BioCyc Web Services
TEST
BioCyc offers several classes of
REST-based
web services that are summarized in the table below. These services include:
- Data retrieval services that return data in XML, JSON, and/or column-delimited formats
(BioCyc data can also be downloaded in a variety of XML and non-XML formats)
- Visualization services, e.g., to map gene expression data onto pathway diagrams
- Services for manipulating SmartTables
Use of the BioCyc web services API is subject to the terms of the
BioCyc Databases Limited Use License. Note that to avoid congestion
on the BioCyc web servers, we respectfully request that when writing
programs that issue large numbers of web service queries, you limit
requests to on average not more than one per second.
Note that in order to access BioCyc web services you must establish
a session (see below) and utilize the returned cookies in subsequent
web-services calls.
Class of Service |
Service |
Input |
Output |
HTTP GET or POST |
Retrieve a Single PGDB Object |
BioCyc object retrieval
|
BioCyc Object ID |
ptools-XML |
GET |
Search and Retrieve a Set of Objects |
Data Retrieval Web Services |
BioCyc Object ID |
BioPAX XML |
GET |
Foreign object-ID (external database identifier) retrieval |
Foreign database ID |
tab delimited file or JSON file |
GET, POST |
Retrieve object sets, e.g., genes-of-pathway, compounds-of-pathway |
BioCyc Object ID |
ptools-XML |
GET |
Evaluate query written in BioVelo query language |
BioVelo Query |
Object set encoded as ptools-XML |
|
Metabolite monoisotopic weight retrieval |
Monoisotopic MW, tolerance |
tab delimited, JSON |
GET, POST |
Metabolite chemical formula retrieval |
Chemical Formula |
tab delimited, JSON |
GET, POST |
Metabolite Translation Service |
|
tab delimited |
GET, POST |
Retrieve objects by name |
BioCyc Object Name |
tab delimited, JSON |
GET, POST |
Retrieve objects by SMILES string |
SMILES String |
tab delimited, JSON |
GET, POST |
Retrieve objects by INCHI string |
INCHI String |
tab delimited, JSON |
GET, POST |
Visualization Services |
Generate Compound Image |
Compound ID |
GIF image |
GET |
Generate Pathway Diagram |
Pathway ID |
GIF image |
GET, POST |
Omics Visualization Services |
Pathway Diagram Painted with Omics Data |
Pathway ID |
HTML |
GET, POST |
Table of Pathway Diagrams Painted with Omics Data |
Pathway ID |
HTML |
GET, POST |
Highlight/Paint Objects on Metabolic Network Diagram |
Object Names and / or IDs |
HTML |
GET |
Paint Omics Data from a File on Metabolic Network Diagram |
Object Names and / or IDs |
HTML |
GET |
SmartTables |
SmartTable Creation |
|
|
POST |
SmartTable Data Retrieval |
|
tab delimited, JSON, csv |
GET |
SmartTable Add Transform Column |
|
|
GET |
SmartTable Add Property Column |
|
|
GET |
SmartTable Add Empty Row |
|
|
GET |
SmartTable Delete Row |
|
|
GET |
SmartTable Add Empty Column |
|
|
GET |
SmartTable Delete Column |
|
|
GET |
SmartTable Modify Cell |
|
|
POST |
SmartTable Modify Name |
|
|
GET |
SmartTable Modify Description |
|
|
GET |
SmartTable Copy |
|
|
GET |
SmartTable Delete |
|
|
GET |
Establishing a Web Services session
To use the BioCyc web services, you must establish a session and log
in to your BioCyc account by POSTing your email and password to
https://websvc.biocyc.org/credentials/login/. The cookies
returned from this request must then be passed back to BioCyc for
every subsequent web service request.
Example using curl
# Log in and save cookies to file biocyc_cookies (POST only):
curl -c biocyc_cookies -d "email=[email]&password=[password]" -X POST https://websvc.biocyc.org/credentials/login/
# Issue web service request, passing cookie file:
curl -b biocyc_cookies https://websvc.biocyc.org/[request]
Example using python Requests module
s = requests.Session() # create session
# Post login credentials to session:
s.post('https://websvc.biocyc.org/credentials/login/', data={'email':'[email]', 'password':'[password]'})
# Issue web service request:
r = s.get('https://websvc.biocyc.org/[request]')
Data Retrieval Web Services: Pathway Tools XML
Any pathway, reaction, compound, gene, protein, RNA or
transcription-unit object in a BioCyc database can be retrieved in
ptools-xml format, an XML format that is based on and closely
resembles the underlying Pathway Tools schema. A single object can be
requested using its BioCyc identifier, or a query can be
issued using either a subset of the Pathway Tools API functions or the
BioVelo query
language to retrieve multiple objects.
The following documents will be useful in interpreting the ptools-xml format:
The Pathway Tools Schema Guide |
A guide to the internal Pathway Tools representation, describing classes and their slots (attributes). |
Guide to ptools-xml |
This document describes the ptools-xml format and the differences between ptools-xml and the Pathway Tools Schema, including the mapping of class and slot names from one to the other. |
ptools-xml.xsd |
An XMLSchema document describing the ptools-xml format |
ptools.wsdl |
A WSDL document describing the ptools-xml-based web services. |
The URLs for retrieving the KB-version is
https://websvc.biocyc.org/kb-version?orgid=[ORGID]
where
- [ORGID] is the identifier for the organism database,
e.g. ECOLI, META, BSUB.
Example URLs:
The default output is a JSON format as follows:
{"kb-version":"19.5"}
Biocyc Object-Id-Based Retrieval of XML Data
The URL to retrieve a single BioCyc object in ptools-xml format is
https://websvc.biocyc.org/getxml?[ORGID]:[OBJECT-ID]
or
https://websvc.biocyc.org/getxml?id=[ORGID]:[OBJECT-id]&detail=[none|low|full]
where
- [ORGID] is the identifier for the organism database,
e.g. ECOLI, META, AFER243159.
- [OBJECT-ID] is in the BioCyc identifier for the
object, e.g. ARGSYN-PWY, EG11025, FRUCTOSE-6P. Note that object identifiers are case-sensitive.
- [none|low|full] indicates whether the returned output should contain no detail, low detail or full detail for the requested object. If no detail parameter is supplied, the request defaults to full detail.
Example URLs:
Search and Retrieve a Set of Objects
Retrieving a Set of Objects Using the Pathway Tools API Functions
The set of Pathway
Tools API functions were defined to allow users who have
downloaded and installed the Pathway Tools software locally (why do this?) to write programs
that operate on the data. A subset of these API functions have been
made available via the web services interface.
The URL to issue an API query that returns a list of objects in
ptools-xml format is
https://websvc.biocyc.org/apixml?fn=[API-FUNCTION]&id=[ORGID]:[OBJECT-ID]&detail=[none|low|full]
where [ORGID], [OBJECT-ID] and detail level are
as for the single object queries described above, and
[API-FUNCTION] is one of the following:
- all-products-of-gene
- binding-site-transcription-factors
- chromosome-of-gene
- compounds-of-pathway
- containers-of
- containing-tus
- direct-activators
- direct-inhibitors
- enzymes-of-gene
- enzymes-of-pathway
- enzymes-of-reaction
- genes-of-pathway
- genes-of-protein
- genes-of-reaction
- genes-regulated-by-gene
- genes-regulating-gene
- get-class-all-instances
- get-class-all-subs
- get-class-direct-supers
- get-class-direct-subs
- modified-containers
- modified-forms
- monomers-of-protein
- pathways-of-compound
- pathways-of-gene
- reactions-of-compound
- reactions-of-enzyme
- reactions-of-gene
- regulator-proteins-of-transcription-unit
- regulon-of-protein
- substrates-of-reaction
- top-containers
- transcription-unit-activators
- transcription-unit-binding-sites
- transcription-unit-genes
- transcription-unit-inhibitors
- transcription-unit-mrna-binding-sites
- transcription-unit-promoter
- transcription-unit-terminators
- transcription-unit-transcription-factors
- transcription-units-of-gene
- transcription-units-of-protein
A more detailed description of each API function is available here.
Example URLs:
Retrieving the Set of Objects Returned by a BioVelo Query
The URL to issue a BioVelo query that returns a list of objects in
ptools-xml format is
https://websvc.biocyc.org/xmlquery?[QUERY] or
https://websvc.biocyc.org/xmlquery?query=[QUERY]&detail=[none|low|full]
where
- [QUERY] is a properly escaped BioVelo query string that
returns a single list of Pathway Tools objects (it is possible to
create BioVelo queries that return multi-column tables -- these are
not appropriate as input for this web service). For more information
about constructing BioVelo queries, see the
Guide to the BioVelo Query Language.
- [none|low|full] indicates whether the returned output should contain no detail (i.e. only object identifiers and links will be included), low detail (names and a handful of other attributes will be included) or full detail for the matching objects. If no detail parameter is supplied, the request defaults to low detail.
NOTE: the BioVelo query needs to be URL encoded if it contains any non-alphanumeric characters. You might look here, or here if you are unfamiliar with URL encoding.
Example URLs:
-
https://websvc.biocyc.org/xmlquery?%5bx%3ax%3c-ecoli%5e%5epathways%5d
Retrieve the complete set of pathways in the EcoCyc database at low detail, where the query [x:x<-ecoli^^pathways]
has been URL encoded as %5bx%3ax%3c-ecoli%5e%5epathways%5d.
-
https://websvc.biocyc.org/xmlquery?query=[x:x<-ecoli^^genes,x^name%3D"trpA"]&detail=full
Retrieve the gene (or genes) in the EcoCyc database with the name "trpA" in full detail,
where the query [x:x<-ecoli^^genes,x^name%3D"trpA"]
has been encoded as %5bx%3ax%3c-ecoli%5e%5egenes%2cx%5ename%253D%22trpA%22%5d.
-
https://websvc.biocyc.org/xmlquery?dbs
Retrieve the set of available organism databases, and the query requires no URL encoding.
-
https://websvc.biocyc.org/xmlquery?%5bx%3ay%3a%3dbsub~argsynbsub-pwy%2cx%3c-(enzymes-of-pathway+y)%5d
Retrieve the set of enzymes that participate in the arginine biosynthesis pathway in Bacillus subtilis,
where the query [x:y:=bsub~argsynbsub-pwy,x<-(enzymes-of-pathway y)]
has been URL encoded as %5bx%3ay%3a%3dbsub~argsynbsub-pwy%2cx%3c-(enzymes-of-pathway+y)%5d.
-
https://websvc.biocyc.org/xmlquery?%5bx%3ax%3c-meta%5e%5eproteins%2c+%22aspartate%22+instringci+x%5enames%26%22kinase%22+instringci+x%5enames%5d
Retrieve the set of proteins in MetaCyc that have the words "aspartate" and "kinase" in their common-name or synonyms
where the query [x:x<-meta^^proteins, "aspartate" instringci x^names&"kinase" instringci x^names]
has been URL encoded as %5bx%3ax%3c-meta%5e%5eproteins%2c+%22aspartate%22+instringci+x%5enames%26%22kinase%22+instringci+x%5enames%5d.
-
https://websvc.biocyc.org/xmlquery?query=%5bx%3ax%3c-ecoli%5e%5epathways%2cecoli~EG10258+in+(pathway-to-genes+x)%5d&detail=none
Retrieve the identifiers of all pathways containing the eno (enolase) gene in Escherichia coli,
where the query [x:x<-ecoli^^pathways,ecoli~EG10258 in (pathway-to-genes x)]
has been encoded as %5bx%3ax%3c-ecoli%5e%5epathways%2cecoli~EG10258+in+(pathway-to-genes+x)%5d.
Data Retrieval Web Services: BioPAX XML
Pathway data for an individual pathway are available in
BioPAX format (both BioPAX Level 2 and Level
3). The URL to access a pathway in BioPAX format is:
https://websvc.biocyc.org/[ORGID]/pathway-biopax?type=[2|3]&object=[PATHWAY]
where
- [ORGID] is the identifier for the organism database,
e.g. ECOLI, META, AFER243159
- [2|3] specifies whether data should use BioPAX Level 2
or Level 3. If the type argument is omitted, BioPAX Level 3 will be generated.
- [PATHWAY] is in the BioCyc identifier for the
pathway, e.g. GLYCOLYSIS, ARGSYN-PWY, PWY0-1299
Example URLs:
Retrieving a BioCyc Object Given a Foreign ID
This service finds the BioCyc ID of an object given a
foreign ID, that is, an identifier of that object in an external database.
This service depends on the foreign ID being stored in the DB-Links slot of
a BioCyc object. All DB-Links in a given PGDB are searched.
Example foreign IDs: Uniprot IDs (P11509) for proteins; KEGG IDs (C00033) for compounds, etc.; Rhea IDs (10743) for reactions.
BioCyc objects such as pathways, reactions, compounds, genes, proteins, RNAs, or transcription-units in a PGDB can be retrieved given a foreign identifier that matches that object.
The URLs to search for objects based on foreign identifier are
https://websvc.biocyc.org/[ORGID]/foreignid?ids=[DATABASE-NAME]:[FOREIGNID]
or
https://websvc.biocyc.org/[ORGID]/foreignid?ids=[DATABASE-NAME]:[FOREIGNID]&fmt=json
where
- [ORGID] is the identifier for the organism database,
e.g. ECOLI, META, AFER243159.
- [DATABASE-NAME] is the name of external database,
e.g. KEGG, PUBCHEM, UNIPROT.
- [FOREIGNID] is the external database identifier. The foreignid input may contain one or more values, which may be separated by commas. Note that foreignids are case-sensitive.
- fmt=json requests output in the JSON format; default output is in tab-delimited format.
This web service can be used if the user is retrieving the results by either the "POST" or "GET" method.
Example URLs:
The default output is a tab-delimited format as follows:
Kegg:C00849 1 ETHYLACETATE
EcoGene:EG11025 1 EG11025
where
column 1 : Input Foreign ID.
column 2 : 1 means that a valid object that matches the foreign ID was found and 0 means that no object that matches the foreign ID was found.
column 3 : The BioCyc identifier of the object that matches the foreign ID.
JSON format:
[{"INPUT":"UniProt:P05653","STATUS":1,"RESULTS":[{"ID":"BSU00070-MONOMER"}]}]
Retrieving a BioCyc Object Given a Chemical Formula
This service finds the BioCyc IDs of all metabolites that exactly match a
supplied chemical formula. This service consults the Chemical-Formula slot of
BioCyc compounds.
The URLs to search metabolites based on chemical formula are
https://websvc.biocyc.org/[ORGID]/CF?cfs=[CHEMICAL-FORMULA]
or
https://websvc.biocyc.org/[ORGID]/CF?cfs=[CHEMICAL-FORMULA]&fmt=json
where
- [ORGID] is the identifier for the organism database,
e.g. ECOLI, META, AFER243159.
- [CHEMICAL-FORMULA] is the chemical formula to be matched, in the format ([element-symbol][coefficient])+. The chemical formula input may contain one or more values, which may be separated by commas.
The search will return all metabolites in the specified database that have the exact
chemical formula(s) provided here.
- fmt=json requests output in JSON format; default output is in tab-delimited format
This web service can be used if the user is retrieving the results by either the "POST" or "GET" method. If multiple Chemical formulas are provided than this web service will search for compounds matching each of the chemical formula.
Example URLs:
The default output is a tab-delimited format as follows:
C6H6 1 BENZENE benzene
H2O3 0
where
column 1 : Input Chemical Formula.
column 2 : 1 means that a valid compound that matches the chemical formula was found; 0 means that no match was found.
column 3 : The BioCyc identifier of the compound that matches the chemical formula.
column 4 : The common-name of the compound.
JSON format:
[{"INPUT":"H2O2","STATUS":1,"RESULTS":[{"ID":"HYDROGEN-PEROXIDE","NAME":"hydrogen peroxide"}]},{"INPUT":"H2O3","STATUS":0}]
Retrieving a BioCyc Compound given a Monoisotopic Weight and Tolerance
Compounds in a PGDB can be retrieved given a monoisotopic molecular weight and tolerance.
The URLs to search for compounds based on monoisotopic molecular weight and tolerance are
https://websvc.biocyc.org/[ORGID]/monoisotopicwt?wts=[MONOISOTOPICMW]&tol=[TOLERANCE]
or
https://websvc.biocyc.org/[ORGID]/monoisotopicwt?wts=[MONOISOTOPICMW]&tol=[TOLERANCE]&fmt=json
where
- [ORGID] is the identifier for the organism database,
e.g. ECOLI, META, AFER243159.
- [MONOISOTOPICMW] is a floating point number, standing for the monoisotopic molecular weight in daltons. One or more monoisotopic molecular weights can be supplied, where multiple values are separated by commas.
- [TOLERANCE] is the search tolerance +/- in ppm.
- fmt=json requests output in the JSON format; default output is in tab-delimited format
This web service can be used if the user is retrieving the results by either the "POST" or "GET" method.
Example URLs:
The default output is a tab-delimited format as follows:
123.009 1 123.008705 3-chloro-L-alanine CHLORALAN-CPD
123.009 1 123.008705 3-chloro-D-alanine 3-CHLORO-D-ALANINE
123.009 1 123.008705 2-chloro-L-alanine CPD0-1475
123.009 1 123.008705 3-chloro-DL-alanine 3-CHLORO-DL-ALANINE
56 0
where
column 1 : Input monoisotopic molecular weight for this search.
column 2 : 1 means the query was successful and 0 means the query found no match.
column 3 : Monoisotopic molecular weight of the compound that is stored in the PGDB
column 4 : Compound name
column 5 : The BioCyc identifier of the compound.
JSON format:
[{"INPUT":"123.009","STATUS":1,"RESULTS":[{"MW":123.008705,"NAME":"3-chloro-L-alanine","ID":"CHLORALAN-CPD"},{"MW":123.008705,"NAME":"3-chloro-D-alanine","ID":"3-CHLORO-D-ALANINE"},{"MW":123.008705,"NAME":"2-chloro-L-alanine","ID":"CPD0-1475"},{"MW":123.008705,"NAME":"3-chloro-DL-alanine","ID":"3-CHLORO-DL-ALANINE"}]},{"INPUT":"56","STATUS":0}]
Metabolite Translation Service
This web service translates metabolite names, identifiers, InChI
strings, InChI keys, monoisotopic molecular weights, and molecular
formula, between metabolite databases. Its input is a set of lines,
one line per metabolite. Each line of the file contains one or more
metabolite names, identifiers, and an optional InChI string, InChI key,
monoisotopic molecular weight, and chemical formula. The service looks up each of the preceding fields
within the specified BioCyc database.
Three cases are possible for each line:
1) None of the provided fields is recognized in the specified BioCyc database, in which case "unknown" is returned, along with the unknown input fields.
2) All of the recognized names, identifiers, InChI string, InChI key, monoisotopic weight, and chemical formula
match a single metabolite, in which case "successful" is returned, along with the following tab-separated
fields:
- BioCyc ID of matching metabolite
- BioCyc common name of matching metabolite
- Additional identifiers present in BioCyc from other databases for the matching metabolite
3) The recognized names, identifiers, InChI string, InChI key, monoisotopic weight, and chemical formula match
more than one metabolite, in which case "ambiguous" is returned, along with the ambiguous fields from the input.
The default input for the file or for pasting data is a tab-delimited format.
Example:
Kegg:C00001 PubChem:125
TRP
ACET
The default output is a tab-delimited format as follows:
ambiguous BioCyc:WATER BioCyc:4-HYDROXY-BENZYL-ALCOHOL
success BioCyc:TRP L-tryptophan MetaboLights:MTBLC57912 HMDB:HMDB00929 IAF1260:33772 ChEBI:57912 PubChem:6923516 KEGG:C00078 CAS:73-22-3
success BioCyc:ACET acetate MetaboLights:MTBLC30089 HMDB:HMDB00042 DrugBank:DB03166 IAF1260:33590 ChemSpider:170 PubChem:175 ChEBI:30089 CAS:64-19-7 KEGG:C00033 CAS:71-50-1
To access the metabolite translation service interactively,
click here
Retrieve BioCyc Objects from a Class by Name
Objects from a specified class in a PGDB can be retrieved by name:
https://websvc.biocyc.org/[ORGID]/name-search?object=[NAME]&class=[CLASS]
or
https://websvc.biocyc.org/[ORGID]/name-search?object=[NAME]&class=[CLASS]&fmt=json
where
- [ORGID] is the identifier for the organism database,
e.g. ECOLI, META, AFER243159.
- [NAME] is is the name of the object to retrieve.
- [CLASS] is the class from which the object is to be retrieved, e.g. Genes.
- fmt=json requests output in the JSON format; default output is in tab-delimited format.
This web service can be used if the user is retrieving the results by either the "POST" or "GET" method.
Example URLs:
The default output is a tab-delimited format as follows. If no results are found then the string EMPTY-RESULT is returned.
EG11024 trpA
where
column 1 : BioCyc Object ID
column 2 : Common Name
JSON format:
{"RESULTS":[{"OBJECT-ID":"EG11024","COMMON-NAME":"trpA"}]}
Retrieve BioCyc Objects by SMILES String
Retrieve compounds whose chemical structure matches a given SMILES string:
https://websvc.biocyc.org/[ORGID]/smiles-search?smiles=[SMILES]&exact=[EXACT]
or
https://websvc.biocyc.org/[ORGID]/smiles-search?smiles=[SMILES]&exact=[EXACT]&fmt=json
where
- [ORGID] is the identifier for the organism database,
e.g. ECOLI, META, AFER243159.
- [SMILES] is the SMILES string,
e.g. CN, CO.
- [EXACT] is a Boolean, either T (true) or F (false).
- fmt=json requests output in the JSON format; default output is in tab-delimited format.
This web service can be used if the user is retrieving the results by either the "POST" or "GET" method.
Example URLs:
The default output is a tab-delimited format as follows. If no results are found then the string EMPTY-RESULT is returned.
CPD-22525 p-aminophenyl-β-D-glucoside C(O)[C@@H]2([C@@H](O)[C@H](O)[C@@H](O)[C@H](OC1(\C=C/C(/N)=C\C=1))O2)
CPD-8122 molybdopterin adenine dinucleotide C(OP(=O)([O-])OP(OC[C@H]2(O[C@H]1(NC3(/N=C(N)\NC(=O)C(/N[C@H]1C(\S)=C2\[S-])=3))))(=O)[O-])[C@H]6(O[C@@H](N4(C5(\C(\N=C/4)=C(N)/N=C\N=5)))[C@H](O)[C@H](O)6)
...
where
column 1 : BioCyc Object ID
column 2 : Common Name
column 3 : Complete SMILES string
JSON format:
{"RESULTS":[{"OBJECT-ID":"CPD-22525","COMMON-NAME":"p<\/i>-aminophenyl-β-D-glucoside","SMILES":"C(O)[C@@H]2([C@@H](O)[C@H](O)[C@@H](O)[C@H](OC1(\\C=C\/C(\/N)=C\\C=1))O2)"},{"OBJECT-ID":"CPD-8122","COMMON-NAME":"molybdopterin adenine dinucleotide","SMILES":"C(OP(=O)([O-])OP(OC[C@H]2(O[C@H]1(NC3(\/N=C(N)\\NC(=O)C(\/N[C@H]1C(\\S)=C2\\[S-])=3))))(=O)[O-])[C@H]6(O[C@@H](N4(C5(\\C(\\N=C\/4)=C(N)\/N=C\\N=5)))[C@H](O)[C@H](O)6)"},...]}
Retrieve BioCyc Objects by InChI String
Retrieve chemical compounds that match a given InChI string:
https://websvc.biocyc.org/[ORGID]/inchi-search?inchi=[INCHI]&exact=[EXACT]
or
https://websvc.biocyc.org/[ORGID]/inchi-search?inchi=[INCHI]&exact=[EXACT]&fmt=json
where
- [ORGID] is the identifier for the organism database,
e.g. ECOLI, META, AFER243159.
- [INCHI] is the InChI string,
e.g. 1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8)
- fmt=json requests output in the JSON format; default output is in tab-delimited format.
This web service can be used if the user is retrieving the results by either the "POST" or "GET" method.
Example URLs:
-
https://websvc.biocyc.org/ECO/inchi-search?inchi=1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8)
Retrieve compounds with INCHIstring 1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8).
-
https://websvc.biocyc.org/ECO/inchi-search?inchi=1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8)&fmt=json
Retrieve compounds with INCHIstring 1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8), using JSON format.
The default output is a tab-delimited format as follows. If no results are found then the string EMPTY-RESULT is returned.
CYTOSINE cytosine InChI=1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8) (1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8) 1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1 1S/C4H5N3O/c5)
where
column 1 : BioCyc Object ID
column 2 : Common Name
column 3 : INCHI String
column 4 : List of INCHI Keys
JSON format:
{"RESULTS":[{"OBJECT-ID":"CYTOSINE","COMMON-NAME":"cytosine","INCHI-STRING":"InChI=1S\/C4H5N3O\/c5-3-1-2-6-4(8)7-3\/h1-2H,(H3,5,6,7,8)","INCHI-KEYS":["1S\/C4H5N3O\/c5-3-1-2-6-4(8)7-3\/h1-2H,(H3,5,6,7,8)","1S\/C4H5N3O\/c5-3-1-2-6-4(8)7-3\/h1","1S\/C4H5N3O\/c5"]}]}
Visualization Services
Generate Compound Image
Compound images may be retrieved in GIF format for incorporation into
other pages. The basic URL to retrieve a compound image is:
https://websvc.biocyc.org/[ORGID]/diagram-only?type=COMPOUND&object=[COMPOUND]
where
- [ORGID] is the identifier for the organism database,
e.g. ECOLI, META, AFER243159
- [COMPOUND] is in the BioCyc identifier for the
compound, e.g. TRP, CPD-560
Example URL:
Generate Pathway Diagram
Pathway images may be generated in GIF format for incorporation into
other pages. These images are fully customizable as to the level of
detail and which elements are included in the diagrams. URLs
to generate a pathway image are of the form:
https://websvc.biocyc.org/[ORGID]/diagram-only?type=PATHWAY&object=[PATHWAY]&[PARAMETER]=[VALUE]
where
- [ORGID] is the identifier for the organism database,
e.g. ECOLI, META, AFER243159
- [PATHWAY] is in the BioCyc identifier for the
pathway, e.g. GLYCOLYSIS, ARGSYN-PWY, PWY0-1299
- Multiple parameter/value pairs can be specified
The following parameters provide customization options for the pathway diagrams:
Parameters to Customize Pathway Appearance
Parameter Name |
Possible Values |
Description |
Default |
detail-level |
0,1,2,3,4 |
Specifies the general detail level for the pathway. The
specific elements shown or hidden can be individually overridden using
the other parameters below.
0 - Minimal detail, only start/end/branchpoint metabolites shown
1 - All main compounds (those along the main pathway backbone)
2 - All main and side compounds, enzyme and gene names, and EC#s
3 - Compound structures for most main compounds
4 - Compound structures for most main and side compounds |
0, 1 or 2, depending on the size and complexity of the
individual pathway. |
enz |
y, n |
Should enzyme names be shown? |
Depends on detail level |
gene |
y, n |
Should gene names be shown? |
Depends on detail level |
ec |
y, n |
Should EC numbers be shown? |
Depends on detail level |
secs |
y, n |
Should side compounds be shown? |
Depends on detail level |
mstruct |
none, most, all |
Should compound structures for main compounds be shown? When
most is selected, structures for some very common compounds,
such as ATP, NAD, etc. are omitted. |
none or most, depending on detail level |
sstruct |
none, most, all |
Should compound structures for side compounds be shown? When
most is selected, structures for some very common compounds,
such as ATP, NAD, etc. are omitted. |
none or most, depending on detail level |
reglinks |
y, n |
If n, omit enzyme regulation icons and feedback inhibition links |
y |
nolinks |
y, n |
If y, suppress showing links to other pathways |
n |
pfontsize |
tiny, very-small, small, normal, large, very-large |
Font size used in diagram |
very-small |
bgcolor |
w, cb, g, bw, tr |
The color scheme for the diagram:
w: Colors on a white background
cb: Colors on a black background
g: Colors on a gray background
bw: Black on a white background
tr: Same colors as for w, but on a transparent background
|
tr |
linear |
snake, horizontal, vertical |
Specify whether linear pathways are drawn horizontally,
vertically, or in a horizontal back-and-forth "snake"-like fashion.
Note that only pathways that contain no cycles or branchpoints
(including branchpoints resulting from links to/from other pathways)
are recognized as linear pathways and therefore sensitive to this parameter. |
snake |
Example URLs:
Omics Visualization Services
Pathway Diagram Painted with Omics Data
Pathway pages can be displayed with omics data superimposed on the
pathway diagrams. This operation navigates to the web page for the
requested pathway. URLs to generate a pathway web page with overlayed
omics data are of the form:
https://websvc.biocyc.org/[ORGID]/new-image?type=PATHWAY&object=[PATHWAY]&[PARAMETER]=[VALUE]
where
- [ORGID] is the identifier for the organism database,
e.g. ECOLI, BSUB, AFER243159
- [PATHWAY] is in the BioCyc identifier for the
pathway, e.g. GLYCOLYSIS, ARGSYN-PWY, PWY0-1299
- Multiple parameter/value pairs can be specified, but two are required in order to show omics data:
- url (for GET) or datafile (for POST) -- The URL of the omics data file
- column1 -- An integer specifying the column number for the data from the omics data file that is to be displayed (column zero is the first column)
The table below outlines the possible paramaters that control the mapping of omics data to pathway diagrams, as well as on the cellular overview diagram (see the next section).
In addition, the options detailed in the previous table can be used to customize the rendering of the pathway itself.
Users can submit omics data using a POST request (which allows the omics data to be private).
For our examples below we make a data file available on a Pathway Tools web server.
Parameters to Customize Pathway and Cellular Overview Omics-Data Visualizations
Parameter Name |
Possible Values |
Pathway (P), Table (T) or Cellular Overview (O) |
Description |
Default |
datafile |
A filename |
P, T |
This parameter is REQUIRED for a POST, and should not be used for a GET. Its value should be a filename.
The file should be tab-delimited, the first column (often referred to as Column 0) being the id of
the gene/protein/compound/reaction/other to which the data in the remaining columns applies. |
REQUIRED for POSTno default |
url |
An example file supplied by the Pathway Tools website administrator |
P, T, O |
This parameter is REQUIRED for a GET, and should not be used for a POST.
Its value should name an example
data file supplied by the Pathway Tools website administrator.
|
REQUIRED for GETno default |
class |
gene, protein, compound, reaction, 'NIL' |
P, T, O |
gene Gene names and/or identifiers
protein Protein names and/or identifiers
compound Compound names and/or identifiers
reaction Reaction identifiers and/or EC numbers
'NIL' Any of the above
The given value declares the type(s) of the ids found in column 0 (the first column) of the data file.
|
gene |
column1 |
numbers separated by space or comma AND/OR,
range of numbers (number pair separated by hyphen) |
P, T, O |
data columns from datafile to be painted on pathway graphic
(e.g. &column1=4-7 9 would select data from columns 4, 5, 6, 7, and 9 in each row of the file.) |
REQUIRED no default |
expressiontype |
relative, absolute |
P, T, O |
relative: the numerical data represents a ratio
(relative to some other dataset or to a control) and is therefore
centered around either 0 or 1 (see log parameter
below). absolute: the numerical data represents
absolute values, e.g. intensities or concentrations, and are all
non-negative. |
relative |
log |
on, off |
P, T, O |
on: 0-centered data off: 1-centered data
- 0-centered scale: implies that the numerical data of your file can contain positive and negative values. The value 0 is considered to be the center of the numerical values provided in your data file.
- 1-centered scale: implies that any negative or zero values in your data file should be skipped. Moreover, the data is centered around the value 1 using a log scale. For example, the value 0.1 is considered to be at the same distance to 1 as the value 10. So, a logarithm of base 10 is applied to your data before the linear coloring mapping is applied.
|
on |
color |
default, specify, rbg, rbg-cutoff, 3-color |
P, T, O |
- default : Orange to gray to blue from data
- specify : Orange to gray to blue with a maximum cutoff (maxcutoff parameter detailed in this table)
- rbg : Red to green from data
- rbg-cutoff : Red to green with a maximum cutoff (maxcutoff parameter detailed in this table)
- 3-color : Three-color display with a threshold
Data values are divided into color bins. You can choose between a color scheme that ranges from orange (most positive values) through gray in the center to blue (most negative values) or from red through blue in the center to green and yellow. For each of these color schemes, two options are available:- The color bins range over the entire spectrum, and the cutoff values for the color bins are derived from the data itself. This means that different experiments could be displayed using different color schemes, making it difficult to directly compare them.
- You may specify a value for the maximum value cutoff (maxcutoff parameter) bin. All displays that use the same maximum value cutoff will use the same color scheme (assuming other settings are the same), and are therefore directly comparable. The maximum cutoff value should be a number, e.g. 2 or 10, etc. All data values greater than the maximum cutoff value will be displayed in the highest bin color.
A final alternative is to use only three color bins, red for data values that exceed some threshold (see parameter below), purple for data values less than the inverse of that threshold, and gray for values in between. The threshold value should be a number, e.g. 2 or 10. |
default |
threshold |
a numeric value |
P, T, O |
Required if 3-color specified. See discussion in 'color' parameter section of this table. |
no default |
maxcutoff |
a numeric value |
P, T, O |
Required if specify or rbg-cutoff specified. See discussion in 'color' parameter section of this table. |
no default |
omicsPopups |
on, unspecified |
P |
If present, display the omics data in popup windows, usually one popup per reaction or metabolite in the pathway. This is the only way to show data in multiple columns. A single column of data can either be shown in popups or (if unspecified) as color coded buttons on the diagram. |
unspecified |
defaultPopup |
bar, plot, heat |
P |
The style of data display in the omics popups: a bar graph, an x-y plot, or a heat map. |
bar |
A single column of gene data from the file displayed with colored "buttons":
A single column of gene data from the file displayed with popups:
Five columns of compound (metabolomics) data from the file displayed with popups and heat map as default popup style:
Table of Pathway Diagrams Painted with Omics Data
This operation navigates to a web page containing a table of
low-detail pathway diagrams, colored to show omics data values. To submit data via the HTTP GET method, use the following URL format:
https://websvc.biocyc.org/[ORGID]/overview-expression-map?pathways=[PATHWAYS]&[PARAMETER]=[VALUE]
where
- [ORGID] is the identifier for the organism database,
e.g. ECOLI, BSUB, AFER243159
- [PATHWAYS] is a comma-separated list of BioCyc identifiers for
the desired pathways, e.g. GLYCOLYSIS, ARGSYN-PWY, PWY0-1299
- Multiple parameter/value pairs can be specified. If none are specified,
then the table will be generated without omics data.
The list of available parameters are those marked T in the
above Omics Data Parameters Table. The
pathway diagrams cannot be customized, and any pathway customization
parameters will be ignored. This view is more useful for gene
expression data than for metabolomics data, as any side metabolites
will not be visible on the pathway diagrams. Popups are also not
available with this view -- if multiple data columns are specified,
the resulting table will contain a column of pathway diagrams for each
data column. The same URL and parameters are used for GET and POST
queries except that GET queries must supply the url
parameter and POST queries must supply the datafile parameter
to upload data from a local file.
Example URL:
Cellular Overview Visualization Services
The following two services navigate to a web page containing the cellular overview (metabolic map) diagram with specified data overlays.
For the highlighting service the objects to be highlighted are specified in the URL itself, and highlighting colors are optionally provided.
For the omics painting service the objects to be highlighted are specified in a POST, and data overlays are derived from omics data values that are mapped to a color scale.
Highlight/Paint Objects on Metabolic Network Diagram
Objects can be specified for highlighting by name, ID or substring.
URLs to highlight specified objects are of the form:
https://websvc.biocyc.org/overviewsWeb/celOv.shtml?orgid=[ORGID]&zoomlevel=[0-3]&[OP]=[VALUES]
where
- [ORGID] is the identifier for the organism database,
e.g. ECOLI, BSUB, AFER243159
- zoomlevel is an integer that indicates the extent to which the diagram has been zoomed. Zoomlevel 0 is the lowest overview magnification, level 3 is the highest magnification. If not supplied, the zoomlevel defaults to 0.
- [OP] specifies a highlighting operation
- [VALUES] consists of one or more values, where multiple values are separated by URL-encoded spaces (i.e., each space is represented by the characters %20).
Each value is of the form [LABEL] [NUMBER] where [LABEL] is the name, ID or substring indicating the object to be highlighted,
and [NUMBER] is an optional omics data value that is mapped to a highlighting color ([LABEL] and [NUMBER] are separated by a URL-encoded space).
An example [OP] plus [VALUES] is "xnids=b1234 35 b3320 86 b2310 45" where b1234 is a gene identifier and 35 is an associated data value.
Multiple highlighting operations can be specified in a single URL. The possible highlighting operations are described in the following table. Note that all these operations correspond to the
operations available from the top menu bar when a Cellular Overview
diagram is displayed. The operation
xnids is special as it accepts
data values as well. A data value can be specified after each name.
Op | Highlight Operation |
rnids | Highlight reaction names or frame ids. |
rsubs | Highlight reaction substrings. |
recns | Highlight reaction EC numbers. |
pnids | Highlight pathway names or frame ids. |
psubs | Highlight pathway substrings. |
gnids | Highlight gene names or frame ids. |
gsubs | Highlight gene substrings. |
enids | Highlight enzyme names or frame ids. |
esubs | Highlight enzyme substrings. |
cnids | Highlight compound names or frame ids. |
csubs | Highlight compound substrings. |
xnids | Highlight a mix of names and frame ids with or without omics data.
|
pcids | Highlight pathways based on curation status. |
rcids | Highlight reactions based on curation status. |
revis | Highlight reactions based on evidence selected. |
pevis | Highlight pathways based on evidence selected. |
gregs | Highlight genes based on regulation selected. |
greps | Highlight genes based on replicons. |
The string specified after the ‘=’ for an operation
must not be quoted, and any special characters must be URL encoded. The
string is not case-sensitive. Multiple values separated by commas may
be supplied for any of the above operations (except xnids, which uses URL-encoded spaces as separators). There is no difference
between suppling multiple comma-separated values for a single
operation versus specifying that operation multiple times, once for
each value. When supplying omics data values using the xnids
operation, the id and the value should be separated by a
URL-encoded space. If multiple objects are specified using the xnids
operation, either all must have data values (resulting in an omics
viewer display), or any data values will be ignored (reverting to a
basic highlighting operation).
Example highlighting URLs are as follows.
URLs with highlighting operations can be automatically generated
by the Cellular Overview by applying the desired highlights using its interactive web interface, and then
right-clicking on the diagram and selecting the command Generate Bookmark for Current Cellular Overview.
Paint Omics Data from a File on Metabolic Network Diagram
The metabolic network diagram can be invoked by using a URL link that specifies an
omics data file that resides on an accessible website. See the
Omics Viewer
section of the Website Users Guide for more information about the
Omics Viewer, including the data file format. This GET request will
navigate to the Cellular Omics Viewer page and load it with data from
the supplied URL and the parameters specified in the request
itself.
URLs to paint omics data on the cellular overview diagram are of the form:
https://websvc.biocyc.org/overviewsWeb/celOv.shtml?orgid=[ORGID]&omics=t&zoomlevel=[0-3]&[PARAMETER]=[VALUE]
where
- [ORGID] is the identifier for the organism database,
e.g. ECOLI, BSUB, AFER243159
- zoomlevel is an integer that indicates the extent to which the diagram has been zoomed. Zoomlevel 0 is the lowest magnification, level 3 is the largest magnification. If not supplied, the zoomlevel defaults to 0.
- Multiple parameter/value pairs can be specified, but two are required:
- url -- The URL of the omics data file
- column1 -- An integer specifying the column number for the data from the omics data file that is to be displayed (column zero is the first column)
The list of available parameters are those marked
O in the
Omics Data Parameters Table.
SmartTables
SmartTable Data Retrieval
SmartTable data can be accessed from a web service in the following formats: JSON, XML, or tab delimited. This web service will request your account username and password.
The basic URL to retrieve a SmartTable is:
https://websvc.biocyc.org/st-service-get?id=[SMARTTABLE-ID]&format=[json|xml|tsv]
where
- [SMARTTABLE-ID] is the identifier of the SmartTable,
e.g. biocyc11-2762-3605383628, biocyc10-NIL-3608637901
- [json|xml|tsv] is the requested format for the SmartTable data. json will return the data in JSON format, xml in XML format, and tsv in tab delimited format.
An example of the JSON structure can be found in the JSON Structure for SmartTables Retrieval and Creation.
Example URL:
SmartTable Creation
To create a SmartTable from data supplied via a file using the web service URL, the user must use a tool that can peform a "PUT" method. The result returned will contain the identifier of the created SmartTable. curl will be used for examples in this documentation section. When using curl, the terminal command may look like the following:
curl -u '[USER@DOMAIN.COM]' -X PUT -T [ST-PATH] http://localhost:1555/st-service-create?id=[ID]&format=[json|xml|tsv]
where
- [USER@DOMAIN.COM] is the user email address associated with their account
- [ST-PATH] is the local path to the file containing SmartTable data, e.g. /tmp/test-st
- [json|xml|tsv] is the data format of the SmartTable data stored at [st-path]
- [ID] (optional) is the identifier for the SmartTable
Example terminal command:
-
curl -u 'USER@DOMAIN.COM' -X PUT -T /tmp/test-st.xml http://www.biocyc.org/st-service-create?format=xml
JSON Structure for SmartTable Data Retrieval and Creation
JSON file structure:
- name (optional) - name field of SmartTable
- description (optional) - description field of SmartTable
- Contents of the short form, which is for creating a single column of values only:
- type: an object class that values will be coerced into for the given database into the SmartTable
- pgdb: an org id for the database in which SmartTable objects will reside and be coerced with the given type
- values: an array of strings, which will be coerced into objects for the SmartTable in a single column
- Contents of the long form, which is for creating multiple columns of values:
- columns: a list (JSON array) of columns, each of which is:
- name (optional): a string that will be the name of the column
- type: an object class that values will be coerced into for the SmartTable
- rows: a JSON array, each element is a dictionary mapping column ids to values. Each value corresponds to one cell in the SmartTable and contains:
- value: a string, number, or {frameid: , pgdb: } which will be coerced into an object for the SmartTable
JSON examples:
// Short form
{"name": "sample short-form group",
"description": "sample short-form description",
"pgdb": "ECOLI",
"type": "Genes",
"values": ["trpA", "trpB"]
}
// long form (2 columns)
{"name": "sample long-form group",
"description": "This is a longer form of JSON used with a SmartTable.",
"columns": [{"name": "Gene",
"type": "Genes"},
{"name": "Expression Level"}]
"rows": [{{"frameid": "EG11204", "pgdb": "ECOLI"},
"1.3"}
{{"frameid": "EG11205", "pgdb": "ECOLI"},
"-2.2"}]
}
XML Structure for SmartTable Data Retrieval and Creation
The XML file structure follows a similar structure to the JSON format. The following is the XML schema:
<xs:schema attributeFormDefault="unqualified" elementFormDefault="qualified" xmlns:xs="http://www.w3.org/2001/XMLSchema">
<xs:element name="GROUP">
<xs:complexType>
<xs:attribute type="xs:string" name="ID"/>
<xs:attribute type="xs:string" name="NAME"/>
<xs:sequence>
<xs:element name="COLUMNS">
<xs:complexType>
<xs:sequence>
<xs:element name="COLUMN" maxOccurs="unbounded" minOccurs="1">
<xs:complexType>
<xs:simpleContent>
<xs:extension base="xs:string">
<xs:attribute type="xs:string" name="NAME" use="optional"/>
<xs:attribute type="xs:string" name="TYPE" use="optional"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="ROWS">
<xs:complexType>
<xs:sequence>
<xs:element name="ROW" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element name="CELL" maxOccurs="unbounded" minOccurs="0">
<xs:complexType mixed="true">
<xs:sequence>
<xs:element name="FRAME" maxOccurs="unbounded" minOccurs="0">
<xs:complexType>
<xs:simpleContent>
<xs:extension base="xs:string">
<xs:attribute type="xs:string" name="ID" use="optional"/>
<xs:attribute type="xs:string" name="PGDB" use="optional"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
</xs:element>
<xs:element type="xs:string" name="VALUE" maxOccurs="unbounded" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:schema>
XML example:
<GROUP ID="biocyc14-2762-3579243971" NAME="Import from snp.txt">
<COLUMNS>
<COLUMN NAME="Position" TYPE="NUMBER"/>
<COLUMN NAME="Gene" TYPE="All-Genes"/>
<COLUMN
NAME="Map to Alicyclobacillus acidocaldarius acidocaldarius DSM 446"
TYPE="All-Genes"/>
<COLUMN NAME="new column"/>
<COLUMN NAME="Binding sites upstream of gene" TYPE="DNA-Binding-Sites"/>
</COLUMNS>
<ROWS>
<ROW>
<CELL><VALUE>10</VALUE></CELL>
<CELL><FRAME ID="EG11024" PGDB="ECOLI"/></CELL>
<CELL><FRAME ID="GCIO-1719" PGDB="AACI521098"/></CELL>
<CELL/>
<CELL>
<FRAME ID="BS00206" PGDB="ECOLI"/>
<FRAME ID="BS0-4061" PGDB="ECOLI"/>
<FRAME ID="BS0-4062" PGDB="ECOLI"/>
</CELL>
</ROW>
</ROWS>
</GROUP>
Other SmartTable Web Services
Various operations to manipulate existing SmartTables can be done with the following web services.
Service Name |
Arguments |
HTTP POST or GET |
Example |
Description |
st-service-transform |
id, transformationid, index
|
GET |
https://websvc.biocyc.org/st-service-transform?id=biocyc11-2762-3605383628&transformid=compound-producing-pathways&index=0 |
Adds a transformation column to an existing SmartTable.
id: SmartTable identifier
transformationid: Name of the transformation to use. See This table for available transformations.
index: Column number to base the new transformation column on. First column starts with 0.
|
st-service-property |
id, propertyid, index
|
GET |
https://websvc.biocyc.org/st-service-property?id=biocyc11-2762-3605383628&propertyid=common-name&index=0 |
Adds a slot property column to an existing SmartTable.
id: SmartTable identifier
propertyid: Name of the slot to use.
index: Column number to base the new transformation column on. First column starts with 0.
|
st-service-add-row |
id
|
GET |
https://websvc.biocyc.org/st-service-add-row?id=biocyc11-2762-3605383628 |
Adds an empty row to an existing SmartTable.
id: SmartTable identifier
|
st-service-delete-rows |
id, indices
|
GET |
https://websvc.biocyc.org/st-service-delete-rows?id=biocyc11-2762-3605383628&indices=0,1 |
Deletes rows from an existing SmartTable.
id: SmartTable identifier
indices: Row numbers to delete. First row starts with 0.
|
st-service-add-column |
id
|
GET |
https://websvc.biocyc.org/st-service-add-column?id=biocyc11-2762-3605383628 |
Adds an empty column to an existing SmartTable.
id: SmartTable identifier
|
st-service-delete-column |
id, index
|
GET |
https://websvc.biocyc.org/st-service-delete-column?id=biocyc11-2762-3605383628&index=0 |
Deletes a column from an existing SmartTable.
id: SmartTable identifier
index: Column number to delete. First column starts with 0.
|
st-service-modify-cell |
id, format, row, column
|
POST |
|
Adds an empty row to an existing SmartTable.
id: SmartTable identifier
format: Cell body format. Can be XML or JSON. (More on cell body format).
row: Row number of the cell to modify. First row starts with 0.
column: Column number of the cell to modify. First column starts with 0.
|
st-service-modify-name |
id, name
|
GET |
https://websvc.biocyc.org/st-service-modify-name?id=biocyc11-2762-3605383628&name=All+Genes |
Modifies the name of an existing SmartTable.
id: SmartTable identifier
name: SmartTable name text.
|
st-service-modify-description |
id, description
|
GET |
https://websvc.biocyc.org/st-service-modify-description?id=biocyc11-2762-3605383628&description=All+Genes+of+Dataset |
Modifies the description of an existing SmartTable.
id: SmartTable identifier
description: SmartTable description text.
|
st-service-copy |
id
|
GET |
https://websvc.biocyc.org/st-service-copy?id=biocyc11-2762-3605383628 |
Creates a copy of an existing SmartTable.
id: SmartTable identifier
|
st-service-delete |
id
|
GET |
https://websvc.biocyc.org/st-service-delete?id=biocyc11-2762-3605383628 |
Deletes an existing SmartTable.
id: SmartTable identifier
|