What sequence ontology to get?
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Hi,
Looks like the sequence ontology has moved from sourceforge to github. The url in chado/load/tt2/load.conf.tt2 no longer works. What is the corresponding url on github? Is it the first so download link of: https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp-simple.obo ? The various choices are at: https://github.com/The-Sequence-Ontology/SO-Ontologies Thanks. Karl <[hidden email]> Free Software: "You don't pay back, you pay forward." -- Robert A. Heinlein ------------------------------------------------------------------------------ _______________________________________________ Gmod-schema mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-schema |
Re: What sequence ontology to get?
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I recommend using purls for all ontologies
E.g. http://purl.obolibrary.org/obo/so.obo These should remain stable allowing the underlying delivery system to change On 22 Jul 2015, at 16:04, Karl O. Pinc wrote: > Hi, > > Looks like the sequence ontology has moved from sourceforge > to github. The url in chado/load/tt2/load.conf.tt2 > no longer works. > > What is the corresponding url on github? > Is it the first so download link of: > https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp-simple.obo > > ? > > The various choices are at: > https://github.com/The-Sequence-Ontology/SO-Ontologies > > Thanks. > > Karl <[hidden email]> > Free Software: "You don't pay back, you pay forward." > -- Robert A. Heinlein > > ------------------------------------------------------------------------------ > _______________________________________________ > Gmod-schema mailing list > [hidden email] > https://lists.sourceforge.net/lists/listinfo/gmod-schema ------------------------------------------------------------------------------ _______________________________________________ Gmod-schema mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-schema |
Re: What sequence ontology to get?
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Hi Chris, I hadn't heard about the purl urls. Is a list of them published somewhere? Thanks, Scott On Wed, Jul 22, 2015 at 7:50 PM, Chris Mungall <[hidden email]> wrote: I recommend using purls for all ontologies ------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ _______________________________________________ Gmod-schema mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-schema |
Re: What sequence ontology to get?
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Yes and no.
The PURL for an OBO always follows the form documented here: http://www.obofoundry.org/id-policy.shtml So you can generate a list by taking the 'namespace' field here and lowercasing: http://obo-registry.googlecode.com/svn/trunk/metadata/ontologies.txt Yes, that is a google code url and we do know it's shutting down. We're going to move the OBO registry to a node server driven from a yaml file but this is just volunteer work at the moment. When it's done, the global metadata file will look like this: https://github.com/OBOFoundry/omb/blob/master/data/repository.yaml On 22 Jul 2015, at 17:05, Scott Cain wrote: > Hi Chris, > > I hadn't heard about the purl urls. Is a list of them published > somewhere? > > Thanks, > Scott > > > On Wed, Jul 22, 2015 at 7:50 PM, Chris Mungall <[hidden email]> > wrote: > >> I recommend using purls for all ontologies >> >> E.g. >> >> http://purl.obolibrary.org/obo/so.obo >> >> These should remain stable allowing the underlying delivery system to >> change >> >> On 22 Jul 2015, at 16:04, Karl O. Pinc wrote: >> >>> Hi, >>> >>> Looks like the sequence ontology has moved from sourceforge >>> to github. The url in chado/load/tt2/load.conf.tt2 >>> no longer works. >>> >>> What is the corresponding url on github? >>> Is it the first so download link of: >>> >> https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp-simple.obo >>> >>> ? >>> >>> The various choices are at: >>> https://github.com/The-Sequence-Ontology/SO-Ontologies >>> >>> Thanks. >>> >>> Karl <[hidden email]> >>> Free Software: "You don't pay back, you pay forward." >>> -- Robert A. Heinlein >>> >>> >> ------------------------------------------------------------------------------ >>> _______________________________________________ >>> Gmod-schema mailing list >>> [hidden email] >>> https://lists.sourceforge.net/lists/listinfo/gmod-schema >> >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> Gmod-schema mailing list >> [hidden email] >> https://lists.sourceforge.net/lists/listinfo/gmod-schema >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot > net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research ------------------------------------------------------------------------------ _______________________________________________ Gmod-schema mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-schema |
Re: What sequence ontology to get?
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In reply to this post by Chris Mungall
On Wed, 22 Jul 2015 16:50:56 -0700
"Chris Mungall" <[hidden email]> wrote: > I recommend using purls for all ontologies > > E.g. > > http://purl.obolibrary.org/obo/so.obo > > These should remain stable allowing the underlying delivery system to > change Ok. Thanks. So the correct SO to download is the so-xp.obo, right? (That's what the prul points to.) > > On 22 Jul 2015, at 16:04, Karl O. Pinc wrote: > > > Hi, > > > > Looks like the sequence ontology has moved from sourceforge > > to github. The url in chado/load/tt2/load.conf.tt2 > > no longer works. > > > > What is the corresponding url on github? > > Is it the first so download link of: > > https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp-simple.obo > > > > ? > > > > The various choices are at: > > https://github.com/The-Sequence-Ontology/SO-Ontologies > > > > Thanks. > > > > Karl <[hidden email]> > > Free Software: "You don't pay back, you pay forward." > > -- Robert A. Heinlein > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > > Gmod-schema mailing list > > [hidden email] > > https://lists.sourceforge.net/lists/listinfo/gmod-schema > Karl <[hidden email]> Free Software: "You don't pay back, you pay forward." -- Robert A. Heinlein ------------------------------------------------------------------------------ _______________________________________________ Gmod-schema mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-schema |
Re: What sequence ontology to get?
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Yes, that's right (it may point to something else in the future, it shouldn't really be exposing the 'so-xp' filename, but this shouldn't affect anything) On Wed, Jul 22, 2015 at 5:21 PM, Karl O. Pinc <[hidden email]> wrote: On Wed, 22 Jul 2015 16:50:56 -0700 ------------------------------------------------------------------------------ _______________________________________________ Gmod-schema mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-schema |
Re: What sequence ontology to get?
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On Mon, 27 Jul 2015 13:44:36 -0700
Chris Mungall <[hidden email]> wrote: > Yes, that's right (it may point to something else in the future, it > shouldn't really be exposing the 'so-xp' filename, but this shouldn't > affect anything) > > On Wed, Jul 22, 2015 at 5:21 PM, Karl O. Pinc <[hidden email]> wrote: > > So the correct SO to download is the so-xp.obo, right? Thanks! Karl <[hidden email]> Free Software: "You don't pay back, you pay forward." -- Robert A. Heinlein ------------------------------------------------------------------------------ _______________________________________________ Gmod-schema mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-schema |
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