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From WABI
This wiki page introduces know-how of Web API for Biology (WABI). Japanese page is here.
It is able to connect from a Web API to other Web API as a workflow by sharing the Input-Output type.
The connection as a workflow can be confirmed with Workflow Navigation System.
Please refer to the following link about Input-Output type.
Contents |
ID search
- Retrieve DDBJ entry by specifying accession number
- Retrieve DNA sequence of DDBJ entry by specifying accession number
- Retrieve PDB entry by specifying EC number
- Retrieve HIT annotation in XML format
- Retrieve amino acid sequence of E.coli by specifying gene name
- Retrieve pathway by specifying pathway ID
- Retrieve organism name of DDBJ entry by specifying accession number
- Retrieve CDS by specifying DDBJ accession number
- Retrieve amino acid sequence by specifying DDBJ accession number
- Retrieve amino acid sequence by specifying DAD accession number
- Retrieve DAD entry by specifying DAD accession number
- Retrieve DAD entry by specifying Protein ID
- Retrieve amino acid sequence in DAD by specifying Protein ID
- Retrieve amino acid sequence by specifying UniProt accession number
- Retrieve UniProt entry by specifying UniProt accession number
- Retrieve amino acid sequence by specifying PDB accession number
- Retrieve PDB entry by specifying PDB accession number
- Retrieve amino acid sequence by specifying PRF accession number
- Retrieve PRF entry by specifying PRF accession number
- Retrieve amino acid sequence and OMIM ID from a protein ID
- GetDDBJVerEntry of GetEntry service does not work
- Retrieve DDBJ entries by specifying gene name and execute BLAST at once
- Retrieve amino acid sequences of ORF whose organism is Herpes virus and whose length is over 50.
- Retrieve genome entry of virus from DDBJ
- Retrieve tree information by GO ID
- Retrieve patent amino acid sequence from JPO/KIPO
- Retrieve patent amino acid sequence from EPO
- Retrieve patent amino acid sequence from USPTO
Keyword search
- Search DDBJ entries by gene name of human
- Search DDBJ entries by free keyword
- Retrieve entries by specifying gene name
- Retrieve entries by specifying organism name
- Search PDB entries by free keyword
- Search KEGG enzyme by free keyword
- Search pathway by gene name
- Retrieve taxonomy information
- Search DAD by free keyword
- Search UniProt/Swiss-Prot by free keyword
- Search UniProt/TrEMBL by free keyword
- Search PRF by free keyword
- Retrieve HIT ID by specifying accession number
- Search OMIM by specified keyword
- Retrieve genotype and frequency from SNP ID
- Search PubMed by Reference SNP ID
- Retrieve entry by specifying sequence length against DDBJ database
- Retrieve cross reference by GO ID
- Phrase search by ARSA
- AND OR search with plural keywords by ARSA
- Search against GO database by function or gene name
- Search DDBJ entries by specifying specimen/strain name
- Search dbSNP by gene name of an acetaldehyde
- Retrieve reference SNP ID that has an amino acid substitution from a protein ID
- Retrieve OMIM record by OMIM ID
- Retrieve sequence details from ID that starts with "NM" or "NC"
Sequence search
- Execute BLAST for homologous sequences
- Execute BLAST for homologous sequences in tab-delimited format
- Execute BLAST with DNA sequence against DDBJ database
- Execute BLAST with amino acid sequence against UniProt/Swiss-Prot database
- Specify reference database same as DDBJ web page in BLAST
- Retrieve result with XML format from BLAST
- Retrieve reference database list of BLAST
- Execute BLAST with local DNA sequence file
- Execute BLAST with accession number
- Specify all DDBJ database for BLAST
- Shorten execution time of BLAST
- Extract specific organism from BLAST execution result
- Retrieve DDBJ entries by specifying gene name and execute BLAST at once
- Execute TBLASTN against large database
- Nr database of default cannot be specified against BLAST
- Execute BLAST asynchronously
- Examine the meaning of each column in the BLAST tab delimited format which is generated by -m 8 option.
- Execute VecScreen with multi-FASTA format file
Multiple alignment
- Execute ClustalW with multiple sequences
- Execute Mafft with multiple sequences
- Execute phylogenetic analysis with multiple alignment
- Generate tree image in JPEG format from Phylip format
Use proxy server
- Use REST service via a proxy server with LWP
- Use REST service via a proxy server with socket(Perl)
- Use REST service via a proxy server with URLConnection(Java)
- Use REST service via a proxy server with socket(Java)
- Use REST service via a proxy server with socket(C)
- Use REST service via a proxy server with socket(Ruby)
- Use REST service via a proxy server with socket(Pyhton)
- Use SOAP service via a proxy server with SOAP::Lite
- Use SOAP service via a proxy server with AXIS
Use query including non alphanumeric character
- Encode query with Perl
- Encode query with Java
- Encode query with C
- Encode query with C Sharp
- Encode query with Ruby
- Encode query with Python
Other know-how
- Execute ClustalW
- Retrieve version of Ensembl service
- Retrieve execution result of asynchronous method
- Solve java.lang.NoClassDefFoundError problem
- Construct SOAP server same as DDBJ
- Execution result cannot be retrieved.
- About the SOAP binding
- Prevent time-out
- SOAP is unavailable with SOAP::Lite 0.69
- Use SOAP with Ruby
- Error occurs in REST execution
- Use DDBJ services in Taverna
- Use DDBJ WebAPI in my service
