From 26bbfaecac44d8a338909d64668cbfbc58f7ddb4 Mon Sep 17 00:00:00 2001
From: Anita Caron <anitac@ebi.ac.uk>
Date: Fri, 16 Jun 2023 18:40:49 +0100
Subject: [PATCH] Add taxon disjoints to subset (#75)

* add taxon disjoints to subset

* update query

* update subset pipeline

* new pipeline for disjoint file in ncbitaxon

* update readme to include disjoint file in ncbitaxon

* Revert "update readme to include disjoint file in ncbitaxon"

This reverts commit 9ef80745f2868faf461a10e457c84a4ce55e79d9.

* Revert "new pipeline for disjoint file in ncbitaxon"

This reverts commit b6c412a66babdae4ab612e17bcc7746a57c15f09.

---------

Co-authored-by: Anita Caron <anitacaron@users.noreply.github.com>
---
 subsets/Makefile               |  5 ++++-
 subsets/add-taxon-disjoints.ru | 22 ++++++++++++++++++++++
 2 files changed, 26 insertions(+), 1 deletion(-)
 create mode 100644 subsets/add-taxon-disjoints.ru

diff --git a/subsets/Makefile b/subsets/Makefile
index 181d2ed..882b453 100644
--- a/subsets/Makefile
+++ b/subsets/Makefile
@@ -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 $@.tmp.owl
+	robot query --input taxslim.owl --format ttl --query add-taxon-disjoints.ru $@.tmp.ttl
+	robot merge --input $@.tmp.owl --input $@.tmp.ttl --output $@
+	rm $@.tmp.owl && rm $@.tmp.ttl
 
 ## The following should not be run as part of CI job.
 ## Admin for this project should run and check in results.
diff --git a/subsets/add-taxon-disjoints.ru b/subsets/add-taxon-disjoints.ru
new file mode 100644
index 0000000..556286e
--- /dev/null
+++ b/subsets/add-taxon-disjoints.ru
@@ -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 .
+}