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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Correct directional RHEA assignments #21534

Open hdrabkin opened 3 years ago

hdrabkin commented 3 years ago

Per this file from @amorgat GO2dirRhea_2021-05-30_118.xlsx Dear Harold, Pascale,

When we tested the search of GO terms in the new web site with Parit, we realized that we still have some GO terms (37) that are mapped to directed Rhea IDs. See attached excel file (GO2dirRhea_2021-05-30_118.xlsx) The column rheaid contains the mapped Rhea ID that should be replaced by the ID of the rhea column (undefined direction). Column direction: BI: bidirectional LR: Left-to-Right RL: Right-to-Left All the best, Anne

hdrabkin commented 3 years ago

Hi @amorgat The first on the list; your suggestion for using RHEA 27318 does not seem right; 27318 is a transport reaction (and is used elsewhere for the GO transporter term. Second one GO:0052936 has been obsoletedd; alt term is GO:0052934. The suggested RHEA:52936 has nothing to do with the former or current GO rxn. Can you please recheck these

hdrabkin commented 3 years ago

Spreadsheet with progress thus far; green means done; brick means 'think about it' ; black means rhea needs to recheck (see above). GO2dirRhea_2021-06-04-hjd.xlsx

hdrabkin commented 2 years ago

@deustp01 , @ukemi ; what do you think?

-RHEA: 21252 GO:0047545 2-hydroxyglutarate dehydrogenase activity ;parent ; exp annotations; 14 -- RHEA: 21254 GO:0061759 alpha-ketoglutarate reductase activity (should add "reverse reaction" to term name to reflect the def) exp annotations: 6 --RHEA:21253 GO:0061758 2-hydroxyglutarate dehydrogenase activity, forward reaction; no annotations.

Should we merge these if forward reaction not used, and reverse only 6?