GenomeNet Tools API

This is a brief specification document for the REST-style GenomeNet Tools API.


Chemical analysis tools

Chemical structure search and comparison

Operation

simcomp - returns a list of compound ID and score similar to a given structure from a chemical database

URL form

http://rest.genome.jp/simcomp/<query>/<database>[/<params>]

<query> = KEGG COMPOUND/DRUG or KNApSAcK entry ID
<database> = compound (default) | drug | knapsack | reaction | 
             KEGG COMPOUND/DRUG or KNApSAcK entry IDs
<params> = <param>[/<params>]
<param> = offset=<num> | limit=<num> | cutoff=<num> | dnode=[0|2] | atom=[0|1|2] | 
          trick=[0|2] | trickatom=[0|1|2] | mode=[local|global] | chiral=[on|off] |
          kcfoutput=[on|off]

Examples

/simcomp/C00022    searches compounds similar to KEGG C00022 (pyruvate) from KEGG COMPOUND
/simcomp/C00022/C00186+C00256+C01432+C00109+C00957/mode=local     
     searches compounds similar to KEGG C00022 from five compounds in KEGG COMPOUND using the local search mode
/simcomp/C00022/compound/cutoff=0.6/dnode=2/atom=2/trick=2/trickatom=0/limit=10/chiral=off     
     searches compounds similar to KEGG C00022 from KEGG COMPOUND using the specified parameters
/simcomp/C00022/knapsack/kcfoutput=on     
     searches compounds similar to KEGG C00022 (pyruvate) from KNApSAcK with KCF alignment outputs.

File upload and SMILES

Use command line tools such as curl   
% curl -F molfile=@<filename> http://rest.genome.jp/simcomp/     
% curl -F kcffile=@<filename> http://rest.genome.jp/simcomp/     
% curl -F smiles='O=C(C(=O)O)C' -F cutoff=0.6 -F limit=10 http://rest.genome.jp/simcomp/     

Parameter details

offset: Number for starting index, e.g. 11 for showing results from the 11th hit
limit: Number of hits shown from the top or the index specified by offset
cutoff: Threshold score; default=0.4
dnode: Docking mode; 0: Atom based; 2: Bond based (default)
atom: Docking atom; 0: Atom species; 1: Atom class; 2: KEGG atom (default)
trick: Enable post-processing; 0: for the largest SCCS; 2: for all SCCSs
trickatom: Docking atom for post-processing; 0: Atom species; 1: Atom class; 2: KEGG atom
mode: local: same as dnode=2, atom=2, trick=0 and trickatom=1
  global: same as dnode=2, atom=2, trick=2 and trickatom=0
chiral: on: enable chiral check (default); off: disable chiral check
kcfoutput: on: enable KCF alignment output; off: output IDs and socres only (default)

See also

SIMCOMP help page

Operation

simcomp2 - returns all to all comparisons for two input sets of chemical structures

URL form

http://rest.genome.jp/simcomp2/<query1>/<query2>[/<params>]

<query1> = <query2> = KEGG COMPOUND/DRUG or KNApSAcK entry IDs
<params> = <param>[/<params>]
<param> = offset=<num> | limit=<num> | cutoff=<num> | dnode=[0|2] | atom=[0|1|2] | 
          trick=[0|2] | trickatom=[0|1|2] | mode=[local|global] | chiral=[on|off] |
          kcfoutput=[on|off] 

Examples

/simcomp2/C00022/C00186    calculate similarity between KEGG C00022 (pyruvate) and C00186 (S-Lactate)
/simcomp2/C00022+C00186/C00256+C01432+C00109+C00957/mode=local     
     calculate all to all similarities between the first and second sets using the local search mode
/simcomp2/C00022+C00186/C00256+C01432+C00109+C00957/cutoff=0.6/dnode=2/atom=2/trick=2/trickatom=0/limit=10/chiral=off     
     calculate all to all similarities between the first and second sets using the specified parameters
/simcomp2/C00022+C00186/C00256+C01432+C00109+C00957/kcfoutput=on     
     calculate all to all similarities between the first and second sets, and output with KCF alignment format

Mol file upload

Use command line tools such as curl   
% curl -F query_file=@<queryfilename> -F target_file=@<targetfilename> http://rest.genome.jp/simcomp2/     
Input files should be single files in the SDF or concatenated MOL format.     
    

Parameter details

Same as simcomp other than the cutoff default is 0.8

See also

SIMCOMP2 help page

Chemical substructure search

Operation

subcomp - returns a list of compound ID and score that includes or is included in a given structure from a chemical database

URL form

http://rest.genome.jp/subcomp/<query>/<database>[/<params>]

<query> = KEGG COMPOUND/DRUG or KNApSAcK entry ID
<database> = compound (default) | drug | knapsack | reaction | 
             KEGG COMPOUND entry IDs
<params> = <param>[/<params>]
<param> = offset=<num> | limit=<num> | cutoff=<num> | mode=[all|sub|sup] | charge=[on|off] |
          valence=[on|off] | coordinate=[on|off] | chiral=[on|off] | kcfoutput=[on|off]

Examples

/subcomp/C00022    searches substructures for KEGG C00022 (pyruvate) from KEGG COMPOUND
/subcomp/C00022/C00048+C00141+C17265+C00109+C00957/mode=sup     
     searches superstructures for KEGG C00022 from five compounds in KEGG COMPOUND
/subcomp/C00022/compound/cutoff=0.6/limit=10/mode=all/charge=on/coordinate=on/valence=on/chiral=on     
     searches substructures for KEGG C00022 from KEGG COMPOUND using the specified parameters
/subcomp/C00022/C00048+C00141+C17265+C00109+C00957/kcfoutput=on     
     searches sub/superstructures for KEGG C00022 from five compounds in KEGG COMPOUND with KCF alignment outputs

File upload and SMILES

Use command line tools such as curl   
% curl -F molfile=@<filename> http://rest.genome.jp/subcomp/     
% curl -F kcffile=@<filename> http://rest.genome.jp/subcomp/     
% curl -F smiles='O=C(C(=O)O)C' -F cutoff=0.8 -F limit=10 http://rest.genome.jp/subcomp/     

Parameter details

offset: Number for starting index, e.g. 11 for showing results from the 11th hit
limit: Number of hits shown from the top or the index specified by offset
cutoff: Threshold score; default=0
mode: Search mode; all: all matches (default); sub: only substructures; sup: only superstructures
charge: Distinguish charged atom, e.g. "OH" from "O-"; default is off
valence: Distinguish valence, e.g. "S<" from "=S="; default is off
coordinate: Consider coordinate bond, e.g. "[X+]-[Y-]" as "X=Y"; default is off
chiral: on: enable chiral check; off: disable chiral check (default)

See also

SUBCOMP help page

Chemical structure conversion

Operation

mol2kcf - returns a KCF formatted chemical structure file for a given MOL formatted structure file

URL form

http://rest.genome.jp/mol2kcf/

This operation only allows file uploads

File upload

Use command line tools such as curl   
% curl -F molfile=@<filename> http://rest.genome.jp/mol2kcf/     

See also

SIMCOMP help page for the KCF (KEGG Chemical Function) format


Last updated: September 10, 2013