DiseaseOntology/SymptomOntology

Invalid syntax in `symp.obo`

Closed this issue · 3 comments

althonos commented

Hi !

Errors

There are a few syntax errors in the current version symp.obo:

  • on line 2246, the xref URL did not properly replace the <new dbxref> placeholder: 
    [URL:http\://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=hyperthermia<new dbxref>]
  • on line 4774 and 5507, several xref URLs are merged together: 
    [URL:http\://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=hemorrhage <http\://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=hemorrhage, wiki:http\://en.wikipedia.org/wiki/Gingival]
  • on lines 5157 and 5186, the placeholder xref has not been replaced 
    xref: ICD9CM_2005:<new dbxref>
    In particular:
    - SYMP:0000816 is probably linking ICD9CM:307.46 or ICD9CM:307.47
    - SYMP:0000821 is probably linking to ICD9CM:786.6

Suggestions

A few suggestions to improve the management of xrefs:

  • xrefs to Wikipedia articles can use the Wikipedia prefix with only the article name, e.g. Wikipedia:Hematemesis.
  • since URLs are valid identifiers, there is no need to prefix URLs to web resources with a url prefix.
  • on line 5616 the URL is invalid (missing leading h in http)
  • the part_of relationship should have an xref referring to BFO:0000050 so that the actual BFO relation can be substituted to the locally defined one as stated in the OBO Semantcis.
lschriml commented

Hello Martin,
thank you for pointing out these fixes in the Symptom Ontology !!

What project are you working on. ?

Edits pushed.

Cheers,
Lynn

althonos commented

Hi Lynn,
I'm trying to improve the semantics of the OBO ontology language to improve conversion from and to the OWL standard. I developed a formal parser (althonos/fastobo) and I'm trying to get all the ontologies of the OBO Foundry to update to the new 1.4 syntax. I'm now working on the OBO to OWL semantics to produce a formally correct obo2owl converter, with Python support, and no need for a Java stack!

althonos commented

Hi Lynn,
this issue has not been fixed completely: SYMP:0000821 still contains an invalid xref (xref: ICD9CM_2005:<new dbxref>) in the latest commit on master branch.