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ModelSEED / Model-SEED-core

The Model SEED is a tool for building, curating, and analyzing gonome-scale metabolic models. Visit the Model SEED homepage for installation instructions and full feature documentation.
http://bionet.mcs.anl.gov/index.php/Model_SEED_Homepage
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Initial draft of Anno factory w/ KBase support #167

Closed devoid closed 12 years ago

devoid commented 12 years ago

@cshenry I'm working on this since Ross requested that we get some models built for him soon. I'm wondering what the function:

ModelSEED::MS::Utilities::GlobalFunctions::functionToRoles does? I can see that in parses the role string but why are we storing compartment, delimiter, and comment? I worry because this compartment is just derived from the string annotation so it won't be consistent with (a) biochemistry compartments, (b) different annotation sources and (c) if the SEED decides to change the annotation "system".

Can I just pull the Contig > Feature > Role schema from the CDMI for Kbase? Do we need "compartment", "delimiter" and "comment" in the FeatureRole object?

cshenry commented 12 years ago

Woh woh. No. This is not how we are going to do this. At least, I don't think so. I am coming back tomorrow. Let's discuss then. In general, before you get sidetracked on this stuff, let me know... I at least want to have discussions on the best way of doing things before ploying down a particulary path. On Jul 17, 2012 4:20 PM, "Scott Devoid" < reply@reply.github.com> wrote:

@cshenry I'm working on this since Ross requested that we get some models built for him soon. I'm wondering what the function:

ModelSEED::MS::Utilities::GlobalFunctions::functionToRoles does? I can see that in parses the role string but why are we storing compartment, delimiter, and comment? I worry because this compartment is just derived from the string annotation so it won't be consistent with (a) biochemistry compartments, (b) different annotation sources and (c) if the SEED decides to change the annotation "system".

Can I just pull the Contig > Feature > Role schema from the CDMI for Kbase? Do we need "compartment", "delimiter" and "comment" in the FeatureRole object?

You can merge this Pull Request by running:

git pull https://github.com/ModelSEED/Model-SEED-corekb-annotation-import

Or you can view, comment on it, or merge it online at:

https://github.com/ModelSEED/Model-SEED-core/pull/167

-- Commit Summary --

  • Initial draft of Anno factory w/ KBase support

-- File Changes --

M Build.PL (1) A lib/Bio/KBase/CDMI/Client.pm (11002) M lib/ModelSEED/MS/Factories/SEEDFactory.pm (298) M t/ms/factories/SEEDFactory.t (85)

-- Patch Links --

https://github.com/ModelSEED/Model-SEED-core/pull/167.patch https://github.com/ModelSEED/Model-SEED-core/pull/167.diff

Reply to this email directly or view it on GitHub: https://github.com/ModelSEED/Model-SEED-core/pull/167

cshenry commented 12 years ago

Well, let me look it over. It could be okay. I would suggest we use the kbase service that issues annotation typed objects. Chris On Jul 17, 2012 5:40 PM, "Chris Henry" chrisshenry@gmail.com wrote:

Woh woh. No. This is not how we are going to do this. At least, I don't think so. I am coming back tomorrow. Let's discuss then. In general, before you get sidetracked on this stuff, let me know... I at least want to have discussions on the best way of doing things before ploying down a particulary path. On Jul 17, 2012 4:20 PM, "Scott Devoid" < reply@reply.github.com> wrote:

@cshenry I'm working on this since Ross requested that we get some models built for him soon. I'm wondering what the function:

ModelSEED::MS::Utilities::GlobalFunctions::functionToRoles does? I can see that in parses the role string but why are we storing compartment, delimiter, and comment? I worry because this compartment is just derived from the string annotation so it won't be consistent with (a) biochemistry compartments, (b) different annotation sources and (c) if the SEED decides to change the annotation "system".

Can I just pull the Contig > Feature > Role schema from the CDMI for Kbase? Do we need "compartment", "delimiter" and "comment" in the FeatureRole object?

You can merge this Pull Request by running:

git pull https://github.com/ModelSEED/Model-SEED-corekb-annotation-import

Or you can view, comment on it, or merge it online at:

https://github.com/ModelSEED/Model-SEED-core/pull/167

-- Commit Summary --

  • Initial draft of Anno factory w/ KBase support

-- File Changes --

M Build.PL (1) A lib/Bio/KBase/CDMI/Client.pm (11002) M lib/ModelSEED/MS/Factories/SEEDFactory.pm (298) M t/ms/factories/SEEDFactory.t (85)

-- Patch Links --

https://github.com/ModelSEED/Model-SEED-core/pull/167.patch https://github.com/ModelSEED/Model-SEED-core/pull/167.diff

Reply to this email directly or view it on GitHub: https://github.com/ModelSEED/Model-SEED-core/pull/167

devoid commented 12 years ago

@cshenry Is there an API that issues annotation typed objects? Or are you talking about an IRIS script? If there's an API call, I'd rather use that (fewer round-trips).

cshenry commented 12 years ago

There should be an API that issues the "Annotated genome" typed object that my "genome_to_fbamodel" command uses as input. Ask Bob about it. I'm virtually certain it exists. If it doesn't exist, one should be written.

Chris

On Jul 19, 2012, at 12:20 PM, Scott Devoid wrote:

@cshenry Is there an API that issues annotation typed objects? Or are you talking about an IRIS script? If there's an API call, I'd rather use that (fewer round-trips).

Reply to this email directly or view it on GitHub: https://github.com/ModelSEED/Model-SEED-core/pull/167#issuecomment-7104768

devoid commented 12 years ago

@cshenry @pfrybar Ready to be merged.