Re: [Biomodels-net-discuss] LSRN abbreviations/Identifiers.org

[Juha M. <juh...@he...>]

Dear Nick
Thank you very much for the information! We are planning to use the id spec in our data format specification (http://varioml.org) which is designed for curated LSDB data submissions and app integration (not bulk HTP data). Ideally would be nice to use URIs, but those may be still bit tricky. Hopefully Identifies.org provides solutions for this!  Now the plan is to use standard name space abbreviations instead, which can be later translated to URIs based on needs.

Could you consider to include different name spaces for different id systems maintained by same name space authority ? E.g would be nice to have HGNC_Symbol there for the symbols and HGNC  or HGNC_ID for numbers. Does this fit with your views ?  Would be practical to include at least well established "display ids"  into the spec. Perhaps no need to split the refseqs like this though.

Cheers, Juha

On Jul 12, 2012, at 1:47 PM, juty wrote:

> Hi Juha,
> 
> Thank you for your email. Hopefully you should find all useful information in LSRN has been incorporated into Identifiers.org. This is no coincidence, since we have been working with the LSRN team to accomplish this task, as LSRN will be shutting down imminently. One of the advantages that Identifiers.org provides is that it has a curated resource at the back end. For instance, the HGNC symbol accession you mention is not functional (http://lsrn.org/HGNC_Symbol:BRCA1). When you use an identifiers.org URL, you can have some confidence in its persistent resolvability. RefSeq could be split into multiple 'sequence types', but we have found this unnecessary at this time.
> 
> We would be interested to know about how you plan to use Identifiers.org! It is always useful to get feedback from our users, so please feel free to contact us with any queries or suggestions.
> 
> You can find more information about Identifiers.org here: http://identifiers.org/pubmed/22140103
> 
> cheers
> 
> NIck
> 
> 
> 
> 
> On 12/07/12 09:37, Juha Muilu wrote:
>> Hi
>> Wondering should I use LSRN abbreviations or name spaces defined in Identifiers.org <http://Identifiers.org> in our data specifications ? LSRN abbreviations seems to address the name space problem in accession number level separating e.g. HGNC Symbols from HGNC IDs. On the other hand not sure should RefSeqs be split based on sequence type(http://lsrn.org/lsrn/registry.html#NCBI_NM and http://lsrn.org/lsrn/registry.html#NCBI_NP), which is understandable of  course but may not be necessary.
>> 
>> Would be great to merge these two useful specs.
>> 
>> Best regards, Juha
>> 
>> 
>> 
>> 
>> 
>> 
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> 
> -- 
> --------------------------------------------------------
> Nick Juty
> Database Curator
> European Bioinformatics Institute
> Cambridge, United Kingdom
> --------------------------------------------------------
> 


---
Juha Muilu, PhD
Senior Researcher
Institute for Molecular Medicine Finland (FIMM)
Nordic EMBL partnership for molecular medicine
University of Helsinki

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