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
[8/21]).
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.
Regards,
Nigam.
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:public-semweb-
[EMAIL PROTECTED] 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
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
<[EMAIL PROTECTED]> 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
<[EMAIL PROTECTED]> wrote:
On Thursday 10 July 2008, Dan Brickley <[EMAIL PROTECTED]>
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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