Reading room

See also: Science Commons reading room

Data sharing


 * Recommendations for independent scholarly publication of data sets

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
 * On The Cusp: A Global Review of the Semantic Web Industry