Re: [Psidev-pi-dev] How stable is the psi-ms.obo URL?

[Ville K. <vi...@ma...>]

Hello Eric,

it sounds like the best we can do in Mascot is to use the latest URL at
the time of releasing the software and keep an eye on the URL for
future revisions. It's unfortunate there isn't a permanent URL
redirection in place, something like http://psidev.info/psi-ms.obo,
that would always point to the latest file.

Regards,
Ville

On Wed, 2017-02-15 at 21:55 -0800, Eric Deutsch wrote:
> Hi Ville, you're right that this CV has seen quite a lot of changes
> recently. This was mostly triggered by the close of Google Code and
> our
> decision to consolidate on GitHub. I think it is very likely that the
> current location will not change again for a long time unless there
> is
> some problem with GitHub.
> 
> I think it is generally intended that readers would use those URIs to
> fetch the ontologies that are referenced, so it is important that the
> URIs
> be correct. That said, I think it is also true that the MS CV is so
> central to most readers and writers of PSI formats that it would be
> common
> for that software to use its internal version of the MS CV, and not
> make
> use of that URI. For example, I think ProteoWizard compiles the
> latest MS
> CV into its source code and does not fetch it from the URI in the
> file. So
> I think it's a bit more important for the CVs other than the MS CV to
> have
> the URI right.
> 
> I think you can find the latest recommended URIs for the CVs in the
> example files at:
> https://github.com/HUPO-PSI/mzIdentML/tree/master/examples/1_2example
> s
> 
> I hope they're consistent.. From the PeptideShaker example:
>        <cv id="PSI-MS"
> uri="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-
> ms.ob
> o" fullName="PSI-MS"/>
>        <cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo"
> fullName="UNIMOD"/>
>        <cv id="UO"
> uri="https://raw.githubusercontent.com/bio-ontology-research-group/un
> it-on
> tology/master/unit.obo" fullName="UNIT-ONTOLOGY"/>
>        <cv id="PRIDE"
> uri="https://github.com/PRIDE-Utilities/pride-ontology/blob/master/pr
> ide_c
> v.obo" fullName="PRIDE"/>
> 
> I notice already one little issue is that sometimes we use the
> raw.githubusercontent form and sometimes the blob form. I don't know
> which
> is preferred, but we should probably just pick one. I think they're
> equivalent, although not sure.
> 
> Regards,
> Eric
> 
> 
> -----Original Message-----
> From: Ville Koskinen [mailto:vi...@ma...]
> Sent: Wednesday, February 15, 2017 3:49 AM
> To: psi...@li...
> Subject: [Psidev-pi-dev] How stable is the psi-ms.obo URL?
> 
> Dear list,
> 
> before moving to GitHub, the psi-ms.obo file's URL was
> 
> http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psims/
> mzML/
> controlledVocabulary/psi-ms.obo
> 
> The URL appears in a number of mzIdentML example files, of course, as
> well
> as the 1.1.0 specification document. But the current URL is now
> 
> https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo
> 
> Should newly exported mzIdentML files use the new URL or keep the old
> URL?
> How stable is the new URL? For example, in October 2015 the new URL
> was
> 
> https://github.com/HUPO-PSI/mzML/blob/master/cv/psi-ms.obo
> 
> but that's of course now dated.
> 
> Or does it make any difference what URL is output in the mzIdentML
> file?
> The mzIdentML 1.1.0 specification for the <cv> element states the uri
> attribute is the "URI of the source CV", but doesn't say whether this
> is
> for the usual namespace purposes (uniform resource
> *identifier*) or for the reader of the file to locate the .obo file
> (uniform resource *locator*). If it's a true URI, is there a table
> somewhere that records what URIs each type of CV should have?
> 
> Regards,
> Ville
> 
> --
> Ville Koskinen
> Matrix Science
> 64 Baker Street
> London W1U 7GB, UK
> Tel: +44 (0)20 7486 1050
> Fax: +44 (0)20 7224 1344
> 
> vi...@ma...
> http://www.matrixscience.com
> 
> Matrix Science Ltd. is registered in England and Wales Company number
> 3533898
> 
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Ville Koskinen
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344

vi...@ma...
http://www.matrixscience.com

Matrix Science Ltd. is registered in England and Wales
Company number 3533898