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Synechocystis PCC 6803 curate-a-thon, 24-28 July; EventBrite
SearchGenomeMetabolism |
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Synechocystis PCC 6803 curate-a-thon, 24-28 July; EventBrite
SearchGenomeMetabolism |
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.
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.
hide
show operations
# 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]
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]')
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
Example URLs:
The default output is a JSON format as follows:
{"kb-version":"19.5"}
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:
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:
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:
https://websvc.biocyc.org/[ORGID]/pathway-biopax?type=[2|3]&object=[PATHWAY]
where
Example URLs:
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
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"}]}]
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
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}]
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
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}]
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:
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
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
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"}]}
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
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
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"]}]}
https://websvc.biocyc.org/[ORGID]/diagram-only?type=COMPOUND&object=[COMPOUND]
where
Example URL:
https://websvc.biocyc.org/[ORGID]/diagram-only?type=PATHWAY&object=[PATHWAY]&[PARAMETER]=[VALUE]
where
The following parameters provide customization options for the pathway diagrams:
| 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:
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.
| 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 |
| 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 |
| 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
|
on |
| color | default, specify, rbg, rbg-cutoff, 3-color | P, T, O |
|
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 |
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:
https://websvc.biocyc.org/overviewsWeb/celOv.shtml?orgid=[ORGID]&zoomlevel=[0-3]&[OP]=[VALUES]
where
| 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.
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
| 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 |
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
An example of the JSON structure can be found in the JSON Structure for SmartTables Retrieval and Creation.
Example URL:
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
Example terminal command:
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"}]
}
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>
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. |
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| 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 |