Re: 'Gene WIki' announced

On Wed, 13 Aug 2008 11:14:36 -0700, Suzanna Lewis <suzi@berkeleybop.org>
wrote:

> You might take a look at http://www.proteopedia.org/

> 
> people can upload their own protein structures as well. its quite nice i
think.

Cool. It's heartening to see such a resource, given my structural roots (I
spent lots of time in grad school analyzing this:
http://www.proteopedia.org/wiki/index.php/2lig ).

If we are facing the rise of a constellation of biomolecule-specific wikis,
as appears to be the case, it will be important to have easy ways to link
them together, to enable users (and tools) to traverse from gene <=> protein
<=> 3D structure <=> metabolite <=> SNP <=> disease <=> etc. Perhaps this is
where the SW will be most useful: to provide some guidelines for creating
such resources so that inter-domain wiki connections can be easily
constructed, navigated, and quality-controlled (removing the wiki-specific
aspect to this, it starts sounding a lot like the charter of the HCLS).

Seems like much of this comes down to naming. An easily discoverable
repository of statements along the lines of "molecule-name A of
molecule-type B has a wiki page at molecule-url X" and ³molecule-name A of
molecule-type B has an associated molecule-type C²  would be a good start.

The NeuroCommons naming project [1] looks great for doing something like
this, but the 'key' part of the URI would be an officially recognized name
of the gene, protein, chemical, etc. rather than a repository-specific
identifier, and there may be no 'database' component in the
molecule-type-name URIs, e.g., http://purl.org/molecule/type/key or perhaps
it would be replaced by organism name (since things like gene symbols can be
organism specific), http://purl.org/molecule/type/organism/key . Has this
type of usage been envisioned? Does it seem reasonable?

Steve

[1] http://neurocommons.org/page/Common_Naming_Project



> On Aug 12, 2008, at 5:08 PM, Steve Chervitz wrote:
> 
>> 
>> On  Thu, 10 Jul 2008 11:15:11 -0500, Bryan Bishop
>> <kanzure@gmail.com> wrote:
>> 
>>> On Thursday 10 July 2008, Dan Brickley <danbri@danbri.org> wrote:
>>>>  From a quick skim I don't see mention of W3C, RDF, Semantic Web etc
>>>> --- I was wondering if anyone here was involved and had contacts,
>>>> since there's doubtless some overlap in interests and approach. In
>>>> particular I was thinking that the Semantic MediaWiki extensions
>>>> (http://semantic-mediawiki.org/wiki/Semantic_MediaWiki) might be
>>>> useful in bridging this work to other datasets.
>>>> 
>>>> thinking out loud,
>>> 
>>> Very interesting, especially considering the already existing protein
>>> database wiki. http://pdbwiki.org/index.php/Main_Page Clearly there are
>>> differences between a protein wiki and a gene wiki, but I'm pretty sure
>>> PDBWiki was not inquiried about this development. Hrm.
>> 
>> Adding to this mix is a wiki for chemical compounds that is
>> constructed by merging Wikipedia content with PubChem data. There is
>> no Semantic Web in it, but it represents a neat approach that
>> creates a domain-specific window into Wikipedia content in an
>> automated fashion. It was created by Rich Apodaca described on his
>> blog here:
>> 
>> http://depth-first.com/articles/2008/05/21/building-chempedia-social-networki

>> ng-applied-to-chemistry
>> http://depth-first.com/articles/2008/07/02/building-chempedia-learning-about-

>> contributors
>> 
>> It inspired me to want to do something analogous for genes
>> (Wikipedia + Entrez Gene, perhaps), and I registered genepedia.org
>> for this purpose, but haven¹t done anything with it yet. Seems like
>> there is a lot of interest in gene-oriented wikis out there. Anyone
>> interested in collaborating on such a project, let me know.
>> 
>> Steve




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