User:Ilya: Difference between revisions

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Registry of Biological Parts software architecture.
__NOTOC__
Contact Ilya Sytchev (Илья Сычёв):
*<math>\mbox{hackdna}</math>@<math>\mbox{gmail.com}</math>
*[[Special:Emailuser/Ilya|send me an email via OpenWetWare]]


Semantic Web: RDF/XML and RDF Schema
==Activities==


Data access interface requirements:
===Current===
*standardized
Developing an integrated data management and analysis system for the [http://winhide.wordpress.com/2011/04/13/setting-up-a-stem-cell-commons/ Stem Cell Commons] project.
*extensible
*human and machine readable
*scalable (distributed registries)


Semantic Web
===Previous===
*allows to model real things, not just documents or database tables
*Systems Engineer at [http://www.genstruct.com/ Genstruct]
*consists of statements about resources in the form of triples:
*[[User:Ilya/OpenWetWare|OpenWetWare]]
SUBJECT -> PROPERTY -> VALUE
*Computing at the Endy Lab:
Every resource is uniquely identified by a URI: don't say "color", say <http://example.com/2005/std6#col>
**[[User:Ilya/BioBrick aligner|BioBrick aligner]]
**[[Endy:Data storage|Data storage]]
**[[User:Ilya/Lab network|Lab network]]
**[[User:Ilya/Win.mit.edu|WIN.MIT.EDU]]
*[[User:Ilya/Yeast/Mating_pheromone_response_pathway|Mating pheromone response pathway]] analysis across [[User:Ilya/Yeast|yeast]] and [[User:Ilya/Yeast/Phylogeny|related species]]


Ontology: controlled vocabulary of concepts and their relationships.
==Miscellaneous==
<html>
<a href="http://www2.clustrmaps.com/user/3e416041">
<img style="float: right" src="http://www2.clustrmaps.com/stats/maps-no_clusters/openwetware.org-wiki-User-Ilya-thumb.jpg" />
</a>
</html>


Examples of ontologies:
*[[Synthetic Biology:Semantic web ontology|Semantic Web Ontology]] for [[Synthetic Biology]] ([[User:Ilya/Registry|Registry notes]])
*Dublin Core
*[[User:Ilya/Notes|Notes]]
**Namespace: http://purl.org/dc/elements/1.1/
*[[User:Ilya/Todo|Todo]]
**Properties: title, creator, publisher, identifier
*[[User:Ilya/Sandbox|Sandbox]]
*Gene Ontology
**Namespace: ftp://ftp.geneontology.org/pub/go/xml/dtd/go.dtd
*Properties: name, definition, isa, association, evidence
*Sequence Ontology: features on a nucleotide or protein sequence
*BioPAX: biological pathway data
*UniProt (planning)


 
[[Category:Steering Committee member]] [[Category:Bioinformaticians]]
References:
#[http://www.w3.org/2005/Talks/0517-boit-tbl/ Berners-Lee - Semantic Web Life Sciences - BioIT World]
#[http://www.w3.org/2003/Talks/05-gartner-tbl/ Web Service - Semantic Web by Tim-Berners Lee]
#[http://www.amk.ca/talks/2004-12-02/ Introduction to the Semantic Web and RDF by A.M. Kuchling]
 
 
Wiki ideas:
 
* '''blacklist''' certain pages from public viewing and/or editing ([http://mail.wikipedia.org/pipermail/mediawiki-l/2004-August/000874.html Blacklist pages from viewing])
 
* use "endy members group" to restrict access to certain pages

Revision as of 18:35, 28 October 2012

Contact Ilya Sytchev (Илья Сычёв):

Activities

Current

Developing an integrated data management and analysis system for the Stem Cell Commons project.

Previous

Miscellaneous

<html> <a href="http://www2.clustrmaps.com/user/3e416041"> <img style="float: right" src="http://www2.clustrmaps.com/stats/maps-no_clusters/openwetware.org-wiki-User-Ilya-thumb.jpg" /> </a> </html>

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