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SysBioChalmers / panYeast-GEM

Reconstruction of a pan-genome metabolic model for S. cerevisiae - the pan model and scripts to make strain-specific models.
Creative Commons Attribution 4.0 International
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Pan genome annotation #7

Closed hongzhonglu closed 6 years ago

hongzhonglu commented 6 years ago

Main improvements in this PR:

Add the mapping relation between the panID and geneID from s288c genome. Based on this mapping relation, the initial panModel could be established. I hereby confirm that I have:

Note: replace [ ] with [X] to check the box. PLEASE DELETE THIS LINE

edkerk commented 6 years ago

@hongzhonglu To clarify, with "nonORF based on ref genome" are meant those panIDs that were not originally derived from S288c, but the genes with this panID have high sequence similarity to the refered S288c gene and therefore likely orthologs? In that case, these should then be annotated in the pan-genome model as OR relationship together with the panID 'directly' coupled to that S288c gene?

Example: YML056C exists as panID 5975-YML056C but also annotated as ortholog for panID 1729-snap_masked-BBH_6-7041. Any grRule with YML056C in yeast-GEM should then be replaced with 5975-YML056C OR 1729-snap_masked-BBH_6-7041. Correct?

hongzhonglu commented 6 years ago

@edkerk You are right! 'Or' relation should be used if one panID(nonORF) and another panID(ORF from s288c genome) are belong to the 'ortholog' relation.