BioCyc Web Services

BioCyc offers several classes of web services that are summarized in the table below. These services include: 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
BioPAX Pathway Data BioCyc Pathway ID BioPAX XML GET
Search and Retrieve a Set of Objects
Retrieve objects by name or accession BioCyc Object Name or Accession tab delimited, JSON, ptools-XML GET, POST
Foreign object-ID (external database identifier) retrieval Foreign database ID tab delimited, JSON, ptools-XML 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, ptools-XML GET, POST
Metabolite chemical formula retrieval Chemical Formula tab delimited, JSON, ptools-XML GET, POST
Metabolite Translation Service tab delimited GET, POST
Retrieve metabolites by SMILES string SMILES String tab delimited, JSON GET, POST
Retrieve metabolites by INCHI string INCHI String tab delimited, JSON, ptools-XML GET, POST
Visualization Services Generate Compound Image Compound ID GIF image GET
Generate Pathway Diagram Pathway ID GIF image GET, POST
Genome Browser Visualization Organism and Replicon Names and / or IDs HTML
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 Single Omics Data from a File on Metabolic Network Diagram Object Names and / or IDs HTML POST
Paint Multi Omics Data From File via POST Multi Omics Text File URL POST
SmartTables
SmartTable Creation PUT
SmartTable Data Retrieval tab delimited, JSON, tsv GET
SmartTable Add Transform Column GET
SmartTable Add Property Column GET
SmartTable Delete Row GET
SmartTable Delete Column GET
SmartTable Modify Name GET
SmartTable Modify Description GET
SmartTable Copy GET
SmartTable Delete GET
SmartTable Enrichment Analysis 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.

Retrieve a Single BioCyc Object

Biocyc KB-Version Retrieval

This service finds the version of the KB and returns the result in JSON format.

The URLs for retrieving the KB-version is

https://websvc.biocyc.org/kb-version?orgid=[ORGID]

where

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

Example URLs:

BioPAX Pathway Data

Pathway data for an individual pathway is available in BioPAX XML 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

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:

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

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:

Retrieve BioCyc Objects from a Class by Name or Accession

Objects from a specified class in a PGDB can be retrieved by name or accession:

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|xml]

where

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"}]}

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|xml]

where

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|xml]

where

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|xml]

where

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:

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 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

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-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

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. 

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

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

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:



Genome Browser Visualization

Genome Explorer can be used to explore one replicon (chromosome or plasmid) at a time, to align conserved regions of multiple replicons, and to analyze high-throughput datasets using tracks. The following are a set of tools that provide customization options for the genome browser via url parameters to achieve the desired effect.



Single Genome Range Request:

Shows the genome within a specific range.

Parameters:
https://websvc.biocyc.org/genbro/genbro.shtml?orgid=[ORGID]&replicon=[REPLICON]&bp-range=[BP-RANGE]

OrgID: The organism's ID.
Format: ECOLI

Replicon: The replicon's ID.
Format: COLI-K12

Bp-Range: A coordinate range (e.g., START/END) to display that region.
Format: 1000/20000

Example:
https://websvc.biocyc.org/genbro/genbro.shtml?orgid=ECOLI&replicon=COLI-K12&bp-range=500000/1000000



Specific Gene in Genome Request:
Show a specific gene within the genome.

Parameters:
https://websvc.biocyc.org/genbro/genbro.shtml?orgid=[ORGID]&replicon=[REPLICON]&gene=[GENE]

OrgID: The organism's ID.
Format: ECOLI

Replicon: The replicon's ID.
Format: COLI-K12

Gene: The gene's ID.
Format: EG10240

Example: https://websvc.biocyc.org/genbro/genbro.shtml?orgid=ECOLI&replicon=COLI-K12&gene=EG10240



Comparative Genome Explorer Request:
Show multiple genes within the same page to compare with each other.

Parameters: https://websvc.biocyc.org/genbro/genbro.shtml?lead-orgid=[LEAD-ORGID]&lead-genes=[LEADGENE]&replicon=[REPLICON]&orgids=[ORGIDS]

Lead OrgID: The leading organism's ID
Format: ECOLI


Lead Gene: The lead gene's ID
Format: EG10240


Replicon: The replicon's ID
Format: COLI-K12


OrgIDs: A list or organism ids, should be seperated by commas. (e.g., ORGID,ORGID2,ORGID3)
Format: ECOLI,GCF_000340255

Example: https://websvc.biocyc.org/genbro/ortho.shtml?lead-orgid=ECOLI&lead-genes=EG10240&replicon=COLI-K12&orgids=ECOLI,GCF_000340255





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

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, O 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 POST
no 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 GET
no 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
  • 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 Required if 3-color specified. See discussion in 'color' parameter section of this table. no default
maxcutoff a numeric value P, T 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

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

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.

Examples of Cellular Overview Highlights
Example URL
Highlight genes with a single color via op xnids https://websvc.biocyc.org/overviewsWeb/celOv.shtml?zoomlevel=0&orgid=ECOLI&xnids=thiE trpA EG10790 b2518 b1704
Highlight genes with integer omics data via op xnids https://websvc.biocyc.org/overviewsWeb/celOv.shtml?zoomlevel=0&orgid=ECOLI&xnids=thiE 4 trpA 6 EG10790 3 b2518 2 b1704 2.5
Highlight metabolites with float omics data via op xnids https://websvc.biocyc.org/overviewsWeb/celOv.shtml?zoomlevel=1&orgid=ECOLI&xnids=L-BETA-ASPARTYL-P%204.0%20L-tryptophan%206.0%20L-LACTATE%203.0%20chorismate%202.0%20TYR%202.5 https://websvc.biocyc.org/overviewsWeb/celOv.shtml?zoomlevel=1&orgid=ECOLI&xnids=L-BETA-ASPARTYL-P 4.0 L-tryptophan 6.0 L-LACTATE 3.0 chorismate 2.0 TYR 2.5
Highlight reactions with omics data via op xnids https://websvc.biocyc.org/overviewsWeb/celOv.shtml?zoomlevel=0&orgid=ECOLI&xnids=DIHYDROFOLATEREDUCT-RXN 4.0 DLACTDEHYDROGNAD-RXN 6.0 PGLUCISOM-RXN 3.0
Highlight reactions with omics data via op xnids https://websvc.biocyc.org/overviewsWeb/celOv.shtml?zoomlevel=0&orgid=ECOLI&xnids=2.0 DIHYDROFOLATEREDUCT-RXN 4.0 DLACTDEHYDROGNAD-RXN&csubs=pyruv
Highlight enzyme based on substrings via op esubs https://websvc.biocyc.org/overviewsWeb/celOv.shtml?zoomlevel=0&orgid=ECOLI&esubs=hydro&esubs=oxy&gsubs=arg,his
Highlight reactions based on evidence code via op revis https://websvc.biocyc.org/overviewsWeb/celOv.shtml?zoomlevel=0&orgid=ECOLI&revis=EV-COMP

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 Single 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

The list of available parameters are those marked O in the Omics Data Parameters Table.

Examples of Cellular Overview Single Omics Data Painting
Example URL
Paint transcriptomics data from a sample data file. To supply your own data use a POST. Six columns of data are provided in this example; click triangle "Start" button to play the animation. https://websvc.biocyc.org/overviewsWeb/celOv.shtml?orgid=ECOLI&omics=t&url=expr-examples/ecoli-feuer-toaerobic-significant.txt&expressiontype=relative&column1=1-6&log=on&class=gene
Paint metabolomics data from a sample data file. To supply your own data use a POST. Five columns of data are provided in this example; click triangle "Start" button to play the animation. https://websvc.biocyc.org/overviewsWeb/celOv.shtml?orgid=HUMAN&omics=t&url=expr-examples/human-metabolomics-syn.txt&expressiontype=relative&column1=1-5&log=on&class=compound

Paint Multi Omics Data From File via POST

The multi omics viewer gives you the ability to upload up to four omics datasets onto the cellular overview. Each dataset is presented via a separate “visual channel.” The available channels are node (metabolite) colors, edge (reaction) colors, node size, and edge thickness. Typically, nodes are used to visualize metabolomics data and edges are used to visualize transcriptomics, proteomics, and reaction-flux data.

The cellular overview can be invoked and passed files via post by calling the overview-multi-omics-process-upr web service. One of the requirements of this post request is that the same session needs to be maintained.

Send a post request to: https://websvc.biocyc.org/overview-multi-omics-process-upr

POST Request Parameters:


Single File POST Request:
Should only be passed one file that would contain the master fields and omics data.

For more information relating to multi omics file formatting go here: link.

Parameters:

orgid:
Expects: The organism id
Required: yes

multifile:
To use single file mode must be false
Expects: t or f
Required: yes

file:
Expects: a file
Includes both the master fields and omics data.
Required: yes

Example:

With the parameters: 

data = {
  "orgid" : "ECOLI",
  "multifile" : "f"
}
files = {  "file" : open("/file1/location/file1.txt "rb") }

Single file example file:
multi-omics-single-file-example.txt

Multi File POST Request:
Will be passed up to five files containing the master fields and omics data.

For more information relating to multi omics file formatting go here: link.

Parameters:

orgid:
Expects: The organism id
Required: yes

multifile:
To use multi file mode, must be true
Expects: t or f
Required: yes

masterfile:
Expects: A master file which includes all of the metafields.
Includes only the master file
Required: yes

file1 - file4:
Expects: a file
Includes only omics data
Required: yes – at minimum file1 and file2

Example:

With the parameters: 

data = {
  "orgid" : "ECOLI",
  "multifile" : "t" 
}

files = {
  "masterfile" : open("/file1/location/masterfile.txt "rb")
  "file1" : open("/file1/location/file1.txt "rb")
  "file2" : open("/file2/location/file2.txt "rb")
  "file3" : open("/file3/location/file3.txt "rb")
  "file4" : open("/file4/location/file4.txt "rb")
}

Multi Omics file example files:
multi-omics-masterfile-example.txt
multi-omics-file1-example.txt
multi-omics-file2-example.txt

Python Library Requirements

The following libraries are needed in order to use the multiomics celov POST request:

requests
selenium
webdriver_manager

Download requirements.txt

To install the packages via the python package manager pip:

pip install -r /path/to/requirements.txt

Python Script Explanation

The script is first creating a session by logging into biocyc. Then after it is successfull, using the same session it makes a POST request to "/overview-multi-omics-process-upr". Afterwords it takes the returned url response, opens up a new firefox window using selenium with your current session, and it will redirect to the cellular overview page which will then load the posted data into the diagram.

What variables need modifed:

login_info: Swap the placeholder values to your biocyc credentials

data: Modify the data variable containing the two parameters to switch if it is single or muilti file mode and which organism id you are selecting.

files: Then change the files variable to reference each file you need for the POST request.

Script for POST request
import requests
from selenium import webdriver
from selenium.webdriver.common.by import By
from selenium.webdriver.firefox.service import Service
from selenium.webdriver.firefox.options import Options
from selenium.webdriver.firefox.firefox_profile import FirefoxProfile
from webdriver_manager.firefox import GeckoDriverManager
	
base_url = "https://websvc.biocyc.org/"
login_url = base_url + "credentials/login/"
login_info = {
	"email" : "your_email",
	"password" : "your_password"
}
	
with requests.Session() as session:
	resp = session.post(login_url, data=login_info)
	if resp.status_code == 200:
		firefox_options = Options()
		firefox_options.add_argument("--start-maximized")
		url =  base_url + "/overview-multi-omics-process-upr"
		data = { "orgid" : "ECOLI", "multifile" : "t"}
		files = {  "masterfile" : open("/masterfile/location/masterfile.txt", "rb"), "file1" : open("/file1/location/file1.txt", "rb") , "file2" : open("/file1/location/file1.txt"", "rb") }
		headers = {'Cache-Control' : 'no-cache, no-store, must-revalidate'}
		response = session.post(url, headers=headers, data=data, files=files)
		print (response.status_code)
		print (response)
		if response.status_code == 200:
			print(response.text)
			omicsurl = "https://" + response.text
			driver = webdriver.Firefox(service=Service(GeckoDriverManager().install()), options=firefox_options)
			driver.get(base_url)
			for cookie in session.cookies:
				if cookie.name == "PTools-session" or cookie.name == "userIdentifier" or cookie.name == "recentOrgID0":
					item = {
						'name': cookie.name,
						'value': cookie.value,
						'domain': cookie.domain,
						'path': cookie.path,
						'expiry': cookie.expires,
						'secure': cookie.secure
					}
					driver.add_cookie(item)
			driver.refresh()
				
			print(response.text)
			driver.get(omicsurl)
			input()
			driver.quit()
	else:
		print (f"failed to render, status code: {response.status_code}")

Download celov_multiomics_post.py

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-get?id=[SMARTTABLE-ID]&format=[json|xml|tsv]

where

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] https://websvc.biocyc.org/st-create?format=[json|xml|tsv]&orgid=[ORGID]&class=[CLASS]

where

Example terminal command:

For tsv (tab-separated-values) input files, the orgid and type args are required; for json and xml input files, those parameters are encoded as part of the file format. For tsv input files, the first row of the file is assumed to contain column headers.

JSON Structure for SmartTable Data Retrieval and Creation

JSON file structure:

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. Unless otherwise indicated, all use the HTTP GET method. In all example URLs, replace "[ID]" with the SmartTable identifier.

Service Name Arguments Example Description
st-transform id, transformid, index
 https://websvc.biocyc.org/st-transform?id=[ID]&transformid=compound-producing-pathways&index=0 Adds a transformation column to an existing SmartTable.
  • id: SmartTable identifier.
  • transformid: Identifier of the transformation to use. See table of available transformations.
  • index: Column number to base the new transformation column on. First column is index 0.
st-property id, propertyid, index
 https://websvc.biocyc.org/st-property?id=[ID]&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 is index 0.
st-delete-rows id, indices
 https://websvc.biocyc.org/st-delete-rows?id=[ID]&indices=0,1 Deletes rows from an existing SmartTable.
  • id: SmartTable identifier.
  • indices: Comma-separated list of row numbers to delete. First row is index 0.
st-delete-column id, index
 https://websvc.biocyc.org/st-delete-column?id=[ID]&index=1 Deletes a column from an existing SmartTable.
  • id: SmartTable identifier
  • index: Column number to delete. First column is index 0.
st-modify-name id, name
 https://websvc.biocyc.org/st-modify-name?id=[ID]&name=All+Genes Modifies the name of an existing SmartTable.
  • id: SmartTable identifier
  • name: SmartTable name text, url-encoded.
st-modify-description id, description
 https://websvc.biocyc.org/st-modify-description?id=[ID]&description=All+Genes+of+Dataset Modifies the description of an existing SmartTable.
  • id: SmartTable identifier
  • description: SmartTable description text, url-encoded.
st-copy id
 https://websvc.biocyc.org/st-copy?id=[ID] Creates a copy of an existing SmartTable.
  • id: SmartTable identifier
st-delete id
 https://websvc.biocyc.org/st-delete?id=[ID] Deletes an existing SmartTable.
  • id: SmartTable identifier
st-enrichment With GET: id, key, type, threshold, statistic, correction

With PUT: format, orgid, class, key, type, threshold, statistic, correction 		https://websvc.biocyc.org/st-enrichment?id=[ID]&type=enrichment&key=enrich-genes-pwys With the GET method, runs an enrichment analysis on the first column of an existing SmartTable. To upload a file of genes or compounds and run an enrichment analysis on it in one step, use the PUT method, and also supply the args needed for the st-create service.
  • id: SmartTable identifier (GET only)
  • key: one value from enrich-all-gen, enrich-go-cc, enrich-go-bp, enrich-go-mf, enrich-genes-regulators-indirect, enrich-genes-regulators, enrich-cpds-pwys, or enrich-genes-pwys
  • type: enrichment, depletion, or enrichment-and-depletion
  • threshold: a number between 0 and 1; only include results with P-value less than this number (default = 0.1)
  • statistic: fisher-exact (default), parent-child-union, or parent-child-intersection
  • correction: none (default), bonferroni, bh (Benjamini-Hochberg), or by (Benjamini-Yekutieli)
  • format: json, xml or tsv; the format of the uploaded data (PUT only)
  • class: Genes or Compounds (PUT, format=tsv only)
  • orgid: the identifier for the organism database (PUT, format=tsv only)