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superphy / spfy

Spfy: an integrated graph database for real-time prediction of Escherichia coli phenotypes and downstream comparative analyses
https://lfz.corefacility.ca/superphy/grouch/
Apache License 2.0
4 stars 2 forks source link

relook at rdfs terms for linking objects #192

Closed kevinkle closed 6 years ago

kevinkle commented 7 years ago

namely: we may want to add rdfs:domain(where it starts from) and rdfs:range(where it ends) to our link_uris(). If this works, we can use the savvy.py script to generate all the graph files, merge them, then use https://github.com/VisualDataWeb/OWL2VOWL to convert and https://github.com/VisualDataWeb/WebVOWL to visualize.

This would be an alternate approach to https://github.com/superphy/reactapp/issues/42

kevinkle commented 7 years ago 
(backend) kevin@scatter:~/Desktop/backend/app$ python -m modules/savvy -i tests/ecoli/GCA_001894495.1_ASM189449v1_genomic.fna
kevin@scatter:~/Desktop/owl2vowl$ java -jar owl2vowl.jar -file /home/kevin/Desktop/backend/app/tests/ecoli/GCA_001894495.1_ASM189449v1_genomic.fna_merged.ttl
kevinkle commented 7 years ago

errors:


10:32:11.380 [main] ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error1152 for type Class
10:32:11.884 [main] ERROR de.uni_stuttgart.vis.vowl.owl2vowl.ConsoleMain - FAILED TO LOAD [-file, /home/kevin/Desktop/backend/app/tests/ecoli/GCA_001894495.1_ASM189449v1_genomic.fna_merged.ttl]
java.lang.StringIndexOutOfBoundsException
String index out of range: -1```