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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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Lots of reactions with status CPDFORMERROR #13

Closed mmundy42 closed 9 years ago

mmundy42 commented 9 years ago

In the master reactions file there are 34,701 eactions of which 6,350 have a status of CPDFORMERROR. The CPDFORMERROR status is set when at least one compound in the reaction does not have a formula or the formula is determined to be invalid. All of the reactions with status CPDFORMERROR are because of the no formula condition.

A quick check showed that some of the reactions are transport reactions for the compound. For example, rxn39240 has stoichiometry -1:cpd30677:0:0:"D-Glucosamine Hydrochloride";1:cpd30677:1:0:"D-Glucosamine Hydrochloride". It has status OK before running the Update_Reaction_Status.pl script but has status CPDFORMERROR after because D-Glucosamine Hydrochloride does not have a formula in the master compounds file.

In the master compounds file there are 27,692 compounds of which 5,068 do not have a formula.

Should there be a special case for transport reactions so that reactions that are transporting one compound between compartments have a status of OK even if there is no compound formula?

Otherwise the reactions aren't going to be usable for models.

samseaver commented 9 years ago

I'd originally thought that all compounds were negated where possible anywhere, before checking formula, so all simply transport reactions should've been marked as OK, I'll check the code.

samseaver commented 9 years ago

OK, based on these commits, I consider this issue to be closed:

https://github.com/ModelSEED/ModelSEEDDatabase/commit/5bfbce792d7f62660f40b4a2bbb2177f723d76a4