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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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Compartment question #6

Closed nconrad closed 9 years ago

nconrad commented 9 years ago

Should all compounds in reactions have compartments?

I see "Pseudomonas aeruginosa LPS core precursor 2" in rxn13866 doesn't:

https://www.patricbrc.org/api/model_reaction/?http_accept=application/json&eq(id,rxn13866)&select(definition)

samseaver commented 9 years ago

I see the problem here. This reaction came from the metabolic model iMO1053 (PA_CORE3s) and the full name of the compound is:

'Pseudomonas aeruginosa LPS core precursor 2 + KDO2-lipidA'

So the ' + ' means you're getting a parsing error, and not retrieving the full name of the compound. This occurs more than once, a quick parse gives me 25 compounds where the name itself contains a ' + ' string, such as:

'(K+ + H+)-ATPase'

I think you'll have to print the equation string using compound identifiers every time, before replacing the identifiers with the relevant names, which can be a pain, but is probably the safest way to do this. In the meantime, we can certainly consider what to do with these rogue ' + ' strings, we can simply remove the spaces so we'd get names like:

'Pseudomonas aeruginosa LPS core precursor 2+KDO2-lipidA' '(K++H+)-ATPase'

mmundy42 commented 9 years ago

I added modifications to the compound and reaction master.mods files to adjust the names that have embedded ' + ' strings to remove the spaces as Sam suggested.

I also found 2 reactions that had an embedded ' <=> ' and I also added a modification to remove the extra spaces.

mmundy42 commented 9 years ago

@nconrad, are you OK with the change to remove spaces? Just wondering if this issue can be closed.

nconrad commented 9 years ago

Yeah, that sounds fine.

I'm on vacation until Monday. I'll address other tickets when I get back. We should regroup when I get back, if possible... And do another push on the site. I've made some progress that I haven't commited yet.

On Wednesday, August 19, 2015, Mike Mundy notifications@github.com wrote:

@nconrad https://github.com/nconrad, are you OK with the change to remove spaces? Just wondering if this issue can be closed.

— Reply to this email directly or view it on GitHub https://github.com/ModelSEED/ModelSEEDDatabase/issues/6#issuecomment-132746317 .

t. 815-508-7951 e. nealconrad@gmail.com