HCLSIG BioRDF Subgroup
With the advent of high-throughput experimentation, there has been an explosion of biomedical data on the Internet. While most of the data is available in Web accessible formats (e.g. HTML), many biomedical researchers rely on the use of Web browsers (e.g., Firefox and Internet Explorer) and search engines like Google to browse and search data on the Internet. Such manual browsing and keyword searching approaches are inadequate for large-scale integration of data on the Web. The Semantic Web transforms the Web into a global database or knowledge base that can be accessed by computer programs/agents through a standard data/ontology format. The Resource Description Framework (RDF) and the Web Ontology Language (OWL) are the W3C standards for encoding data/knowledge. This task group explores how to use RDF and OWL (as well as their enabling technologies) to better enable the computer to represent, identify, publish, query and integrate data/knowledge in the health care and life science domain.
The task coordinator is MScottMarshall (firstname.lastname@example.org)
- Enhance the HCLS KBs. Currently there are two HCLS KBs: HCLS KB hosted by DERI and HCLS KB hosted by Free University Berlin. As part of the enhancement, we would like to incorporate new data sets that help the KB span from bench to bedside.
- Increase the value and use of the HCLS KBs by identifying scientific use cases
- Work on a human-friendly UI, explore mechanisms for updating the data sources, and adding new data sets.
- Document our finding to help accelerate adoption of the Semantic Web.
Translating standards into practice - One Semantic Web API for Gene Expression Helena F Deus, Eric Prud’hommeaux, Michael Miller, Jun Zhao, James Malone, Tomasz Adamusiak, Jim McCusker, Sudeshna Das, Philippe Rocca-Serra, Ronan Fox, M. Scott Marshall Journal of Biomedical Informatics, Special Issue: Standards in Practice, 24 Mar 2012
Helena Deus, Jun Zhao, Satya Sahoo, Matthias Samwald, Eric Prud'hommeaux, Michael Miller, M.Scott Marshall and Kei-Hoi Cheung. Provenance of Microarray Experiments for a Better Understanding of Experiment Results (SWPM2010 Workshop wiki page, pdf)
Cheung KH, Frost HR, Marshall MS, Prud'hommeaux E, Samwald M, Zhao J, Paschke A. (2009). A Journey to Semantic Web Query Federation in Life Sciences. BMC Bioinformatics, 10(Suppl 10):S10.
Zhao J, Jentzsch A, Samwald M, Cheung KH. Linked Data for Connnecting Traditional Chinese Medicine and Western Medicine. Data Integration in the Life Sciences Workshops (DILS 09), University of Manchester, UK (poster presentation) -- this work is in collaboration with the LoDD task force.
- Query Federation
- BioSIOC / aTags
- Linking TCM with LoDD Datasets
- Deep Knowledge Representation Challenge
- Kei Cheung (Yale University)
- Matthias Samwald (Medical University of Vienna)
- Rob Frost (Vector C)
- Adrian Paschke (Freie Universitat Berlin)
- Eric Prud'hommeaux (W3C)
- Don Doherty (Brainstage)
- Susie Stephens (Johnson & Johnson Pharmaceutical Research & Development)
- Scott Marshall (University of Amsterdam)
- TN Bhat (NIST)
- Huajun Chen (Zhejiang University)
- Jun Zhao (Oxford University)
- Kingsley Idehen (OpenLink Software)
- Helena Deus (University of Texas)
- Satya Sahoo (Wright State University)
We welcome new participants.
- Querying Distributed RDF Data Sources with SPARQL
- AllegroGraph documentation
- SPARQL Service Bus middleware
- Vocabulary of Interlinked Dataset
- The RDF dump of the TCMGeneDIT Database
- The new release of RDF dump of the TCMGeneDIT Database
- OpenLink Virtuoso - Quad Store and Linked Data Deployment
- Live Virtuoso Instance - NeuroCommons, Bio2Rdf, Uniprot, Yago, and other data sets from the Linked Data Cloud (note: Live SPARQL endpoint)
- C-SHALS 2009
- DILS 2009
- BioRDF update F2F 2009
- BioRDF breakout session F2F 2009