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RE: 'Gene WIki' announced

From: Nigam Shah <nigam@stanford.edu>
Date: Thu, 21 Aug 2008 15:49:05 -0700
To: "'Kei Cheung'" <kei.cheung@yale.edu>
Cc: "'w3c semweb hcls'" <public-semweb-lifesci@w3.org>
Message-ID: <008e01c903e0$1e0065f0$5a0131d0$@edu>

Hi Kei,

Wikis are certainly gaining ground. If there are ways in which NCBO
can contribute ontology services to such projects, we would be very
happy to help. We can start simple by promoting the use of ontology
term URIs provided by BioPortal (see Mark's message from earlier today

If multiple wiki projects started using ontology term URIs from NCBO,
it might go a long way to jump-starting the cross-linkage among
bio-wikis and other structured descriptions of bio-entities. We have
already spoken to wikiproffesional (knewco) and they are onboard with
the idea.


>-----Original Message-----
>From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-
>lifesci-request@w3.org] On Behalf Of Kei Cheung
>Sent: Tuesday, August 19, 2008 8:34 PM
>To: Steve Chervitz
>Cc: Suzanna Lewis; w3c semweb hcls
>Subject: Re: 'Gene WIki' announced
>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
>called "Visual Web Meets Semantic Web" to the list of HCSLIG project
>ideas (http://esw.w3.org/topic/HCLSIG/Project_Ideas/). Neurons are
>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
>collected on neurons (for both human and model organisms). Such
>information can be mashed up with other types of data (e.g., genes,
>SNPs, proteins, pathways, diseases, chemical drugs, etc). Therefore
>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
>3D electron images of neuron cells or 3D animation of neuron models
>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
>> 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:
>> 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,
>> starts sounding a lot like the charter of the HCLS).
>> Seems like much of this comes down to naming. An easily
>> repository of statements along the lines of "molecule-name A of
>> molecule-type B has a wiki page at molecule-url X" and
>> 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
>> organism name (since things like gene symbols can be organism
>> specific), http://purl.org/molecule/type/organism/key . Has this
>> 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>
>>>>>> From a quick skim I don't see mention of W3C, RDF, Semantic Web
>>>>>> --- I was wondering if anyone here was involved and had
>>>>>> since there's doubtless some overlap in interests and approach.
>>>>>> particular I was thinking that the Semantic MediaWiki
>>>>>> (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
>>>>> database wiki. http://pdbwiki.org/index.php/Main_Page Clearly
>>>>> differences between a protein wiki and a gene wiki, but I'm
>> 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
>>>> 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
>>>> blog here:
>>>> ng-applied-to-chemistry
>> http://depth-first.com/articles/2008/07/02/building-chempedia-
>>>> contributors
>>>> It inspired me to want to do something analogous for genes
>>>> (Wikipedia + Entrez Gene, perhaps), and I registered
>>>> for this purpose, but haven't done anything with it yet. Seems
>>>> there is a lot of interest in gene-oriented wikis out there.
>>>> interested in collaborating on such a project, let me know.
>>>> Steve
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Received on Thursday, 21 August 2008 22:49:45 UTC

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