Author: buildbot
Date: Thu Jul 14 19:15:33 2016
New Revision: 992830
Log:
Staging update by buildbot for taverna
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websites/staging/taverna/trunk/cgi-bin/ (props changed)
websites/staging/taverna/trunk/content/ (props changed)
websites/staging/taverna/trunk/content/introduction/chemistry-web-services.html
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Modified:
websites/staging/taverna/trunk/content/introduction/chemistry-web-services.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/chemistry-web-services.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/chemistry-web-services.html
Thu Jul 14 19:15:33 2016
@@ -194,32 +194,54 @@ Instead it shows <a class="alert-link" h
visibility: hidden;
}
h2:hover > .headerlink, h3:hover > .headerlink, h1:hover > .headerlink,
h6:hover > .headerlink, h4:hover > .headerlink, h5:hover > .headerlink,
dt:hover > .elementid-permalink { visibility: visible }</style>
+<h2 id="overview">Overview<a class="headerlink" href="#overview"
title="Permanent link">¶</a></h2>
<p>This document describes a set of chemistry services provided by <a
href="#chemspider">ChemSpider</a>, <a href="#chebi">ChEBI</a> and <a
href="#pubchem">PubChem</a>
that can be used for the construction of chemistry workflows from the
Taverna Workbench.</p>
-<p>Example workflows contained in the document show how some of the operations
from the services in the set can
- be invoked.
+<p>Example workflows contained in the document show how some of the operations
from the services in the set can
+ be invoked.
They can also be downloaded as part of the <a
href="http://www.myexperiment.org/packs/136";>Chemistry Workflows pack</a> at
myExperiment.</p>
+<h3 id="contents">Contents<a class="headerlink" href="#contents"
title="Permanent link">¶</a></h3>
+<div class="toc">
+<ul>
+<li><a href="#overview">Overview</a><ul>
+<li><a href="#contents">Contents</a></li>
+</ul>
+</li>
+<li><a href="#chemspider">ChemSpider</a><ul>
+<li><a href="#inchi-web-service">InChi Web service</a></li>
+<li><a href="#openbabel-web-service">OpenBabel Web service</a></li>
+<li><a href="#mass-spec-api-web-service">Mass spec API Web service</a></li>
+<li><a href="#spectra-web-service">Spectra Web service</a></li>
+<li><a href="#compound-search-web-service">Compound search Web service</a></li>
+<li><a href="#synonyms">Synonyms</a></li>
+</ul>
+</li>
+<li><a href="#chebi">ChEBI</a></li>
+<li><a href="#pubchem">PubChem</a></li>
+</ul>
+</div>
+<hr />
<p><a name="chemspider"></a></p>
-<h2 id="chemspider"><h2>ChemSpider<a class="headerlink" href="#chemspider"
title="Permanent link">¶</a></h2>
-<p><a href="http://www.chemspider.com/";>ChemSpider</a> is a chemistry search
engine that has been built with the intention of aggregating and indexing
- chemical structures and their associated information into a single
searchable repository and making it
+<h2 id="chemspider">ChemSpider<a class="headerlink" href="#chemspider"
title="Permanent link">¶</a></h2>
+<p><a href="http://www.chemspider.com/";>ChemSpider</a> is a chemistry search
engine that has been built with the intention of aggregating and indexing
+ chemical structures and their associated information into a single
searchable repository and making it
freely available to everybody.</p>
<p>ChemSpider provides several Web services, and these are listed below
together with their WSDL locations.</p>
<h3 id="inchi-web-service">InChi Web service<a class="headerlink"
href="#inchi-web-service" title="Permanent link">¶</a></h3>
<p>WSDL: <a
href="http://www.chemspider.com/InChI.asmx?WSDL";>http://www.chemspider.com/InChI.asmx?WSDL</a></p>
-<p><img src="/img/biocatalogue-smallcog.png" alt="BioCatalogue icon"
width="16" height="16" />
+<p><img src="/img/biocatalogue-smallcog.png" alt="BioCatalogue icon"
width="16" height="16" />
In BioCatalogue: <a
href="http://www.biocatalogue.org/services/2164";>http://www.biocatalogue.org/services/2164</a></p>
-<p>The InChI Web service provides operations to manipulate InChI Strings and
InChIKeys,
- including the conversion to and from the MOL file format, validity
checking of InChI identifiers,
+<p>The InChI Web service provides operations to manipulate InChI Strings and
InChIKeys,
+ including the conversion to and from the MOL file format, validity
checking of InChI identifiers,
and searching ChemSpider using InChI inputs.</p>
-<p>Some of the Web service’s operations listed below require a
“security token”.
-A security token can be obtained by completing the registration process for
ChemSpider at
+<p>Some of the Web service’s operations listed below require a
“security token”.
+A security token can be obtained by completing the registration process for
ChemSpider at
<a
href="http://www.chemspider.com/Register.aspx";>http://www.chemspider.com/Register.aspx</a>.</p>
<p>The following operations are contained within the InChI Web service:</p>
<ul>
<li>
<p>CSIDToMol <br />
- Converts a ChemSpider identifier to a MOL file. A security token is
required to get access to this
+ Converts a ChemSpider identifier to a MOL file. A security token is
required to get access to this
service. <br />
<a href="http://www.myexperiment.org/workflows/1418";>Example workflow</a></p>
</li>
@@ -235,7 +257,7 @@ A security token can be obtained by comp
</li>
<li>
<p>GenerateInChIKey <br />
- Returns a hashed InChI key which is a fixed length (25 character) condensed
digital representation of
+ Returns a hashed InChI key which is a fixed length (25 character) condensed
digital representation of
the input InChI string that is not human-understandable. <br />
<a href="http://www.myexperiment.org/workflows/1389";>Example workflow</a></p>
</li>
@@ -303,20 +325,20 @@ A security token can be obtained by comp
<p>WSDL: <a
href="http://www.chemspider.com/OpenBabel.asmx?WSDL";>http://www.chemspider.com/OpenBabel.asmx?WSDL</a></p>
<ul>
<li>convert <br />
- Converts a molecule represented in one format to another.
- For a list of valid format values, please visit <a
href="http://openbabel.org/wiki/Category:Formats";>openbabel</a>.
+ Converts a molecule represented in one format to another.
+ For a list of valid format values, please visit <a
href="http://openbabel.org/wiki/Category:Formats";>openbabel</a>.
An empty string is returned in case of failure. <br />
<a href="http://www.myexperiment.org/workflows/1401";>Example workflow</a></li>
</ul>
<h3 id="mass-spec-api-web-service">Mass spec API Web service<a
class="headerlink" href="#mass-spec-api-web-service" title="Permanent
link">¶</a></h3>
<p>WSDL: <a
href="http://www.chemspider.com/MassSpecAPI.asmx?WSDL";>http://www.chemspider.com/MassSpecAPI.asmx?WSDL</a>
<br />
-<img src="/img/biocatalogue-smallcog.png" alt="BioCatalogue icon" width="16"
height="16" />
+<img src="/img/biocatalogue-smallcog.png" alt="BioCatalogue icon" width="16"
height="16" />
In BioCatalogue: <a
href="http://www.biocatalogue.org/services/2040";>http://www.biocatalogue.org/services/2040</a></p>
<ul>
<li>
<p>GetCompressedRecordsSdf <br />
- Returns a SDF file containing records of compounds found by an asynchronous
search operation.
- A security token associated with ‘Service Subscriber’
+ Returns a SDF file containing records of compounds found by an asynchronous
search operation.
+ A security token associated with ‘Service Subscriber’
role is required to access this operation. <br />
Example workflow not available since a ‘Service Subscriber’
role is required by the user.</p>
</li>
@@ -327,33 +349,33 @@ In BioCatalogue: <a href="http://www.bio
</li>
<li>
<p>GetExtendedCompoundInfo <br />
- Returns extended record details for a given ChemSpider identifier.
+ Returns extended record details for a given ChemSpider identifier.
A security token is required to access this service. <br />
<a href="http://www.myexperiment.org/workflows/1405";>Example workflow</a></p>
</li>
<li>
<p>GetExtendedCompoundInfoArray <br />
- Returns an array of extended record details from an array of ChemSpider
identifiers.
+ Returns an array of extended record details from an array of ChemSpider
identifiers.
A security token is required to access this service. <br />
<a href="http://www.myexperiment.org/workflows/1406";>Example workflow</a></p>
</li>
<li>
<p>GetRecordMol <br />
- Returns a ChemSpider record in MOL format or an empty string in case of
failure.
- The cacl3d parameter specifies whether 3D coordinates should be calculated
before returning record data.
+ Returns a ChemSpider record in MOL format or an empty string in case of
failure.
+ The cacl3d parameter specifies whether 3D coordinates should be calculated
before returning record data.
A security token is required to access this service. <br />
<a href="http://www.myexperiment.org/workflows/1407";>Example workflow</a></p>
</li>
<li>
<p>GetRecordsSdf <br />
Returns a SDF file containing records found by an asynchronous search
operation.<br />
- A security token associated with the ‘Service Subscriber’
+ A security token associated with the ‘Service Subscriber’
role is required to access this operation. <br />
Example workflow not available since a Service Subscriber role is required
by the user.</p>
</li>
<li>
<p>SearchByFormula <br />
- Search ChemSpider compounds by molecular formula within a specified list
of datasources.
+ Search ChemSpider compounds by molecular formula within a specified list
of datasources.
This operation is deprecated and will be removed soon – use
SearchByFormulaAsync instead. <br />
Example workflow not available since this operation is deprecated.</p>
</li>
@@ -364,13 +386,13 @@ In BioCatalogue: <a href="http://www.bio
</li>
<li>
<p>SearchByFormulaAsync <br />
- Searches ChemSpider compounds by molecular formula within a specified
datasources list.
+ Searches ChemSpider compounds by molecular formula within a specified
datasources list.
Security token is required to get access to this service. <br />
<a href="http://www.myexperiment.org/workflows/1420";>Example workflow</a></p>
</li>
<li>
<p>SearchByMass <br />
- Searches ChemSpider compounds by mass +/- range within specified
datasources list.
+ Searches ChemSpider compounds by mass +/- range within specified
datasources list.
This operation is deprecated and will be removed soon – use
SearchByMassAsync instead. <br />
Example workflow not available since this operation is deprecated.</p>
</li>
@@ -381,7 +403,7 @@ In BioCatalogue: <a href="http://www.bio
</li>
<li>
<p>SearchByMassAsync <br />
- Searches ChemSpider compounds by mass +/- range within a specified
datasources list.
+ Searches ChemSpider compounds by mass +/- range within a specified
datasources list.
A security token is required to access this service.</p>
</li>
</ul>
@@ -406,14 +428,15 @@ In BioCatalogue: <a href="http://www.bio
</ul>
<h3 id="compound-search-web-service">Compound search Web service<a
class="headerlink" href="#compound-search-web-service" title="Permanent
link">¶</a></h3>
<p>WSDL: <a
href="http://www.chemspider.com/Search.asmx?WSDL";>http://www.chemspider.com/Search.asmx?WSDL</a>
<br />
-<img src="/pages/wp-content/uploads/2010/07/biocatalogue-smallcog.png"
alt="BioCatalogue icon" width="16" height="16" /> In BioCatalogue: </span><a
href="http://www.biocatalogue.org/services/1932";
target="_blank">http://www.biocatalogue.org/services/1932</a></p>
+<img src="/pages/wp-content/uploads/2010/07/biocatalogue-smallcog.png"
alt="BioCatalogue icon" width="16" height="16" /> In BioCatalogue: </span>
+<a href="http://www.biocatalogue.org/services/1932";
target="_blank">http://www.biocatalogue.org/services/1932</a></p>
<ul>
<li>
<p>AsyncSimpleSearch <br />
- Searches for molecules based on the entered search terms.
- The operation returns a transaction ID which can be used to access the
status of the search and results.
+ Searches for molecules based on the entered search terms.
+ The operation returns a transaction ID which can be used to access the
status of the search and results.
A security token is required to access this service. <br />
- The result of this operation is a hash number which can be used to retrieve
the actual results using
+ The result of this operation is a hash number which can be used to retrieve
the actual results using
the GetAsyncSearchResult operation below. <br />
<a href="http://www.myexperiment.org/workflows/1411";>Example workflow</a></p>
</li>
@@ -424,65 +447,65 @@ In BioCatalogue: <a href="http://www.bio
</li>
<li>
<p>GetAsyncSearchResult <br />
- Returns a list of identifiers found by the asynchronous search operation.
+ Returns a list of identifiers found by the asynchronous search operation.
A security token is required to access this service. <br />
<a href="http://www.myexperiment.org/workflows/1411";>Example workflow</a></p>
</li>
<li>
<p>GetAsyncSearchStatus <br />
- Queries the asynchronous operation status.
+ Queries the asynchronous operation status.
A security token is required to access this service. <br />
<a href="http://www.myexperiment.org/workflows/1411";>Example workflow</a></p>
</li>
<li>
<p>GetCompoundInfo <br />
- Returns the record details (CSID, InChIKey, InChI, SMILES) of a molecule by
its ChemSpider identifier.
+ Returns the record details (CSID, InChIKey, InChI, SMILES) of a molecule by
its ChemSpider identifier.
A security token is required to access this service. <br />
<a href="http://www.myexperiment.org/workflows/1412";>Example workflow</a></p>
</li>
<li>
<p>GetCompoundThumbnail <br />
- Returns an image of a molecule’s 2D structure in PNG format.
+ Returns an image of a molecule’s 2D structure in PNG format.
A security token is required to access this service. <br />
<a href="http://www.myexperiment.org/workflows/1414";>Example workflow</a></p>
</li>
<li>
<p>GetRecordDetails <br />
- Returns a record details: CSID, InChIKey, InChI, SMILES.
+ Returns a record details: CSID, InChIKey, InChI, SMILES.
This operation is deprecated and will be removed soon – use
GetCompoundInfo instead. <br />
No example workflow due to deprecation of this operation.</p>
</li>
<li>
<p>GetRecordImage <br />
- Returns an image of a molecule’s structure in PNG format.
+ Returns an image of a molecule’s structure in PNG format.
This operation is deprecated and will be removed soon – use
GetCompoundThumbnail instead. <br />
No example workflow due to deprecation of this operation.</p>
</li>
<li>
<p>Mol2CSID <br />
- Searches for structures matching a given MOL file within a given range.
- Returns a list of ChemSpider identifiers associated with matching
structures.
+ Searches for structures matching a given MOL file within a given range.
+ Returns a list of ChemSpider identifiers associated with matching
structures.
A security token with the ‘specific’ role is required to access
this service. <br />
No example workflow due to specific role required for the operation.</p>
</li>
<li>
<p>MolAndDS2CSID <br />
- Searches for structures matching a given MOL file within the range
specified by search options and
+ Searches for structures matching a given MOL file within the range
specified by search options and
within the specified list of datasources.<br />
- Returns a list of ChemSpider identifiers.
+ Returns a list of ChemSpider identifiers.
A security token with the ‘specific’ role is required to access
this service. <br />
No example workflow due to specific role required for the operation.</p>
</li>
<li>
<p>SimpleSearch <br />
- Performs a search using a given set of terms. Returns a list of ChemSpider
identifiers.
+ Performs a search using a given set of terms. Returns a list of ChemSpider
identifiers.
A security token is required to access this service. <br />
<a href="http://www.myexperiment.org/workflows/1427";>Example workflow</a></p>
</li>
<li>
<p>SimpleSearch2IdList <br />
- Tries to find whatever is entered.
- Returns a list of ChemSpider IDs.
+ Tries to find whatever is entered.
+ Returns a list of ChemSpider IDs.
This operation is deprecated and will be removed soon – use
SimpleSearch instead. <br />
No example workflow due to deprecation of this operation.</p>
</li>
@@ -494,38 +517,39 @@ In BioCatalogue: <a href="http://www.bio
Returns synonym names for a given compound represented by its MOL file. <br
/>
<a href="http://www.myexperiment.org/workflows/1415";>Example workflow</a></li>
</ul>
+<hr />
<p><a name="chebi"></a></p>
<h2 id="chebi">ChEBI<a class="headerlink" href="#chebi" title="Permanent
link">¶</a></h2>
-<p>Chemical Entities of Biological Interest (<a
href="http://www.ebi.ac.uk/chebi/";>ChEBI</a>) is a freely available database of
molecular entities
+<p>Chemical Entities of Biological Interest (<a
href="http://www.ebi.ac.uk/chebi/";>ChEBI</a>) is a freely available database of
molecular entities
focused on ‘small’ chemical compounds.<br />
The term ‘molecular entity’ refers to any constitutionally or
isotopically distinct atom, molecule,
- ion, ion pair, radical, radical ion, complex or conformer, identifiable as
a separately distinguishable
- entity.
-ChEBI incorporates an ontological classification, whereby the relationships
between molecular entities or
+ ion, ion pair, radical, radical ion, complex or conformer, identifiable as
a separately distinguishable
+ entity.
+ChEBI incorporates an ontological classification, whereby the relationships
between molecular entities or
classes of entities and their parents and/or children are specified.</p>
<p>ChEBI provides the following Web service with 7 operations.
WSDL: <a
href="http://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl";>http://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl</a>
<br />
-<img src="/img/biocatalogue-smallcog.png" alt="BioCatalogue icon" width="16"
height="16" />
+<img src="/img/biocatalogue-smallcog.png" alt="BioCatalogue icon" width="16"
height="16" />
In BioCatalogue: <a
href="http://www.biocatalogue.org/services/2174";>http://www.biocatalogue.org/services/2174</a></p>
<ul>
<li>
<p>getLiteEntity <br />
- Retrieves a list of “lite” entities containing only the ChEBI
ASCII name and ChEBI identifier.
- The input parameters are a search string and a search category.
- If the search category is null then it will search under all fields.
- The search string accepts the wildcard character “*” and also
unicode characters.
+ Retrieves a list of “lite” entities containing only the ChEBI
ASCII name and ChEBI identifier.
+ The input parameters are a search string and a search category.
+ If the search category is null then it will search under all fields.
+ The search string accepts the wildcard character “*” and also
unicode characters.
A maximum 5000 entries can be retrieved at a time. <br />
<a href="http://www.myexperiment.org/workflows/1419";>Example workflow</a></p>
</li>
<li>
<p>getCompleteEntity <br />
- Retrieves the complete record of a molecule including synonyms, database
links and chemical structures,
+ Retrieves the complete record of a molecule including synonyms, database
links and chemical structures,
using the ChEBI identifier. <br />
<a href="http://www.myexperiment.org/workflows/1421";>Example workflow</a></p>
</li>
<li>
<p>getCompleteEntityByList <br />
- Given a list of ChEBI accession numbers,
+ Given a list of ChEBI accession numbers,
retrieves the complete entity record associated with each accession
number.<br />
The maximum size of a given list is 50. <br />
<a href="http://www.myexperiment.org/workflows/1422";>Example workflow</a></p>
@@ -551,35 +575,36 @@ In BioCatalogue: <a href="http://www.bio
<a href="http://www.myexperiment.org/workflows/1426";>Example workflow</a></p>
</li>
</ul>
+<hr />
<p><a name="pubchem"></a></p>
<h2 id="pubchem">PubChem<a class="headerlink" href="#pubchem" title="Permanent
link">¶</a></h2>
-<p><a href="http://pubchem.ncbi.nlm.nih.gov/";>PubChem</a> is a free database
of chemical structures of small organic molecules and information on
- their biological activities provided by the National Center for
Biotechnology Information (<a
href="http://en.wikipedia.org/wiki/National_Center_for_Biotechnology_Information";>NCBI</a>),
+<p><a href="http://pubchem.ncbi.nlm.nih.gov/";>PubChem</a> is a free database
of chemical structures of small organic molecules and information on
+ their biological activities provided by the National Center for
Biotechnology Information (<a
href="http://en.wikipedia.org/wiki/National_Center_for_Biotechnology_Information";>NCBI</a>),
part of the United States National Institutes of Health (<a
href="http://en.wikipedia.org/wiki/National_Institutes_of_Health";>NIH</a>).</p>
<p>PubChem provides the following Web service with 28 operations.
WSDL: <a
href="http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap.cgi?wsdl";>http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap.cgi?wsdl</a>
-<img src="/img/biocatalogue-smallcog.png" alt="BioCatalogue icon" width="16"
height="16" />
+<img src="/img/biocatalogue-smallcog.png" alt="BioCatalogue icon" width="16"
height="16" />
In BioCatalogue: <a
href="http://www.biocatalogue.org/services/2176";>http://www.biocatalogue.org/services/2176</a></p>
<ul>
<li>
<p>AssayDownload <br />
- Given an assay key, prepares a file for download which contains an assay
data table in the selected format.
- See the assay query section of the PUG service documentation
- (<a
href="http://pubchem.ncbi.nlm.nih.gov/pug/pughelp.html";>http://pubchem.ncbi.nlm.nih.gov/pug/pughelp.html</a>)
for more details on the supported formats.
+ Given an assay key, prepares a file for download which contains an assay
data table in the selected format.
+ See the assay query section of the PUG service documentation
+ (<a
href="http://pubchem.ncbi.nlm.nih.gov/pug/pughelp.html";>http://pubchem.ncbi.nlm.nih.gov/pug/pughelp.html</a>)
for more details on the supported formats.
Compression is optional and defaults to gzip (.gz). Returns a download
key. Asynchronous.</p>
</li>
<li>
<p>Download <br />
- Given a list key, prepares a file for downloading which contains those
records in the selected format.
- See the web download service documentation
- (<a
href="http://pubchem.ncbi.nlm.nih.gov/pc_fetch/pc_fetch-help.html";>http://pubchem.ncbi.nlm.nih.gov/pc_fetch/pc_fetch-help.html</a>)
- for more detail on the supported formats and file types.
+ Given a list key, prepares a file for downloading which contains those
records in the selected format.
+ See the web download service documentation
+ (<a
href="http://pubchem.ncbi.nlm.nih.gov/pc_fetch/pc_fetch-help.html";>http://pubchem.ncbi.nlm.nih.gov/pc_fetch/pc_fetch-help.html</a>)
+ for more detail on the supported formats and file types.
Returns a download key. Asynchronous. <br />
<a href="http://www.myexperiment.org/workflows/1435";>Example workflow</a></p>
</li>
<li>
<p>GetAssayColumnDescription <br />
- Returns the description of a column (readout) in a BioAssay, which may be
the outcome, score,
+ Returns the description of a column (readout) in a BioAssay, which may be
the outcome, score,
or a TID from the given AID. Synchronous.</p>
</li>
<li>
@@ -588,7 +613,7 @@ In BioCatalogue: <a href="http://www.bio
</li>
<li>
<p>GetAssayDescription <br />
- Returns the descriptive information for a BioAssay, including the number of
user-specified readouts (TIDs)
+ Returns the descriptive information for a BioAssay, including the number of
user-specified readouts (TIDs)
and whether a score readout is present.<br />
Optionally get version information. Synchronous.</p>
</li>
@@ -598,13 +623,13 @@ In BioCatalogue: <a href="http://www.bio
</li>
<li>
<p>GetEntrezKey <br />
- Given a list key, returns an Entrez history key (db, query key, and
WebEnv) corresponding to that list.
+ Given a list key, returns an Entrez history key (db, query key, and
WebEnv) corresponding to that list.
Synchronous. <br />
<a href="http://www.myexperiment.org/workflows/1431";>Example workflow</a></p>
</li>
<li>
<p>GetEntrezUrl <br />
- Given an Entrez history key (db, query key, and WebEnv), returns an HTTP
URL that may be used to view the
+ Given an Entrez history key (db, query key, and WebEnv), returns an HTTP
URL that may be used to view the
list in Entrez. Synchronous.
<a href="http://www.myexperiment.org/workflows/1431";>Example
workflow</a></p>
</li>
@@ -619,119 +644,119 @@ In BioCatalogue: <a href="http://www.bio
</li>
<li>
<p>GetOperationStatus <br />
- Given a key for any asynchronous operation, returns the status of that
operation.
- Possible return values are: Success, the operation completed normally;
HitLimit, TimeLimit: the operation
- finished normally, but one of the limits was reached (e.g. before the
entire database was searched);
- ServerError, InputError, DataError, Stopped: there was a problem with
the input or on the server,
- and the job has died; Queued: the operation is waiting its turn in the
public queue; Running:
+ Given a key for any asynchronous operation, returns the status of that
operation.
+ Possible return values are: Success, the operation completed normally;
HitLimit, TimeLimit: the operation
+ finished normally, but one of the limits was reached (e.g. before the
entire database was searched);
+ ServerError, InputError, DataError, Stopped: there was a problem with
the input or on the server,
+ and the job has died; Queued: the operation is waiting its turn in the
public queue; Running:
the operation is in progress. Synchronous. <br />
<a href="http://www.myexperiment.org/workflows/1431";>Example workflow</a></p>
</li>
<li>
<p>GetStandardizedCID <br />
- Given a structure key that has been processed by Standardize, returns the
corresponding PubChem Compound
+ Given a structure key that has been processed by Standardize, returns the
corresponding PubChem Compound
database CID, or an empty value if the structure is not present in
PubChem. Synchronous.</p>
</li>
<li>
<p>GetStandardizedStructure <br />
- Given a structure key that has been processed by Standardize, returns the
chemical structure in as SMILES
+ Given a structure key that has been processed by Standardize, returns the
chemical structure in as SMILES
or InChI strings. Synchronous.</p>
</li>
<li>
<p>GetStandardizedStructureBase64 <br />
- Given a structure key that has been processed by Standardize, returns the
chemical structure as ASN, XML,
+ Given a structure key that has been processed by Standardize, returns the
chemical structure as ASN, XML,
or SDF, returned as a Base64-encoded string. Synchronous.</p>
</li>
<li>
<p>GetStatusMessage <br />
- Given a key for any asynchronous operation, returns any system messages
(error messages, job info, etc.)
+ Given a key for any asynchronous operation, returns any system messages
(error messages, job info, etc.)
associated with the operation, if any. Synchronous.</p>
</li>
<li>
<p>IdentitySearch <br />
- Searches PubChem Compound for structures identical to the one given by the
structure key input based on
- a user-selected level of chemical identity: connectivity only, match
isotopes and/or stereo, etc.
- The search may be limited by elapsed time or number of records found, or
restricted to search only within
- a previous result set (given by a list key).
+ Searches PubChem Compound for structures identical to the one given by the
structure key input based on
+ a user-selected level of chemical identity: connectivity only, match
isotopes and/or stereo, etc.
+ The search may be limited by elapsed time or number of records found, or
restricted to search only within
+ a previous result set (given by a list key).
Returns a list key. Asynchronous. <br />
<a href="http://www.myexperiment.org/workflows/1433";>Example workflow</a></p>
</li>
<li>
<p>InputAssay <br />
- Specifies an assay table from a BioAssay AID.
- The table may be complete, concise, or include a ListKey-specified set of
readouts (TIDs).
- By default, all tested substances are included, but can be restricted to a
ListKey-specified set of SIDs
+ Specifies an assay table from a BioAssay AID.
+ The table may be complete, concise, or include a ListKey-specified set of
readouts (TIDs).
+ By default, all tested substances are included, but can be restricted to a
ListKey-specified set of SIDs
or CIDs. Returns an assay key. Synchronous.</p>
</li>
<li>
<p>InputEntrez <br />
- Configures an Entrez history key (db, query key, and WebEnv).
+ Configures an Entrez history key (db, query key, and WebEnv).
Returns a list key. Synchronous.</p>
</li>
<li>
<p>InputList <br />
- Configures a set of identifiers for a PubChem database, as an array of
integers.
+ Configures a set of identifiers for a PubChem database, as an array of
integers.
Returns a list key. Synchronous.</p>
</li>
<li>
<p>InputListText <br />
- Configures a set of identifiers for a PubChem database, as a simple string
of integer values separated
+ Configures a set of identifiers for a PubChem database, as a simple string
of integer values separated
by commas and/or whitespace. Returns a list key. Synchronous.</p>
</li>
<li>
<p>InputStructure
- Configures a chemical structure as a simple (one-line) string, either
SMILES or InChI.
+ Configures a chemical structure as a simple (one-line) string, either
SMILES or InChI.
Returns a structure key. Synchronous. <br />
<a href="http://www.myexperiment.org/workflows/1433";>Example workflow</a></p>
</li>
<li>
<p>InputStructureBase64 <br />
- Configures a chemical structure in ASN.1 (text or binary), XML, or SDF
format.
- The structure must be encoded as a Base64 string.
- Currently only single structures are supported.
+ Configures a chemical structure in ASN.1 (text or binary), XML, or SDF
format.
+ The structure must be encoded as a Base64 string.
+ Currently only single structures are supported.
Returns a structure key. Synchronous. <br />
<a href="http://www.myexperiment.org/workflows/1431";>Example workflow</a></p>
</li>
<li>
<p>MFSearch <br />
Searches PubChem Compound for structures of a given molecular formula,<br />
- optionally allowing elements not specified to be present.
- The search may be limited by elapsed time or number of records found, or
restricted to search only
+ optionally allowing elements not specified to be present.
+ The search may be limited by elapsed time or number of records found, or
restricted to search only
within a previous result set (given by a list key). Returns a list key.
Asynchronous.</p>
</li>
<li>
<p>ScoreMatrix <br />
- Computes a matrix of scores from one or two lists of IDs (if one, the IDs
will be self-scored),
+ Computes a matrix of scores from one or two lists of IDs (if one, the IDs
will be self-scored),
of the selected type and in the selected format.<br />
Compression is optional and defaults to gzip (.gz). Returns a download key.
Asynchronous.</p>
</li>
<li>
<p>SimilaritySearch2D <br />
- Searches PubChem Compound for structures similar to the one given by the
structure key input,
+ Searches PubChem Compound for structures similar to the one given by the
structure key input,
based on the given Tanimoto-based similarity score.<br />
The search may be limited by elapsed time or number of records found,<br />
- or restricted to search only within a previous result set (given by a
list key).
+ or restricted to search only within a previous result set (given by a
list key).
Returns a list key. Asynchronous. <br />
<a href="http://www.myexperiment.org/workflows/1431";>Example workflow</a></p>
</li>
<li>
<p>Standardize <br />
- Standardizes the structure given by the structure key input,
- using the same algorithm PubChem uses to construct the Compound
database.
+ Standardizes the structure given by the structure key input,
+ using the same algorithm PubChem uses to construct the Compound database.
Returns a structure key. Asynchronous.</p>
</li>
<li>
<p>SubstructureSearch <br />
- Searches PubChem Compound for structures containing the one given by the
structure key input,
- based on a user-selected level of chemical identity: connectivity only,
match isotopes and/or stereo, etc.
- The search may be limited by elapsed time or number of records found,
- or restricted to search only within a previous result set (given by a
list key).
+ Searches PubChem Compound for structures containing the one given by the
structure key input,
+ based on a user-selected level of chemical identity: connectivity only,
match isotopes and/or stereo, etc.
+ The search may be limited by elapsed time or number of records found,
+ or restricted to search only within a previous result set (given by a
list key).
Returns a list key. Asynchronous. <br />
<a href="http://www.myexperiment.org/workflows/1434";>Example workflow</a></p>
</li>
<li>
<p>SuperstructureSearch <br />
- Searches PubChem Compound for structures contained within the one given by
the structure key input,
+ Searches PubChem Compound for structures contained within the one given by
the structure key input,
based on a user-selected level of chemical identity: connectivity only,
match isotopes and/or stereo, etc. The search may be limited by elapsed time
or number of records found, or restricted to search only within a previous
result set (given by a list key). Returns a list key. Asynchronous.</li></p>
</li>
</ul></div>
