W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > August 2008

Re: 'Gene WIki' announced

From: Kei Cheung <kei.cheung@yale.edu>
Date: Tue, 19 Aug 2008 23:33:30 -0400
Message-ID: <48AB908A.5040304@yale.edu>
To: Steve Chervitz <Steve_Chervitz@affymetrix.com>
CC: Suzanna Lewis <suzi@berkeleybop.org>, w3c semweb hcls <public-semweb-lifesci@w3.org>

Hi Steve, Suzanna et al,

It sounds like "wikinomics" is becoming real. If more 
biological/clinical data (including high-throughput data) are made 
available through semantic wiki, community-based data collection, 
annotation, and integration can be more facilitated via collaborative 

I'm exploring the idea of creating "Wiki Neuron" based on my past 
activities in the HCLSIG. I've recently added a description of this idea 
called "Visual Web Meets Semantic Web" to the list of HCSLIG project 
ideas (http://esw.w3.org/topic/HCLSIG/Project_Ideas/). Neurons are the 
one of the fundamental life science entities that neuroscientists are 
studying. Diverse types of information/experimental data (e.g., 
physiological measurements, computational models, images, etc) have been 
collected on neurons (for both human and model organisms). Such neuronal 
information can be mashed up with other types of data (e.g., genes, 
SNPs, proteins, pathways, diseases, chemical drugs, etc). Therefore it 
would be meaningful and important to link Wiki Neuron to other 
bio-Wikis. Yes, URI's are key to establishing such links.

Also included in my project proposal is 3D Web/Virtual Web. Like 3D 
protein structures that can be displayed on wiki pages of proteopedia, 
3D electron images of neuron cells or 3D animation of neuron models can 
be displayed via Wiki Neuron. 3D virtual world can help simulate a 
virtual organization or community where scientists (avatars) can 
interact with each other.

I wonder if people are interested in such an idea of a collaborative 



Steve Chervitz wrote:

> 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 “molecule-name 
> A of molecule-type B has an associated molecule-type C” 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) 
> <http://semantic-mediawiki.org/wiki/Semantic_MediaWiki%29> 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 
> s ure
>>>> 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 haven’t 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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Received on Wednesday, 20 August 2008 03:33:14 UTC

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