Author: gnaylor
Date: Thu Jul 14 19:53:01 2016
New Revision: 1752736
URL: http://svn.apache.org/viewvc?rev=1752736&view=rev
Log:
Make all operation names BOLD
Modified:
incubator/taverna/site/trunk/content/introduction/chemistry-web-services.md
Modified:
incubator/taverna/site/trunk/content/introduction/chemistry-web-services.md
URL:
http://svn.apache.org/viewvc/incubator/taverna/site/trunk/content/introduction/chemistry-web-services.md?rev=1752736&r1=1752735&r2=1752736&view=diff
==============================================================================
--- incubator/taverna/site/trunk/content/introduction/chemistry-web-services.md
(original)
+++ incubator/taverna/site/trunk/content/introduction/chemistry-web-services.md
Thu Jul 14 19:53:01 2016
@@ -122,7 +122,7 @@ The following operations are contained w
### OpenBabel Web service
WSDL: [http://www.chemspider.com/OpenBabel.asmx?WSDL][26]
- - convert
+ - **convert**
Converts a molecule represented in one format to another.
For a list of valid format values, please visit [openbabel][27].
An empty string is returned in case of failure.
@@ -135,77 +135,77 @@ WSDL: [http://www.chemspider.com/MassSpe
In BioCatalogue: [http://www.biocatalogue.org/services/2040][30]
- - GetCompressedRecordsSdf
+ - **GetCompressedRecordsSdf**
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.
Example workflow not available since a ‘Service Subscriber’
role is required by the user.
- - GetDatabases
+ - **GetDatabases**
Returns a list of datasources in ChemSpider.
[Example workflow][31]
- - GetExtendedCompoundInfo
+ - **GetExtendedCompoundInfo**
Returns extended record details for a given ChemSpider identifier.
A security token is required to access this service.
[Example workflow][32]
- - GetExtendedCompoundInfoArray
+ - **GetExtendedCompoundInfoArray**
Returns an array of extended record details from an array of ChemSpider
identifiers.
A security token is required to access this service.
[Example workflow][33]
- - GetRecordMol
+ - **GetRecordMol**
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.
[Example workflow][34]
- - GetRecordsSdf
+ - **GetRecordsSdf**
Returns a SDF file containing records found by an asynchronous search
operation.
A security token associated with the ‘Service Subscriber’
role is required to access this operation.
Example workflow not available since a Service Subscriber role is required
by the user.
- - SearchByFormula
+ - **SearchByFormula**
Search ChemSpider compounds by molecular formula within a specified list
of datasources.
This operation is deprecated and will be removed soon – use
SearchByFormulaAsync instead.
Example workflow not available since this operation is deprecated.
- - SearchByFormula2
+ - **SearchByFormula2**
Search ChemSpider compounds by molecular formula.
Example workflow not available since this operation is deprecated.
- - SearchByFormulaAsync
+ - **SearchByFormulaAsync**
Searches ChemSpider compounds by molecular formula within a specified
datasources list.
Security token is required to get access to this service.
[Example workflow][35]
- - SearchByMass
+ - **SearchByMass**
Searches ChemSpider compounds by mass +/- range within specified
datasources list.
This operation is deprecated and will be removed soon – use
SearchByMassAsync instead.
Example workflow not available since this operation is deprecated.
- - SearchByMass2
+ - **SearchByMass2**
Search ChemSpider compounds by mass +/- range.
Example workflow not available since this operation is deprecated.
- - SearchByMassAsync
+ - **SearchByMassAsync**
Searches ChemSpider compounds by mass +/- range within a specified
datasources list.
A security token is required to access this service.
### Spectra Web service
WSDL: [http://www.chemspider.com/Spectra.asmx?WSDL][36]
- - GetAllSpectraInfo
+ - **GetAllSpectraInfo**
Returns information for all open access spectra in ChemSpider
[Example workflow][37]
- - GetCompoundSpectraInfo
+ - **GetCompoundSpectraInfo**
Returns information about spectra associated with a particular compound
identified by the cmp_id parameter
[Example workflow][38]
- - GetSpectrumInfo
+ - **GetSpectrumInfo**
Returns information about a particular spectrum identified by its spc_id
parameter
[Example workflow][39]
@@ -214,7 +214,7 @@ WSDL: [http://www.chemspider.com/Search.
<img src="/img/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>
- - AsyncSimpleSearch
+ - **AsyncSimpleSearch**
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.
@@ -222,59 +222,59 @@ WSDL: [http://www.chemspider.com/Search.
the GetAsyncSearchResult operation below.
[Example workflow][41]
- - CSID2ExtRefs
+ - **CSID2ExtRefs**
Returns a list of external references (data sources) for a given compound.
A security token with the relevant role is required to access this service.
- - GetAsyncSearchResult
+ - **GetAsyncSearchResult**
Returns a list of identifiers found by the asynchronous search operation.
A security token is required to access this service.
[Example workflow][42]
- - GetAsyncSearchStatus
+ - **GetAsyncSearchStatus**
Queries the asynchronous operation status.
A security token is required to access this service.
[Example workflow][43]
- - GetCompoundInfo
+ - **GetCompoundInfo**
Returns the record details (CSID, InChIKey, InChI, SMILES) of a molecule by
its ChemSpider identifier.
A security token is required to access this service.
[Example workflow][44]
- - GetCompoundThumbnail
+ - **GetCompoundThumbnail**
Returns an image of a molecule’s 2D structure in PNG format.
A security token is required to access this service.
[Example workflow][45]
- - GetRecordDetails
+ - **GetRecordDetails**
Returns a record details: CSID, InChIKey, InChI, SMILES.
This operation is deprecated and will be removed soon – use
GetCompoundInfo instead.
No example workflow due to deprecation of this operation.
- - GetRecordImage
+ - **GetRecordImage**
Returns an image of a molecule’s structure in PNG format.
This operation is deprecated and will be removed soon – use
GetCompoundThumbnail instead.
No example workflow due to deprecation of this operation.
- - Mol2CSID
+ - **Mol2CSID**
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.
No example workflow due to specific role required for the operation.
- - MolAndDS2CSID
+ - **MolAndDS2CSID**
Searches for structures matching a given MOL file within the range
specified by search options and
within the specified list of datasources.
Returns a list of ChemSpider identifiers.
A security token with the ‘specific’ role is required to access
this service.
No example workflow due to specific role required for the operation.
- - SimpleSearch
+ - **SimpleSearch**
Performs a search using a given set of terms. Returns a list of ChemSpider
identifiers.
A security token is required to access this service.
[Example workflow][46]
- - SimpleSearch2IdList
+ - **SimpleSearch2IdList**
Tries to find whatever is entered.
Returns a list of ChemSpider IDs.
This operation is deprecated and will be removed soon – use
SimpleSearch instead.
@@ -283,7 +283,7 @@ WSDL: [http://www.chemspider.com/Search.
### Synonyms
WSDL: [http://www.chemspider.com/Synonyms.asmx?WSDL][47]
- - GetStructureSynonyms
+ - **GetStructureSynonyms**
Returns synonym names for a given compound represented by its MOL file.
[Example workflow][48]
@@ -304,7 +304,7 @@ WSDL: [http://www.ebi.ac.uk/webservices/
<img src="/img/biocatalogue-smallcog.png" alt="BioCatalogue icon" width="16"
height="16" />
In BioCatalogue: [http://www.biocatalogue.org/services/2174][51]
- - getLiteEntity
+ - **getLiteEntity**
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.
@@ -312,30 +312,30 @@ In BioCatalogue: [http://www.biocatalogu
A maximum 5000 entries can be retrieved at a time.
[Example workflow][52]
- - getCompleteEntity
+ - **getCompleteEntity**
Retrieves the complete record of a molecule including synonyms, database
links and chemical structures,
using the ChEBI identifier.
[Example workflow][53]
- - getCompleteEntityByList
+ - **getCompleteEntityByList**
Given a list of ChEBI accession numbers,
retrieves the complete entity record associated with each accession
number.
The maximum size of a given list is 50.
[Example workflow][54]
- - getOntologyParents
+ - **getOntologyParents**
Retrieves the ontology parents of an entity including the relationship
type, using a ChEBI identifier.
[Example workflow][55]
- - getOntologyChildren
+ - **getOntologyChildren**
Retrieves the ontology children of an entity including the relationship
type, using a ChEBI identifier.
[Example workflow][56]
- - getAllOntologyChildrenInPath
+ - **getAllOntologyChildrenInPath**
Retrieves the ontology children of an entity including the relationship
type, using a ChEBI identifier.
No example workflow available.
- - getStructureSearch
+ - **getStructureSearch**
Does a substructure, similarity or identity search using a query structure.
[Example workflow][57]
@@ -349,16 +349,17 @@ In BioCatalogue: [http://www.biocatalogu
PubChem provides the following Web service with 28 operations.
WSDL: [http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap.cgi?wsdl][61]
+
<img src="/img/biocatalogue-smallcog.png" alt="BioCatalogue icon" width="16"
height="16" />
In BioCatalogue: [http://www.biocatalogue.org/services/2176][62]
- - AssayDownload
+ - **AssayDownload**
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
([http://pubchem.ncbi.nlm.nih.gov/pug/pughelp.html][63]) for more details
on the supported formats.
Compression is optional and defaults to gzip (.gz). Returns a download
key. Asynchronous.
- - Download
+ - **Download**
Given a list key, prepares a file for downloading which contains those
records in the selected format.
See the web download service documentation
([http://pubchem.ncbi.nlm.nih.gov/pc_fetch/pc_fetch-help.html][64])
@@ -366,39 +367,39 @@ In BioCatalogue: [http://www.biocatalogu
Returns a download key. Asynchronous.
[Example workflow][65]
- - GetAssayColumnDescription
+ - **GetAssayColumnDescription**
Returns the description of a column (readout) in a BioAssay, which may be
the outcome, score,
or a TID from the given AID. Synchronous.
- - GetAssayColumnDescriptions
+ - **GetAssayColumnDescriptions**
Returns the description of all columns (readouts) in a BioAssay.
Synchronous.
- - GetAssayDescription
+ - **GetAssayDescription**
Returns the descriptive information for a BioAssay, including the number of
user-specified readouts (TIDs)
and whether a score readout is present.
Optionally get version information. Synchronous.
- - GetDownloadUrl
+ - **GetDownloadUrl**
Given a download key, returns an FTP URL that may be used to download the
requested file. Synchronous.
- - GetEntrezKey
+ - **GetEntrezKey**
Given a list key, returns an Entrez history key (db, query key, and
WebEnv) corresponding to that list.
Synchronous.
[Example workflow][66]
- - GetEntrezUrl
+ - **GetEntrezUrl**
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.
[Example workflow][67]
- - GetIDList
+ - **GetIDList**
Given a list key, returns the identifiers as an array of integers.
Synchronous.
[Example workflow][68]
- - GetListItemsCount
+ - **GetListItemsCount**
Returns the number of IDs in the set represented by a given list key.
Synchronous.
- - GetOperationStatus
+ - **GetOperationStatus**
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);
@@ -407,23 +408,23 @@ In BioCatalogue: [http://www.biocatalogu
the operation is in progress. Synchronous.
[Example workflow][69]
- - GetStandardizedCID
+ - **GetStandardizedCID**
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.
- - GetStandardizedStructure
+ - **GetStandardizedStructure**
Given a structure key that has been processed by Standardize, returns the
chemical structure in as SMILES
or InChI strings. Synchronous.
- - GetStandardizedStructureBase64
+ - **GetStandardizedStructureBase64**
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.
- - GetStatusMessage
+ - **GetStatusMessage**
Given a key for any asynchronous operation, returns any system messages
(error messages, job info, etc.)
associated with the operation, if any. Synchronous.
- - IdentitySearch
+ - **IdentitySearch**
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
@@ -431,48 +432,48 @@ In BioCatalogue: [http://www.biocatalogu
Returns a list key. Asynchronous.
[Example workflow][70]
- - InputAssay
+ - **InputAssay**
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.
- - InputEntrez
+ - **InputEntrez**
Configures an Entrez history key (db, query key, and WebEnv).
Returns a list key. Synchronous.
- - InputList
+ - **InputList**
Configures a set of identifiers for a PubChem database, as an array of
integers.
Returns a list key. Synchronous.
- - InputListText
+ - **InputListText**
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.
- - InputStructure
+ - **InputStructure**
Configures a chemical structure as a simple (one-line) string, either
SMILES or InChI.
Returns a structure key. Synchronous.
[Example workflow][71]
- - InputStructureBase64
+ - **InputStructureBase64**
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.
[Example workflow][72]
- - MFSearch
+ - **MFSearch**
Searches PubChem Compound for structures of a given molecular formula,
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.
- - ScoreMatrix
+ - **ScoreMatrix**
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.
Compression is optional and defaults to gzip (.gz). Returns a download key.
Asynchronous.
- - SimilaritySearch2D
+ - **SimilaritySearch2D**
Searches PubChem Compound for structures similar to the one given by the
structure key input,
based on the given Tanimoto-based similarity score.
The search may be limited by elapsed time or number of records found,
@@ -480,12 +481,12 @@ In BioCatalogue: [http://www.biocatalogu
Returns a list key. Asynchronous.
[Example workflow][73]
- - Standardize
+ - **Standardize**
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.
- - SubstructureSearch
+ - **SubstructureSearch**
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,
@@ -493,7 +494,7 @@ In BioCatalogue: [http://www.biocatalogu
Returns a list key. Asynchronous.
[Example workflow][74]
- - SuperstructureSearch
+ - **SuperstructureSearch**
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>
