Bio2RDF: moving forward as a community

 Last week we held our first virtual meeting towards re-invigorating the Bio2RDF project with a significantly larger and vested community. From discussions, we plan to establish 3 focus groups around :

A. policy (information, governance, sustainability, outreach)

B. technical (architecture, infrastructure and RDFization)

C. social (user experience and social networking)

The next step then is for groups to:

1. identify and certify discussion leads (responsibilities: set meeting times and agenda, facilitate and encourage discussion among members, draft reports)

2. identify additional people to recruit from the wider community that would provide additional expertise (interested, but didn't attend the first? sign up now !)

3. extend and prioritize discussion items (what exactly will this group focus its efforts on in the short and long term)

4. identify and assign bite-sized tasks (so we can get things done one step at a time :)

5. collate results and present to the wider community

I suggest that groups self-organize a first meeting in the next two weeks to deal with items 1-4, and either meet again or use the Google documents to collaboratively report findings.

Finally, I'd like for us to hold another meeting with times that are much more accommodating for Europe + North America ;)  Please fill the doodle poll (http://www.doodle.com/fsuz6mgs5cztf2e2)

As always, feel free to contact me if you have any questions, and please sign up to the Bio2RDF mailing list for all future discussions.

Biocuration 2010 presentation

Here is the presentation given at Biocuration 2010 , October 13th

W4 4 marc-alexandre-nolin-v2

View more presentations from nolmar01.

Bio2RDF return to Japan

Bio2RDF is returning in Japan again this year. We will give a talk about Bio2RDF at Biocuration 2010 . Biocuration is from October 11th to October 14th at Odaiba, Tokyo.

Video on Bio2RDF and Beyond! Large Scale, Distributed Biological Data Integration

Invited by former student Alexander De Leon and host Oscar Corcho, Michel Dumontier gave a talk on "Bio2RDF and Beyond! Large Scale, Distributed Biological Data Integration" [video] to the Ontology Engineering group at the Universidad Politécnica de Madrid (UPM).

Bio2RDF Cognoscope presentation at BioHackathon 2010 in Tokyo

François Belleau from the Bio2RDF project was invited as an early Semantic Web technology adopter to present the Bio2RDF project at the annual BioHackathon 2010 held each year in Tokyo.

Bio2RDF@BH2010

View more presentations from François Belleau.

Registry for original provider HTML pages

If you weren't aware, the Bio2RDF project offers both RDF, and a service that redirects to either HTML, images, or other non-RDF sources that could be useful.

The HTML redirect service is particularly useful, because one can start at the Bio2RDF page, and follow a link that looks like "http://bio2rdf.org/html/namespace:identifier", to get to the original providers web page.

There are currently 142 namespaces that are registered along with HTML pages. Examples of these links are, the NextBio page for Amyloid Beta precursor protein (http://bio2rdf.org/nextbio:1445), the NCBI Entrez Geneid page for Superoxide dismutase 1 (http://bio2rdf.org/geneid:6647), the Pharmgkb page for Superoxide dismutase 1(http://bio2rdf.org/pharmgkb:PA334), and the HGNC page for Superoxide dismutase 1 (http://bio2rdf.org/hugo:SOD1).

The list below, details the namespace prefixes that are currently registered with Bio2RDF for this service. A full set of details about what services are provided for any particular namespaces are provided at here, and the entire RDF configuration that makes the Bio2RDF system work is available here (RDF/XML)

aceview, agi_locuscode, arrayexpress, asap, aspgd, aspgd_locus, aspgd_ref, bind, biogrid, biomodels, biopatml, biosystems, brenda, cas, cath, ccds, cdd, cgd, cgsc, chebi, chemidplus, cid, citations, cog, cpath, cpd, dbpedia, dbsnp, ddbj, dictybase, dictybase_trials, dip, doi, dr, drugbank_drugs, ec, echobase, eck, ecogene, embl, ensembl, enzyme, flybase, gdb, genbank, genedb_pfalciparum, genedb_spombe, geneid, gi, gl, go, goa_ref, gopubmed, gr, gr_gene, gr_protein, gr_qtl, gr_ref, h-invdb, h_inv, hgnc, homologene, hpa, hpa_antibody, hprd, huge_navigator, hugo, intact, interpro, ipi, iproclass, isbn, issn, keywords, lifedb, linkedct_trials, ma, mesh, metacyc, mgc, mgi, msdchem, myexp_user, myexp_workflow, nar, ncbi, nextbio, nist_chemistry_webbook, nmrshiftdb_molecule, oclc, omim, pamgo_vmd, path, pathguide, pdb, pdbsum, pfam, pharmgkb, phosphosite, po, prints, prodom, prosite, pseudocap, psimod, pubchem, pubmed, reactome, rebase, refseq, rgd, rn, scop, seed, sgd, sgd_locus, sgd_ref, sgn, sgn_ref, sid, sider_drugs, sider_sideeffects, smart, so, srs, swoogle, symbol, tair_arabidopsis, taxon, taxonomy, tc, tgd_locus, tgd_ref, um-bbd, uniparc, uniprot, uniref, unists, wikipathways, wikipedia, xenbase, zfin

If you know of a biological database that has webpages for their items and is not listed here then feel free to comment about it here or email the group at bio2rdf@googlegroups.com

Linking Open Drug Data wins the Triplify challenge

Congratulations to Kei's group and their Linking Open Drug Data (LODD) project for winning the Triplify challenge.

http://blog.aksw.org/2009/triplification-challenge-2009-winners/

http://triplify.org/files/challenge_2009/LODD.pdf

It is a new contribution to the LOD cloud and they have linked those new datasets to Bio2RDF and DBpedia URIs. That is the right way to do it !