= 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) * gene_id http://www.ncbi.nlm.nih.gov/gene/ENTRYID (NCBI gene ID) = 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 * URL which returns prototype RDF * http://sabi.ddbj.nig.ac.jp/ddbj/data/ e.g. http://sabi.ddbj.nig.ac.jp/ddbj/data/Z48241 * URL which returns in flatfile format * http://sabi.ddbj.nig.ac.jp/ddbj/ e.g. http://sabi.ddbj.nig.ac.jp/ddbj/Z48241 * URL 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: 730,602 triples) * http://www.hgc.jp/~shuichi/biohack2010/kegg-genes2kegg-ko.ttl (KEGG GENES2KO / KEGG KO2GENES turtle: 3,687,074 triples) * http://www.hgc.jp/~shuichi/biohack2010/kegg-ko2kegg-pathway.ttl (KEGG KO2PATHWAY / KEGG PATHWAY2KO turtle) * http://www.hgc.jp/~shuichi/biohack2010/kegg-genes2kegg-ko.ttl (KEGG GENES2NCBI GENE-ID / NCBI GENE-ID2KEGG GENES turtle: 3,687,074 triples) = 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 - http://192.168.11.61:8892/sparql/ * KEGG - * DDBJ - Facet * Bio2RDF KEGG - http://192.168.11.61:8890/fct/ * Bio2RDF PDB - http://192.168.11.61:8891/fct/ * PDBj - http://192.168.11.61:8892/fct/ * KEGG - * DDBJ - = Validating RDF/XML format = * http://librdf.org/parse = How to load data to virtuoso = First, in the '''virtuoso.ini''' file, set the following parameter {{{ DirsAllowed = ., /usr/local/virtuoso-opensource/share/virtuoso/vad, /tmp }}} So the directory /tmp is allowed to have data to be loaded. Then put the data file in /tmp (e.g., all.ttl, ddbj.rdf). {{{ % cat load.isql DB.DBA.TTLP_MT(file_to_string_output('/tmp/all.ttl'), '' ,'http://www.pdbj.org'); checkpoint; DB.DBA.RDF_LOAD_RDFXML(file_to_string_output('/tmp/lala.rdf'), '' ,'http://www.pdbj.org'); checkpoint; % isql 1111 dba dba < load.isql }}} Here the third argument for the functions '''TTLP_MT''' and '''RDF_LOAD_RDFXML''' is the name of the graph (in this case, it's '''http://www.pdbj.org'''). = Results? = [[wiki:DDBJ-KEGG-PDBj/Results]] Developed the following on-the-fly DDBJ interface of RDF, Web API and HTML page * URL which returns prototype RDF * http://sabi.ddbj.nig.ac.jp/ddbj/data/ e.g. http://sabi.ddbj.nig.ac.jp/ddbj/data/Z48241 * URL which returns in flatfile format (URI?) * http://sabi.ddbj.nig.ac.jp/ddbj/ e.g. http://sabi.ddbj.nig.ac.jp/ddbj/Z48241 * URL which redirects HTML page * http://sabi.ddbj.nig.ac.jp/ddbj/html/ e.g. http://sabi.ddbj.nig.ac.jp/ddbj/html/Z48241 Installed the following virtuoso at DDBJ site * http://sabi.ddbj.nig.ac.jp:8080/sparql