) + HYDROGEN SULFATE + [SO3(OH)](-) + CHEBI:45696 + + hydrogensulfate + + + + + Gmelin:2121 + Gmelin + + + + + hydrogen(tetraoxidosulfate)(1-) + IUPAC + + + + + + hydrogensulfate + IUPAC + + + + + hydrogensulfate(1-) + IUPAC + + + + + + hydrogentetraoxosulfate(1-) + IUPAC + + + + + + hydrogentetraoxosulfate(VI) + IUPAC + + + + + + hydroxidotrioxidosulfate(1-) + IUPAC + + + + + + HSO4(-) + IUPAC + + + + + HYDROGEN SULFATE + PDBeChem + + + + + [SO3(OH)](-) + IUPAC + + + + @@ -6215,6 +9340,40 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + chebi_ontology + Schwefeloxide + oxides of sulfur + sulfur oxides + CHEBI:48154 + + sulfur oxide + + + + + Schwefeloxide + ChEBI + + + + + oxides of sulfur + ChEBI + + + + + sulfur oxides + ChEBI + + + + @@ -6295,6 +9454,60 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + chebi_ontology + CHEBI:50312 + + onium compound + + + + + + + + + Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families. + onium cations + chebi_ontology + onium cations + onium ion + onium ions + CHEBI:50313 + + onium cation + + + + + onium cations + IUPAC + + + + + + onium cations + ChEBI + + + + + onium ion + ChEBI + + + + + onium ions + ChEBI + + + + @@ -6350,6 +9563,71 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + A poison that interferes with the functions of the nervous system. + CHEBI:50911 + Wikipedia:Neurotoxin + chebi_ontology + agente neurotoxico + nerve poison + nerve poisons + neurotoxic agent + neurotoxic agents + neurotoxicant + neurotoxins + CHEBI:50910 + + neurotoxin + + + + + agente neurotoxico + ChEBI + + + + + nerve poison + ChEBI + + + + + nerve poisons + ChEBI + + + + + neurotoxic agent + ChEBI + + + + + neurotoxic agents + ChEBI + + + + + neurotoxicant + ChEBI + + + + + neurotoxins + ChEBI + + + + @@ -6364,6 +9642,48 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + CHEBI:25556 + CHEBI:7594 + KEGG:C06061 + chebi_ontology + Nitrogenous compounds + nitrogen compounds + nitrogen molecular entities + CHEBI:51143 + + nitrogen molecular entity + + + + + Nitrogenous compounds + KEGG_COMPOUND + + + + + nitrogen compounds + ChEBI + + + + + nitrogen molecular entities + ChEBI + + + + @@ -6377,6 +9697,33 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + A role played by the molecular entity or part thereof which causes the development of a pathological process. + chebi_ontology + etiopathogenetic agent + etiopathogenetic role + CHEBI:52209 + + aetiopathogenetic role + + + + + etiopathogenetic agent + ChEBI + + + + + etiopathogenetic role + ChEBI + + + + @@ -6402,6 +9749,61 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + A reagent that forms a bond to its reaction partner (the electrophile) by donating both bonding electrons. + chebi_ontology + nucleophile + nucleophiles + nucleophilic reagents + CHEBI:59740 + + nucleophilic reagent + + + + + nucleophile + ChEBI + + + + + nucleophiles + ChEBI + + + + + nucleophilic reagents + ChEBI + + + + + + + + + An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one. + chebi_ontology + a monovalent cation + CHEBI:60242 + + monovalent inorganic cation + + + + + a monovalent cation + UniProt + + + + @@ -6422,6 +9824,83 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + Any substance that causes disturbance to organisms by chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by the organism. + Wikipedia:Poison + chebi_ontology + poisonous agent + poisonous agents + poisonous substance + poisonous substances + poisons + toxic agent + toxic agents + toxic substance + toxic substances + CHEBI:64909 + + poison + + + + + poisonous agent + ChEBI + + + + + poisonous agents + ChEBI + + + + + poisonous substance + ChEBI + + + + + poisonous substances + ChEBI + + + + + poisons + ChEBI + + + + + toxic agent + ChEBI + + + + + toxic agents + ChEBI + + + + + toxic substance + ChEBI + + + + + toxic substances + ChEBI + + + + @@ -6486,6 +9965,40 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus). + chebi_ontology + Mus musculus metabolite + Mus musculus metabolites + mouse metabolites + CHEBI:75771 + + mouse metabolite + + + + + Mus musculus metabolite + ChEBI + + + + + Mus musculus metabolites + ChEBI + + + + + mouse metabolites + ChEBI + + + + @@ -6506,66 +10019,273 @@ For example, A and B may be gene products and binding of B by A positively regul baker's yeast secondary metabolites CHEBI:75772 - Saccharomyces cerevisiae metabolite + Saccharomyces cerevisiae metabolite + + + + + S. cerevisiae metabolite + ChEBI + + + + + S. cerevisiae metabolites + ChEBI + + + + + S. cerevisiae secondary metabolite + ChEBI + + + + + S. cerevisiae secondary metabolites + ChEBI + + + + + Saccharomyces cerevisiae metabolites + ChEBI + + + + + Saccharomyces cerevisiae secondary metabolites + ChEBI + + + + + baker's yeast metabolite + ChEBI + + + + + baker's yeast metabolites + ChEBI + + + + + baker's yeast secondary metabolite + ChEBI + + + + + baker's yeast secondary metabolites + ChEBI + + + + + + + + + Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea. + chebi_ontology + prokaryotic metabolites + CHEBI:75787 + + prokaryotic metabolite + + + + + prokaryotic metabolites + ChEBI + + + + + + + + + Any enzyme inhibitor that interferes with the action of a hydrolase (EC 3.*.*.*). + Wikipedia:Hydrolase + chebi_ontology + EC 3.* (hydrolase) inhibitors + EC 3.* inhibitor + EC 3.* inhibitors + EC 3.*.*.* inhibitor + EC 3.*.*.* inhibitors + hydrolase (EC 3.*) inhibitor + hydrolase (EC 3.*) inhibitors + hydrolase inhibitor + hydrolase inhibitors + CHEBI:76759 + + EC 3.* (hydrolase) inhibitor + + + + + EC 3.* (hydrolase) inhibitors + ChEBI + + + + + EC 3.* inhibitor + ChEBI + + + + + EC 3.* inhibitors + ChEBI + + + + + EC 3.*.*.* inhibitor + ChEBI + + + + + EC 3.*.*.* inhibitors + ChEBI + + + + + hydrolase (EC 3.*) inhibitor + ChEBI + + + + + hydrolase (EC 3.*) inhibitors + ChEBI + + + + + hydrolase inhibitor + ChEBI + + + + + hydrolase inhibitors + ChEBI + + + + + + + + + Any hydrolase inhibitor that interferes with the action of a hydrolase acting on C-N bonds, other than peptide bonds (EC 3.5.*.*). + chebi_ontology + EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitor + EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitors + EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitor + EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitors + EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitors + EC 3.5.* inhibitor + EC 3.5.* inhibitors + CHEBI:76764 + + EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor - + - S. cerevisiae metabolite + EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitor ChEBI - + - S. cerevisiae metabolites + EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitors ChEBI - + - S. cerevisiae secondary metabolite + EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitor ChEBI - + - S. cerevisiae secondary metabolites + EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitors ChEBI - + - Saccharomyces cerevisiae metabolites + EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitors ChEBI - + - Saccharomyces cerevisiae secondary metabolites + EC 3.5.* inhibitor ChEBI - + - baker's yeast metabolite + EC 3.5.* inhibitors ChEBI + + + + + + + + An EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor that interferes with the action of any non-peptide linear amide C-N hydrolase (EC 3.5.1.*). + chebi_ontology + EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitors + EC 3.5.1.* inhibitor + EC 3.5.1.* inhibitors + non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitor + non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitors + CHEBI:76807 + + EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor + - + - baker's yeast metabolites + EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitors ChEBI - + - baker's yeast secondary metabolite + EC 3.5.1.* inhibitor ChEBI - + - baker's yeast secondary metabolites + EC 3.5.1.* inhibitors + ChEBI + + + + + non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitor + ChEBI + + + + + non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitors ChEBI @@ -6593,6 +10313,55 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + Any prokaryotic metabolite produced during a metabolic reaction in bacteria. + CHEBI:75760 + CHEBI:76970 + chebi_ontology + CHEBI:76969 + + bacterial metabolite + + + + + + + + + Any bacterial metabolite produced during a metabolic reaction in Escherichia coli. + chebi_ontology + E.coli metabolite + E.coli metabolites + Escherichia coli metabolites + CHEBI:76971 + + Escherichia coli metabolite + + + + + E.coli metabolite + ChEBI + + + + + E.coli metabolites + ChEBI + + + + + Escherichia coli metabolites + ChEBI + + + + @@ -6636,6 +10405,153 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the action of amidase (EC 3.5.1.4). + Wikipedia:Amidase + chebi_ontology + EC 3.5.1.4 (amidase) inhibitors + EC 3.5.1.4 inhibitor + EC 3.5.1.4 inhibitors + N-acetylaminohydrolase inhibitor + N-acetylaminohydrolase inhibitors + acylamidase inhibitor + acylamidase inhibitors + acylamide amidohydrolase inhibitor + acylamide amidohydrolase inhibitors + amidase (EC 3.5.1.4) inhibitor + amidase (EC 3.5.1.4) inhibitors + amidase inhibitor + amidase inhibitors + amidohydrolase inhibitor + amidohydrolase inhibitors + deaminase inhibitor + deaminase inhibitors + fatty acylamidase inhibitor + fatty acylamidase inhibitors + CHEBI:77941 + + EC 3.5.1.4 (amidase) inhibitor + + + + + EC 3.5.1.4 (amidase) inhibitors + ChEBI + + + + + EC 3.5.1.4 inhibitor + ChEBI + + + + + EC 3.5.1.4 inhibitors + ChEBI + + + + + N-acetylaminohydrolase inhibitor + ChEBI + + + + + N-acetylaminohydrolase inhibitors + ChEBI + + + + + acylamidase inhibitor + ChEBI + + + + + acylamidase inhibitors + ChEBI + + + + + acylamide amidohydrolase inhibitor + ChEBI + + + + + acylamide amidohydrolase inhibitors + ChEBI + + + + + amidase (EC 3.5.1.4) inhibitor + ChEBI + + + + + amidase (EC 3.5.1.4) inhibitors + ChEBI + + + + + amidase inhibitor + ChEBI + + + + + amidase inhibitors + ChEBI + + + + + amidohydrolase inhibitor + ChEBI + + + + + amidohydrolase inhibitors + ChEBI + + + + + deaminase inhibitor + ChEBI + + + + + deaminase inhibitors + ChEBI + + + + + fatty acylamidase inhibitor + ChEBI + + + + + fatty acylamidase inhibitors + ChEBI + + + + @@ -6670,6 +10586,27 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + A substance used in a thermodynamic heat pump cycle or refrigeration cycle that undergoes a phase change from a gas to a liquid and back. Refrigerants are used in air-conditioning systems and freezers or refrigerators and are assigned a "R" number (by ASHRAE - formerly the American Society of Heating, Refrigerating and Air Conditioning Engineers), which is determined systematically according to their molecular structure. + Wikipedia:Refrigerant + chebi_ontology + refrigerants + CHEBI:78433 + + refrigerant + + + + + refrigerants + ChEBI + + + + @@ -6730,6 +10667,20 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An elemental molecular entity in which all of the atoms have atomic number 26. + chebi_ontology + CHEBI:82663 + + elemental iron + + + + @@ -6853,6 +10804,50 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione. + Wikipedia:Sulfur_metabolism + sulfur metabolism + sulphur metabolic process + sulphur metabolism + biological_process + GO:0006790 + + + + + + sulfur compound metabolic process + + + + + The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione. + GOC:ai + + + + @@ -6927,6 +10922,45 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. + nitrogen compound metabolism + biological_process + GO:0006807 + + + nitrogen compound metabolic process + + + + + The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. + GOC:jl + ISBN:0198506732 + + + + @@ -7318,6 +11352,47 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + The chemical reactions and pathways involving the ammonium ion. + pr + 2011-09-28T04:21:30Z + ammonium ion metabolism + biological_process + ammonium metabolic process + GO:0097164 + ammonium ion metabolic process + + + + + The chemical reactions and pathways involving the ammonium ion. + GOC:dhl + GOC:tb + PMID:14671018 + + + + diff --git a/src/ontology/imports/pco_import.owl b/src/ontology/imports/pco_import.owl index 7d23f2c..46670ab 100644 --- a/src/ontology/imports/pco_import.owl +++ b/src/ontology/imports/pco_import.owl @@ -7,11 +7,12 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"> + xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + - 2022-01-01 + 2022-03-12 @@ -87,6 +88,12 @@ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/imports/po_import.owl b/src/ontology/imports/po_import.owl index 3173e6d..f5497ba 100644 --- a/src/ontology/imports/po_import.owl +++ b/src/ontology/imports/po_import.owl @@ -14,9 +14,9 @@ xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + - 2022-01-01 + 2022-03-12 @@ -52,7 +52,9 @@ - + + definition + @@ -286,7 +288,9 @@ - + + has_exact_synonym + @@ -2651,7 +2655,7 @@ For example, A and B may be gene products and binding of B by A positively regul panicle development (related) - GRO:0007157 + GRO:0007157 @@ -4720,13 +4724,13 @@ For example, A and B may be gene products and binding of B by A positively regul cycle (broad) - FNA:d42df0a9-60f4-4c24-9c0b-ba815272f2fe + FNA:d42df0a9-60f4-4c24-9c0b-ba815272f2fe verticil (broad) - FNA:12607624-3d2a-4113-bd86-0e2557f2f473 + FNA:12607624-3d2a-4113-bd86-0e2557f2f473 @@ -5294,7 +5298,7 @@ For example, A and B may be gene products and binding of B by A positively regul megasporangia (exact, plural) - FNA:39beb98a-e588-4996-8a2d-57c9967dc8ab + FNA:39beb98a-e588-4996-8a2d-57c9967dc8ab @@ -5320,7 +5324,7 @@ For example, A and B may be gene products and binding of B by A positively regul macrosporangia (related) - FNA:6102371f-fcdd-47cd-b0fd-2d24e2d5c8cc + FNA:6102371f-fcdd-47cd-b0fd-2d24e2d5c8cc diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index df9382c..34918dd 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -16,9 +16,9 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + - 2022-01-01 + 2022-03-12 @@ -54,7 +54,9 @@ - + + definition + @@ -202,6 +204,12 @@ + + + + + + @@ -214,6 +222,12 @@ + + + + + + @@ -252,7 +266,9 @@ - + + has_exact_synonym + diff --git a/src/ontology/imports/stato_import.owl b/src/ontology/imports/stato_import.owl index f68ea66..53d4dc3 100644 --- a/src/ontology/imports/stato_import.owl +++ b/src/ontology/imports/stato_import.owl @@ -9,10 +9,11 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"> + xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" + xmlns:terms="http://purl.org/dc/terms/"> - - 2022-01-01 + + 2022-03-12 @@ -60,7 +61,40 @@ - + + definition + definition + textual definition + + The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition + definition + textual definition + @@ -136,12 +170,47 @@ + + + + + + + + + + Description may include but is not limited to: an abstract, + table of contents, reference to a graphical representation + of content or a free-text account of the content. + An account of the content of the resource. + + Description + Description + + + + + + + + + + + + + + Mark Miller + 2018-05-11T13:47:29Z + + + + @@ -448,6 +517,51 @@ every c that is a concretization of g specifically denotes r + + + + + + + + + + inheres in + this fragility inheres in this vase + this red color inheres in this apple + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + A dependent inheres in its bearer at all times for which the dependent exists. + inheres_in + + + inheres in + + + + + + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + + bearer of + + + + diff --git a/src/ontology/imports/uo_import.owl b/src/ontology/imports/uo_import.owl index 5054cce..8da8ce2 100644 --- a/src/ontology/imports/uo_import.owl +++ b/src/ontology/imports/uo_import.owl @@ -8,8 +8,8 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:oboInOwl="oboInOwl:"> - - 2022-01-01 + + 2022-03-12 @@ -65,6 +65,24 @@ + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/reports/srpdio-edit.owl-obo-report.tsv b/src/ontology/reports/srpdio-edit.owl-obo-report.tsv index 729186c..14e5fe2 100644 --- a/src/ontology/reports/srpdio-edit.owl-obo-report.tsv +++ b/src/ontology/reports/srpdio-edit.owl-obo-report.tsv @@ -1 +1,837 @@ Level Rule Name Subject Property Value +ERROR multiple_labels concentration of elemental scandium in top soil rdfs:label concentration of chemical entity in soil +ERROR multiple_labels concentration of elemental scandium in top soil rdfs:label concentration of elemental scandium in top soil +ERROR multiple_labels concentration of elemental scandium in environmental material rdfs:label concentration of chemical entity in liquid water +ERROR multiple_labels concentration of elemental scandium in environmental material rdfs:label concentration of elemental scandium in environmental material +ERROR multiple_definitions concentration of elemental scandium in top soil IAO:0000115 The concentration of chemical entity when measured in soil. +ERROR multiple_definitions concentration of elemental scandium in top soil IAO:0000115 The concentration of elemental scandium when measured in top soil. +ERROR multiple_definitions concentration of elemental scandium in environmental material IAO:0000115 The concentration of chemical entity when measured in liquid water. +ERROR multiple_definitions concentration of elemental scandium in environmental material IAO:0000115 The concentration of elemental scandium when measured in environmental material. +ERROR multiple_equivalent_class_definitions concentration of elemental scandium in top soil owl:equivalentClass blank node +ERROR multiple_equivalent_class_definitions concentration of elemental scandium in environmental material owl:equivalentClass blank node +WARN multiple_equivalent_classes concentration of elemental scandium in top soil owl:equivalentClass blank node +WARN multiple_equivalent_classes concentration of elemental scandium in environmental material owl:equivalentClass blank node +INFO missing_superclass alkaline of fresh water rdfs:subClassOf +INFO missing_superclass electrical conductivity of fresh water rdfs:subClassOf +INFO missing_superclass acidity of fresh water rdfs:subClassOf +INFO missing_superclass temperature of fresh water rdfs:subClassOf +INFO missing_superclass alkaline of soil rdfs:subClassOf +INFO missing_superclass water composition of soil rdfs:subClassOf +INFO missing_superclass alkaline of environmental material rdfs:subClassOf +INFO missing_superclass electrical conductivity of environmental material rdfs:subClassOf +INFO missing_superclass acidity of environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental aluminium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental antimony in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental arsenic in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental barium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental beryllium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental bismuth in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental boron in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental cadmium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental caesium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental calcium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental cerium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental chromium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental cobalt in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental copper in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental gallium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental gold in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental indium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental iron in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental lanthanum in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental lead in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental lithium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental magnesium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental manganese in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental mercury in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental molybdenum in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental nickel in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental niobium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental phosphorus in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental potassium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental rubidium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental selenium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental silicon in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental silver in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental sodium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental strontium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental sulfur in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental tellurium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental thallium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental thorium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental tin in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental titanium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental tungsten in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental uranium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental vanadium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental yttrium in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental zinc in shoot system rdfs:subClassOf +INFO missing_superclass concentration of elemental aluminium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental antimony in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental arsenic in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental barium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental beryllium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental bismuth in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental boron in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental cadmium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental caesium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental calcium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental cerium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental chromium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental cobalt in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental copper in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental gallium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental gold in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental indium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental iron in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental lanthanum in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental lead in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental lithium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental magnesium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental manganese in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental mercury in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental molybdenum in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental nickel in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental niobium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental phosphorus in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental potassium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental rubidium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental selenium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental silicon in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental silver in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental sodium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental strontium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental sulfur in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental tellurium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental thallium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental thorium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental tin in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental titanium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental tungsten in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental uranium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental vanadium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental yttrium in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental zinc in plant structure rdfs:subClassOf +INFO missing_superclass concentration of elemental aluminium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental antimony in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental arsenic in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental barium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental beryllium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental bismuth in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental boron in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental cadmium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental caesium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental calcium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental cerium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental chromium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental cobalt in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental copper in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental gallium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental gold in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental indium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental iron in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental lanthanum in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental lead in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental lithium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental magnesium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental manganese in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental mercury in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental molybdenum in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental nickel in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental niobium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental phosphorus in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental potassium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental rubidium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental selenium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental silicon in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental silver in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental sodium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental strontium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental sulfur in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental tellurium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental thallium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental thorium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental tin in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental titanium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental tungsten in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental uranium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental vanadium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental yttrium in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental zinc in bulb rdfs:subClassOf +INFO missing_superclass concentration of elemental aluminium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental antimony in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental arsenic in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental barium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental beryllium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental bismuth in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental boron in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental cadmium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental caesium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental calcium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental cerium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental chromium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental cobalt in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental copper in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental gallium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental gold in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental indium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental iron in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental lanthanum in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental lead in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental lithium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental magnesium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental manganese in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental mercury in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental molybdenum in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental nickel in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental niobium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental phosphorus in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental potassium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental rubidium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental selenium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental silicon in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental silver in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental sodium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental strontium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental sulfur in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental tellurium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental thallium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental thorium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental tin in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental titanium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental tungsten in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental uranium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental vanadium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental yttrium in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental zinc in fruit rdfs:subClassOf +INFO missing_superclass concentration of elemental aluminium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental antimony in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental arsenic in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental barium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental beryllium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental bismuth in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental boron in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental cadmium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental caesium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental calcium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental cerium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental chromium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental cobalt in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental copper in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental gallium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental gold in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental indium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental iron in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental lanthanum in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental lead in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental lithium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental magnesium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental manganese in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental mercury in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental molybdenum in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental nickel in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental niobium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental phosphorus in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental potassium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental rubidium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental selenium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental silicon in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental silver in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental sodium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental strontium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental sulfur in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental tellurium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental thallium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental thorium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental tin in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental titanium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental tungsten in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental uranium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental vanadium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental yttrium in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental zinc in infructescence rdfs:subClassOf +INFO missing_superclass concentration of elemental aluminium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental antimony in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental arsenic in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental barium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental beryllium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental bismuth in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental boron in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental cadmium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental caesium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental calcium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental cerium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental chromium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental cobalt in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental copper in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental gallium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental gold in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental indium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental iron in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental lanthanum in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental lead in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental lithium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental magnesium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental manganese in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental mercury in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental molybdenum in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental nickel in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental niobium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental phosphorus in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental potassium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental rubidium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental selenium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental silicon in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental silver in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental sodium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental strontium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental sulfur in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental tellurium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental thallium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental thorium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental tin in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental titanium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental tungsten in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental uranium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental vanadium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental yttrium in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental zinc in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of elemental aluminium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental antimony in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental arsenic in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental barium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental beryllium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental bismuth in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental boron in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental cadmium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental caesium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental calcium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental cerium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental chromium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental cobalt in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental copper in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental gallium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental gold in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental indium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental iron in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental lanthanum in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental lead in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental lithium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental magnesium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental manganese in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental mercury in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental molybdenum in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental nickel in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental niobium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental phosphorus in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental potassium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental rubidium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental selenium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental silicon in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental silver in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental sodium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental strontium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental sulfur in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental tellurium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental thallium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental thorium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental tin in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental titanium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental tungsten in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental uranium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental vanadium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental yttrium in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental zinc in seed rdfs:subClassOf +INFO missing_superclass concentration of elemental aluminium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental antimony in root rdfs:subClassOf +INFO missing_superclass concentration of elemental arsenic in root rdfs:subClassOf +INFO missing_superclass concentration of elemental barium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental beryllium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental bismuth in root rdfs:subClassOf +INFO missing_superclass concentration of elemental boron in root rdfs:subClassOf +INFO missing_superclass concentration of elemental cadmium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental caesium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental calcium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental cerium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental chromium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental cobalt in root rdfs:subClassOf +INFO missing_superclass concentration of elemental copper in root rdfs:subClassOf +INFO missing_superclass concentration of elemental gallium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental gold in root rdfs:subClassOf +INFO missing_superclass concentration of elemental indium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental iron in root rdfs:subClassOf +INFO missing_superclass concentration of elemental lanthanum in root rdfs:subClassOf +INFO missing_superclass concentration of elemental lead in root rdfs:subClassOf +INFO missing_superclass concentration of elemental lithium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental magnesium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental manganese in root rdfs:subClassOf +INFO missing_superclass concentration of elemental mercury in root rdfs:subClassOf +INFO missing_superclass concentration of elemental molybdenum in root rdfs:subClassOf +INFO missing_superclass concentration of elemental nickel in root rdfs:subClassOf +INFO missing_superclass concentration of elemental niobium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental phosphorus in root rdfs:subClassOf +INFO missing_superclass concentration of elemental potassium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental rubidium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental selenium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental silicon in root rdfs:subClassOf +INFO missing_superclass concentration of elemental silver in root rdfs:subClassOf +INFO missing_superclass concentration of elemental sodium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental strontium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental sulfur in root rdfs:subClassOf +INFO missing_superclass concentration of elemental tellurium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental thallium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental thorium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental tin in root rdfs:subClassOf +INFO missing_superclass concentration of elemental titanium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental tungsten in root rdfs:subClassOf +INFO missing_superclass concentration of elemental uranium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental vanadium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental yttrium in root rdfs:subClassOf +INFO missing_superclass concentration of elemental zinc in root rdfs:subClassOf +INFO missing_superclass concentration of elemental aluminium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental antimony in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental arsenic in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental barium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental beryllium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental bismuth in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental boron in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental cadmium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental caesium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental calcium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental cerium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental chromium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental cobalt in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental copper in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental gallium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental gold in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental indium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental iron in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental lanthanum in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental lead in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental lithium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental magnesium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental manganese in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental mercury in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental molybdenum in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental nickel in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental niobium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental phosphorus in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental potassium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental rubidium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental selenium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental silicon in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental silver in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental sodium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental strontium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental sulfur in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental tellurium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental thallium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental thorium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental tin in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental titanium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental tungsten in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental uranium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental vanadium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental yttrium in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental zinc in tuber rdfs:subClassOf +INFO missing_superclass concentration of elemental aluminium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental antimony in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental arsenic in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental barium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental beryllium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental bismuth in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental boron in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental cadmium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental caesium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental calcium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental cerium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental chromium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental cobalt in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental copper in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental gallium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental gold in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental indium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental iron in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental lanthanum in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental lead in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental lithium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental magnesium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental manganese in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental mercury in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental molybdenum in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental nickel in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental niobium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental phosphorus in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental potassium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental rubidium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental selenium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental silicon in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental silver in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental sodium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental strontium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental sulfur in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental tellurium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental thallium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental thorium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental tin in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental titanium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental tungsten in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental uranium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental vanadium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental yttrium in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental zinc in root system rdfs:subClassOf +INFO missing_superclass concentration of chemical entity in plant structure rdfs:subClassOf +INFO missing_superclass concentration of chemical entity in shoot system rdfs:subClassOf +INFO missing_superclass concentration of chemical entity in bulb rdfs:subClassOf +INFO missing_superclass concentration of chemical entity in fruit rdfs:subClassOf +INFO missing_superclass concentration of chemical entity in infructescence rdfs:subClassOf +INFO missing_superclass concentration of chemical entity in vascular leaf rdfs:subClassOf +INFO missing_superclass concentration of chemical entity in seed rdfs:subClassOf +INFO missing_superclass concentration of chemical entity in root rdfs:subClassOf +INFO missing_superclass concentration of chemical entity in tuber rdfs:subClassOf +INFO missing_superclass concentration of chemical entity in root system rdfs:subClassOf +INFO missing_superclass concentration of elemental aluminium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental antimony in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental arsenic in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental barium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental beryllium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental bismuth in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental boron in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental cadmium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental caesium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental calcium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental cerium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental chromium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental cobalt in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental copper in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental gallium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental gold in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental indium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental iron in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental lanthanum in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental lead in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental lithium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental magnesium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental manganese in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental mercury in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental molybdenum in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental nickel in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental niobium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental phosphorus in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental potassium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental rubidium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental selenium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental silicon in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental silver in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental sodium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental strontium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental sulfur in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental tellurium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental thallium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental thorium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental tin in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental titanium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental tungsten in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental uranium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental vanadium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental yttrium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental zinc in environmental material rdfs:subClassOf +INFO missing_superclass concentration of elemental aluminium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental antimony in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental arsenic in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental barium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental beryllium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental bismuth in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental boron in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental cadmium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental caesium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental calcium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental cerium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental chromium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental cobalt in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental copper in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental gallium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental gold in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental indium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental iron in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental lanthanum in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental lead in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental lithium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental magnesium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental manganese in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental mercury in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental molybdenum in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental nickel in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental niobium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental phosphorus in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental potassium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental rubidium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental selenium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental silicon in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental silver in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental sodium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental strontium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental sulfur in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental tellurium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental thallium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental thorium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental tin in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental titanium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental tungsten in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental uranium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental vanadium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental yttrium in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental zinc in soil rdfs:subClassOf +INFO missing_superclass concentration of elemental aluminium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental antimony in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental arsenic in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental barium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental beryllium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental bismuth in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental boron in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental cadmium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental caesium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental calcium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental cerium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental chromium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental cobalt in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental copper in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental gallium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental gold in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental indium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental iron in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental lanthanum in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental lead in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental lithium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental magnesium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental manganese in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental mercury in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental molybdenum in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental nickel in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental niobium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental phosphorus in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental potassium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental rubidium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental selenium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental silicon in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental silver in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental sodium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental strontium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental sulfur in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental tellurium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental thallium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental thorium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental tin in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental titanium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental tungsten in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental uranium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental vanadium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental yttrium in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental zinc in liquid water rdfs:subClassOf +INFO missing_superclass concentration of elemental aluminium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental antimony in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental arsenic in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental barium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental beryllium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental bismuth in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental boron in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental cadmium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental caesium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental calcium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental cerium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental chromium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental cobalt in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental copper in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental gallium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental gold in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental indium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental iron in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental lanthanum in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental lead in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental lithium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental magnesium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental manganese in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental mercury in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental molybdenum in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental nickel in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental niobium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental phosphorus in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental potassium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental rubidium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental selenium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental silicon in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental silver in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental sodium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental strontium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental sulfur in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental tellurium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental thallium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental thorium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental tin in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental titanium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental tungsten in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental uranium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental vanadium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental yttrium in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental zinc in garden soil rdfs:subClassOf +INFO missing_superclass concentration of elemental aluminium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental antimony in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental arsenic in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental barium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental beryllium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental bismuth in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental boron in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental cadmium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental caesium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental calcium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental cerium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental chromium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental cobalt in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental copper in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental gallium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental gold in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental indium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental iron in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental lanthanum in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental lead in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental lithium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental magnesium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental manganese in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental mercury in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental molybdenum in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental nickel in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental niobium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental phosphorus in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental potassium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental rubidium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental selenium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental silicon in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental silver in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental sodium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental strontium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental sulfur in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental tellurium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental thallium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental thorium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental tin in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental titanium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental tungsten in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental uranium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental vanadium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental yttrium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental zinc in fresh water rdfs:subClassOf +INFO missing_superclass concentration of elemental aluminium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental antimony in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental arsenic in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental barium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental beryllium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental bismuth in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental boron in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental cadmium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental caesium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental calcium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental cerium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental chromium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental cobalt in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental copper in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental gallium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental gold in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental indium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental iron in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental lanthanum in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental lead in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental lithium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental magnesium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental manganese in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental mercury in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental molybdenum in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental nickel in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental niobium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental phosphorus in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental potassium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental rubidium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental selenium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental silicon in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental silver in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental sodium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental strontium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental sulfur in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental tellurium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental thallium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental thorium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental tin in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental titanium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental tungsten in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental uranium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental vanadium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental yttrium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental zinc in top soil rdfs:subClassOf +INFO missing_superclass concentration of ammonium in fresh water rdfs:subClassOf +INFO missing_superclass concentration of iron(2+) in fresh water rdfs:subClassOf +INFO missing_superclass concentration of bromide in fresh water rdfs:subClassOf +INFO missing_superclass concentration of chloride in fresh water rdfs:subClassOf +INFO missing_superclass concentration of fluoride in fresh water rdfs:subClassOf +INFO missing_superclass concentration of nitrite in fresh water rdfs:subClassOf +INFO missing_superclass concentration of nitrate in fresh water rdfs:subClassOf +INFO missing_superclass concentration of phosphate(3-) in fresh water rdfs:subClassOf +INFO missing_superclass concentration of sulfate in fresh water rdfs:subClassOf +INFO missing_superclass concentration of chemical entity in environmental material rdfs:subClassOf +INFO missing_superclass concentration of chemical entity in material entity rdfs:subClassOf +INFO missing_superclass concentration of elemental scandium in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental scandium in environmental material rdfs:subClassOf +INFO missing_superclass concentration of chemical entity in garden soil rdfs:subClassOf +INFO missing_superclass concentration of chemical entity in fresh water rdfs:subClassOf +INFO missing_superclass concentration of chemical entity in top soil rdfs:subClassOf +INFO missing_superclass concentration of elemental aluminium in distilled water rdfs:subClassOf +INFO missing_superclass concentration of elemental arsenic in distilled water rdfs:subClassOf +INFO missing_superclass concentration of elemental barium in distilled water rdfs:subClassOf +INFO missing_superclass concentration of elemental beryllium in distilled water rdfs:subClassOf +INFO missing_superclass concentration of elemental cadmium in distilled water rdfs:subClassOf +INFO missing_superclass concentration of elemental chromium in distilled water rdfs:subClassOf +INFO missing_superclass concentration of elemental copper in distilled water rdfs:subClassOf +INFO missing_superclass concentration of elemental lead in distilled water rdfs:subClassOf +INFO missing_superclass concentration of elemental manganese in distilled water rdfs:subClassOf +INFO missing_superclass concentration of elemental nickel in distilled water rdfs:subClassOf +INFO missing_superclass concentration of elemental zinc in distilled water rdfs:subClassOf +INFO missing_superclass concentration of elemental aluminium in tap water rdfs:subClassOf +INFO missing_superclass concentration of elemental arsenic in tap water rdfs:subClassOf +INFO missing_superclass concentration of elemental barium in tap water rdfs:subClassOf +INFO missing_superclass concentration of elemental beryllium in tap water rdfs:subClassOf +INFO missing_superclass concentration of elemental cadmium in tap water rdfs:subClassOf +INFO missing_superclass concentration of elemental chromium in tap water rdfs:subClassOf +INFO missing_superclass concentration of elemental copper in tap water rdfs:subClassOf +INFO missing_superclass concentration of elemental lead in tap water rdfs:subClassOf +INFO missing_superclass concentration of elemental manganese in tap water rdfs:subClassOf +INFO missing_superclass concentration of elemental nickel in tap water rdfs:subClassOf +INFO missing_superclass concentration of elemental zinc in tap water rdfs:subClassOf +INFO missing_superclass concentration of chemical entity in distilled water rdfs:subClassOf +INFO missing_superclass concentration of chemical entity in tap water rdfs:subClassOf +INFO missing_superclass data item about some civilian status rdfs:subClassOf +INFO missing_superclass data item about some disability status rdfs:subClassOf +INFO missing_superclass data item about some educational attainment rdfs:subClassOf +INFO missing_superclass data item about some computer and internet access rdfs:subClassOf +INFO missing_superclass data item about some internet access rdfs:subClassOf +INFO missing_superclass data item about some computing device status rdfs:subClassOf +INFO missing_superclass data item about some age rdfs:subClassOf +INFO missing_superclass data item about some grandparent age category rdfs:subClassOf +INFO missing_superclass data item about some grandparent responsibility for grandchildren rdfs:subClassOf +INFO missing_superclass data item about some housing quality rdfs:subClassOf +INFO missing_superclass data item about some group quarters type rdfs:subClassOf +INFO missing_superclass data item about some income quality rdfs:subClassOf +INFO missing_superclass data item about some poverty status rdfs:subClassOf +INFO missing_superclass data item about some Food Stamps or SNAP status rdfs:subClassOf +INFO missing_superclass data item about some health insurance coverage rdfs:subClassOf +INFO missing_superclass data item about some household size rdfs:subClassOf +INFO missing_superclass data item about some househould mortgage status rdfs:subClassOf +INFO missing_superclass data item about some employment and labor status rdfs:subClassOf +INFO missing_superclass data item about some employment status rdfs:subClassOf +INFO missing_superclass data item about some labor force status rdfs:subClassOf +INFO missing_superclass data item about some veteran status rdfs:subClassOf +INFO missing_superclass data item about some ACS race or ethnicity rdfs:subClassOf +INFO missing_superclass data item about some quality about langauge spoken rdfs:subClassOf +INFO missing_superclass data item about some language spoken at home rdfs:subClassOf +INFO missing_superclass data item about some belongs to a minority group rdfs:subClassOf +INFO missing_superclass measurement datum about some concentration of chemical entity in material entity rdfs:subClassOf +INFO missing_superclass measurement datum about some concentration of carbon dioxide in an atmosphere rdfs:subClassOf +INFO missing_superclass measurement datum about some concentration of chemical entity in environmental material rdfs:subClassOf +INFO missing_superclass measurement datum about some concentration of chemical entity in plant structure rdfs:subClassOf diff --git a/src/ontology/srpdio-edit.owl b/src/ontology/srpdio-edit.owl index 394a136..396b6bd 100644 --- a/src/ontology/srpdio-edit.owl +++ b/src/ontology/srpdio-edit.owl @@ -25,6 +25,7 @@ Import( Import() Import() Import() +Import() Annotation(dce:description "An ontology for use with the NIEHS Superfund Research Project.") Annotation(dce:title "Superfund Research Project Data Integration Ontology") Annotation(dcterms:license ) diff --git a/src/patterns/data/default/chemical_concentration.txt b/src/patterns/data/default/chemical_concentration.txt new file mode 100644 index 0000000..0b66008 --- /dev/null +++ b/src/patterns/data/default/chemical_concentration.txt @@ -0,0 +1,385 @@ +http://purl.obolibrary.org/obo/SRPDIO_2020061 +http://purl.obolibrary.org/obo/CHEBI_33966 +http://purl.obolibrary.org/obo/SRPDIO_2020029 +http://purl.obolibrary.org/obo/SRPDIO_2020048 +http://purl.obolibrary.org/obo/CHEBI_33609 +http://purl.obolibrary.org/obo/SRPDIO_2020283 +http://purl.obolibrary.org/obo/SRPDIO_2020217 +http://purl.obolibrary.org/obo/CHEBI_33464 +http://purl.obolibrary.org/obo/SRPDIO_2020054 +http://purl.obolibrary.org/obo/SRPDIO_2020249 +http://purl.obolibrary.org/obo/SRPDIO_2020109 +http://purl.obolibrary.org/obo/CHEBI_155865 +http://purl.obolibrary.org/obo/SRPDIO_2020188 +http://purl.obolibrary.org/obo/SRPDIO_2020305 +http://purl.obolibrary.org/obo/SRPDIO_2020275 +http://purl.obolibrary.org/obo/SRPDIO_2020257 +http://purl.obolibrary.org/obo/CHEBI_155925 +http://purl.obolibrary.org/obo/SRPDIO_2020141 +http://purl.obolibrary.org/obo/SRPDIO_2020155 +http://purl.obolibrary.org/obo/SRPDIO_2020238 +http://purl.obolibrary.org/obo/SRPDIO_2020166 +http://purl.obolibrary.org/obo/SRPDIO_2020272 +http://purl.obolibrary.org/obo/SRPDIO_2020018 +http://purl.obolibrary.org/obo/SRPDIO_2020268 +http://purl.obolibrary.org/obo/SRPDIO_2020297 +http://purl.obolibrary.org/obo/SRPDIO_2020279 +http://purl.obolibrary.org/obo/SRPDIO_2020184 +http://purl.obolibrary.org/obo/SRPDIO_2020065 +http://purl.obolibrary.org/obo/SRPDIO_2020286 +http://purl.obolibrary.org/obo/CHEBI_37404 +http://purl.obolibrary.org/obo/CHEBI_155921 +http://purl.obolibrary.org/obo/SRPDIO_2020245 +http://purl.obolibrary.org/obo/SRPDIO_2020177 +http://purl.obolibrary.org/obo/CHEBI_18367 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