Standards and formats

• S ee the BioSharing listing at http://www.biosharing.org/standards for names of the standards.

Semantic Web technologies

• RDF
• Resource Description Framework
• http://www.w3.org/RDF/
• Turtle
• Terse RDF Triple Language
• http://www.w3.org/TeamSubmission/turtle/
• see also N-Triples, Notation 3, RDF/XML and SPARQL/XML
• OWL
• Web Ontology Language
• http://www.w3.org/TR/owl2-overview/
• SPARQL
• SPARQL Protocol and RDF Query Language
• http://www.w3.org/TR/rdf-sparql-protocol/
• http://www.w3.org/TR/rdf-sparql-query/
• SPIN
• SPARQL Inferencing Notation
• http://www.w3.org/Submission/spin-overview/
• http://spinrdf.org
• DL
• Description Logic
• http://en.wikipedia.org/wiki/Description_logic
• TC
• Transitive Closure
• http://en.wikipedia.org/wiki/Transitive_closure
• Entailment
• http://en.wikipedia.org/wiki/Entailment

• Dublin Core
• A vocabulary of fifteen properties for use in resource description
• http://dublincore.org/
• FOAF
• Friend of a Friend
• http://www.foaf-project.org/
• VoID
• Vocavulary of Interlinked Datasets
• http://www.w3.org/TR/void/
• SKOS
• Simple Knowledge Organization System
• http://www.w3.org/TR/skos-reference/
• SERV
• Semantic Entity Resolution Vocabulary
• http://code.google.com/p/semanticscience/wiki/serv
• BFO
• Basic Formal Ontology
• http://www.ifomis.org/bfo/
• SIO
• Semanticscience Integrated Ontology
• http://code.google.com/p/semanticscience/wiki/SIO
• EDAM
• EMBRACE Data and Methods ontology
• http://edamontology.sourceforge.net/
• myGrid
• myGrid/Moby service ontology
• http://www.mygrid.org.uk/tools/service-management/mygrid-ontology/
• SIOC
• Semantically-Interlinked Online Communities
• http://sioc-project.org/ontology
• SIOC types and health care and life sciences
• http://www.w3.org/TR/hcls-sioc/
• OBI
• Ontology for Biomedical Investigations
• http://obi-ontology.org/
• OBO
• Open Biological and Biomedical Ontologies
• http://www.obofoundry.org/
• GO
• Gene Ontology
• http://www.geneontology.org/
• SO
• Sequence Ontology
• http://www.sequenceontology.org/
• CCO
• Cell Cycle Ontology
• http://www.cellcycleontology.org/
• SBO
• Systems Biology Ontology
• http://www.ebi.ac.uk/sbo/
• AO
• Annotation Ontology
• http://code.google.com/p/annotation-ontology/
• PAV
• Provenance Authoring and Versioning ontology
• http://code.google.com/p/pav-ontology/
• OLS
• Ontology Lookup Service (@ EBI)
• http://www.ebi.ac.uk/ontology-lookup/
• CDAO
• Comparative Data Analysis Ontology
• http://sourceforge.net/apps/mediawiki/cdao/index.php?title=Main_Page

S ee http://www.biosharing.org/standards for more!

Communities and projects

• SWAT4LS
• Semantic Web Applications and Tools for Life Sciences workshop (December 9, 2011 @ London, UK)
• http://www.swat4ls.org/2011/
• ISWC
• International Semantic Web Conference (October 23-27, 2011 @ Bonn, Germany)
• http://iswc2011.semanticweb.org/
• ICBO
• International Conference on Biomedical Ontology (July 26-30, 2011 @ University at Buffalo, NY)
• http://icbo.buffalo.edu/
• SemTech
• Semantic Technology Conference (June 5-9, 2011 @ San Francisco, CA)
• http://semtech2011.semanticweb.com/
• W3C HCLC
• World Wide Web Consortium Semantic Web Health Care and Life Sciences interest group
• http://www.w3.org/2001/sw/hcls/
• BioPortal
• Portal to access and share ontologies that are actively used in biomedical communities
• http://bioportal.bioontology.org/
• BioLOD
• Biological Linked Open Data is a database of biological open data
• http://biolod.org/
• SharedNames
• Assign URIs as names for publicly available biomedical information records
• http://sharedname.org/
• BioXSD
• Common exchange format for basic bioinfomatics data
• http://bioxsd.org/
• BioDBcore
• Community defined, uniform, generic description of the core attributes of biological databases
• http://biocurator.org/biodbcore.shtml
• BioCatalogue
• Curated catalogue of life science web services
• http://www.biocatalogue.org/
• myExperiment
• Find, use and share scientific workflows
• http://www.myexperiment.org/
• BioModels
• Standards for model curation in systems biology
• http://biomodels.net/
• BioSharing
• Data sharing policies and reporting standards
• http://www.biosharing.org/
• ISA
• Investication/Study/Assay infrastructure -- general purpose format and software suite
• http://isatab.sourceforge.net/
• ISB
• International Society for Biocuration
• http://www.biocurator.org/
• MIBBI
• Minimum Information for Biological and Biomedical Investigations
• http://www.mibbi.org/
• MIABi
• Minimum Information About a Bioinformatics investigation
• http://www.biomedcentral.com/1471-2164/11/S4/S27/additional/
• MIAPA
• Minimal Information for a Phylogenetic Analysis
• http://www.nescent.org/sites/evoio/MIAPA
• PSI
• HUPO Proteomics Standards Initiative
• http://www.psidev.info/
• Dryad
• International repository of data underlying peer-reviewed articles in the basic and applied biosciences.
• http://www.datadryad.org/
• FuGE
• Functional Genomics Experiment
• http://fuge.sourceforge.net/
• GSC
• Genomic Standard Consortium
• http://gensc.org/
• SIGS
• Standards in Genomic Sciences
• http://www.standardsingenomics.org/
• Science Commons
• Expand the use of Creative Commons licenses to scientific and technical research
• http://creativecommons.org/science
• TOPSAN
• Share information about protein three-dimensional structures
• http://www.topsan.org/

Institutions and organizations

• JST
• Japan Science and Technology Agency [Japan]
• http://www.jst.go.jp/
• NBDC
• National Bioscience Database Center [Japan]
• http://biosciencedbc.jp/
• ROIS
• Research Organization of Information and Systems [Japan]
• http://www.rois.ac.jp/
• DBCLS
• Database Center for Life Science [Japan]
• http://dbcls.rois.ac.jp/
• DDBJ
• DNA Data Bank of Japan (Web API for Biology) [Japan]
• http://wabi.ddbj.nig.ac.jp/
• PDBj
• Protein Data Bank JapanDictionary (SOAP, REST API) [Japan]
• http://www.pdbj.org/doc/
• KEGG
• Kyoto Encyclopedia of Genes and Genomes (KEGG API) [Japan]
• http://www.genome.jp/kegg/soap/
• CBRC
• Computational Biology Research Center [Japan]
• http://www.cbrc.jp/
• NCBC
• National Center for Biomedical Computing
• http://www.ncbcs.org/
• NCBO
• National Center for Biomedical Ontology
• http://www.bioontology.org/
• NCBI
• National Center for BIotechnology Information (Entrez Utilities)
• http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
• UCSC
• University of California Santa Cruz (Genome Bioinformatics)
• http://genome.ucsc.edu/
• BBSRC
• Biotechnology and Biological Sciences Research Council
• http://www.bbsrc.ac.uk/
• EMBRACE
• European Model for Bioinformatics Research and Community Education
• http://www.embracegrid.info/
• EBI
• European Bioinformatics Institute (Web services)
• http://www.ebi.ac.uk/Tools/webservices/
• IFOMIS
• Institute for Formal Ontology and Medical Information Science
• http://www.ifomis.org/
• OBF
• Open Bioinformatics Foundation
• http://www.open-bio.org/

• BioPerl
• Bioinformatics library for Perl language
• http://bioperl.org/
• BioPython
• Bioinformatics library for Python language
• http://biopython.org/
• BioRuby
• Bioinformatics library for Ruby language
• http://bioruby.org/
• BioJava
• Bioinformatics library for Java language
• http://biojava.org/
• Protege
• Ontology editor
• http://protege.stanford.edu/
• Taverna
• Workflow construction tool
• http://www.taverna.org.uk/
• Cytoscape
• Graph visualization tool
• http://www.cytoscape.org/
• OLSVis
• A visual browser for EBI's OLS
• http://ols.wordvis.com/

Generic Web technologies