Chemical Analysis Tools API

This is a brief specification document for the REST-style GenomeNet chamical analysis tools API.

[ GenomeNet | Chemical Tools API | Genome Tools API | LinkDB API | DBGET API ]

Contents

simcomp: similar chemical structure search

simcomp2: all vs. all similarity calculation

subcomp: substructure search

mol2kcf/sdf2kcf: MOL or SDF file converstion to KCF format

ezyme: enzyme ortholog prediction

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|none] | 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 (default); none: disable post-processing
trickatom: Docking atom for post-processing; 0: Atom species (default); 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|none] | trickatom=[0|1|2] | mode=[local|global] | chiral=[on|off] |
          kcfoutput=[on|off]

Examples

/simcomp2/C00022/C00186    calculates similarity between KEGG C00022 (pyruvate) and C00186 (S-Lactate)
/simcomp2/C00022+C00186/C00256+C01432+C00109+C00957/mode=local     
     calculates 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     
     calculates all to all similarities between the first and second sets using the specified parameters
/simcomp2/C00022+C00186/C00256+C01432+C00109+C00957/kcfoutput=on     
     calculates 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/     
    

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
sdf2kcf - returns a KCF formatted chemical structure file for a given SDF formatted structure file

URL form

http://rest.genome.jp/mol2kcf/
http://rest.genome.jp/sdf2kcf/

This operation only allows file uploads

File upload

Use command line tools such as curl   
% curl -F molfile=@<filename> http://rest.genome.jp/mol2kcf/
% curl -F sdffile=@<filename> http://rest.genome.jp/sdf2kcf/ 		    

See also

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

Enzyme ortholog prediction

Operation

ezyme - returns a list of predicted KEGG Ortholog ID (KO), Ortholog Cluster ID (OC) and Reactant pair ID (RP) for a given pair of reactants.

URL form

http://rest.genome.jp/ezyme/<query1>/<query2>[/version=1]

<query1> = <query2> = KEGG COMPOUND/DRUG, PubChem or KNApSAcK entry IDs

version=1 option is for the older version of e-zyme that predicts EC subsubclasses

Examples

/ezyme/C00077/C00327    predicts ortholog candidates for the reaction from C00077 (Ornithine) to C00327 (Citrulline)
/ezyme/D08302/C00327    KEGG DRUG ID (D08302 for Ornithine) can be used instead of COMPOUND ID
/ezyme/CID6262/C00327    PubChem CID (CID6262 for Ornithine) can be used
/ezyme/SID3377/C00327    PubChem SID (SID3377 for Ornithine) can be used
/ezyme/C00001384/C00327    KNApSAcK ID (C00001384 for Ornithine) can be used

File upload

Use command line tools such as curl   
% curl -F substrate_file=@<filename1> -F product_file=@<filename2> http://rest.genome.jp/ezyme/
    

See also

E-zyme2 web page

Last updated: December 4, 2015