Only use accessions from species_isolates (closes #6)

EVORA-project · Nov 7, 2024 · 2269384 · 2269384
1 parent 256b9fe
commit 2269384
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diff --git a/create_ontologies.py b/create_ontologies.py
@@ -88,10 +88,10 @@ def main():
             if not pd.isna(node.abbrev_csv):
                 g.add((class_iri, URIRef(SYNONYM), Literal(node.abbrev_csv)))
 
-            if not pd.isna(node.genbank_accession_csv):
-                add_xrefs(g, class_iri, node.genbank_accession_csv, 'genbank:')
-            if not pd.isna(node.refseq_accession_csv):
-                add_xrefs(g, class_iri, node.refseq_accession_csv, 'refseq:')
+            # if not pd.isna(node.genbank_accession_csv):
+            #     add_xrefs(g, class_iri, node.genbank_accession_csv, 'genbank:')
+            # if not pd.isna(node.refseq_accession_csv):
+            #     add_xrefs(g, class_iri, node.refseq_accession_csv, 'refseq:')
 
             taxnode_isolates = isolates[isolates['taxnode_id'] == node.taxnode_id]
 

diff --git a/ols_config.json b/ols_config.json
@@ -1,28 +1,28 @@
 {
   "ontologies": [
     {
-      "id": "ictv_2023",
-      "ontology_purl": "./out/ictv_2023.owl.ttl",
+      "id": "ictv_1987",
+      "ontology_purl": "./out/ictv_1987.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_2018a",
-      "ontology_purl": "./out/ictv_2018a.owl.ttl",
+      "id": "ictv_1997",
+      "ontology_purl": "./out/ictv_1997.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_1971",
-      "ontology_purl": "./out/ictv_1971.owl.ttl",
+      "id": "ictv_2012",
+      "ontology_purl": "./out/ictv_2012.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_2018b",
-      "ontology_purl": "./out/ictv_2018b.owl.ttl",
+      "id": "ictv_1996",
+      "ontology_purl": "./out/ictv_1996.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_2017",
-      "ontology_purl": "./out/ictv_2017.owl.ttl",
+      "id": "ictv_2013",
+      "ontology_purl": "./out/ictv_2013.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
@@ -31,168 +31,168 @@
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_1987",
-      "ontology_purl": "./out/ictv_1987.owl.ttl",
+      "id": "ictv_1984",
+      "ontology_purl": "./out/ictv_1984.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_2005",
-      "ontology_purl": "./out/ictv_2005.owl.ttl",
+      "id": "ictv_2008",
+      "ontology_purl": "./out/ictv_2008.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_1974",
-      "ontology_purl": "./out/ictv_1974.owl.ttl",
+      "id": "ictv_1979",
+      "ontology_purl": "./out/ictv_1979.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_2012",
-      "ontology_purl": "./out/ictv_2012.owl.ttl",
+      "id": "ictv_2019",
+      "ontology_purl": "./out/ictv_2019.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_2020",
-      "ontology_purl": "./out/ictv_2020.owl.ttl",
+      "id": "ictv_2009",
+      "ontology_purl": "./out/ictv_2009.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_2014",
-      "ontology_purl": "./out/ictv_2014.owl.ttl",
+      "id": "ictv_1978",
+      "ontology_purl": "./out/ictv_1978.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_2008",
-      "ontology_purl": "./out/ictv_2008.owl.ttl",
+      "id": "ictv_1995",
+      "ontology_purl": "./out/ictv_1995.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_1976",
-      "ontology_purl": "./out/ictv_1976.owl.ttl",
+      "id": "ictv_1971",
+      "ontology_purl": "./out/ictv_1971.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_1982",
-      "ontology_purl": "./out/ictv_1982.owl.ttl",
+      "id": "ictv_1974",
+      "ontology_purl": "./out/ictv_1974.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_1998",
-      "ontology_purl": "./out/ictv_1998.owl.ttl",
+      "id": "ictv_2018b",
+      "ontology_purl": "./out/ictv_2018b.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_1999a",
-      "ontology_purl": "./out/ictv_1999a.owl.ttl",
+      "id": "ictv_2002a",
+      "ontology_purl": "./out/ictv_2002a.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_2009",
-      "ontology_purl": "./out/ictv_2009.owl.ttl",
+      "id": "ictv_1990",
+      "ontology_purl": "./out/ictv_1990.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_1991",
-      "ontology_purl": "./out/ictv_1991.owl.ttl",
+      "id": "ictv_1999b",
+      "ontology_purl": "./out/ictv_1999b.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_1979",
-      "ontology_purl": "./out/ictv_1979.owl.ttl",
+      "id": "ictv_2015",
+      "ontology_purl": "./out/ictv_2015.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_1997",
-      "ontology_purl": "./out/ictv_1997.owl.ttl",
+      "id": "ictv_2005",
+      "ontology_purl": "./out/ictv_2005.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_1975",
-      "ontology_purl": "./out/ictv_1975.owl.ttl",
+      "id": "ictv_2023",
+      "ontology_purl": "./out/ictv_2023.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_1993",
-      "ontology_purl": "./out/ictv_1993.owl.ttl",
+      "id": "ictv_2022",
+      "ontology_purl": "./out/ictv_2022.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_2021",
-      "ontology_purl": "./out/ictv_2021.owl.ttl",
+      "id": "ictv_1998",
+      "ontology_purl": "./out/ictv_1998.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_2002b",
-      "ontology_purl": "./out/ictv_2002b.owl.ttl",
+      "id": "ictv_1975",
+      "ontology_purl": "./out/ictv_1975.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_2002a",
-      "ontology_purl": "./out/ictv_2002a.owl.ttl",
+      "id": "ictv_1991",
+      "ontology_purl": "./out/ictv_1991.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_1999b",
-      "ontology_purl": "./out/ictv_1999b.owl.ttl",
+      "id": "ictv_1981",
+      "ontology_purl": "./out/ictv_1981.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_2019",
-      "ontology_purl": "./out/ictv_2019.owl.ttl",
+      "id": "ictv_2004",
+      "ontology_purl": "./out/ictv_2004.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_1978",
-      "ontology_purl": "./out/ictv_1978.owl.ttl",
+      "id": "ictv_2014",
+      "ontology_purl": "./out/ictv_2014.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_1995",
-      "ontology_purl": "./out/ictv_1995.owl.ttl",
+      "id": "ictv_2020",
+      "ontology_purl": "./out/ictv_2020.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_1996",
-      "ontology_purl": "./out/ictv_1996.owl.ttl",
+      "id": "ictv_2002b",
+      "ontology_purl": "./out/ictv_2002b.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_2013",
-      "ontology_purl": "./out/ictv_2013.owl.ttl",
+      "id": "ictv_2018a",
+      "ontology_purl": "./out/ictv_2018a.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_1981",
-      "ontology_purl": "./out/ictv_1981.owl.ttl",
+      "id": "ictv_2016",
+      "ontology_purl": "./out/ictv_2016.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_2016",
-      "ontology_purl": "./out/ictv_2016.owl.ttl",
+      "id": "ictv_1993",
+      "ontology_purl": "./out/ictv_1993.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_1984",
-      "ontology_purl": "./out/ictv_1984.owl.ttl",
+      "id": "ictv_1999a",
+      "ontology_purl": "./out/ictv_1999a.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_2022",
-      "ontology_purl": "./out/ictv_2022.owl.ttl",
+      "id": "ictv_1976",
+      "ontology_purl": "./out/ictv_1976.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_2004",
-      "ontology_purl": "./out/ictv_2004.owl.ttl",
+      "id": "ictv_2017",
+      "ontology_purl": "./out/ictv_2017.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_2015",
-      "ontology_purl": "./out/ictv_2015.owl.ttl",
+      "id": "ictv_1982",
+      "ontology_purl": "./out/ictv_1982.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     },
     {
-      "id": "ictv_1990",
-      "ontology_purl": "./out/ictv_1990.owl.ttl",
+      "id": "ictv_2021",
+      "ontology_purl": "./out/ictv_2021.owl.ttl",
       "preferredPrefix": "https://ictv.global/taxonomy/taxondetails?taxnode_id="
     }
   ]