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1 parent 1a70dad commit 9aa02f16eaa065e0c0bc1c069c068698bed89c8c @pbuttigieg pbuttigieg committed Jun 26, 2017
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Showing with 55,854 additions and 43,137 deletions.
  1. +6,116 −4,786 envo.json
  2. +635 −136 envo.obo
  3. +6,120 −4,790 envo.owl
  4. +51 −2 imports/chebi_import.obo
  5. +87 −2 imports/chebi_import.owl
  6. +4 −0 imports/chebi_seed.owl
  7. +5 −3 imports/foodon_import.obo
  8. +18 −4 imports/foodon_import.owl
  9. +2 −1 imports/foodon_terms.txt
  10. +1 −0 imports/iao_import.owl
  11. +1 −1 imports/iao_terms.txt
  12. +21 −0 imports/ncbitaxon_import.obo
  13. +29 −0 imports/ncbitaxon_import.owl
  14. +1 −0 imports/ncbitaxon_terms.txt
  15. +5 −0 imports/pato_import.obo
  16. +9 −0 imports/pato_import.owl
  17. +1 −0 imports/pato_seed.owl
  18. +29 −24 imports/uberon_import.obo
  19. +45 −32 imports/uberon_import.owl
  20. +5,351 −4,323 src/envo/envo-simple.owl
  21. +6,116 −4,786 src/envo/envo.json
  22. +635 −136 src/envo/envo.obo
  23. +6,120 −4,790 src/envo/envo.owl
  24. +51 −2 src/envo/imports/chebi_import.obo
  25. +5 −3 src/envo/imports/foodon_import.obo
  26. +18 −4 src/envo/imports/foodon_import.owl
  27. +21 −0 src/envo/imports/ncbitaxon_import.obo
  28. +5 −0 src/envo/imports/pato_import.obo
  29. +29 −24 src/envo/imports/uberon_import.obo
  30. +45 −32 src/envo/imports/uberon_import.owl
  31. +20 −1 src/envo/subsets/EnvO-Lite-GSC.obo
  32. +56 −4 src/envo/subsets/EnvO-Lite-GSC.owl
  33. +64 −48 src/envo/subsets/environmental_hazards.owl
  34. +5,214 −4,186 src/envo/subsets/envo-basic.json
  35. +497 −94 src/envo/subsets/envo-basic.obo
  36. +5,243 −4,215 src/envo/subsets/envo-basic.owl
  37. +912 −947 src/envo/subsets/envoPolar.owl
  38. +52 −52 src/envo/subsets/nlcd2011.owl
  39. +11 −11 src/envo/subsets/ro-eco.owl
  40. +57 −57 src/envo/subsets/wwfBiome-metadata.txt
  41. +13 −13 src/envo/subsets/wwfBiome.owl
  42. +20 −1 subsets/EnvO-Lite-GSC.obo
  43. +56 −4 subsets/EnvO-Lite-GSC.owl
  44. +57 −57 subsets/environmental_hazards-metadata.txt
  45. +64 −48 subsets/environmental_hazards.owl
  46. +5,214 −4,186 subsets/envo-basic.json
  47. +497 −94 subsets/envo-basic.obo
  48. +5,243 −4,215 subsets/envo-basic.owl
  49. +912 −947 subsets/envoPolar.owl
  50. +52 −52 subsets/nlcd2011.owl
  51. +11 −11 subsets/ro-eco.owl
  52. +13 −13 subsets/wwfBiome.owl
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10,902 envo.json

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771 envo.obo

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10,910 envo.owl

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53 imports/chebi_import.obo
@@ -1,6 +1,6 @@
format-version: 1.2
ontology: envo/imports/chebi_import
-property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/chebi/151/chebi.owl
+property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/chebi/152/chebi.owl
[Term]
id: CHEBI:131621
@@ -13,6 +13,11 @@ name: dicarboxylic acids and O-substituted derivatives
is_a: CHEBI:36586 ! carbonyl compound
[Term]
+id: CHEBI:133331
+name: metal oxide
+is_a: CHEBI:24836 ! inorganic oxide
+
+[Term]
id: CHEBI:13389
name: NAD
is_a: CHEBI:25524 ! NAD(P)
@@ -230,7 +235,7 @@ id: CHEBI:17347
name: testosterone
is_a: CHEBI:131621 ! C19-steroid
is_a: CHEBI:35343 ! 17beta-hydroxy steroid
-is_a: CHEBI:47788 ! 3-oxo steroid
+is_a: CHEBI:47909 ! 3-oxo-Delta(4) steroid
is_a: CHEBI:50402 ! androstanoid
[Term]
@@ -1300,6 +1305,11 @@ name: copper(0)
is_a: CHEBI:37404 ! elemental copper
[Term]
+id: CHEBI:30187
+name: aluminium oxide
+is_a: CHEBI:33623 ! aluminium oxides
+
+[Term]
id: CHEBI:30356
name: isobutyl group
is_a: CHEBI:22323 ! alkyl group
@@ -1834,6 +1844,12 @@ name: aluminium molecular entity
is_a: CHEBI:33581 ! boron group molecular entity
[Term]
+id: CHEBI:33623
+name: aluminium oxides
+is_a: CHEBI:133331 ! metal oxide
+is_a: CHEBI:33620 ! aluminium molecular entity
+
+[Term]
id: CHEBI:33627
name: monoatomic aluminium
is_a: CHEBI:33238 ! monoatomic entity
@@ -3001,6 +3017,12 @@ name: dinucleotide
is_a: CHEBI:36976 ! nucleotide
[Term]
+id: CHEBI:47909
+name: 3-oxo-Delta(4) steroid
+is_a: CHEBI:47788 ! 3-oxo steroid
+is_a: CHEBI:51689 ! enone
+
+[Term]
id: CHEBI:48041
name: microcystin
is_a: CHEBI:24533 ! heterodetic cyclic peptide
@@ -3208,6 +3230,11 @@ is_a: CHEBI:33415 ! elemental carbon
is_a: CHEBI:50795 ! nanostructure
[Term]
+id: CHEBI:50816
+name: iron oxide
+is_a: CHEBI:24873 ! iron molecular entity
+
+[Term]
id: CHEBI:50860
name: organic molecular entity
is_a: CHEBI:33582 ! carbon group molecular entity
@@ -3263,6 +3290,17 @@ name: organic univalent group
is_a: CHEBI:33247 ! organic group
[Term]
+id: CHEBI:51689
+name: enone
+is_a: CHEBI:51721 ! alpha,beta-unsaturated ketone
+is_a: CHEBI:78840 ! olefinic compound
+
+[Term]
+id: CHEBI:51721
+name: alpha,beta-unsaturated ketone
+is_a: CHEBI:17087 ! ketone
+
+[Term]
id: CHEBI:51958
name: organic polycyclic compound
is_a: CHEBI:33635 ! polycyclic compound
@@ -3676,6 +3714,11 @@ name: carbohydrates and carbohydrate derivatives
is_a: CHEBI:36963 ! organooxygen compound
[Term]
+id: CHEBI:78840
+name: olefinic compound
+is_a: CHEBI:50860 ! organic molecular entity
+
+[Term]
id: CHEBI:79387
name: trivalent inorganic anion
is_a: CHEBI:24834 ! inorganic anion
@@ -3706,6 +3749,12 @@ name: pheophytin
is_a: CHEBI:38252 ! phorbines
[Term]
+id: CHEBI:82661
+name: diatomaceous earth
+is_a: CHEBI:30563 ! silicon dioxide
+is_a: CHEBI:46662 ! mineral
+
+[Term]
id: CHEBI:82663
name: elemental iron
is_a: CHEBI:24873 ! iron molecular entity
View
89 imports/chebi_import.owl
@@ -7,7 +7,7 @@
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:dc="http://purl.org/dc/elements/1.1/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/envo/imports/chebi_import.owl">
- <dc:source rdf:resource="http://purl.obolibrary.org/obo/chebi/151/chebi.owl"/>
+ <dc:source rdf:resource="http://purl.obolibrary.org/obo/chebi/152/chebi.owl"/>
</owl:Ontology>
@@ -41,6 +41,15 @@
+ <!-- http://purl.obolibrary.org/obo/CHEBI_133331 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_133331">
+ <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">metal oxide</rdfs:label>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_24836"/>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/CHEBI_13389 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_13389">
@@ -404,7 +413,7 @@
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">testosterone</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_131621"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_35343"/>
- <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_47788"/>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_47909"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_50402"/>
</owl:Class>
@@ -2252,6 +2261,15 @@
+ <!-- http://purl.obolibrary.org/obo/CHEBI_30187 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_30187">
+ <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aluminium oxide</rdfs:label>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33623"/>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/CHEBI_30356 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_30356">
@@ -3178,6 +3196,16 @@
+ <!-- http://purl.obolibrary.org/obo/CHEBI_33623 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_33623">
+ <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aluminium oxides</rdfs:label>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_133331"/>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33620"/>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/CHEBI_33627 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_33627">
@@ -5181,6 +5209,16 @@
+ <!-- http://purl.obolibrary.org/obo/CHEBI_47909 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_47909">
+ <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">3-oxo-Delta(4) steroid</rdfs:label>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_47788"/>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_51689"/>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/CHEBI_48041 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_48041">
@@ -5540,6 +5578,15 @@
+ <!-- http://purl.obolibrary.org/obo/CHEBI_50816 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_50816">
+ <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">iron oxide</rdfs:label>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_24873"/>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/CHEBI_50860 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_50860">
@@ -5639,6 +5686,25 @@
+ <!-- http://purl.obolibrary.org/obo/CHEBI_51689 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_51689">
+ <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">enone</rdfs:label>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_51721"/>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_78840"/>
+ </owl:Class>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/CHEBI_51721 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_51721">
+ <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">alpha,beta-unsaturated ketone</rdfs:label>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_17087"/>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/CHEBI_51958 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_51958">
@@ -6372,6 +6438,15 @@
+ <!-- http://purl.obolibrary.org/obo/CHEBI_78840 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_78840">
+ <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">olefinic compound</rdfs:label>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_50860"/>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/CHEBI_79387 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_79387">
@@ -6426,6 +6501,16 @@
+ <!-- http://purl.obolibrary.org/obo/CHEBI_82661 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_82661">
+ <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">diatomaceous earth</rdfs:label>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_30563"/>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_46662"/>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/CHEBI_82663 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_82663">
View
4 imports/chebi_seed.owl
@@ -5,6 +5,10 @@ Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(CHEBI:=<http://purl.obolibrary.org/obo/CHEBI_>)
Ontology(<http://purl.obolibrary.org/obo/envo/imports/chebi_seed.owl>
+Declaration(Class(CHEBI:46662)) ## mineral
+Declaration(Class(CHEBI:82661)) ## diatomaceous earth
+Declaration(Class(CHEBI:50816)) ## iron oxide
+Declaration(Class(CHEBI:30187)) ## aluminium oxide
Declaration(Class(CHEBI:49936)) ## uranium(0)
Declaration(Class(CHEBI:30050)) ## gold(0)
Declaration(Class(CHEBI:82664)) ## iron(0)
View
8 imports/foodon_import.obo
@@ -19,12 +19,14 @@ is_a: FOODON:00001002 ! product type, foodon
[Term]
id: FOODON:00001287
name: mushroom
+def: "A mushroom (or toadstool) is the fleshy, spore-bearing fruiting body of a fungus, typically produced above ground on soil or on its food source." []
+synonym: "fungi" BROAD []
+synonym: "wild mushroom" NARROW []
xref: LANGUAL:B1467
is_a: FOODON:00001143 ! fungal product
is_a: FOODON:03412035 ! basidiomycetes
-property_value: hasSynonym "fungi" xsd:string
-property_value: hasSynonym "wild mushroom" xsd:string
property_value: IAO:0000114 IAO:0000428
+property_value: IAO:0000119 WIKIPEDIA:Mushroom xsd:string
property_value: IAO:0000412 http://langual.org xsd:string
[Term]
@@ -56,7 +58,7 @@ property_value: IAO:0000412 http://langual.org xsd:string
id: FOODON:03412035
name: basidiomycetes
def: "*Basidiomycota* is one of two large phyla that, together with the *Ascomycota*, constitute the subkingdom *Dikarya* (often referred to as the \"higher fungi\") within the kingdom Fungi. More specifically the *Basidiomycota* include these groups: mushrooms, puffballs, stinkhorns, bracket fungi, other polypores, jelly fungi, boletes, chanterelles, earth stars, smuts, bunts, rusts, mirror yeasts, and the human pathogenic yeast *Cryptococcus*." []
-synonym: "NCBITaxon:5204" BROAD []
+synonym: "Basidiomycota" BROAD [http://purl.obolibrary.org/obo/NCBITaxon_5204, ITIS:623881]
xref: http://eol.org/pages/5664
xref: LANGUAL:B2035
is_a: FOODON:03411261 ! fungus
View
22 imports/foodon_import.owl
@@ -59,6 +59,12 @@
+ <!-- http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym -->
+
+ <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym"/>
+
+
+
<!-- http://www.geneontology.org/formats/oboInOwl#hasSynonym -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasSynonym"/>
@@ -115,12 +121,13 @@
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/FOODON_00001143"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/FOODON_03412035"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
+ <obo:IAO_0000115 xml:lang="en">A mushroom (or toadstool) is the fleshy, spore-bearing fruiting body of a fungus, typically produced above ground on soil or on its food source.</obo:IAO_0000115>
+ <obo:IAO_0000119>WIKIPEDIA:Mushroom</obo:IAO_0000119>
<obo:IAO_0000412>http://langual.org</obo:IAO_0000412>
+ <oboInOwl:hasBroadSynonym xml:lang="en">fungi</oboInOwl:hasBroadSynonym>
<oboInOwl:hasDbXref>LANGUAL:B1467</oboInOwl:hasDbXref>
- <oboInOwl:hasSynonym xml:lang="en">fungi</oboInOwl:hasSynonym>
- <oboInOwl:hasSynonym xml:lang="en">wild mushroom</oboInOwl:hasSynonym>
+ <oboInOwl:hasNarrowSynonym xml:lang="en">wild mushroom</oboInOwl:hasNarrowSynonym>
<rdfs:label xml:lang="en">mushroom</rdfs:label>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mushroom</rdfs:label>
</owl:Class>
@@ -170,7 +177,7 @@
<obo:IAO_0000115 xml:lang="en">*Basidiomycota* is one of two large phyla that, together with the *Ascomycota*, constitute the subkingdom *Dikarya* (often referred to as the &quot;higher fungi&quot;) within the kingdom Fungi. More specifically the *Basidiomycota* include these groups: mushrooms, puffballs, stinkhorns, bracket fungi, other polypores, jelly fungi, boletes, chanterelles, earth stars, smuts, bunts, rusts, mirror yeasts, and the human pathogenic yeast *Cryptococcus*.</obo:IAO_0000115>
<obo:IAO_0000119>WIKIPEDIA:Basidiomycota</obo:IAO_0000119>
<obo:IAO_0000412>http://langual.org</obo:IAO_0000412>
- <oboInOwl:hasBroadSynonym rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_5204"/>
+ <oboInOwl:hasBroadSynonym>Basidiomycota</oboInOwl:hasBroadSynonym>
<oboInOwl:hasDbXref>LANGUAL:B2035</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>http://eol.org/pages/5664</oboInOwl:hasDbXref>
<oboInOwl:hasSynonym xml:lang="en">basidiomycota</oboInOwl:hasSynonym>
@@ -181,6 +188,13 @@
<oboInOwl:hasSynonym xml:lang="en">ustomycetes</oboInOwl:hasSynonym>
<rdfs:label xml:lang="en">basidiomycetes</rdfs:label>
</owl:Class>
+ <owl:Axiom>
+ <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/FOODON_03412035"/>
+ <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym"/>
+ <owl:annotatedTarget>Basidiomycota</owl:annotatedTarget>
+ <oboInOwl:hasDbXref rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_5204"/>
+ <oboInOwl:hasDbXref>ITIS:623881</oboInOwl:hasDbXref>
+ </owl:Axiom>
</rdf:RDF>
View
3 imports/foodon_terms.txt
@@ -1 +1,2 @@
-http://purl.obolibrary.org/obo/FOODON_00001287 # mushroom
+http://purl.obolibrary.org/obo/FOODON_00001287 # mushroom
+
View
1 imports/iao_import.owl
@@ -188,3 +188,4 @@
<!-- Generated by the OWL API (version 0.0.1+91bea50) https://github.com/owlcs/owlapi -->
+
View
2 imports/iao_terms.txt
@@ -5,4 +5,4 @@ http://purl.obolibrary.org/obo/IAO_0000584 # time sampled measurement data set
http://purl.obolibrary.org/obo/IAO_0000582 # time stamped measurement datum
http://purl.obolibrary.org/obo/IAO_0000032 # scalar measurement datum
http://purl.obolibrary.org/obo/IAO_0000136 # is about
-http://purl.obolibrary.org/obo/IAO_0000221 # is quality measurement of
+http://purl.obolibrary.org/obo/IAO_0000221 # is quality measurement of
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