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Rothamsted / knetbuilder

KnetBuilder data integration platform for building knowledge graphs. Previously known as ondex.
https://knetminer.com
MIT License
12 stars 11 forks source link

UniProt parser: Parse GO class and remove GO file parameter #5

Closed KeywanHP closed 7 years ago

KeywanHP commented 7 years ago

The GO file parameter in the UniProt parser was used to lookup the ontology class P, F or C for each GO annotation in order to create the correct Concept Class and Relation Type. The ontology class information is now included in the UniProt XML itself and therefore the additional GO file is not needed any longer.

I suggest we improve the Parser code to parse F, P or C flags in UniProt XML GO annotations...

<dbReference type="GO" id="GO:0004497">
    <property type="term" value="F:monooxygenase activity"/>
    <property type="evidence" value="ECO:0000501"/>
    <property type="project" value="UniProtKB-KW"/>
 </dbReference>
AjitPS commented 7 years ago

Currently working to resolve this, needs more work

AjitPS commented 7 years ago

Fixed and implemented in recent commits: https://github.com/Rothamsted/ondex-knet-builder/commit/e0d041e6d2c09b11d06286027925454dc948ac9f and https://github.com/Rothamsted/ondex-knet-builder/commit/b07c6469c7631a82bce65a46226abcaa0d3a2a00 thanks @KeywanHP

AjitPS commented 7 years ago

can be closed now