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=<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/<ACCESSION>

e.g.  http://sabi.ddbj.nig.ac.jp/ddbj/data/Z48241

• URI which returns in flatfile format
•  http://sabi.ddbj.nig.ac.jp/ddbj/<ACCESSION>

e.g.  http://sabi.ddbj.nig.ac.jp/ddbj/Z48241

• URI which redirects HTML page
•  http://sabi.ddbj.nig.ac.jp/ddbj/html/<ACCESSION>

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

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 -