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Add taxon disjoints to subset #75

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merged 7 commits into from
Jun 16, 2023
Merged

Add taxon disjoints to subset #75

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8ebfb4f
add taxon disjoints to subset
anitacaron Jun 15, 2023
2eb9ca5
update query
anitacaron Jun 16, 2023
3fc0d82
update subset pipeline
anitacaron Jun 16, 2023
b6c412a
new pipeline for disjoint file in ncbitaxon
anitacaron Jun 16, 2023
9ef8074
update readme to include disjoint file in ncbitaxon
anitacaron Jun 16, 2023
49f119a
Revert "update readme to include disjoint file in ncbitaxon"
anitacaron Jun 16, 2023
87f70fe
Revert "new pipeline for disjoint file in ncbitaxon"
anitacaron Jun 16, 2023
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10 changes: 8 additions & 2 deletions Makefile
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
.PHONY: all
all: ncbitaxon.owl ncbitaxon.obo ncbitaxon.json ncbi_diff_latest_current_obo.txt
all: ncbitaxon.owl.gz ncbitaxon.obo.gz ncbitaxon.json.gz
all: ncbitaxon.owl ncbitaxon.obo ncbitaxon.json ncbi_diff_latest_current_obo.txt ncbitaxon-disjoint-over-in-taxon.owl
all: ncbitaxon.owl.gz ncbitaxon.obo.gz ncbitaxon.json.gz ncbitaxon-disjoint-over-in-taxon.owl.gz

ROBOT=robot

Expand Down Expand Up @@ -76,3 +76,9 @@ build/ncbitaxon.owl: ncbitaxon.ttl

.PHONY: test
test: build/Nov2019/ncbitaxon.diff build/Nov2019/ncbitaxon_robot.diff

ncbitaxon-disjoint-over-in-taxon.owl: ncbitaxon.owl
OWLTOOLS_MEMORY=16G owltools $< --create-taxon-disjoint-over-in-taxon --root NCBITaxon:1 --output [email protected]
robot query --input $< --format ttl --query add-taxon-disjoints.ru [email protected]
robot merge --input [email protected] --input [email protected] --output $@
rm [email protected] && rm [email protected]
2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -65,7 +65,7 @@ If you specifically wish to cite the OBO/OWL translation, use the URL for this p
3. `make all -B`
4. `cd ..`
2. gh release create v2021-06-10
3. gh release upload v2021-06-10 ncbitaxon.json ncbitaxon.json.gz ncbitaxon.obo ncbitaxon.obo.gz ncbitaxon.owl ncbitaxon.owl.gz subsets/taxslim-disjoint-over-in-taxon.owl subsets/taxslim.obo subsets/taxslim.owl subsets/taxslim.json
3. gh release upload v2021-06-10 ncbitaxon.json ncbitaxon.json.gz ncbitaxon.obo ncbitaxon.obo.gz ncbitaxon.owl ncbitaxon.owl.gz subsets/taxslim-disjoint-over-in-taxon.owl subsets/taxslim.obo subsets/taxslim.owl subsets/taxslim.json ncbitaxon-disjoint-over-in-taxon.owl ncbitaxon-disjoint-over-in-taxon.owl.gz

### Using Monarch Jenkins

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5 changes: 4 additions & 1 deletion subsets/Makefile
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Expand Up @@ -13,7 +13,10 @@ taxslim: taxon-subset-ids.txt
robot convert -i taxslim.owl -f json -o taxslim.json

taxslim-disjoint-over-in-taxon.owl: taxslim
owltools taxslim.owl --create-taxon-disjoint-over-in-taxon --root NCBITaxon:1
owltools taxslim.owl --create-taxon-disjoint-over-in-taxon --root NCBITaxon:1 --output [email protected]
robot query --input taxslim.owl --format ttl --query add-taxon-disjoints.ru [email protected]
robot merge --input [email protected] --input [email protected] --output $@
rm [email protected] && rm [email protected]

## The following should not be run as part of CI job.
## Admin for this project should run and check in results.
Expand Down
22 changes: 22 additions & 0 deletions subsets/add-taxon-disjoints.ru
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@@ -0,0 +1,22 @@
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162>
CONSTRUCT {
[
a owl:Restriction ;
owl:onProperty in_taxon: ;
owl:someValuesFrom ?subtaxon ;
owl:disjointWith [
a owl:Restriction ;
owl:onProperty in_taxon: ;
owl:someValuesFrom [
a owl:Class ;
owl:complementOf ?subtaxon
]
]
] .
}
WHERE {
?subtaxon rdf:type owl:Class .
}