[[PageOutline]] = 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. * [http://sourceforge.net/apps/mediawiki/bio2rdf/index.php Bio2RDF] [http://sourceforge.net/apps/mediawiki/bio2rdf/index.php?title=Namespace Namespace] * 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/ * [http://neurocommons.org/page/Main_Page 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/ * CardioSHARE * [http://biordf.net/cardioSHARE/predicates.html CardioSHARE demo - Available predicates] * Linked Data * [wiki:DBCLS_RDFs] 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 [http://togodb.dbcls.jp/ TogoDB] should be exported as RDF through [http://togows.dbcls.jp/ TogoWS] at DBCLS