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Posted to commits@taverna.apache.org by bu...@apache.org on 2016/07/14 19:53:09 UTC
svn commit: r992839 - in /websites/staging/taverna/trunk: cgi-bin/ content/
content/introduction/chemistry-web-services.html
Author: buildbot
Date: Thu Jul 14 19:53:08 2016
New Revision: 992839
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 Thu Jul 14 19:53:08 2016
@@ -1 +1 @@
-1752734
+1752736
Propchange: websites/staging/taverna/trunk/content/
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--- cms:source-revision (original)
+++ cms:source-revision Thu Jul 14 19:53:08 2016
@@ -1 +1 @@
-1752734
+1752736
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 19:53:08 2016
@@ -319,7 +319,7 @@ A security token can be obtained by comp
<h3 id="openbabel-web-service">OpenBabel Web service<a class="headerlink" href="#openbabel-web-service" title="Permanent link">¶</a></h3>
<p>WSDL: <a href="http://www.chemspider.com/OpenBabel.asmx?WSDL">http://www.chemspider.com/OpenBabel.asmx?WSDL</a></p>
<ul>
-<li>convert <br />
+<li><strong>convert</strong> <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>.
An empty string is returned in case of failure. <br />
@@ -331,73 +331,73 @@ A security token can be obtained by comp
In BioCatalogue: <a href="http://www.biocatalogue.org/services/2040">http://www.biocatalogue.org/services/2040</a></p>
<ul>
<li>
-<p>GetCompressedRecordsSdf <br />
+<p><strong>GetCompressedRecordsSdf</strong> <br />
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>
<li>
-<p>GetDatabases <br />
+<p><strong>GetDatabases</strong> <br />
Returns a list of datasources in ChemSpider. <br />
<a href="http://www.myexperiment.org/workflows/1404">Example workflow</a></p>
</li>
<li>
-<p>GetExtendedCompoundInfo <br />
+<p><strong>GetExtendedCompoundInfo</strong> <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">Example workflow</a></p>
</li>
<li>
-<p>GetExtendedCompoundInfoArray <br />
+<p><strong>GetExtendedCompoundInfoArray</strong> <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">Example workflow</a></p>
</li>
<li>
-<p>GetRecordMol <br />
+<p><strong>GetRecordMol</strong> <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">Example workflow</a></p>
</li>
<li>
-<p>GetRecordsSdf <br />
+<p><strong>GetRecordsSdf</strong> <br />
Returns a SDF file containing records found by an asynchronous search operation.<br />
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 />
+<p><strong>SearchByFormula</strong> <br />
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>
<li>
-<p>SearchByFormula2 <br />
+<p><strong>SearchByFormula2</strong> <br />
Search ChemSpider compounds by molecular formula. <br />
Example workflow not available since this operation is deprecated.</p>
</li>
<li>
-<p>SearchByFormulaAsync <br />
+<p><strong>SearchByFormulaAsync</strong> <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">Example workflow</a></p>
</li>
<li>
-<p>SearchByMass <br />
+<p><strong>SearchByMass</strong> <br />
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>
<li>
-<p>SearchByMass2 <br />
+<p><strong>SearchByMass2</strong> <br />
Search ChemSpider compounds by mass +/- range. <br />
Example workflow not available since this operation is deprecated.</p>
</li>
<li>
-<p>SearchByMassAsync <br />
+<p><strong>SearchByMassAsync</strong> <br />
Searches ChemSpider compounds by mass +/- range within a specified datasources list.
A security token is required to access this service.</p>
</li>
@@ -406,17 +406,17 @@ In BioCatalogue: <a href="http://www.bio
<p>WSDL: <a href="http://www.chemspider.com/Spectra.asmx?WSDL">http://www.chemspider.com/Spectra.asmx?WSDL</a></p>
<ul>
<li>
-<p>GetAllSpectraInfo <br />
+<p><strong>GetAllSpectraInfo</strong> <br />
Returns information for all open access spectra in ChemSpider <br />
<a href="http://www.myexperiment.org/workflows/1408">Example workflow</a></p>
</li>
<li>
-<p>GetCompoundSpectraInfo <br />
+<p><strong>GetCompoundSpectraInfo</strong> <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">Example workflow</a></p>
</li>
<li>
-<p>GetSpectrumInfo <br />
+<p><strong>GetSpectrumInfo</strong> <br />
Returns information about a particular spectrum identified by its spc_id parameter <br />
<a href="http://www.myexperiment.org/workflows/1410">Example workflow</a></p>
</li>
@@ -427,7 +427,7 @@ In BioCatalogue: <a href="http://www.bio
<a href="http://www.biocatalogue.org/services/1932" target="_blank">http://www.biocatalogue.org/services/1932</a></p>
<ul>
<li>
-<p>AsyncSimpleSearch <br />
+<p><strong>AsyncSimpleSearch</strong> <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.
A security token is required to access this service. <br />
@@ -436,55 +436,55 @@ In BioCatalogue: <a href="http://www.bio
<a href="http://www.myexperiment.org/workflows/1411">Example workflow</a></p>
</li>
<li>
-<p>CSID2ExtRefs <br />
+<p><strong>CSID2ExtRefs</strong> <br />
Returns a list of external references (data sources) for a given compound.<br />
A security token with the relevant role is required to access this service.</p>
</li>
<li>
-<p>GetAsyncSearchResult <br />
+<p><strong>GetAsyncSearchResult</strong> <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">Example workflow</a></p>
</li>
<li>
-<p>GetAsyncSearchStatus <br />
+<p><strong>GetAsyncSearchStatus</strong> <br />
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 />
+<p><strong>GetCompoundInfo</strong> <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">Example workflow</a></p>
</li>
<li>
-<p>GetCompoundThumbnail <br />
+<p><strong>GetCompoundThumbnail</strong> <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">Example workflow</a></p>
</li>
<li>
-<p>GetRecordDetails <br />
+<p><strong>GetRecordDetails</strong> <br />
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 />
+<p><strong>GetRecordImage</strong> <br />
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 />
+<p><strong>Mol2CSID</strong> <br />
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 />
+<p><strong>MolAndDS2CSID</strong> <br />
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.
@@ -492,13 +492,13 @@ In BioCatalogue: <a href="http://www.bio
No example workflow due to specific role required for the operation.</p>
</li>
<li>
-<p>SimpleSearch <br />
+<p><strong>SimpleSearch</strong> <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">Example workflow</a></p>
</li>
<li>
-<p>SimpleSearch2IdList <br />
+<p><strong>SimpleSearch2IdList</strong> <br />
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 />
@@ -508,7 +508,7 @@ In BioCatalogue: <a href="http://www.bio
<h3 id="synonyms">Synonyms<a class="headerlink" href="#synonyms" title="Permanent link">¶</a></h3>
<p>WSDL: <a href="http://www.chemspider.com/Synonyms.asmx?WSDL">http://www.chemspider.com/Synonyms.asmx?WSDL</a></p>
<ul>
-<li>GetStructureSynonyms <br />
+<li><strong>GetStructureSynonyms</strong> <br />
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>
@@ -528,7 +528,7 @@ WSDL: <a href="http://www.ebi.ac.uk/webs
In BioCatalogue: <a href="http://www.biocatalogue.org/services/2174">http://www.biocatalogue.org/services/2174</a></p>
<ul>
<li>
-<p>getLiteEntity <br />
+<p><strong>getLiteEntity</strong> <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.
@@ -537,35 +537,35 @@ In BioCatalogue: <a href="http://www.bio
<a href="http://www.myexperiment.org/workflows/1419">Example workflow</a></p>
</li>
<li>
-<p>getCompleteEntity <br />
+<p><strong>getCompleteEntity</strong> <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">Example workflow</a></p>
</li>
<li>
-<p>getCompleteEntityByList <br />
+<p><strong>getCompleteEntityByList</strong> <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">Example workflow</a></p>
</li>
<li>
-<p>getOntologyParents <br />
+<p><strong>getOntologyParents</strong> <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">Example workflow</a></p>
</li>
<li>
-<p>getOntologyChildren <br />
+<p><strong>getOntologyChildren</strong> <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">Example workflow</a></p>
</li>
<li>
-<p>getAllOntologyChildrenInPath <br />
+<p><strong>getAllOntologyChildrenInPath</strong> <br />
Retrieves the ontology children of an entity including the relationship type, using a ChEBI identifier. <br />
No example workflow available.</p>
</li>
<li>
-<p>getStructureSearch <br />
+<p><strong>getStructureSearch</strong> <br />
Does a substructure, similarity or identity search using a query structure. <br />
<a href="http://www.myexperiment.org/workflows/1426">Example workflow</a></p>
</li>
@@ -577,19 +577,19 @@ In BioCatalogue: <a href="http://www.bio
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" />
+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></p>
+<p><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 />
+<p><strong>AssayDownload</strong> <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.
Compression is optional and defaults to gzip (.gz). Returns a download key. Asynchronous.</p>
</li>
<li>
-<p>Download <br />
+<p><strong>Download</strong> <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>)
@@ -598,47 +598,47 @@ In BioCatalogue: <a href="http://www.bio
<a href="http://www.myexperiment.org/workflows/1435">Example workflow</a></p>
</li>
<li>
-<p>GetAssayColumnDescription <br />
+<p><strong>GetAssayColumnDescription</strong> <br />
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>
-<p>GetAssayColumnDescriptions <br />
+<p><strong>GetAssayColumnDescriptions</strong> <br />
Returns the description of all columns (readouts) in a BioAssay. Synchronous.</p>
</li>
<li>
-<p>GetAssayDescription <br />
+<p><strong>GetAssayDescription</strong> <br />
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>
<li>
-<p>GetDownloadUrl <br />
+<p><strong>GetDownloadUrl</strong> <br />
Given a download key, returns an FTP URL that may be used to download the requested file. Synchronous.</p>
</li>
<li>
-<p>GetEntrezKey <br />
+<p><strong>GetEntrezKey</strong> <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">Example workflow</a></p>
</li>
<li>
-<p>GetEntrezUrl <br />
+<p><strong>GetEntrezUrl</strong> <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">Example workflow</a></p>
</li>
<li>
-<p>GetIDList <br />
+<p><strong>GetIDList</strong> <br />
Given a list key, returns the identifiers as an array of integers. Synchronous. <br />
<a href="http://www.myexperiment.org/workflows/1433">Example workflow</a></p>
</li>
<li>
-<p>GetListItemsCount <br />
+<p><strong>GetListItemsCount</strong> <br />
Returns the number of IDs in the set represented by a given list key. Synchronous.</p>
</li>
<li>
-<p>GetOperationStatus <br />
+<p><strong>GetOperationStatus</strong> <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);
@@ -648,27 +648,27 @@ In BioCatalogue: <a href="http://www.bio
<a href="http://www.myexperiment.org/workflows/1431">Example workflow</a></p>
</li>
<li>
-<p>GetStandardizedCID <br />
+<p><strong>GetStandardizedCID</strong> <br />
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 />
+<p><strong>GetStandardizedStructure</strong> <br />
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 />
+<p><strong>GetStandardizedStructureBase64</strong> <br />
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 />
+<p><strong>GetStatusMessage</strong> <br />
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 />
+<p><strong>IdentitySearch</strong> <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
@@ -677,35 +677,35 @@ In BioCatalogue: <a href="http://www.bio
<a href="http://www.myexperiment.org/workflows/1433">Example workflow</a></p>
</li>
<li>
-<p>InputAssay <br />
+<p><strong>InputAssay</strong> <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
or CIDs. Returns an assay key. Synchronous.</p>
</li>
<li>
-<p>InputEntrez <br />
+<p><strong>InputEntrez</strong> <br />
Configures an Entrez history key (db, query key, and WebEnv).
Returns a list key. Synchronous.</p>
</li>
<li>
-<p>InputList <br />
+<p><strong>InputList</strong> <br />
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 />
+<p><strong>InputListText</strong> <br />
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
+<p><strong>InputStructure</strong>
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 />
+<p><strong>InputStructureBase64</strong> <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.
@@ -713,20 +713,20 @@ In BioCatalogue: <a href="http://www.bio
<a href="http://www.myexperiment.org/workflows/1431">Example workflow</a></p>
</li>
<li>
-<p>MFSearch <br />
+<p><strong>MFSearch</strong> <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
within a previous result set (given by a list key). Returns a list key. Asynchronous.</p>
</li>
<li>
-<p>ScoreMatrix <br />
+<p><strong>ScoreMatrix</strong> <br />
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 />
+<p><strong>SimilaritySearch2D</strong> <br />
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 />
@@ -735,13 +735,13 @@ In BioCatalogue: <a href="http://www.bio
<a href="http://www.myexperiment.org/workflows/1431">Example workflow</a></p>
</li>
<li>
-<p>Standardize <br />
+<p><strong>Standardize</strong> <br />
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 />
+<p><strong>SubstructureSearch</strong> <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,
@@ -750,7 +750,7 @@ In BioCatalogue: <a href="http://www.bio
<a href="http://www.myexperiment.org/workflows/1434">Example workflow</a></p>
</li>
<li>
-<p>SuperstructureSearch <br />
+<p><strong>SuperstructureSearch</strong> <br />
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>