Cambridge Semantic Web Monthly Meetup

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Agenda:

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6:00-6:15 Introduction/News

6:15-6:55 Drupal 7 and schema.org (http://schema.org/) for a more structured Web Stéphane Corlosquet, Software engineer and Drupal developer at MIND Informatics Schema.org is a joint initiative from the major search engines to build a collection of schemas that webmasters can use to markup their HTML pages. Search engines including Bing, Google, Yahoo! and Yandex rely on this markup to improve the display of search results, making it easier for people to find the right web pages. Drupal 7 makes it easy to markup pages withschema.org (http://schema.org/), allowing to quickly build pages with structured data that can be understood by Google and displayed as Rich Snippets.

Drupal Module: http://drupal.org/project/schemaorg

Bio: http://openspring.net/scor

6:55-7:25pm

Oliver Ruebenacker ( http://www.oliver.curiousworld.org/ )

Turning biological knowledge into mathematical models, automated (http://www.sbpax.org/)

Living organisms are so enormously complex that we need computer simulations to understand the biochemical details. An increasing part of the biochemical details is becoming known, and an increasing part of that knowledge is becoming available on the web in machine-readable formats, especially in the form of the RDF/OWL-based community standard Biological Pathways Exchange (BioPAX) (http://www.biopax.org/). For example, the web portal Pathway Commons (http://www.pathwaycommons.org/) aggregates biochemical knowledge from nine popular databases and allows query and export to BioPAX comprising about 1,700 pathways from 414 organisms, including about 440,000 interactions involving 86,000 substances. This data is fully linked with open controlled terminologies such as gene ontology (http://www.geneontology.org/) (e.g. anatomical features) and free online databases such as ChEBI (http://www.ebi.ac.uk/chebi/) (chemicals), KEGG (http://www.genome.jp/kegg/)(genes a.o.),UniProt (http://www.uniprot.org/)(proteins) and PubMed (http://www.ncbi.nlm.nih.gov/pubmed/)(publications).

A significant recent break-through for computer simulations of biological organisms has been the development of Systems Biology Pathway Exchange (SBPAX) (http://www.sbpax.org/) a BioPAX extension for the inclusion of quantitative data and systems biology terms, especially the Systems Biology Ontology (SBO) (http://www.ebi.ac.uk/sbo/main/). Two pathway databases with significant quantitative data - Signaling Gateway Molecule Pages (SGMP) (http://www.signaling-gateway.org/molecule/) and System for the Analysis of Biochemical Pathways - Reaction Kinetics (SABIO-RK) (http://sabio.villa-bosch.de/) - have prototypes that can export to SBPAX, and the Virtual Cell (http://vcell.org/) has a prototype that can import SBPAX to build and annotate models. This makes it possible to increasingly automate model building.