Datasets

Lists currently available and still missing datasets (as Linked Data / RDF).

Available resources

Let's make a list of all RDF resources currently available and evaluate them according to its contents and quality. Extraction of meaningful triples (relations) from original data sources requires good understanding of their contents and it could be a key for the resulting usefulness.

•  Bio2RDF  Namespace
  •  Banff_Manifesto
  • Ensembl - genes
  • OBO - GO terms, ChEBI compounds
  • NCBI - genes, sequences, mesh terms, disease (omim), pubmed articles
  • KEGG - pathways, genes, enzymes, compounds, drugs, glycans, reactions
  • MGI - genes
  • PDB - structures
  • UniProt - proteins, keywords, taxonomy
  •  http://quebec.bio2rdf.org/download/virtuoso/V6/
•  NeuroCommons Project
  •  http://sparql.neurocommons.org/
  •  http://sparql.neurocommons.org/sparql? -- SPARQL endpoint
  •  http://neurocommons.org/page/RDF_distribution
  •  http://neurocommons.org/page/Bundles
  •  http://ashby.csail.mit.edu/presentations/The_Neurocommons_Common_names_and_ontologies_for_open_source_knowledge_integration_on_the_Semantic_Web.pdf
• uniprot RDF
  •  http://dev.isb-sib.ch/projects/uniprot-rdf/
  •  http://dev.isb-sib.ch/projects/uniprot-rdf/migration.html
  •  http://dev.isb-sib.ch/projects/uniprot-rdf/shorthand.html
  •  http://dev.isb-sib.ch/projects/uniprot-rdf/owl/
  •  Jerven Bolleman, Thomas Kappler, and the UniProt Consortium (2009) Weekend Triple Billionaire Maintaining a Large RDF Data Set in the Life Sciences
•  LinkedLifeData
  •  http://linkedlifedata.com/sources
  •  http://linkedlifedata.com/sparql
  •  http://linkedlifedata.com/relfinder
  •  http://linkedlifedata.com/convention
  •  ftp://ftp.ontotext.com/pub/lld
  •  http://linkedlifedata.com/about

* CardioSHARE

•  CardioSHARE demo - Available predicates

• Linked Data
  •  Tim Berners-Lee on the next Web | Video on TED.com
    •  Hans Rosling shows the best stats you've ever seen | Video on TED.com
• DBCLS_RDFs
• TreeBASE
  •  URL API, serialization formats
• RDF example from SciNeS, RIKEN
  •  https://database.riken.jp/sw/download/cria110s1ria110s222i~archives~semantics~external_id.rdf.xml
• SystemsBiology?
• Semantic Systems Biology  http://www.semantic-systems-biology.org/

We should categorize these according to their format (e.g. RDF) and extracted relationships (not only by their original source databases).

Missing resources

Not sure that they are actually unavailable, but let's lists wanted relations (triples) to solve biological queries.

• Taxonomy <-> Pathway module
• Taxonomy <-> Ortholog cluster
• Gene <-> Expression patterns (from multiple experiments)
• Enzyme <-> Activity
• Protein architectures (domain combinations) <-> Taxonomy

We should add intended reasons (what for these relations are required).

• Contents of the  TogoDB should be exported as RDF through  TogoWS at DBCLS