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PathwayCommons / cpath2

Biological pathway data integration and access platform (Pathway Commons)
http://www.pathwaycommons.org/pc2/
MIT License
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too many parent pathways in extended SIF (esp. in KEGG's) #238

Closed IgorRodchenkov closed 8 years ago

IgorRodchenkov commented 8 years ago

This was reported (emailed) by one of our users (Georges, Katija from DFCI, Harvard):

Sorry to bother you again with a question about pathway commons v8. Please, let me know, if I should rather direct my questions to someone else.

"...have been confused by finding quite some "PPIs" (protein pairs) in the pathway commons v8 file that have many many pathways associated with them. Please, find below an example. When we look up both enzymes in Uniprot and KEGG, then they don't seem to be involved in the same metabolic pathway at all and are neither individually associated with most of the listed pathways below. Can you please, help us understand how we have to interpret the annotations provided in pathway commons? ... AHCYL1 catalysis-precedes GNMT KEGG Alanine, aspartate and glutamate metabolism;Amino sugar and nucleotide sugar metabolism;Aminoacyl-tRNA biosynthesis;Arginine and proline metabolism;Ascorbate and aldarate metabolism;Biotin metabolism;Butanoate metabolism;Citrate cycle (TCA cycle);Cyanoamino acid metabolism;Cysteine and methionine metabolism;D-Glutamine and D-glutamate metabolism;Ether lipid metabolism;Fatty acid biosynthesis;Fatty acid elongation;Fatty acid metabolism;Folate biosynthesis;Fructose and mannose metabolism;Galactose metabolism;Glutathione metabolism;Glycerolipid metabolism;Glycerophospholipid metabolism;Glycine, serine and threonine metabolism;Glycolysis / Gluconeogenesis;Glycosphingolipid biosynthesis - ganglio series;Glycosphingolipid biosynthesis - globo series;Glycosphingolipid biosynthesis - lacto and neolacto series;Glycosylphosphatidylinositol(GPI)-anchor biosynthesis;Glyoxylate and dicarboxylate metabolism;Histidine metabolism;Inositol phosphate metabolism;Lipoic acid metabolism;Lysine biosynthesis;Lysine degradation;Metabolic pathways;N-Glycan biosynthesis;Nicotinate and nicotinamide metabolism;Nitrogen metabolism;One carbon pool by folate;Pantothenate and CoA biosynthesis;Pentose and glucuronate interconversions;Pentose phosphate pathway;Phenylalanine metabolism;Phenylalanine, tyrosine and tryptophan biosynthesis;Porphyrin and chlorophyll metabolism;Primary bile acid biosynthesis;Propanoate metabolism;Purine metabolism;Pyrimidine metabolism;Pyruvate metabolism;Sphingolipid metabolism;Starch and sucrose metabolism;Steroid biosynthesis;Steroid hormone biosynthesis;Sulfur metabolism;Synthesis and degradation of ketone bodies;Taurine and hypotaurine metabolism;Terpenoid backbone biosynthesis;Tryptophan metabolism;Tyrosine metabolism;Ubiquinone and other terpenoid-quinone biosynthesis;Valine, leucine and isoleucine biosynthesis;Valine, leucine and isoleucine degradation;beta-Alanine metabolism http://purl.org/pc2/8/Catalysis_74e3feb762c18a8c692052fc87f383c4;http://purl.org/pc2/8/Catalysis_21de9a19c1e7cbb3d88e107af391930e;http://purl.org/pc2/8/BiochemicalReaction_6c5f265ef62f3259d5514ba79bf611be;http://purl.org/pc2/8/BiochemicalReaction_a8928e36dfa30ff2179bacf1de0d11f2 ..."

This is mostly about KEGG's (loopy interweaved pathways) data, but it makes sense to fix for all - by printing only direct parent pathway names (of corresp. mediator interactions).

IgorRodchenkov commented 8 years ago

Fixed in Paxtools (pattern module); will be fixed for PC2 v8 after re-exporting to extended SIF format, and re-building/restarting the web service (to fix it for the web queries)...

IgorRodchenkov commented 8 years ago

Fixed. SIF archives were updated.