TogoWS: REST

Integration of the bioinformatics web services

http://togows.dbcls.jp/entry/database/entry_id[,entry_id2,...]/field[.format]

Related resources

• Status log of Japanese web services


• Database of sample codes for Japanese web services (for Perl, Python, Ruby and Java)


• Database of methods provided by EBI, NCBI, and Japanese web services (in Japanese)


• Database of documentations provided by EBI, NCBI, and Japanese web services (in Japanese)

Towards an integrated web service in life science

TogoWS REST service

REST URI conventions

• http://togows.dbcls.jp/entry/database/entry_id[,entry_id2,...]/field[.format]
• http://togows.dbcls.jp/search/database/query+string[.format][/offset,limit[.format]]
• http://togows.dbcls.jp/convert/data_source.format

Entry retrieval

http://togows.dbcls.jp/entry/database/entry_id[,entry_id2,...]/field[.format]

• database:
  • KEGG: gene, orthology, enzyme, compound, drug, glycan, reaction
  • DDBJ: ddbj, dad
  • PDBj: pdb
  • NCBI: gene, genome, genomeprj, geo, journals, mesh, nucleotide, omim, pmc, protein, pubmed, taxonomy, cdd, popset, snp, unigene, homologene, nuccore, nucest, nucgss, unists
  • EBI: biomodels, chebi, ensembl, go, interpro, reactome, uniprot, uniparc, uniref100, uniref90, uniref50, msdchem, msdpdb
• format:
  • xml, json, gff, fasta etc.
• samples:
  • http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN,A1AG1_MOUSE
  • http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN,A1AG1_MOUSE.fasta
  • http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN,A1AG1_MOUSE.gff
  • http://togows.dbcls.jp/entry/pubmed/16381885
  • http://togows.dbcls.jp/entry/pubmed/16381885/authors
  • http://togows.dbcls.jp/entry/pubmed/16381885/authors.json

Database search

http://togows.dbcls.jp/search/database/query+string[.format][/offset,limit[.format]]

• query+string:
  • Format of "query string" follows the Common Query Language
• samples:
  • http://togows.dbcls.jp/search/uniprot/lung+cancer
  • http://togows.dbcls.jp/search/uniprot/lung+cancer/count
  • http://togows.dbcls.jp/search/uniprot/lung+cancer/1,10

Data format conversion

http://togows.dbcls.jp/convert/data_source.format

• data_source:
  • genbank, blast, fasta, psl, sim4, hmmer, exonerate, wise etc.
• protocol:
  • Use POST protocol to upload data sourse as a text
• samples:
  • http://togows.dbcls.jp/convert/blast.gff

Examples - NCBI GenBank

• http://togows.dbcls.jp/entry/genbank/HUMIGHAF
• http://togows.dbcls.jp/entry/genbank/HUMIGHAF.xml
• http://togows.dbcls.jp/entry/genbank/HUMIGHAF.fasta
• http://togows.dbcls.jp/entry/genbank/HUMIGHAF/definition
• http://togows.dbcls.jp/entry/genbank/HUMIGHAF/seq
• http://togows.dbcls.jp/entry/genbank/J00231
• http://togows.dbcls.jp/entry/genbank/J00231.1
• http://togows.dbcls.jp/entry/genbank/185041

TODO

• http://togows.dbcls.jp/entry/genbank/HUMIGHAF/references # -> PMIDs
• http://togows.dbcls.jp/entry/genbank/HUMIGHAF/features # -> GFF
• http://togows.dbcls.jp/entry/genbank/HUMIGHAF.gff # features

Examples - NCBI PubMed

• http://togows.dbcls.jp/entry/pubmed/16381885
• http://togows.dbcls.jp/entry/pubmed/16381885.xml
• http://togows.dbcls.jp/entry/pubmed/16381885.ttl
• http://togows.dbcls.jp/entry/pubmed/16381885/abstract
• http://togows.dbcls.jp/entry/pubmed/16381885/au
• http://togows.dbcls.jp/entry/pubmed/16381885/authors
• http://togows.dbcls.jp/entry/pubmed/16381885/so
• http://togows.dbcls.jp/entry/pubmed/16381885/mesh
• http://dx.doi.org/ + http://togows.dbcls.jp/entry/pubmed/16381885/doi

Examples - EMBL

• http://togows.dbcls.jp/entry/embl/J00231
• http://togows.dbcls.jp/entry/embl/J00231.xml
• http://togows.dbcls.jp/entry/embl/J00231.fasta
• http://togows.dbcls.jp/entry/embl/J00231/entry_id
• http://togows.dbcls.jp/entry/embl/J00231/definition
• http://togows.dbcls.jp/entry/embl/J00231/seq (alias to "sequence", "naseq"?)

TODO

• http://togows.dbcls.jp/entry/embl/J00231/references # rx -> PMIDs
• http://togows.dbcls.jp/entry/embl/J00231/features # ft -> GFF
• http://togows.dbcls.jp/entry/embl/J00231.gff # features
• http://togows.dbcls.jp/entry/embl/J00231/created_date # dt (Hash)
• http://togows.dbcls.jp/entry/embl/J00231/updated_date # dt (Hash)
• http://togows.dbcls.jp/entry/embl/J00231/keywords # kw
• http://togows.dbcls.jp/entry/embl/J00231/common_name # os
• http://togows.dbcls.jp/entry/embl/J00231/organism # os
• http://togows.dbcls.jp/entry/embl/J00231/taxonomy # oc
• http://togows.dbcls.jp/entry/embl/J00231/dr # cross_ref (Hash)
• http://togows.dbcls.jp/entry/embl/J00231/comment # cc (field str)
• http://togows.dbcls.jp/entry/embl/J00231/composition # sq (Hash)

Examples - UniProt

• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN.xml (XSD)
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN.fasta
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN/entry_id
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN/definition
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN/seq (alias to "sequence", "aaseq"?)

TODO

• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN/references # rx -> PMIDs
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN/dois # rx -> DOIs
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN/features # Protein DAS
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN.gff # Protein DAS
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN/created_date # dt
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN/sequence_updated(_date?) # dt
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN/annotation_updated(_date?) # dt
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN/sequence_version
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN/entry_version
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN/gene_name # gn
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN/synonyms # gn
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN/common_name # os (Hash)
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN/organism # os (Hash)
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN/taxonomy # oc
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN/tax_id # ox
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN/comments # cc (Hash)
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN/dr # cross_ref (Hash)
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN/keywords # kw
• http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN/composition # sq

Examples - DDBJ DDBJ

• http://togows.dbcls.jp/entry/ddbj/AB000100
• http://togows.dbcls.jp/entry/dad/AB000100-2

Examples - DDBJ DAD

• http://togows.dbcls.jp/entry/dad/AB000100-2

Examples - PDBj

• http://togows.dbcls.jp/entry/pdb/1a4u
• http://togows.dbcls.jp/entry/pdb/1a4u/accession # downcase?
• http://togows.dbcls.jp/entry/pdb/1a4u/keywords
• http://togows.dbcls.jp/entry/pdb/1a4u/chains
• http://togows.dbcls.jp/entry/pdb/1a4u/models

TODO

• http://togows.dbcls.jp/entry/pdb/1a4u/atoms
• http://togows.dbcls.jp/entry/pdb/1a4u/seq # seqres
• http://togows.dbcls.jp/entry/pdb/1a4u/remark
• http://togows.dbcls.jp/entry/pdb/1a4u/jrnl # no PMID?
• http://togows.dbcls.jp/entry/pdb/1a4u/data # ?
• http://togows.dbcls.jp/entry/pdb/1a4u/helix # ?
• http://togows.dbcls.jp/entry/pdb/1a4u/turn # ?
• http://togows.dbcls.jp/entry/pdb/1a4u/sheet # ?
• http://togows.dbcls.jp/entry/pdb/1a4u/dbref # ?

Examples - KEGG ENZYME

• http://togows.dbcls.jp/entry/enzyme/1.1.1.1
• http://togows.dbcls.jp/entry/enzyme/1.1.1.1/entry_id
• http://togows.dbcls.jp/entry/enzyme/1.1.1.1/names
• http://togows.dbcls.jp/entry/enzyme/1.1.1.1/name
• http://togows.dbcls.jp/entry/enzyme/1.1.1.1/classes
• http://togows.dbcls.jp/entry/enzyme/1.1.1.1/sysname
• http://togows.dbcls.jp/entry/enzyme/1.1.1.1/reaction
• http://togows.dbcls.jp/entry/enzyme/1.1.1.1/all_reac
• http://togows.dbcls.jp/entry/enzyme/1.1.1.1/iubmb_reactions
• http://togows.dbcls.jp/entry/enzyme/1.1.1.1/kegg_reactions
• http://togows.dbcls.jp/entry/enzyme/1.1.1.1/substrates
• http://togows.dbcls.jp/entry/enzyme/1.1.1.1/products
• http://togows.dbcls.jp/entry/enzyme/1.1.1.1/inhibitors
• http://togows.dbcls.jp/entry/enzyme/1.1.1.1/cofactors
• http://togows.dbcls.jp/entry/enzyme/1.1.1.1/comment

TODO

• http://togows.dbcls.jp/entry/enzyme/1.1.1.1/references # cross_ref (PMIDs)
• http://togows.dbcls.jp/entry/enzyme/1.1.1.1/pathways # cross_ref (field string)
• http://togows.dbcls.jp/entry/enzyme/1.1.1.1/orthologs # cross_ref (field string)
• http://togows.dbcls.jp/entry/enzyme/1.1.1.1/genes # cross_ref (field string)
• http://togows.dbcls.jp/entry/enzyme/1.1.1.1/structures # cross_ref (PDBs)
• http://togows.dbcls.jp/entry/enzyme/1.1.1.1/dblinks # cross_ref (field string)

Examples - KEGG GENES

• http://togows.dbcls.jp/entry/gene/eco:b0002
• http://togows.dbcls.jp/entry/gene/eco:b0002/entry_id
• http://togows.dbcls.jp/entry/gene/eco:b0002/division
• http://togows.dbcls.jp/entry/gene/eco:b0002/organism
• http://togows.dbcls.jp/entry/gene/eco:b0002/name
• http://togows.dbcls.jp/entry/gene/eco:b0002/genes
• http://togows.dbcls.jp/entry/gene/eco:b0002/gene
• http://togows.dbcls.jp/entry/gene/eco:b0002/definition
• http://togows.dbcls.jp/entry/gene/eco:b0002/eclinks
• http://togows.dbcls.jp/entry/gene/eco:b0002/position
• http://togows.dbcls.jp/entry/gene/eco:b0002/chromosome
• http://togows.dbcls.jp/entry/gene/eco:b0002/gbposition
• http://togows.dbcls.jp/entry/gene/eco:b0002/aaseq
• http://togows.dbcls.jp/entry/gene/eco:b0002/aalen
• http://togows.dbcls.jp/entry/gene/eco:b0002/ntseq
• http://togows.dbcls.jp/entry/gene/eco:b0002/ntlen

TODO

• http://togows.dbcls.jp/entry/gene/eco:b0002/orthologs # cross_ref
• http://togows.dbcls.jp/entry/gene/eco:b0002/pathways # cross_ref
• http://togows.dbcls.jp/entry/gene/eco:b0002/motif # cross_ref
• http://togows.dbcls.jp/entry/gene/eco:b0002/dblinks # cross_ref
• http://togows.dbcls.jp/entry/gene/eco:b0002/codon_usage # Hash

Examples - KEGG ORTHOLOGY

• http://togows.dbcls.jp/entry/orthology/K00001
• http://togows.dbcls.jp/entry/orthology/K00001/entry_id
• http://togows.dbcls.jp/entry/orthology/K00001/names
• http://togows.dbcls.jp/entry/orthology/K00001/definition
• http://togows.dbcls.jp/entry/orthology/K00001/keggclasses
• http://togows.dbcls.jp/entry/orthology/K00001/pathways

TODO

• http://togows.dbcls.jp/entry/orthology/K00001/dblinks # cross_ref (dblinks_as_hash)
• http://togows.dbcls.jp/entry/orthology/K00001/genes # cross_ref (genes_as_hash)

Examples - KEGG COMPOUND

• http://togows.dbcls.jp/entry/compound/C00001
• http://togows.dbcls.jp/entry/compound/C00001/entry_id
• http://togows.dbcls.jp/entry/compound/C00001/name
• http://togows.dbcls.jp/entry/compound/C00001/names
• http://togows.dbcls.jp/entry/compound/C00001/formula
• http://togows.dbcls.jp/entry/compound/C00001/mass
• http://togows.dbcls.jp/entry/compound/C00001/remark
• http://togows.dbcls.jp/entry/compound/C00001/glycans
• http://togows.dbcls.jp/entry/compound/C00001/reactions
• http://togows.dbcls.jp/entry/compound/C00001/rpairs
• http://togows.dbcls.jp/entry/compound/C00001/enzymes
• http://togows.dbcls.jp/entry/compound/C00001/kcf
• http://togows.dbcls.jp/entry/compound/C00001/comment

TODO

• http://togows.dbcls.jp/entry/compound/C00001/pathways # cross_ref
• http://togows.dbcls.jp/entry/compound/C00001/dblinks # cross_ref

Examples - KEGG DRUG

• http://togows.dbcls.jp/entry/drug/D00001
• http://togows.dbcls.jp/entry/drug/D00001/entry_id
• http://togows.dbcls.jp/entry/drug/D00001/name
• http://togows.dbcls.jp/entry/drug/D00001/names
• http://togows.dbcls.jp/entry/drug/D00001/formula
• http://togows.dbcls.jp/entry/drug/D00001/mass
• http://togows.dbcls.jp/entry/drug/D00001/activity
• http://togows.dbcls.jp/entry/drug/D00001/remark
• http://togows.dbcls.jp/entry/drug/D00001/comment
• http://togows.dbcls.jp/entry/drug/D00001/kcf

TODO

• http://togows.dbcls.jp/entry/drug/D00001/pathways # cross_ref
• http://togows.dbcls.jp/entry/drug/D00001/dblinks # cross_ref

Examples - KEGG GLYCAN

• http://togows.dbcls.jp/entry/glycan/G00001
• http://togows.dbcls.jp/entry/glycan/G00001/entry_id
• http://togows.dbcls.jp/entry/glycan/G00001/name
• http://togows.dbcls.jp/entry/glycan/G00001/mass
• http://togows.dbcls.jp/entry/glycan/G00001/keggclass
• http://togows.dbcls.jp/entry/glycan/G00001/compounds
• http://togows.dbcls.jp/entry/glycan/G00001/reactions
• http://togows.dbcls.jp/entry/glycan/G00001/enzymes
• http://togows.dbcls.jp/entry/glycan/G00001/orthologs # cross_ref
• http://togows.dbcls.jp/entry/glycan/G00001/comment
• http://togows.dbcls.jp/entry/glycan/G00001/remark
• http://togows.dbcls.jp/entry/glycan/G00001/references
• http://togows.dbcls.jp/entry/glycan/G00001/dblinks # cross_ref
• http://togows.dbcls.jp/entry/glycan/G00001/kcf

TODO

• http://togows.dbcls.jp/entry/glycan/G00001/composition # Hash
• http://togows.dbcls.jp/entry/glycan/G00001/pathways # cross_ref

Examples - KEGG REACTION

• http://togows.dbcls.jp/entry/reaction/R00005
• http://togows.dbcls.jp/entry/reaction/R00005/entry_id
• http://togows.dbcls.jp/entry/reaction/R00005/name
• http://togows.dbcls.jp/entry/reaction/R00005/definition
• http://togows.dbcls.jp/entry/reaction/R00005/equation
• http://togows.dbcls.jp/entry/reaction/R00005/enzymes

TODO

• http://togows.dbcls.jp/entry/reaction/R00005/rpairs # cross_ref
• http://togows.dbcls.jp/entry/reaction/R00005/pathways # cross_ref