problems with HumanDO_xp.obo

[obophenotype-user]

There are many problems with this file.

It is full of mistakes such as 'pneumonic plague' = 'lung disease' and located_in some lung

Many classes share the same logical definition.

Perhaps this was caused by a problem in an oboedit beta?

I am attaching a list of problematic cases that could be found automatically. There may be many more that are not so obviously wrong.

Note you can run your test for yourself using obo-check-xps.pl https://github.com/cmungall/obo-scripts

I also recommend releasing with oort, this will spot these problems too

Reported by: cmungall

Original Ticket: diseaseontology/feature-requests/24

[obophenotype-user]

Original comment by: cmungall

[obophenotype-user]

Thank you for pointing this out. Agreed. This is an issue. We hope to address this in the near future.

Regards, Lynn

Original comment by: lschriml

[obophenotype-user]

• assigned_to: nobody --> lynn_schriml

Original comment by: lschriml

[obophenotype-user]

We plan to start a new logical definition file in 2013 that will address these issues. Lynn

Original comment by: lschriml

[obophenotype-user]

• status: open --> pending

Original comment by: lschriml

[obophenotype-user]

See also:

https://code.google.com/p/phenotype-ontologies/source/browse/\#svn%2Ftrunk%2Fsrc%2Fontology%2Fdoid%2Fmappings

Original comment by: cmungall

[obophenotype-user]

• status: pending --> open

Original comment by: cmungall

[obophenotype-user]

• status: open --> wont-fix
• Group: --> Next Release (example)

Original comment by: lschriml

[obophenotype-user]

The HumanDO_xp file will be revamped and replaced. Lynn

Original comment by: lschriml