= URL = * PDBj http://www.pdbj.org/PDBID (PDBID = 1gof, 1a00, ...) This is a fake URL. * KEGG http://togows.dbcls.jp/entry/kegg-DBNAME/ENTRYID * DDBJ http://togows.dbcls.jp/entry/ddbj/ENTRYID * !UniProt http://www.uniprot.org/uniprot/ENTRYID * !PubMed http://www.ncbi.nlm.nih.gov/pubmed/ENTRYID * Taxonomy http://www.ncbi.nlm.nih.gov/Taxonomy/TAXID (this is invalid URL) * HapMap http://www.khapmap.org/ENTRYID (this is invalid URL) = PDB things = * ftp://ftp.protein.osaka-u.ac.jp/pub/pdb/data/structures/all/XML-noatom/{PDBID}-noatom.xml.gz * /PDBx:datablock/PDBx:entity_src_genCategory/PDBx:entity_src_gen/PDBx:pdbx_gene_src_ncbi_taxonomy_id where {PDBID} should be something like "1a00" (in lowercase). = DDBJ things = * http://xml.nig.ac.jp/rest/Invoke?service=DDBJ&method=getXMLEntry&accession= e.g. http://xml.nig.ac.jp/rest/Invoke?service=DDBJ&method=getXMLEntry&accession=AL121903 * URI which returns prototype RDF * http://sabi.ddbj.nig.ac.jp/ddbj/data/ e.g. http://sabi.ddbj.nig.ac.jp/ddbj/data/Z48241 * URI which returns in flatfile format * http://sabi.ddbj.nig.ac.jp/ddbj/ e.g. http://sabi.ddbj.nig.ac.jp/ddbj/Z48241 * URI which redirects HTML page * http://sabi.ddbj.nig.ac.jp/ddbj/html/ e.g. http://sabi.ddbj.nig.ac.jp/ddbj/html/Z48241 = KEGG things = * Draft KEGG RDF download site (temporal) : http://www.hgc.jp/~shuichi/biohack2010/ * Note: I wouldn't recommend to display the following files in your web browsers because it's large text file. * http://www.hgc.jp/~shuichi/biohack2010/kegg-genes2pdb.ttl (KEGG GENES2PDB / PDB2KEGG GENES turtle) * http://www.hgc.jp/~shuichi/biohack2010/kegg-genes2kegg-ko.ttl (KEGG GENES2KO / KEGG KO2GENES turtle) * http://www.hgc.jp/~shuichi/biohack2010/kegg-ko2kegg-pathway.ttl (KEGG KO2PATHWAY / KEGG PATHWAY2KO turtle) = Reflect for pubmed = To use reflect on pubmed: http://reflect.cbs.dtu.dk/TEST/GetEntities?uri=http://www.ncbi.nlm.nih.gov/pubmed/20146332&entity_types=9606 The result will contain XML code like seen at [http://reflect.cbs.dtu.dk/restAPI.html http://reflect.cbs.dtu.dk/restAPI.html] = SPARQL endpoint = Room 415 network * Bio2RDF KEGG - http://192.168.11.61:8890/sparql/ * Bio2RDF PDB - http://192.168.11.61:8891/sparql/ * PDBj - * KEGG - * DDBJ - Facet * Bio2RDF KEGG - http://192.168.11.61:8890/fct/ * Bio2RDF PDB - http://192.168.11.61:8891/fct/ * PDBj - * KEGG - * DDBJ -