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BaderLab / EnrichmentMap_monthlyGenesetBuild

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October 2020-March 2021 issues with genesets - panther and Wikipathway #15

Open risserlin opened 3 years ago

risserlin commented 3 years ago

but might be for all genesets Panther genesets are mix of all species identifiers Wikipathways are losing identifiers with the new ensembl id annotator, need to figure out why. comparing_genesets_between_releases.xlsx

veroniquevoisin commented 1 year ago

I have just noticed this issue (Human_GOBP_AllPathways_no_GO_iea_January_01_2022_symbol.gmt) with lower and upper case format in the PANTHER pathways. I'm wondering how the PANTHER pathways are curated. I'm not sure how a pathway can contain a mix of identifiers. Does it make these pathways less reliable? If yes, should they still be included or removed from the build?

risserlin commented 1 year ago

this was fixed with the commit 8b440d6bb162b2562945ead4c8be60d8b40d39de From June 2022 there were only species specific ids in the panther pathways.

veroniquevoisin commented 1 year ago

Thanks!