replace skos:exactMatch with semapv:crossSpeciesExactMatch in hp-mp m…

…appings
EBISPOT · Sep 25, 2024 · 313ae2a · 313ae2a
1 parent b095e6e
commit 313ae2a
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Showing 10 changed files with 19 additions and 12 deletions.
diff --git a/00_fetch_data/sssom/fetch.sh b/00_fetch_data/sssom/fetch.sh
@@ -1,14 +1,21 @@
 #!/bin/bash
 
-rm -f *.sssom.tsv.gz
-
-curl -L https://data.monarchinitiative.org/mappings/latest/gene_mappings.sssom.tsv | gzip > gene_mappings.sssom.tsv.gz
-curl -L https://data.monarchinitiative.org/mappings/latest/hp_mesh.sssom.tsv | gzip > hp_mesh.sssom.tsv.gz
-curl -L https://data.monarchinitiative.org/mappings/latest/mesh_chebi_biomappings.sssom.tsv | gzip > mesh_chebi_biomappings.sssom.tsv.gz
-curl -L https://data.monarchinitiative.org/mappings/latest/mondo.sssom.tsv | gzip > mondo.sssom.tsv.gz
-curl -L https://data.monarchinitiative.org/mappings/latest/umls_hp.sssom.tsv | gzip > umls_hp.sssom.tsv.gz
-curl -L https://data.monarchinitiative.org/mappings/latest/upheno_custom.sssom.tsv | gzip > upheno_custom.sssom.tsv.gz
-
-curl -L https://raw.githubusercontent.com/mapping-commons/mh_mapping_initiative/master/mappings/mp_hp_mgi_all.sssom.tsv | gzip > mp_hp_mgi_all.sssom.tsv.gz
-curl -L https://raw.githubusercontent.com/obophenotype/bio-attribute-ontology/master/src/mappings/oba-efo.sssom.tsv | gzip > oba-efo.sssom.tsv.gz
-curl -L https://raw.githubusercontent.com/obophenotype/bio-attribute-ontology/master/src/mappings/oba-vt.sssom.tsv | gzip > oba-vt.sssom.tsv.gz
+rm -f *.sssom.tsv.gz *.sssom.tsv
+
+wget https://data.monarchinitiative.org/mappings/latest/gene_mappings.sssom.tsv 
+wget https://data.monarchinitiative.org/mappings/latest/hp_mesh.sssom.tsv
+wget https://data.monarchinitiative.org/mappings/latest/mesh_chebi_biomappings.sssom.tsv 
+wget https://data.monarchinitiative.org/mappings/latest/mondo.sssom.tsv 
+wget https://data.monarchinitiative.org/mappings/latest/umls_hp.sssom.tsv 
+wget https://data.monarchinitiative.org/mappings/latest/upheno_custom.sssom.tsv 
+
+wget https://raw.githubusercontent.com/mapping-commons/mh_mapping_initiative/master/mappings/mp_hp_mgi_all.sssom.tsv 
+wget https://raw.githubusercontent.com/obophenotype/bio-attribute-ontology/master/src/mappings/oba-efo.sssom.tsv
+wget https://raw.githubusercontent.com/obophenotype/bio-attribute-ontology/master/src/mappings/oba-vt.sssom.tsv 
+
+sed -i 's/skos:exactMatch/semapv:crossSpeciesExactMatch/g' mp_hp_mgi_all.sssom.tsv
+
+for f in *.sssom.tsv; do
+  gzip $f
+done
+
diff --git a/00_fetch_data/sssom/gene_mappings.sssom.tsv.gz b/00_fetch_data/sssom/gene_mappings.sssom.tsv.gz
diff --git a/00_fetch_data/sssom/hp_mesh.sssom.tsv.gz b/00_fetch_data/sssom/hp_mesh.sssom.tsv.gz
diff --git a/00_fetch_data/sssom/mesh_chebi_biomappings.sssom.tsv.gz b/00_fetch_data/sssom/mesh_chebi_biomappings.sssom.tsv.gz
diff --git a/00_fetch_data/sssom/mondo.sssom.tsv.gz b/00_fetch_data/sssom/mondo.sssom.tsv.gz
diff --git a/00_fetch_data/sssom/mp_hp_mgi_all.sssom.tsv.gz b/00_fetch_data/sssom/mp_hp_mgi_all.sssom.tsv.gz
diff --git a/00_fetch_data/sssom/oba-efo.sssom.tsv.gz b/00_fetch_data/sssom/oba-efo.sssom.tsv.gz
diff --git a/00_fetch_data/sssom/oba-vt.sssom.tsv.gz b/00_fetch_data/sssom/oba-vt.sssom.tsv.gz
diff --git a/00_fetch_data/sssom/umls_hp.sssom.tsv.gz b/00_fetch_data/sssom/umls_hp.sssom.tsv.gz
diff --git a/00_fetch_data/sssom/upheno_custom.sssom.tsv.gz b/00_fetch_data/sssom/upheno_custom.sssom.tsv.gz