Reading room

See also: Science Commons reading room

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.

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

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