Reading room
See also: Science Commons reading room
Data sharing
NeuroCommons prototype
- Alan Ruttenberg, Jonathan A. Rees, Matthias Samwald, and M. Scott Marshall. "Life sciences on the Semantic Web: the Neurocommons and beyond." Briefings in Bioinformatics 2009; doi: 10.1093/bib/bbp004. abstract, full text, PDF
- Ruttenberg et al. Advancing translational research with the Semantic Web. BMC Bioinformatics 8:S2, 2007.
- Scott Marshall et al. A prototype knowledge base for the life sciences. W3C interest group note, 2008.
Data integration
- Good and Wilkinson. The life sciences Semantic Web is full of creeps! Briefings in Bioinformatics 7:275-286, 2006.
- Carole Goble. The seven deadly sins of bioinformatics. Presentation, 2007.
- Rod Page. Biodiversity informatics: the challenge of linking data and the role of shared identifiers. Briefings in Bioinformatics 9:345-354, 2008.
- Lincoln Stein. Creating a bioinformatics nation. Nature, 2002. Keynote speech transcribed by a contributor to the Veterinary Sciences Tomorrow web site.
- Mike Bergman "I have yet to metadata I didn't like," article on data integration with RDF
Ontology
- Barry Smith et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology 25, 1251-1255 (2007)
- OBO Foundry Principles
- Gene Ontology
- John Sowa criticizing SUMO, W3C, RDF, and everyone else
Naming
- Use/mention distinction (wikipedia)
- Hayes and Halpin "In defense of ambiguity"
- ARK (Archival Resource Key)
- MIRIAM
- bio2rdf
- OKKAM
- LSID
Technical standards
- RFC 3896 URI generic syntax
- RDF semantics
- OWL 1, OWL 2
- SPARQL
- SPARUL
- httpRange-14 resolution
- XRDS-simple draft
- Discovery and HTTP
Semantic Web
