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Use Chobo for OBO parsing #1164

Closed kimrutherford closed 8 years ago

kimrutherford commented 8 years ago

The loading/updating should be a bit faster if we use Chobo.

kimrutherford commented 8 years ago

I've put this on high priority as we need it for #28.

kimrutherford commented 8 years ago

The code changes are done and I'm about to try loading the ontologies for the test Canto.

kimrutherford commented 8 years ago

The code changes are done and I'm about to try loading the ontologies for the test Canto.

It seemed to work but with many warnings: pombase/chobo#6

kimrutherford commented 8 years ago

It seemed to work but with many warnings:

Most of the warnings are fixed. There are a few left but I can't see any that would cause a problem. This code has been in the test Canto for a week and I haven't seen any problems.

Here's an example warning:

new "def" tag of this stanza (from /var/pomcur/sources/pato-simple.obo line 19366) differs from previously seen value (from /var/pomcur/canto-sources/pombase_fypo_git_for_canto/release/fypo-simple.obo line 69110) "Inverse of part_of." - ignoring new value: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2."

while merging: [Typedef] id: has_part name: has_part comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. def: Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. namespace: quality

into existing term: [Typedef] id: has_part name: has_part comment: Example: operon has_part gene. def: Inverse of part_of. namespace: sequence