Invalid syntax in `symp.obo`

[althonos]

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]

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

What project are you working on. ?

Edits pushed.

Cheers, Lynn

[althonos]

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]

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.