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

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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.

cheers,
Erick

On 5 March 2014 02:37, Chris Mungall <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...
> > 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...>
> > Tel: 734-615-8231 (O)
> > http://www.hegroup.org/
> >
> > **********************************************************
> > Electronic Mail is not secure, may not be read every day, and should
> > not be used for urgent or sensitive issues
> >
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