Skip to content

Commit

Permalink
initial pass at #4
Browse files Browse the repository at this point in the history
  • Loading branch information
@cmungall
cmungall committed Dec 16, 2015
1 parent 767385c commit aedc4e5
Show file tree
Hide file tree
Showing 16 changed files with 524 additions and 0 deletions.
0 ontology/catalog-v001.xml → src/ontology/catalog-v001.xml
View file
File renamed without changes.
0 ontology/chebi_imports.owl → src/ontology/chebi_imports.owl
View file
File renamed without changes.
4 changes: 4 additions & 0 deletions src/ontology/curie_map.yaml
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
ENVO: http://purl.obolibrary.org/obo/ENVO_
CHEBI: http://purl.obolibrary.org/obo/CHEBI_
PATO: http://purl.obolibrary.org/obo/PATO_
RO: http://purl.obolibrary.org/obo/RO_
0 ontology/envo-p.owl → src/ontology/envo-p.owl
View file
File renamed without changes.
0 ontology/envo_imports.owl → src/ontology/envo_imports.owl
View file
File renamed without changes.
3 changes: 3 additions & 0 deletions src/ontology/modules/entity_attribute_location-gci.owl
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
Prefix(:=<http://purl.obolibrary.org/obo/>)
Ontology(<http://purl.obolibrary.org/obo/auto-gci>
)
78 changes: 78 additions & 0 deletions src/ontology/modules/entity_attribute_location-main.owl
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,78 @@
Prefix: : <http://purl.obolibrary.org/obo/>
Prefix: IAO: <http://purl.obolibrary.org/obo/IAO_>
Prefix: DOSDP: <http://geneontology.org/foo/>
Prefix: oio: <http://www.geneontology.org/formats/oboInOwl#>

## Auto-generated

Ontology: <http://purl.obolibrary.org/obo/auto>
AnnotationProperty: IAO:0000115
AnnotationProperty: oba/patterns/entity_attribute/location
AnnotationProperty: oba/patterns/entity_attribute/entity
AnnotationProperty: oba/patterns/entity_attribute/attribute
AnnotationProperty: DOSDP:applies-pattern
AnnotationProperty: oio:hasExactSynonym
ObjectProperty: RO_0000052 ## inheres in
ObjectProperty: BFO_0000050 ## part of
ObjectProperty: RO_0002314 ## inheres in part of
## Auto-generated classes

Class: ENVO:00010483 ## environmental material
Class: CHEBI:27594 ## carbon atom
Class: PATO:0001986 ## dissolved
## {"location": "ENVO:00010483", "entity": "CHEBI:27594", "attribute": "PATO:0001986"}
Class: <urn:uuid:7c80b706-4055-4f86-a86b-874c0cdf68f9>
Annotations: rdfs:label "dissolved of carbon atom in environmental material"
Annotations: IAO:0000115 "The dissolved of a carbon atom when measured in environmental material."
Annotations: oio:hasExactSynonym "environmental material carbon atom dissolved"
EquivalentTo: PATO:0001986 and RO_0000052 some (CHEBI:27594 and BFO_0000050 some ENVO:00010483) ## dissolved and 'inheres in' some (carbon atom and 'part of' some environmental material)

Class: ENVO:00001998 ## soil
Class: CHEBI:27594 ## carbon atom
Class: PATO:0001986 ## dissolved
## {"location": "ENVO:00001998", "entity": "CHEBI:27594", "attribute": "PATO:0001986"}
Class: <urn:uuid:68f3826f-471f-4116-9c9c-8be58518b728>
Annotations: rdfs:label "dissolved of carbon atom in soil"
Annotations: IAO:0000115 "The dissolved of a carbon atom when measured in soil."
Annotations: oio:hasExactSynonym "soil carbon atom dissolved"
EquivalentTo: PATO:0001986 and RO_0000052 some (CHEBI:27594 and BFO_0000050 some ENVO:00001998) ## dissolved and 'inheres in' some (carbon atom and 'part of' some soil)

Class: ENVO:00002006 ## water
Class: CHEBI:27594 ## carbon atom
Class: PATO:0001986 ## dissolved
## {"location": "ENVO:00002006", "entity": "CHEBI:27594", "attribute": "PATO:0001986"}
Class: <urn:uuid:25e8add5-a480-4808-b7b6-b0d90f0239ff>
Annotations: rdfs:label "dissolved of carbon atom in water"
Annotations: IAO:0000115 "The dissolved of a carbon atom when measured in water."
Annotations: oio:hasExactSynonym "water carbon atom dissolved"
EquivalentTo: PATO:0001986 and RO_0000052 some (CHEBI:27594 and BFO_0000050 some ENVO:00002006) ## dissolved and 'inheres in' some (carbon atom and 'part of' some water)

Class: ENVO:00010483 ## environmental material
Class: CHEBI:25555 ## nitrogen atom
Class: PATO:0001986 ## dissolved
## {"location": "ENVO:00010483", "entity": "CHEBI:25555", "attribute": "PATO:0001986"}
Class: <urn:uuid:43403064-30e8-441f-812f-eb1fbddf8695>
Annotations: rdfs:label "dissolved of nitrogen atom in environmental material"
Annotations: IAO:0000115 "The dissolved of a nitrogen atom when measured in environmental material."
Annotations: oio:hasExactSynonym "environmental material nitrogen atom dissolved"
EquivalentTo: PATO:0001986 and RO_0000052 some (CHEBI:25555 and BFO_0000050 some ENVO:00010483) ## dissolved and 'inheres in' some (nitrogen atom and 'part of' some environmental material)

Class: ENVO:00001998 ## soil
Class: CHEBI:25555 ## nitrogen atom
Class: PATO:0001986 ## dissolved
## {"location": "ENVO:00001998", "entity": "CHEBI:25555", "attribute": "PATO:0001986"}
Class: <urn:uuid:4bd6c5ae-d634-47a0-8256-dde0ea800908>
Annotations: rdfs:label "dissolved of nitrogen atom in soil"
Annotations: IAO:0000115 "The dissolved of a nitrogen atom when measured in soil."
Annotations: oio:hasExactSynonym "soil nitrogen atom dissolved"
EquivalentTo: PATO:0001986 and RO_0000052 some (CHEBI:25555 and BFO_0000050 some ENVO:00001998) ## dissolved and 'inheres in' some (nitrogen atom and 'part of' some soil)

Class: ENVO:00002006 ## water
Class: CHEBI:25555 ## nitrogen atom
Class: PATO:0001986 ## dissolved
## {"location": "ENVO:00002006", "entity": "CHEBI:25555", "attribute": "PATO:0001986"}
Class: <urn:uuid:0ce13dc5-def1-4fba-aab5-f9d7c5cfe793>
Annotations: rdfs:label "dissolved of nitrogen atom in water"
Annotations: IAO:0000115 "The dissolved of a nitrogen atom when measured in water."
Annotations: oio:hasExactSynonym "water nitrogen atom dissolved"
EquivalentTo: PATO:0001986 and RO_0000052 some (CHEBI:25555 and BFO_0000050 some ENVO:00002006) ## dissolved and 'inheres in' some (nitrogen atom and 'part of' some water)
202 changes: 202 additions & 0 deletions src/ontology/modules/entity_attribute_location.owl
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,202 @@
Prefix: : <http://purl.obolibrary.org/obo/>
Prefix: IAO: <http://purl.obolibrary.org/obo/IAO_>
Prefix: DOSDP: <http://geneontology.org/foo/>
Prefix: oio: <http://www.geneontology.org/formats/oboInOwl#>
Prefix: ENVO: <http://purl.obolibrary.org/obo/ENVO_>
Prefix: CHEBI: <http://purl.obolibrary.org/obo/CHEBI_>
Prefix: PATO: <http://purl.obolibrary.org/obo/PATO_>
Prefix: RO: <http://purl.obolibrary.org/obo/RO_>

## Auto-generated

Ontology: <http://purl.obolibrary.org/obo/auto>
AnnotationProperty: IAO:0000115
AnnotationProperty: oba/patterns/entity_attribute/location
AnnotationProperty: oba/patterns/entity_attribute/entity
AnnotationProperty: oba/patterns/entity_attribute/attribute
AnnotationProperty: DOSDP:applies-pattern
AnnotationProperty: oio:hasExactSynonym
ObjectProperty: RO_0000052 ## inheres in
ObjectProperty: RO_0002314 ## inheres in part of
ObjectProperty: BFO_0000050 ## part of
## Auto-generated classes

Class: ENVO:00010483 ## environmental material
Class: CHEBI:27594 ## carbon atom
Class: PATO:0001536 ## solubility
## {"location": "ENVO:00010483", "entity": "CHEBI:27594", "attribute": "PATO:0001536"}
Class: <urn:uuid:a59ed7f2-ecb9-4c27-b053-e72ba441fa8b>
Annotations: rdfs:label "solubility of carbon atom in environmental material"
Annotations: IAO:0000115 "The solubility of a carbon atom when measured in environmental material."
Annotations: oio:hasExactSynonym "environmental material carbon atom solubility"
EquivalentTo: PATO:0001536 and RO_0000052 some (CHEBI:27594 and BFO_0000050 some ENVO:00010483) ## solubility and 'inheres in' some (carbon atom and 'part of' some environmental material)

Class: ENVO:00001998 ## soil
Class: CHEBI:27594 ## carbon atom
Class: PATO:0001536 ## solubility
## {"location": "ENVO:00001998", "entity": "CHEBI:27594", "attribute": "PATO:0001536"}
Class: <urn:uuid:c2212744-e32f-476c-aafd-420a5fe6e0b8>
Annotations: rdfs:label "solubility of carbon atom in soil"
Annotations: IAO:0000115 "The solubility of a carbon atom when measured in soil."
Annotations: oio:hasExactSynonym "soil carbon atom solubility"
EquivalentTo: PATO:0001536 and RO_0000052 some (CHEBI:27594 and BFO_0000050 some ENVO:00001998) ## solubility and 'inheres in' some (carbon atom and 'part of' some soil)

Class: ENVO:00002006 ## water
Class: CHEBI:27594 ## carbon atom
Class: PATO:0001536 ## solubility
## {"location": "ENVO:00002006", "entity": "CHEBI:27594", "attribute": "PATO:0001536"}
Class: <urn:uuid:fc0df622-9f2d-484a-812c-4ea4d0165804>
Annotations: rdfs:label "solubility of carbon atom in water"
Annotations: IAO:0000115 "The solubility of a carbon atom when measured in water."
Annotations: oio:hasExactSynonym "water carbon atom solubility"
EquivalentTo: PATO:0001536 and RO_0000052 some (CHEBI:27594 and BFO_0000050 some ENVO:00002006) ## solubility and 'inheres in' some (carbon atom and 'part of' some water)

Class: ENVO:00010483 ## environmental material
Class: CHEBI:27594 ## carbon atom
Class: PATO:0000070 ## amount
## {"location": "ENVO:00010483", "entity": "CHEBI:27594", "attribute": "PATO:0000070"}
Class: <urn:uuid:b81eaabe-513b-472a-9846-40960b0e99a0>
Annotations: rdfs:label "amount of carbon atom in environmental material"
Annotations: IAO:0000115 "The amount of a carbon atom when measured in environmental material."
Annotations: oio:hasExactSynonym "environmental material carbon atom amount"
EquivalentTo: PATO:0000070 and RO_0000052 some (CHEBI:27594 and BFO_0000050 some ENVO:00010483) ## amount and 'inheres in' some (carbon atom and 'part of' some environmental material)

Class: ENVO:00001998 ## soil
Class: CHEBI:27594 ## carbon atom
Class: PATO:0000070 ## amount
## {"location": "ENVO:00001998", "entity": "CHEBI:27594", "attribute": "PATO:0000070"}
Class: <urn:uuid:06cc4c4e-c72f-4974-bfc9-cf7eb5c8445e>
Annotations: rdfs:label "amount of carbon atom in soil"
Annotations: IAO:0000115 "The amount of a carbon atom when measured in soil."
Annotations: oio:hasExactSynonym "soil carbon atom amount"
EquivalentTo: PATO:0000070 and RO_0000052 some (CHEBI:27594 and BFO_0000050 some ENVO:00001998) ## amount and 'inheres in' some (carbon atom and 'part of' some soil)

Class: ENVO:00002006 ## water
Class: CHEBI:27594 ## carbon atom
Class: PATO:0000070 ## amount
## {"location": "ENVO:00002006", "entity": "CHEBI:27594", "attribute": "PATO:0000070"}
Class: <urn:uuid:035884ad-f240-41c8-b964-99165c819f8b>
Annotations: rdfs:label "amount of carbon atom in water"
Annotations: IAO:0000115 "The amount of a carbon atom when measured in water."
Annotations: oio:hasExactSynonym "water carbon atom amount"
EquivalentTo: PATO:0000070 and RO_0000052 some (CHEBI:27594 and BFO_0000050 some ENVO:00002006) ## amount and 'inheres in' some (carbon atom and 'part of' some water)

Class: ENVO:00010483 ## environmental material
Class: CHEBI:27594 ## carbon atom
Class: PATO:0000033 ## concentration of
## {"location": "ENVO:00010483", "entity": "CHEBI:27594", "attribute": "PATO:0000033"}
Class: <urn:uuid:4155b153-87d6-4dd7-b806-00766021be9a>
Annotations: rdfs:label "concentration of of carbon atom in environmental material"
Annotations: IAO:0000115 "The concentration of of a carbon atom when measured in environmental material."
Annotations: oio:hasExactSynonym "environmental material carbon atom concentration of"
EquivalentTo: PATO:0000033 and RO_0000052 some (CHEBI:27594 and BFO_0000050 some ENVO:00010483) ## concentration of and 'inheres in' some (carbon atom and 'part of' some environmental material)

Class: ENVO:00001998 ## soil
Class: CHEBI:27594 ## carbon atom
Class: PATO:0000033 ## concentration of
## {"location": "ENVO:00001998", "entity": "CHEBI:27594", "attribute": "PATO:0000033"}
Class: <urn:uuid:e17ea55b-2b22-41ca-8781-0ace9ea20c0c>
Annotations: rdfs:label "concentration of of carbon atom in soil"
Annotations: IAO:0000115 "The concentration of of a carbon atom when measured in soil."
Annotations: oio:hasExactSynonym "soil carbon atom concentration of"
EquivalentTo: PATO:0000033 and RO_0000052 some (CHEBI:27594 and BFO_0000050 some ENVO:00001998) ## concentration of and 'inheres in' some (carbon atom and 'part of' some soil)

Class: ENVO:00002006 ## water
Class: CHEBI:27594 ## carbon atom
Class: PATO:0000033 ## concentration of
## {"location": "ENVO:00002006", "entity": "CHEBI:27594", "attribute": "PATO:0000033"}
Class: <urn:uuid:d79212a5-24b1-4b71-a815-571306fbf0ff>
Annotations: rdfs:label "concentration of of carbon atom in water"
Annotations: IAO:0000115 "The concentration of of a carbon atom when measured in water."
Annotations: oio:hasExactSynonym "water carbon atom concentration of"
EquivalentTo: PATO:0000033 and RO_0000052 some (CHEBI:27594 and BFO_0000050 some ENVO:00002006) ## concentration of and 'inheres in' some (carbon atom and 'part of' some water)

Class: ENVO:00010483 ## environmental material
Class: CHEBI:25555 ## nitrogen atom
Class: PATO:0001536 ## solubility
## {"location": "ENVO:00010483", "entity": "CHEBI:25555", "attribute": "PATO:0001536"}
Class: <urn:uuid:84e01e8e-06b2-4108-a450-8d926bc9be6e>
Annotations: rdfs:label "solubility of nitrogen atom in environmental material"
Annotations: IAO:0000115 "The solubility of a nitrogen atom when measured in environmental material."
Annotations: oio:hasExactSynonym "environmental material nitrogen atom solubility"
EquivalentTo: PATO:0001536 and RO_0000052 some (CHEBI:25555 and BFO_0000050 some ENVO:00010483) ## solubility and 'inheres in' some (nitrogen atom and 'part of' some environmental material)

Class: ENVO:00001998 ## soil
Class: CHEBI:25555 ## nitrogen atom
Class: PATO:0001536 ## solubility
## {"location": "ENVO:00001998", "entity": "CHEBI:25555", "attribute": "PATO:0001536"}
Class: <urn:uuid:905f2eb9-29d1-4874-8c78-1881333d374c>
Annotations: rdfs:label "solubility of nitrogen atom in soil"
Annotations: IAO:0000115 "The solubility of a nitrogen atom when measured in soil."
Annotations: oio:hasExactSynonym "soil nitrogen atom solubility"
EquivalentTo: PATO:0001536 and RO_0000052 some (CHEBI:25555 and BFO_0000050 some ENVO:00001998) ## solubility and 'inheres in' some (nitrogen atom and 'part of' some soil)

Class: ENVO:00002006 ## water
Class: CHEBI:25555 ## nitrogen atom
Class: PATO:0001536 ## solubility
## {"location": "ENVO:00002006", "entity": "CHEBI:25555", "attribute": "PATO:0001536"}
Class: <urn:uuid:3d2d8a10-f613-4dbb-b3cf-44cc9216ab70>
Annotations: rdfs:label "solubility of nitrogen atom in water"
Annotations: IAO:0000115 "The solubility of a nitrogen atom when measured in water."
Annotations: oio:hasExactSynonym "water nitrogen atom solubility"
EquivalentTo: PATO:0001536 and RO_0000052 some (CHEBI:25555 and BFO_0000050 some ENVO:00002006) ## solubility and 'inheres in' some (nitrogen atom and 'part of' some water)

Class: ENVO:00010483 ## environmental material
Class: CHEBI:25555 ## nitrogen atom
Class: PATO:0000070 ## amount
## {"location": "ENVO:00010483", "entity": "CHEBI:25555", "attribute": "PATO:0000070"}
Class: <urn:uuid:46ea3981-0690-4e1d-a962-94ebfa89990b>
Annotations: rdfs:label "amount of nitrogen atom in environmental material"
Annotations: IAO:0000115 "The amount of a nitrogen atom when measured in environmental material."
Annotations: oio:hasExactSynonym "environmental material nitrogen atom amount"
EquivalentTo: PATO:0000070 and RO_0000052 some (CHEBI:25555 and BFO_0000050 some ENVO:00010483) ## amount and 'inheres in' some (nitrogen atom and 'part of' some environmental material)

Class: ENVO:00001998 ## soil
Class: CHEBI:25555 ## nitrogen atom
Class: PATO:0000070 ## amount
## {"location": "ENVO:00001998", "entity": "CHEBI:25555", "attribute": "PATO:0000070"}
Class: <urn:uuid:7b1fb203-f3c1-488a-a93f-38b087149f19>
Annotations: rdfs:label "amount of nitrogen atom in soil"
Annotations: IAO:0000115 "The amount of a nitrogen atom when measured in soil."
Annotations: oio:hasExactSynonym "soil nitrogen atom amount"
EquivalentTo: PATO:0000070 and RO_0000052 some (CHEBI:25555 and BFO_0000050 some ENVO:00001998) ## amount and 'inheres in' some (nitrogen atom and 'part of' some soil)

Class: ENVO:00002006 ## water
Class: CHEBI:25555 ## nitrogen atom
Class: PATO:0000070 ## amount
## {"location": "ENVO:00002006", "entity": "CHEBI:25555", "attribute": "PATO:0000070"}
Class: <urn:uuid:caca08cc-e46d-43dc-8809-a1aa906271fa>
Annotations: rdfs:label "amount of nitrogen atom in water"
Annotations: IAO:0000115 "The amount of a nitrogen atom when measured in water."
Annotations: oio:hasExactSynonym "water nitrogen atom amount"
EquivalentTo: PATO:0000070 and RO_0000052 some (CHEBI:25555 and BFO_0000050 some ENVO:00002006) ## amount and 'inheres in' some (nitrogen atom and 'part of' some water)

Class: ENVO:00010483 ## environmental material
Class: CHEBI:25555 ## nitrogen atom
Class: PATO:0000033 ## concentration of
## {"location": "ENVO:00010483", "entity": "CHEBI:25555", "attribute": "PATO:0000033"}
Class: <urn:uuid:791ec6e7-2f18-43d6-8dea-c7ec10f311ad>
Annotations: rdfs:label "concentration of of nitrogen atom in environmental material"
Annotations: IAO:0000115 "The concentration of of a nitrogen atom when measured in environmental material."
Annotations: oio:hasExactSynonym "environmental material nitrogen atom concentration of"
EquivalentTo: PATO:0000033 and RO_0000052 some (CHEBI:25555 and BFO_0000050 some ENVO:00010483) ## concentration of and 'inheres in' some (nitrogen atom and 'part of' some environmental material)

Class: ENVO:00001998 ## soil
Class: CHEBI:25555 ## nitrogen atom
Class: PATO:0000033 ## concentration of
## {"location": "ENVO:00001998", "entity": "CHEBI:25555", "attribute": "PATO:0000033"}
Class: <urn:uuid:f7b8a0ae-fcf6-455a-aaa7-cbde2b83eefb>
Annotations: rdfs:label "concentration of of nitrogen atom in soil"
Annotations: IAO:0000115 "The concentration of of a nitrogen atom when measured in soil."
Annotations: oio:hasExactSynonym "soil nitrogen atom concentration of"
EquivalentTo: PATO:0000033 and RO_0000052 some (CHEBI:25555 and BFO_0000050 some ENVO:00001998) ## concentration of and 'inheres in' some (nitrogen atom and 'part of' some soil)

Class: ENVO:00002006 ## water
Class: CHEBI:25555 ## nitrogen atom
Class: PATO:0000033 ## concentration of
## {"location": "ENVO:00002006", "entity": "CHEBI:25555", "attribute": "PATO:0000033"}
Class: <urn:uuid:1e327425-05b1-44e8-a360-bb760179dd6f>
Annotations: rdfs:label "concentration of of nitrogen atom in water"
Annotations: IAO:0000115 "The concentration of of a nitrogen atom when measured in water."
Annotations: oio:hasExactSynonym "water nitrogen atom concentration of"
EquivalentTo: PATO:0000033 and RO_0000052 some (CHEBI:25555 and BFO_0000050 some ENVO:00002006) ## concentration of and 'inheres in' some (nitrogen atom and 'part of' some water)
19 changes: 19 additions & 0 deletions src/ontology/modules/entity_attribute_location.tsv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
attribute attribute label entity entity label location location label
PATO:0001536 solubility CHEBI:27594 carbon atom ENVO:00010483 environmental material
PATO:0001536 solubility CHEBI:27594 carbon atom ENVO:00001998 soil
PATO:0001536 solubility CHEBI:27594 carbon atom ENVO:00002006 water
PATO:0000070 amount CHEBI:27594 carbon atom ENVO:00010483 environmental material
PATO:0000070 amount CHEBI:27594 carbon atom ENVO:00001998 soil
PATO:0000070 amount CHEBI:27594 carbon atom ENVO:00002006 water
PATO:0000033 concentration of CHEBI:27594 carbon atom ENVO:00010483 environmental material
PATO:0000033 concentration of CHEBI:27594 carbon atom ENVO:00001998 soil
PATO:0000033 concentration of CHEBI:27594 carbon atom ENVO:00002006 water
PATO:0001536 solubility CHEBI:25555 nitrogen atom ENVO:00010483 environmental material
PATO:0001536 solubility CHEBI:25555 nitrogen atom ENVO:00001998 soil
PATO:0001536 solubility CHEBI:25555 nitrogen atom ENVO:00002006 water
PATO:0000070 amount CHEBI:25555 nitrogen atom ENVO:00010483 environmental material
PATO:0000070 amount CHEBI:25555 nitrogen atom ENVO:00001998 soil
PATO:0000070 amount CHEBI:25555 nitrogen atom ENVO:00002006 water
PATO:0000033 concentration of CHEBI:25555 nitrogen atom ENVO:00010483 environmental material
PATO:0000033 concentration of CHEBI:25555 nitrogen atom ENVO:00001998 soil
PATO:0000033 concentration of CHEBI:25555 nitrogen atom ENVO:00002006 water
3 changes: 3 additions & 0 deletions src/ontology/modules/entity_quality_location-gci.owl
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
Prefix(:=<http://purl.obolibrary.org/obo/>)
Ontology(<http://purl.obolibrary.org/obo/auto-gci>
)
Loading

0 comments on commit aedc4e5

Please sign in to comment.