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fixed the patterns and modules and added ebi_biomes.csv
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@kaiiam
kaiiam committed Mar 1, 2019
1 parent 5c0f7fc commit 448eded
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6 changes: 3 additions & 3 deletions src/envo/Makefile
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Expand Up @@ -7,7 +7,7 @@

OBO=http://purl.obolibrary.org/obo
USECAT= --catalog-xml catalog-v001.xml
MODS = entity_attribute_location entity_quality_location entity_attribute process_attribute
MODS = entity_attribute_location entity_quality_location entity_attribute process_attribute chemical_concentration
ALL_MODS_OWL = $(patsubst %, modules/%.owl, $(MODS))
ALL_MODS_CSV = $(patsubst %, modules/%.csv, $(MODS))
ROBOT= robot
Expand Down Expand Up @@ -347,8 +347,8 @@ all_modules_owl: $(ALL_MODS_OWL)
all_modules_obo: $(patsubst %, modules/%.obo, $(MODS))

modules/%.owl: modules/%.csv patterns/%.yaml curie_map.yaml
./run.sh dosdp-tools --table-format=csv --template=./patterns/$*.yaml --outfile=modules/$*.tmp.owl --obo-prefixes=true generate --infile=modules/$*.csv
./run.sh robot annotate --input modules/$*.tmp.owl -O http://purl.obolibrary.org/obo/envo/modules/$*.owl --output modules/$*.owl && rm modules/$*.tmp.owl
dosdp-tools --table-format=csv --template=./patterns/$*.yaml --outfile=modules/$*.tmp.owl --obo-prefixes=true generate --infile=modules/$*.csv
robot annotate --input modules/$*.tmp.owl -O http://purl.obolibrary.org/obo/envo/modules/$*.owl --output modules/$*.owl && rm modules/$*.tmp.owl

modules/%.obo: modules/%.owl
owltools $< -o -f obo $@.tmp && grep -v ^owl-axioms $@.tmp > $@
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62 changes: 31 additions & 31 deletions src/envo/modules/chemical_concentration.csv
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@@ -1,31 +1,31 @@
iri,class iri,attribute,attribute label,entity,entity label
ENVO:3100001,,CHEBI:15422,Adenosine 5-triphosphate,ENVO:00002006,water
ENVO:3100002,,CHEBI:28315,alloxanthine,ENVO:00002006,water
ENVO:3100003,,CHEBI:28425,alpha-carotene,ENVO:00002006,water
ENVO:3100004,,CHEBI:28938,ammonium,ENVO:00002006,water
ENVO:3100005,,CHEBI:30033,bacteriochlorophyll a,ENVO:00002006,water
ENVO:3100006,,CHEBI:17579,beta-carotene,ENVO:00002006,water
ENVO:3100007,,CHEBI:23042,carotene,ENVO:00002006,water
ENVO:3100008,,CHEBI:18230,chlorophyll a,ENVO:00002006,water
ENVO:3100009,,CHEBI:27888,chlorophyll b,ENVO:00002006,water
ENVO:3100010,,CHEBI:16900,chlorophyllide a,ENVO:00002006,water
ENVO:3100011,,CHEBI:15379,dioxygen,ENVO:00002006,water
ENVO:3100012,,CHEBI:73113,divinyl chlorophyll a,ENVO:00002006,water
ENVO:3100013,,CHEBI:73115,divinyl chlorophyll b,ENVO:00002006,water
ENVO:3100014,,CHEBI:5186,fucoxanthin,ENVO:00002006,water
ENVO:3100015,,CHEBI:15996,Guanosine 5-triphosphate,ENVO:00002006,water
ENVO:3100016,,CHEBI:16240,hydrogen peroxide,ENVO:00002006,water
ENVO:3100017,,CHEBI:16136,hydrogen sulfide,ENVO:00002006,water
ENVO:3100018,,CHEBI:16136,hydrogen sulfide,ENVO:00002006,water
ENVO:3100019,,CHEBI:28838,lutein,ENVO:00002006,water
ENVO:3100020,,CHEBI:16183,methane,ENVO:00002006,water
ENVO:3100021,,CHEBI:25501,neoxanthin,ENVO:00002006,water
ENVO:3100022,,CHEBI:17632 ,nitrate ,ENVO:00002006,water
ENVO:3100023,,CHEBI:16301,nitrite,ENVO:00002006,water
ENVO:3100024,,CHEBI:17045,nitrous oxide,ENVO:00002006,water
ENVO:3100025,,CHEBI:44882,peridinin,ENVO:00002006,water
ENVO:3100026,,CHEBI:26020,phosphate,ENVO:00002006,water
ENVO:3100027,,CHEBI:29241,silicate(4-),ENVO:00002006,water
ENVO:3100028,,CHEBI:27295,violaxanthin,ENVO:00002006,water
ENVO:3100029,,CHEBI:27547,zeaxanthin,ENVO:00002006,water
ENVO:3100034,,CHEBI:26675,silicic acid,ENVO:00002006,water
defined_class,defined_class_label,attribute,attribute_label,entity,entity_label
ENVO:3100001,,CHEBI:15422,Adenosine 5-triphosphate,ENVO:00002006,water
ENVO:3100002,,CHEBI:28315,alloxanthine,ENVO:00002006,water
ENVO:3100003,,CHEBI:28425,alpha-carotene,ENVO:00002006,water
ENVO:3100004,,CHEBI:28938,ammonium,ENVO:00002006,water
ENVO:3100005,,CHEBI:30033,bacteriochlorophyll a,ENVO:00002006,water
ENVO:3100006,,CHEBI:17579,beta-carotene,ENVO:00002006,water
ENVO:3100007,,CHEBI:23042,carotene,ENVO:00002006,water
ENVO:3100008,,CHEBI:18230,chlorophyll a,ENVO:00002006,water
ENVO:3100009,,CHEBI:27888,chlorophyll b,ENVO:00002006,water
ENVO:3100010,,CHEBI:16900,chlorophyllide a,ENVO:00002006,water
ENVO:3100011,,CHEBI:15379,dioxygen,ENVO:00002006,water
ENVO:3100012,,CHEBI:73113,divinyl chlorophyll a,ENVO:00002006,water
ENVO:3100013,,CHEBI:73115,divinyl chlorophyll b,ENVO:00002006,water
ENVO:3100014,,CHEBI:5186,fucoxanthin,ENVO:00002006,water
ENVO:3100015,,CHEBI:15996,Guanosine 5-triphosphate,ENVO:00002006,water
ENVO:3100016,,CHEBI:16240,hydrogen peroxide,ENVO:00002006,water
ENVO:3100017,,CHEBI:16136,hydrogen sulfide,ENVO:00002006,water
ENVO:3100018,,CHEBI:16136,hydrogen sulfide,ENVO:00002006,water
ENVO:3100019,,CHEBI:28838,lutein,ENVO:00002006,water
ENVO:3100020,,CHEBI:16183,methane,ENVO:00002006,water
ENVO:3100021,,CHEBI:25501,neoxanthin,ENVO:00002006,water
ENVO:3100022,,CHEBI:17632 ,nitrate ,ENVO:00002006,water
ENVO:3100023,,CHEBI:16301,nitrite,ENVO:00002006,water
ENVO:3100024,,CHEBI:17045,nitrous oxide,ENVO:00002006,water
ENVO:3100025,,CHEBI:44882,peridinin,ENVO:00002006,water
ENVO:3100026,,CHEBI:26020,phosphate,ENVO:00002006,water
ENVO:3100027,,CHEBI:29241,silicate(4-),ENVO:00002006,water
ENVO:3100028,,CHEBI:27295,violaxanthin,ENVO:00002006,water
ENVO:3100029,,CHEBI:27547,zeaxanthin,ENVO:00002006,water
ENVO:3100034,,CHEBI:26675,silicic acid,ENVO:00002006,water
183 changes: 183 additions & 0 deletions src/envo/modules/chemical_concentration.obo
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format-version: 1.2
ontology: envo/modules/chemical_concentration

[Term]
id: ENVO:3100001
name: Adenosine 5-triphosphate of water
def: "The concentration of Adenosine 5-triphosphate when measured in water." []
synonym: "water Adenosine 5-triphosphate concentration" EXACT []

[Term]
id: ENVO:3100002
name: alloxanthine of water
def: "The concentration of alloxanthine when measured in water." []
synonym: "water alloxanthine concentration" EXACT []

[Term]
id: ENVO:3100003
name: alpha-carotene of water
def: "The concentration of alpha-carotene when measured in water." []
synonym: "water alpha-carotene concentration" EXACT []

[Term]
id: ENVO:3100004
name: ammonium of water
def: "The concentration of ammonium when measured in water." []
synonym: "water ammonium concentration" EXACT []

[Term]
id: ENVO:3100005
name: bacteriochlorophyll a of water
def: "The concentration of bacteriochlorophyll a when measured in water." []
synonym: "water bacteriochlorophyll a concentration" EXACT []

[Term]
id: ENVO:3100006
name: beta-carotene of water
def: "The concentration of beta-carotene when measured in water." []
synonym: "water beta-carotene concentration" EXACT []

[Term]
id: ENVO:3100007
name: carotene of water
def: "The concentration of carotene when measured in water." []
synonym: "water carotene concentration" EXACT []

[Term]
id: ENVO:3100008
name: chlorophyll a of water
def: "The concentration of chlorophyll a when measured in water." []
synonym: "water chlorophyll a concentration" EXACT []

[Term]
id: ENVO:3100009
name: chlorophyll b of water
def: "The concentration of chlorophyll b when measured in water." []
synonym: "water chlorophyll b concentration" EXACT []

[Term]
id: ENVO:3100010
name: chlorophyllide a of water
def: "The concentration of chlorophyllide a when measured in water." []
synonym: "water chlorophyllide a concentration" EXACT []

[Term]
id: ENVO:3100011
name: dioxygen of water
def: "The concentration of dioxygen when measured in water." []
synonym: "water dioxygen concentration" EXACT []

[Term]
id: ENVO:3100012
name: divinyl chlorophyll a of water
def: "The concentration of divinyl chlorophyll a when measured in water." []
synonym: "water divinyl chlorophyll a concentration" EXACT []

[Term]
id: ENVO:3100013
name: divinyl chlorophyll b of water
def: "The concentration of divinyl chlorophyll b when measured in water." []
synonym: "water divinyl chlorophyll b concentration" EXACT []

[Term]
id: ENVO:3100014
name: fucoxanthin of water
def: "The concentration of fucoxanthin when measured in water." []
synonym: "water fucoxanthin concentration" EXACT []

[Term]
id: ENVO:3100015
name: Guanosine 5-triphosphate of water
def: "The concentration of Guanosine 5-triphosphate when measured in water." []
synonym: "water Guanosine 5-triphosphate concentration" EXACT []

[Term]
id: ENVO:3100016
name: hydrogen peroxide of water
def: "The concentration of hydrogen peroxide when measured in water." []
synonym: "water hydrogen peroxide concentration" EXACT []

[Term]
id: ENVO:3100017
name: hydrogen sulfide of water
def: "The concentration of hydrogen sulfide when measured in water." []
synonym: "water hydrogen sulfide concentration" EXACT []

[Term]
id: ENVO:3100018
name: hydrogen sulfide of water
def: "The concentration of hydrogen sulfide when measured in water." []
synonym: "water hydrogen sulfide concentration" EXACT []

[Term]
id: ENVO:3100019
name: lutein of water
def: "The concentration of lutein when measured in water." []
synonym: "water lutein concentration" EXACT []

[Term]
id: ENVO:3100020
name: methane of water
def: "The concentration of methane when measured in water." []
synonym: "water methane concentration" EXACT []

[Term]
id: ENVO:3100021
name: neoxanthin of water
def: "The concentration of neoxanthin when measured in water." []
synonym: "water neoxanthin concentration" EXACT []

[Term]
id: ENVO:3100022
name: http://purl.obolibrary.org/obo/CHEBI_17632 of water
def: "The concentration of http://purl.obolibrary.org/obo/CHEBI_17632 when measured in water." []
synonym: "water http://purl.obolibrary.org/obo/CHEBI_17632 concentration" EXACT []

[Term]
id: ENVO:3100023
name: nitrite of water
def: "The concentration of nitrite when measured in water." []
synonym: "water nitrite concentration" EXACT []

[Term]
id: ENVO:3100024
name: nitrous oxide of water
def: "The concentration of nitrous oxide when measured in water." []
synonym: "water nitrous oxide concentration" EXACT []

[Term]
id: ENVO:3100025
name: peridinin of water
def: "The concentration of peridinin when measured in water." []
synonym: "water peridinin concentration" EXACT []

[Term]
id: ENVO:3100026
name: phosphate of water
def: "The concentration of phosphate when measured in water." []
synonym: "water phosphate concentration" EXACT []

[Term]
id: ENVO:3100027
name: silicate(4-) of water
def: "The concentration of silicate(4-) when measured in water." []
synonym: "water silicate(4-) concentration" EXACT []

[Term]
id: ENVO:3100028
name: violaxanthin of water
def: "The concentration of violaxanthin when measured in water." []
synonym: "water violaxanthin concentration" EXACT []

[Term]
id: ENVO:3100029
name: zeaxanthin of water
def: "The concentration of zeaxanthin when measured in water." []
synonym: "water zeaxanthin concentration" EXACT []

[Term]
id: ENVO:3100034
name: silicic acid of water
def: "The concentration of silicic acid when measured in water." []
synonym: "water silicic acid concentration" EXACT []

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