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Posted to commits@taverna.apache.org by bu...@apache.org on 2015/02/24 16:57:05 UTC
svn commit: r941342 - in /websites/staging/taverna/trunk: cgi-bin/ content/
content/introduction/chemistry-web-services.html
Author: buildbot
Date: Tue Feb 24 15:57:05 2015
New Revision: 941342
Log:
Staging update by buildbot for taverna
Modified:
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
Propchange: websites/staging/taverna/trunk/cgi-bin/
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--- cms:source-revision (original)
+++ cms:source-revision Tue Feb 24 15:57:05 2015
@@ -1 +1 @@
-1661993
+1661994
Propchange: websites/staging/taverna/trunk/content/
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--- cms:source-revision (original)
+++ cms:source-revision Tue Feb 24 15:57:05 2015
@@ -1 +1 @@
-1661993
+1661994
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 Tue Feb 24 15:57:05 2015
@@ -177,7 +177,7 @@ Instead it shows <a class="alert-link" h
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.
-They can also be downloaded as part of the <a href="http://www.myexperiment.org/packs/136.html">Chemistry Workflows pack</a> at myExperiment.</p>
+They can also be downloaded as part of the <a href="http://www.myexperiment.org/packs/136">Chemistry Workflows pack</a> at myExperiment.</p>
<p><a name="chemspider"></a></p>
<h2 id="wzxhzdk2chemspider"><h2>ChemSpider</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
@@ -200,73 +200,73 @@ A security token can be obtained by comp
<p>CSIDToMol <br />
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.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1418">Example workflow</a></p>
</li>
<li>
<p>GenerateInChI <br />
Generates an InChI string for a given chemical represented by its SMILES string, SDF or MOL file. <br />
-<a href="href="http://www.myexperiment.org/workflows/1387.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1387">Example workflow</a></p>
</li>
<li>
<p>GenerateInChIInfo <br />
Returns information relating to the InChI string for a given chemical compound. <br />
-<a href="http://www.myexperiment.org/workflows/1388.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1388">Example workflow</a></p>
</li>
<li>
<p>GenerateInChIKey <br />
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.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1389">Example workflow</a></p>
</li>
<li>
<p>InChIKeyToCSID <br />
Converts an InChI key to a ChemSpider identifier. <br />
-<a href="http://www.myexperiment.org/workflows/1390.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1390">Example workflow</a></p>
</li>
<li>
<p>InChIKeyToInChI <br />
Converts an InChI key to an InChI string. <br />
-<a href="http://www.myexperiment.org/workflows/1391.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1391">Example workflow</a></p>
</li>
<li>
<p>InChIKeyToMol <br />
Converts an InChI key to a MOL file. <br />
-<a href="http://www.myexperiment.org/workflows/1392.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1392">Example workflow</a></p>
</li>
<li>
<p>InChIToCSID <br />
Convets an InChI string to a ChemSpider identifier. <br />
-<a href="http://www.myexperiment.org/workflows/1393.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1393">Example workflow</a></p>
</li>
<li>
<p>InChIToInChIKey <br />
Converts an InChI string to an InChI key. This only works for 1.02b InChI strings. <br />
-<a href="http://www.myexperiment.org/workflows/1394.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1394">Example workflow</a></p>
</li>
<li>
<p>InChIToMol <br />
Converts an InChI string to a MOL file. Uses <a href="http://openbabel.org/wiki/Main_Page">OpenBabel</a> internally to perform this operation. <br />
-<a href="http://www.myexperiment.org/workflows/1395.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1395">Example workflow</a></p>
</li>
<li>
<p>InChIToSMILES <br />
Converts an InChI string to a SMILES string. Uses <a href="http://openbabel.org/wiki/Main_Page">OpenBabel</a></a> internally to perform this operation. <br />
-<a href="http://www.myexperiment.org/workflows/1396.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1396">Example workflow</a></p>
</li>
<li>
<p>IsValidInChIKey <br />
Checks that an InChI key is valid. Works only for v1.02b InChI keys. <br />
-<a href="http://www.myexperiment.org/workflows/1397.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1397">Example workflow</a></p>
</li>
<li>
<p>MolToInChI <br />
Converts a MOL file into an InChI string (v1.02s). <br />
-<a href="http://www.myexperiment.org/workflows/1398.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1398">Example workflow</a></p>
</li>
<li>
<p>MolToInChIKey <br />
Converts a MOL file into an v1.02s InChI key. <br />
-<a href="http://www.myexperiment.org/workflows/1399.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1399">Example workflow</a></p>
</li>
<li>
<p>ResolveInChIKey <br />
@@ -275,7 +275,7 @@ A security token can be obtained by comp
<li>
<p>SMILESToInChI <br />
Converts a SMILES string to an InChI string. The result is returned as a v1.02s InChI string. <br />
-<a href="http://www.myexperiment.org/workflows/1400.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1400">Example workflow</a></p>
</li>
</ul>
<h3 id="openbabel-web-service">OpenBabel Web service</h3>
@@ -285,7 +285,7 @@ A security token can be obtained by comp
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.html">Example workflow</a></li>
+<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</h3>
<p>WSDL: <a href="http://www.chemspider.com/MassSpecAPI.asmx?WSDL">http://www.chemspider.com/MassSpecAPI.asmx?WSDL</a> <br />
@@ -302,26 +302,26 @@ In BioCatalogue: <a href="http://www.bio
<li>
<p>GetDatabases <br />
Returns a list of datasources in ChemSpider. <br />
-<a href="http://www.myexperiment.org/workflows/1404.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1404">Example workflow</a></p>
</li>
<li>
<p>GetExtendedCompoundInfo <br />
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.html">Example workflow</a></p>
+<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.
A security token is required to access this service. <br />
-<a href="http://www.myexperiment.org/workflows/1406.html">Example workflow</a></p>
+<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.
A security token is required to access this service. <br />
-<a href="http://www.myexperiment.org/workflows/1407.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1407">Example workflow</a></p>
</li>
<li>
<p>GetRecordsSdf <br />
@@ -345,7 +345,7 @@ In BioCatalogue: <a href="http://www.bio
<p>SearchByFormulaAsync <br />
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.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1420">Example workflow</a></p>
</li>
<li>
<p>SearchByMass <br />
@@ -370,17 +370,17 @@ In BioCatalogue: <a href="http://www.bio
<li>
<p>GetAllSpectraInfo <br />
Returns information for all open access spectra in ChemSpider <br />
-<a href="http://www.myexperiment.org/workflows/1408.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1408">Example workflow</a></p>
</li>
<li>
<p>GetCompoundSpectraInfo <br />
Returns information about spectra associated with a particular compound identified by the cmp_id parameter <br />
-<a href="http://www.myexperiment.org/workflows/1409.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1409">Example workflow</a></p>
</li>
<li>
<p>GetSpectrumInfo <br />
Returns information about a particular spectrum identified by its spc_id parameter <br />
-<a href="http://www.myexperiment.org/workflows/1410.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1410">Example workflow</a></p>
</li>
</ul>
<h3 id="compound-search-web-service">Compound search Web service</h3>
@@ -394,7 +394,7 @@ In BioCatalogue: <a href="http://www.bio
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 GetAsyncSearchResult operation below. <br />
-<a href="http://www.myexperiment.org/workflows/1411.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1411">Example workflow</a></p>
</li>
<li>
<p>CSID2ExtRefs <br />
@@ -405,25 +405,25 @@ In BioCatalogue: <a href="http://www.bio
<p>GetAsyncSearchResult <br />
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.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1411">Example workflow</a></p>
</li>
<li>
<p>GetAsyncSearchStatus <br />
Queries the asynchronous operation status.
A security token is required to access this service. <br />
-<a href="http://www.myexperiment.org/workflows/1411.html">Example workflow</a></p>
+<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.
A security token is required to access this service. <br />
-<a href="http://www.myexperiment.org/workflows/1412.html">Example workflow</a></p>
+<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.
A security token is required to access this service. <br />
-<a href="http://www.myexperiment.org/workflows/1414.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1414">Example workflow</a></p>
</li>
<li>
<p>GetRecordDetails <br />
@@ -456,7 +456,7 @@ In BioCatalogue: <a href="http://www.bio
<p>SimpleSearch <br />
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.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1427">Example workflow</a></p>
</li>
<li>
<p>SimpleSearch2IdList <br />
@@ -471,7 +471,7 @@ In BioCatalogue: <a href="http://www.bio
<ul>
<li>GetStructureSynonyms <br />
Returns synonym names for a given compound represented by its MOL file. <br />
-<a href="http://www.myexperiment.org/workflows/1415.html">Example workflow</a></li>
+<a href="http://www.myexperiment.org/workflows/1415">Example workflow</a></li>
</ul>
<p><a name="chebi"></a></p>
<h2 id="chebi">ChEBI</h2>
@@ -494,30 +494,30 @@ In BioCatalogue: <a href="http://www.bio
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.html">Example workflow</a></p>
+<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,
using the ChEBI identifier. <br />
-<a href="http://www.myexperiment.org/workflows/1421.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1421">Example workflow</a></p>
</li>
<li>
<p>getCompleteEntityByList <br />
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.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1422">Example workflow</a></p>
</li>
<li>
<p>getOntologyParents <br />
Retrieves the ontology parents of an entity including the relationship type, using a ChEBI identifier. <br />
-<a href="http://www.myexperiment.org/workflows/1423.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1423">Example workflow</a></p>
</li>
<li>
<p>getOntologyChildren <br />
Retrieves the ontology children of an entity including the relationship type, using a ChEBI identifier. <br />
-<a href="http://www.myexperiment.org/workflows/1424.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1424">Example workflow</a></p>
</li>
<li>
<p>getAllOntologyChildrenInPath <br />
@@ -527,7 +527,7 @@ In BioCatalogue: <a href="http://www.bio
<li>
<p>getStructureSearch <br />
Does a substructure, similarity or identity search using a query structure. <br />
-<a href="http://www.myexperiment.org/workflows/1426.html">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1426">Example workflow</a></p>
</li>
</ul>
<p><a name="pubchem"></a></p>
@@ -538,7 +538,7 @@ In BioCatalogue: <a href="http://www.bio
<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" />
-In BioCatalogue: <a href="href="http://www.biocatalogue.org/services/2176">http://www.biocatalogue.org/services/2176</a></p>
+In BioCatalogue: <a href="http://www.biocatalogue.org/services/2176">http://www.biocatalogue.org/services/2176</a></p>
<ul>
<li>
<p>AssayDownload <br />
@@ -554,7 +554,7 @@ In BioCatalogue: <a href="href="htt
(<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.html?version=2">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1435">Example workflow</a></p>
</li>
<li>
<p>GetAssayColumnDescription <br />
@@ -579,18 +579,18 @@ In BioCatalogue: <a href="href="htt
<p>GetEntrezKey <br />
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.html?version=2">Example workflow</a></p>
+<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
list in Entrez. Synchronous.
- <a href="http://www.myexperiment.org/workflows/1431.html?version=2">Example workflow</a></p>
+ <a href="http://www.myexperiment.org/workflows/1431">Example workflow</a></p>
</li>
<li>
<p>GetIDList <br />
Given a list key, returns the identifiers as an array of integers. Synchronous. <br />
-<a href="http://www.myexperiment.org/workflows/1433.html?version=2">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1433">Example workflow</a></p>
</li>
<li>
<p>GetListItemsCount <br />
@@ -604,7 +604,7 @@ In BioCatalogue: <a href="href="htt
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.html?version=2">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1431">Example workflow</a></p>
</li>
<li>
<p>GetStandardizedCID <br />
@@ -633,7 +633,7 @@ In BioCatalogue: <a href="href="htt
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.html?version=2">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1433">Example workflow</a></p>
</li>
<li>
<p>InputAssay <br />
@@ -661,7 +661,7 @@ In BioCatalogue: <a href="href="htt
<p>InputStructure
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.html?version=2">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1433">Example workflow</a></p>
</li>
<li>
<p>InputStructureBase64 <br />
@@ -669,7 +669,7 @@ In BioCatalogue: <a href="href="htt
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.html?version=2">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1431">Example workflow</a></p>
</li>
<li>
<p>MFSearch <br />
@@ -691,7 +691,7 @@ In BioCatalogue: <a href="href="htt
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).
Returns a list key. Asynchronous. <br />
-<a href="http://www.myexperiment.org/workflows/1431.html?version=2">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1431">Example workflow</a></p>
</li>
<li>
<p>Standardize <br />
@@ -706,7 +706,7 @@ In BioCatalogue: <a href="href="htt
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.html?version=2">Example workflow</a></p>
+<a href="http://www.myexperiment.org/workflows/1434">Example workflow</a></p>
</li>
<li>
<p>SuperstructureSearch <br />