loading the ontology go_daily-termdb-data.owl
Traceback (most recent call last):
File "/anaconda3/lib/python3.6/xml/sax/expatreader.py", line 217, in feed
self._parser.Parse(data, isFinal)
xml.parsers.expat.ExpatError: syntax error: line 1, column 0
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "dishin.py", line 39, in
semanticbase.create(sb_file, db_file, name_prefix, relation, annotation_file)
File "/Users/imran/Desktop/thesis/aligners/dishln/DiShIn/semanticbase.py", line 94, in create
g.load(owl_file)
File "/anaconda3/lib/python3.6/site-packages/rdflib/graph.py", line 1050, in load
self.parse(source, publicID, format)
File "/anaconda3/lib/python3.6/site-packages/rdflib/graph.py", line 1043, in parse
parser.parse(source, self, **args)
File "/anaconda3/lib/python3.6/site-packages/rdflib/plugins/parsers/rdfxml.py", line 578, in parse
self._parser.parse(source)
File "/anaconda3/lib/python3.6/xml/sax/expatreader.py", line 111, in parse
xmlreader.IncrementalParser.parse(self, source)
File "/anaconda3/lib/python3.6/xml/sax/xmlreader.py", line 125, in parse
self.feed(buffer)
File "/anaconda3/lib/python3.6/xml/sax/expatreader.py", line 221, in feed
self._err_handler.fatalError(exc)
File "/anaconda3/lib/python3.6/xml/sax/handler.py", line 38, in fatalError
raise exception
xml.sax._exceptions.SAXParseException: file:///Users/imran/Desktop/thesis/aligners/dishln/DiShIn/go_daily-termdb-data.owl:1:0: syntax error
Hi wget http://archive.geneontology.org/latest-termdb/go_daily-termdb.owl.gz was not available so i downloaded wget http://archive.geneontology.org/latest-termdb/go_daily-termdb-data.gz and extracted and renamed to go_daily-termdb-data.owl and when i ran
python dishin.py go_daily-termdb-data.owl go.db http://purl.org/obo/owl/GO# http://www.w3.org/2000/01/rdf-schema#subClassOf goa_uniprot_all_noiea.gafI get this exception