SWAN (Semantic Web Applications in Neuromedicine)

Welcome to the SWAN project!

SWAN (Semantic Web Applications in Neuromedicine) is a Web-based collaborative program that aims to organize and annotate scientific knowledge about Alzheimer disease (AD) and other neurodegenerative disorders. Its goal is to facilitate the formation, development and testing of hypotheses about the disease. The ultimate goal of this project is to create tools and resources to manage the evolving universe of data and information about AD in such a way that researchers can easily comprehend their larger context ("what hypothesis does this support or contradict?"), compare and contrast hypotheses ("where do these two hypotheses agree and disagree?"), identify unanswered questions and synthesize concepts and data into ever more comprehensive and useful hypotheses and treatment targets for this disease.

DISCO - DISCOvery

NIF Interoperation Capabilities
What is DISCO?

DISCO is an information integration approach designed to facilitate interoperation among Internet resources. It consists of a set of tools and services that allows resource providers who maintain information to share it with automated systems such as NIF. NIF is then able to “harvest” the information and keep those sets of information up-to-date.
How is this accomplished?

By using a series of files and/or scripts which are then placed in the root directory of the resource developer’s resource. (NIF can also host the files on its servers and crawl for changes there.) Once the files of the resource providers are in place, and DISCO is notified, the DISCO server can then recognize and "consume" the information shared, providing machine understandable information to NIF Integrator Servers (also known as Aggregators) about your resource.

http://www.springerlink.com/content/c613m0l225p072g5/fulltext.html

DOMEO

DOMEO - Document Metadata Organizer

Ciccarese P, Ocana M, Clark, T. DOMEO: a web-based tool for semantic annotation of online documents. Paper at Bio-Ontologies 2011, Vienna, Austria. Accepted

So highlight text in the web (eg. Pubmed article) and hit Annotate. Loads ontology data when annotating as well. Also lets you share annotations.

http://code.google.com/p/domeo/

http://www.slideshare.net/paolociccarese/swan-annotation-framework-text-mining

An Uber-comparison of RDFa, Microdata and Microformats

http://manu.sporny.org/2011/uber-comparison-rdfa-md-uf/

Google and bioinformatics

Semantic web sounds like a nice way of retrieving biological data by asking questions ... http://www.io-informatics.com/ Putting semantic web ideas to work
http://mndoci.com/blog/2007/07/13/what-is-a-google-for-bioinformatics/

Google Does Bioinformatics Venture Deal
This should be controversial: Google announced in a filing at the close today that it has invested $3.9-million into a bioinformatics startup called 23andMe. The company's co-founder is Ann Wojcicki, Google co-founder Sergey Brin's new spouse. According to the filing, Ann's company helps consumers understand and browse their genome.
https://www.23andme.com/

Google jobs
http://www.google.com/support/jobs/bin/static.py?page=students.html&sid=resume
https://tbe.taleo.net/NA2/ats/careers/searchResults.jsp?org=TWENTYTHREEANDME&cws=1

Too lazy to start a new post, so I'm adding a great Cytoscape plugin called MiMI (Michigan Molecular Interactions) http://www.eecs.umich.edu/db/mimi/ In a nutshell, MiMI integrates major protein-protein interactions (ppi) databases like MIPS, MINT, BioGRID, HPRD and DIP into one so users like me don't have to scavange around each database to find data :D ...
Jayapandian M, Chapman A, Tarcea VG, Yu C, Elkiss A, Ianni A, Liu B, Nandi A,
Santos C, Andrews P, Athey B, States D, Jagadish HV.
Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together.
Nucleic Acids Res. 2006 Nov 27; [Epub ahead of print]