Orphanet benchmark

config/OrphaNet/data_processing/generate_orpha_gene_disease_benchmarks.py

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+import csv
+import requests
+import xmltodict
+
+# use this if loading data from raw xml file (up-to-date as of 2/15/2023)
+# with open('../en_product6.xml') as xml_file:
+#    data_dict = xmltodict.parse(xml_file.read())
+
+# us this if extracting from link from http://www.orphadata.org/cgi-bin/index.php
+# Note, that file name is likely to change for newer versions and will require updating
+r = requests.get('http://www.orphadata.org/data/xml/en_product6.xml')
+data_dict = xmltodict.parse(r.content)
+
+x = [['Disease_Curie', 'Disease_Name', 'Gene_Curie', 'Gene_Name']]
+for data in data_dict['JDBOR']['DisorderList']['Disorder']:
+    orpha_code = 'ORPHANET:{}'.format(data['OrphaCode'])
+    orpha_name = data['Name']['#text']
+    associations = data['DisorderGeneAssociationList']['DisorderGeneAssociation']
+    if type(associations) is not list:
+        associations = [associations]
+        for association in associations:
+            gene_name = association['Gene']['Name']['#text']
+            references = association['Gene']['ExternalReferenceList']['ExternalReference']
+            found = False
+            if type(references) is not list:
+                references = [references]
+            for reference in references:
+                if reference['Source'] == 'Ensembl':
+                    gene_curie = 'ENSEMBL:{}'.format(reference['Reference'])
+                    x.append([orpha_code, orpha_name, gene_curie, gene_name])
+                    found = True
+                    break
+with open('../data.tsv', 'w', newline='') as f:
+    writer = csv.writer(f, delimiter='\t')
+    writer.writerows(x)
+