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Re: 'Gene WIki' announced

From: Maged N.K. Boulos <mnkboulos@gmail.com>
Date: Fri, 22 Aug 2008 07:35:57 +0100
Message-ID: <dad227630808212335nd287b0ai2e66235da1a71101@mail.gmail.com>
To: public-semweb-lifesci@w3.org
Hi All,

here is a link to a recent paper we published with Kei about the 3D
component he is describing below; I hope it can give readers a more detailed
view about the potential of these technologies:
Kamel Boulos MN, Scotch M, Cheung K-H, Burden D. *Web GIS in practice VI: a
demo "playlist" of geo-mashups for public health neogeographers*.
*International
Journal of Health
Geographics<http://www.ij-healthgeographics.com/content/pdf/1476-072X-7-38.pdf>
*. 2008;7:38
*http://www.ij-healthgeographics.com/content/pdf/1476-072X-7-38.pdf*<http://www.ij-healthgeographics.com/content/pdf/1476-072X-7-38.pdf>

You can find more pointers at: http://healthcybermap.org/sl.htm

Best wishes,



--*Maged N Kamel Boulos*, MBBCh, MSc (Derm), MSc (Med Inform), PhD, FRGS,
FHEA, UKCHIP-L3 Member
Senior Member of IEEE, the Institute of Electrical and Electronics
Engineers, and of IEEE EMBS
Senior (Principal) Lecturer in Health Informatics, Faculty of Health and
Social Work, University of Plymouth
Centre Court, 73 Exeter Street, Drake Circus, Plymouth, Devon PL4 8AA, UK
Tel: +44 (0)1752 586530 - Fax: +44 (0)8709 157698 - E-mail:
mnkamelboulos@plymouth.ac.uk
Web: http://www.plymouth.ac.uk/staff/mnkamelboulos
Editor-in-Chief, *Int** J Health Geogr* (indexed in MEDLINE—ISI tracked)
http://ij-healthgeographics.com/

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On Wed, Aug 20, 2008 at 4:33 AM, Kei Cheung <kei.cheung@yale.edu> wrote:

>
> 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 ontologies.
>
> 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
> project.
>
> Best,
>
> -Kei
>
> 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 Saturday, 23 August 2008 13:29:40 GMT

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