Re: [Obo-discuss] Request namespaces for INO (Interaction Network Ontology) and HINO (Human INO)

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indeed, even better.

On 5 March 2014 09:49, Nicolas Le Novere <n.l...@gm...> wrote:

> On 05/03/14 08:05, Erick Antezana wrote:
> > Hi,
> >
> > I agree with Chris: the proliferation of namespaces should be to some
> extent controlled...
> >
> > My take on this issue would be:
> >
> > - continue keeping namespaces in the OBO foundry which *only* correspond
> to domain ontologies
> > - maintain a separate resource, something such as
> http://www.geneontology.org/cgi-bin/xrefs.cgi, for application ontologies.
>
> Something like
>
> http://identifiers.org?
>
> > cheers,
> > Erick
> >
> >
> > On 5 March 2014 02:37, Chris Mungall <cjm...@lb... <mailto:
> cjm...@lb...>> wrote:
> >
> >     Hi Oliver,
> >
> >     I have a general concern, maybe I'm not getting something.
> >
> >     There are a very large number of databases out there. Many of these
> can
> >     be translated to an ontology.
> >
> >     It's not clear that there's always a clear win in doing this (but
> that's
> >     a question that may be best answered by doing further experimentation
> >     such as what you're doing).
> >
> >     But in doing this we should not be creating an administrative burden
> by
> >     registering new OBO namespaces for every database X species
> combination
> >     out there. And we definitely should not be contributing to the ID
> >     mapping curse by minting yet another set of numeric IDs.
> >
> >     Do you really need this to be an OBO library ontology? I know we have
> >     something of a precedent here with things like the NCBITaxonomy, but
> >     perhaps not every translated resource needs to have the magic OBO
> purl.
> >
> >     If you really want to have these translations be in the OBO space,
> why
> >     don't we set up one generic ID space and put everything under that,
> >     relaxing the URI guidelines? For example, let's say you wanted to
> grab
> >     an ID space "OMICS". You could then use this to prefix the URIs of
> >     database-sourced entities retaining the original ID. E.g.
> >     purl....obo/OMICS/REACTOME_12345. This way we don't end up with a
> >     proliferation of "ontologies", and you have the freedom to keep
> adding
> >     new entities (as you most likely will).
> >
> >
> >
> >
> >
> >     On 4 Mar 2014, at 12:18, He, Yongqun wrote:
> >
> >      > Additional information:
> >      >
> >      > INO/HINO website:
> >      > http://www.ino-ontology.org/
> >      >
> >      > INO in Ontobee: http://www.ontobee.org/browser/index.php?o=INO
> >      > HINO in Ontobee: http://www.ontobee.org/browser/index.php?o=HINO
> >      >
> >      > Best,
> >      > Oliver
> >      >
> >      >
> >      > From: He, Yongqun
> >      > Sent: Tuesday, March 04, 2014 3:16 PM
> >      > To: obo...@li... <mailto:
> obo...@li...>
> >      > Cc: He, Yongqun
> >      > Subject: Request namespaces for INO (Interaction Network
> Ontology) and
> >      > HINO (Human INO)
> >      >
> >      > Dear OBO-discuss:
> >      >
> >      > Here I would like to request two related namespaces for inclusion
> in
> >      > the OBO Foundry ontology library:
> >      > (1) INO: Interaction Network Ontology
> >      > (2) HINO: Human Interaction Network Ontology, which is an
> extension of
> >      > INO.
> >      >
> >      > INO is aligned with BFO. INO was initially developed to classify
> and
> >      > represent different levels of interaction keywords used for
> literature
> >      > mining of genetic interaction networks. The literature mining
> strategy
> >      > and the INO name were described in our ontology-based literature
> >      > mining paper in 2011:
> >      >       Ozgur A, Xiang Z, Radev D, He Y. Mining of
> vaccine-associated
> >      > IFN-γ gene interaction networks using the Vaccine Ontology.
> Journal
> >      > of Biomedical Semantics. 2011, 2(Suppl 2):S8. PMID: 21624163.
> >      > http://www.ncbi.nlm.nih.gov/pubmed/21624163
> >      >
> >      > HINO is an extension of INO. HINO targets for ontologically
> >      > representing human interactions and networks. The rationale for
> HINO
> >      > development is as follows:
> >      >      Many resources, such as Reactome and KEGG, store manually
> curated
> >      > interactions and pathways. However, there is no BFO-aligned
> >      > interaction pathway ontology that specifies the information
> stored in
> >      > Reactome and other databases. The curated data are commonly
> >      > represented in BioPAX, an OWL-based biological pathway data
> exchange
> >      > format. BioPAX represents these interactions and pathways as
> >      > instances. BioPAX is successful in facilitating data exchange.
> >      > However, individual entities, interactions, and pathways
> represented
> >      > in BioPAX are all temporary instance IDs and cannot be exchanged
> among
> >      > different resources. Given appropriate conditions, these
> interactions
> >      > and pathways in Reactome and KEGG always occur. Therefore, they
> are
> >      > more appropriately represented as ontology classes instead of
> >      > instances. The HINO is aimed to provide non-redundant
> representations
> >      > of human molecular interactions, pathways, and  networks. HINO was
> >      > presented in ICBO-2013 as a poster:
> >      > http://ceur-ws.org/Vol-1060/icbo2013_submission_70.pdf
> >      >     More detail about HINO was recently published in a preprint in
> >      > arXiv:
> >      >
> >      > -          Abstract: http://arxiv.org/abs/1311.3355
> >      >
> >      > -          PDF full text:
> >      > http://arxiv.org/ftp/arxiv/papers/1311/1311.3355.pdf
> >      >
> >      > Currently HINO only represents human molecular interactions and
> >      > networks knowledge stored in Reactome. We are working to add more
> >      > results from other interaction and pathway databases.
> Cross-references
> >      > to the original database sources will be provided.
> >      >
> >      > Suggestions, comments, and collaborations are welcome and
> appreciated.
> >      >
> >      > Thanks for your consideration,
> >      >
> >      > Oliver
> >      >
> >      > Yongqun "Oliver" He, DVM, PhD
> >      > Associate Professor
> >      > Unit for Laboratory Animal Medicine
> >      > Department of Microbiology and Immunology
> >      > Center for Computational Medicine and Bioinformatics
> >      > and Comprehensive Cancer Center
> >      > University of Michigan Medical School
> >      > Mail: 018 ARF, 1150 W. Medical Center Dr.
> >      > Ann Arbor, MI 48109
> >      > Email: yon...@me... <mailto:yon...@me...
> ><mailto:yon...@me... <mailto:yon...@me...>>
> >      > Tel: 734-615-8231 (O)
> >      > http://www.hegroup.org/
> >      >
> >      > **********************************************************
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> >      > not be used for urgent or sensitive issues
> >      >
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>
> --
> Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT
> Tel: +441223496433   Mob:+447833147074   n.l...@gm...
> orcid.org//0000-0002-6309-7327  http://lenoverelab.org/perso/lenov/
> Skype:n.lenovere  twitter:@lenovere  http://nlenov.wordpress.com/
>
>
>
>
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