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ModelSEED / ModelSEEDDatabase

This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach
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potential cpd issue #28

Closed nconrad closed 8 years ago

nconrad commented 8 years ago

User submitted...

In the meantime I have found a compound entry with some possible errors: cpd11684

This compound looks to be the same than CHEBI:16042 (http://www.ebi.ac.uk/chebi/searchId.do?chebiId=16042) or http://metacyc.org/META/NEW-IMAGE?type=COMPOUND&object=Halide-Anions

So it can be bromide, chloride, fluoride or iodide. In consequence its mass should be unknown because is the mass of one of those 4. Not 1 for sure. And its charge should be -1 according to ChEBI and MetaCyc.

samseaver commented 8 years ago

What compound? I mean, did they give you a ModelSEED identifier?

nconrad commented 8 years ago

whoops. updated ticket. It's cpd11684

samseaver commented 8 years ago

Yes, its mass should be unknown, and that can be updated in the database. Its charge is listed as zero because its also associated with this KEGG compound:

http://rest.kegg.jp/get/C00462

which has a formula that includes a proton.

Generally speaking however, the compound is of little concern as we cannot use it in flux balance analysis.

samseaver commented 8 years ago

Fixed here:

https://github.com/ModelSEED/ModelSEEDDatabase/commit/e528f4fa20e4b4833b4e695e1793a073ef32171e