PUG SOAP Web Service Reference

Table of Contents

Overview

Description

This document contains Web Service descriptions for the following services.

Web Services
Name  Description 
PUG SOAP 

PUG SOAP Web Service

See Also

Methods | Complex Types | Simple Types

Methods: PUG SOAP

Methods
Name  Description 
AssayDownload  Given an assay key, prepare for download a file containing 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) for more detail on the supported formats. Compression is optional and defaults to gzip (.gz). Returns a download key. Asynchronous.
Download  Given a list key, prepare for download a file containing those records in the selected format. See the web download service documentation (http://pubchem.ncbi.nlm.nih.gov/pc_fetch/pc_fetch-help.html) for more detail on the supported formats and file types. Returns a download key. Asynchronous. Note that if SynchronousSingleRecord is set to true, and the ListKey contains only a single ID, then a Base64 string of data is returned synchronously in the response, instead of going through the download file.
GetAssayColumnDescription  Get the description of column (readout) in a BioAssay, which may be the outcome, score, or a TID from the given AID. Synchronous.
GetAssayColumnDescriptions  Get the description of all columns (readouts) in a BioAssay. Synchronous.
GetAssayDescription  Get the descriptive information for a BioAssay, including the number of user-specified readouts (TIDs) and whether a score readout is present. Optionally get version and SID/CID count information. If GetFullDataBlob is set to true, then a Base64 string of data is returned in the response instead, containing the full PubChem Assay description in the requested format (ASN or XML only). Synchronous.
GetDownloadUrl  Given a download key, return an FTP URL that may be used to download the requested file. Synchronous.
GetEntrezKey  Given a list key, return an Entrez history key (db, query key, and WebEnv) corresponding to that list. Synchronous.
GetEntrezUrl  Given an Entrez history key (db, query key, and WebEnv), return an HTTP URL that may be used to view the list in Entrez. Synchronous.
GetIDList  Given a list key, return the identifiers as an array of integers. Note that this method expects there to be at least one identifier in the list, and will fault if the list is empty; see GetListItemsCount, which can be used to check for an empty list prior to calling GetIDList. The optional Start (zero-based) and Count parameters can be used to return smaller portions of the list, useful especially for large lists. Synchronous.
GetListItemsCount  Return the number of IDs in the set represented by the given list key. Synchronous.
GetOperationStatus  Given a key for any asynchronous operation, return 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.
GetStandardizedCID  Given a structure key that has been processed by Standardize, return the corresponding PubChem Compound database CID, or an empty value if the structure is not present in PubChem. Synchronous.
GetStandardizedStructure  Given a structure key that has been processed by Standardize, return the chemical structure in as SMILES or InChI strings. Synchronous.
GetStandardizedStructureBase64  Given a structure key that has been processed by Standardize, return the chemical structure as ASN, XML, or SDF, returned as a Base64-encoded string. Synchronous.
GetStatusMessage  Given a key for any asynchronous operation, return any system messages (error messages, job info, etc.) associated with the operation, if any. Synchronous.
IdentitySearch  Search 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.
IDExchange  Convert IDs from one type to another, using any one of a variety of CID matching algorithms. Output can be a list or a downloaded file; download file compression is optional and defaults to gzip (.gz). Returns a list or download key. Asynchronous.
InputAssay  Specify 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  Input an Entrez history key (db, query key, and WebEnv). Returns a list key. Synchronous.
InputList  Input a set of identifiers for a PubChem database, as an array of integers. Returns a list key. Synchronous.
InputListString  Input a set of identifiers for a PubChem database, as an array of strings. Returns a list key. Synchronous.
InputListText  Input 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  Input a chemical structure as a simple (one-line) string, either SMILES or InChI. Returns a structure key. Synchronous.
InputStructureBase64  Input 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.
MFSearch  Search 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  Compute 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  Search 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, or restricted to search only within a previous result set (given by a list key). Returns a list key. Asynchronous.
Standardize  Standardize 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  Search 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.
SuperstructureSearch  Search 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.

Method: AssayDownload

Description

Given an assay key, prepare for download a file containing 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) for more detail on the supported formats. Compression is optional and defaults to gzip (.gz). Returns a download key. Asynchronous.

Action

http://pubchem.ncbi.nlm.nih.gov/AssayDownload

Input (Literal)

The input of this method is the argument AssayDownload having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:AssayKey  s:string  1..1 
tns:AssayFormat  tns:AssayFormatType  1..1 
tns:eCompress  tns:CompressType  0..1 
Output (Literal)

The output of this method is the argument AssayDownloadResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:DownloadKey  s:string  1..1 

Method: Download

Description

Given a list key, prepare for download a file containing those records in the selected format. See the web download service documentation (http://pubchem.ncbi.nlm.nih.gov/pc_fetch/pc_fetch-help.html) for more detail on the supported formats and file types. Returns a download key. Asynchronous. Note that if SynchronousSingleRecord is set to true, and the ListKey contains only a single ID, then a Base64 string of data is returned synchronously in the response, instead of going through the download file.

Action

http://pubchem.ncbi.nlm.nih.gov/Download

Input (Literal)

The input of this method is the argument Download having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:ListKey  s:string  1..1 
tns:eFormat  tns:FormatType  1..1 
tns:eCompress  tns:CompressType  0..1 
tns:Use3D  s:boolean  0..1 
tns:N3DConformers  s:int  0..1 
tns:SynchronousSingleRecord  s:boolean  0..1 
Output (Literal)

The output of this method is the argument DownloadResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:DownloadKey  s:string  0..1 
tns:DataBlob  tns:DataBlobType  0..1 

Method: GetAssayColumnDescription

Description

Get the description of column (readout) in a BioAssay, which may be the outcome, score, or a TID from the given AID. Synchronous.

Action

http://pubchem.ncbi.nlm.nih.gov/GetAssayColumnDescription

Input (Literal)

The input of this method is the argument GetAssayColumnDescription having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:AID  s:int  1..1 
tns:Heading  tns:HeadingType  1..1 
tns:TID  s:int  0..1 
Output (Literal)

The output of this method is the argument GetAssayColumnDescriptionResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:ColumnDescription  tns:ColumnDescriptionType  1..1 

Method: GetAssayColumnDescriptions

Description

Get the description of all columns (readouts) in a BioAssay. Synchronous.

Action

http://pubchem.ncbi.nlm.nih.gov/GetAssayColumnDescriptions

Input (Literal)

The input of this method is the argument GetAssayColumnDescriptions having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:AID  s:int  1..1 
Output (Literal)

The output of this method is the argument GetAssayColumnDescriptionsResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:ColumnDescription  tns:ColumnDescriptionType  1..* 

Method: GetAssayDescription

Description

Get the descriptive information for a BioAssay, including the number of user-specified readouts (TIDs) and whether a score readout is present. Optionally get version and SID/CID count information. If GetFullDataBlob is set to true, then a Base64 string of data is returned in the response instead, containing the full PubChem Assay description in the requested format (ASN or XML only). Synchronous.

Action

http://pubchem.ncbi.nlm.nih.gov/GetAssayDescription

Input (Literal)

The input of this method is the argument GetAssayDescription having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:AID  s:int  1..1 
tns:GetVersion  s:boolean  0..1 
tns:GetCounts  s:boolean  0..1 
tns:GetFullDataBlob  s:boolean  0..1 
tns:eFormat  tns:FormatType  0..1 
Output (Literal)

The output of this method is the argument GetAssayDescriptionResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:AssayDescription  tns:AssayDescriptionType  0..1 
tns:DataBlob  tns:DataBlobType  0..1 

Method: GetDownloadUrl

Description

Given a download key, return an FTP URL that may be used to download the requested file. Synchronous.

Action

http://pubchem.ncbi.nlm.nih.gov/GetDownloadUrl

Input (Literal)

The input of this method is the argument GetDownloadUrl having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:DownloadKey  s:string  1..1 
Output (Literal)

The output of this method is the argument GetDownloadUrlResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:url  s:string  1..1 

Method: GetEntrezKey

Description

Given a list key, return an Entrez history key (db, query key, and WebEnv) corresponding to that list. Synchronous.

Action

http://pubchem.ncbi.nlm.nih.gov/GetEntrezKey

Input (Literal)

The input of this method is the argument GetEntrezKey having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:ListKey  s:string  1..1 
Output (Literal)

The output of this method is the argument GetEntrezKeyResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:EntrezKey  tns:EntrezKey  1..1 

Method: GetEntrezUrl

Description

Given an Entrez history key (db, query key, and WebEnv), return an HTTP URL that may be used to view the list in Entrez. Synchronous.

Action

http://pubchem.ncbi.nlm.nih.gov/GetEntrezUrl

Input (Literal)

The input of this method is the argument GetEntrezUrl having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:EntrezKey  tns:EntrezKey  1..1 
Output (Literal)

The output of this method is the argument GetEntrezUrlResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:url  s:string  1..1 

Method: GetIDList

Description

Given a list key, return the identifiers as an array of integers. Note that this method expects there to be at least one identifier in the list, and will fault if the list is empty; see GetListItemsCount, which can be used to check for an empty list prior to calling GetIDList. The optional Start (zero-based) and Count parameters can be used to return smaller portions of the list, useful especially for large lists. Synchronous.

Action

http://pubchem.ncbi.nlm.nih.gov/GetIDList

Input (Literal)

The input of this method is the argument GetIDList having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:ListKey  s:string  1..1 
tns:Start  s:int  0..1 
tns:Count  s:int  0..1 
Output (Literal)

The output of this method is the argument GetIDListResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:IDList  tns:ArrayOfInt  1..1 

Method: GetListItemsCount

Description

Return the number of IDs in the set represented by the given list key. Synchronous.

Action

http://pubchem.ncbi.nlm.nih.gov/GetListItemsCount

Input (Literal)

The input of this method is the argument GetListItemsCount having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:ListKey  s:string  1..1 
Output (Literal)

The output of this method is the argument GetListItemsCountResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:count  s:int  1..1 

Method: GetOperationStatus

Description

Given a key for any asynchronous operation, return 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.

Action

http://pubchem.ncbi.nlm.nih.gov/GetOperationStatus

Input (Literal)

The input of this method is the argument GetOperationStatus of type tns:AnyKeyType having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:AnyKey  s:string  1..1 
Output (Literal)

The output of this method is the argument GetOperationStatusResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:status  tns:StatusType  1..1 

Method: GetStandardizedCID

Description

Given a structure key that has been processed by Standardize, return the corresponding PubChem Compound database CID, or an empty value if the structure is not present in PubChem. Synchronous.

Action

http://pubchem.ncbi.nlm.nih.gov/GetStandardizedCID

Input (Literal)

The input of this method is the argument GetStandardizedCID having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:StrKey  s:string  1..1 
Output (Literal)

The output of this method is the argument GetStandardizedCIDResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:CID  s:int  1..1 

Method: GetStandardizedStructure

Description

Given a structure key that has been processed by Standardize, return the chemical structure in as SMILES or InChI strings. Synchronous.

Action

http://pubchem.ncbi.nlm.nih.gov/GetStandardizedStructure

Input (Literal)

The input of this method is the argument GetStandardizedStructure having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:StrKey  s:string  1..1 
tns:format  tns:FormatType  1..1 
Output (Literal)

The output of this method is the argument GetStandardizedStructureResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:structure  s:string  1..1 

Method: GetStandardizedStructureBase64

Description

Given a structure key that has been processed by Standardize, return the chemical structure as ASN, XML, or SDF, returned as a Base64-encoded string. Synchronous.

Action

http://pubchem.ncbi.nlm.nih.gov/GetStandardizedStructureBase64

Input (Literal)

The input of this method is the argument GetStandardizedStructureBase64 having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:StrKey  s:string  1..1 
tns:format  tns:FormatType  1..1 
Output (Literal)

The output of this method is the argument GetStandardizedStructureBase64Response having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:structure  s:base64Binary  1..1 

Method: GetStatusMessage

Description

Given a key for any asynchronous operation, return any system messages (error messages, job info, etc.) associated with the operation, if any. Synchronous.

Action

http://pubchem.ncbi.nlm.nih.gov/GetStatusMessage

Input (Literal)

The input of this method is the argument GetStatusMessage of type tns:AnyKeyType having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:AnyKey  s:string  1..1 
Output (Literal)

The output of this method is the argument GetStatusMessageResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:message  s:string  1..1 

Method: IdentitySearch

Description

Search 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.

Action

http://pubchem.ncbi.nlm.nih.gov/IdentitySearch

Input (Literal)

The input of this method is the argument IdentitySearch having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:StrKey  s:string  1..1 
tns:idOptions  tns:IdentitySearchOptions  1..1 
tns:limits  tns:LimitsType  0..1 
Output (Literal)

The output of this method is the argument IdentitySearchResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:ListKey  s:string  1..1 

Method: IDExchange

Description

Convert IDs from one type to another, using any one of a variety of CID matching algorithms. Output can be a list or a downloaded file; download file compression is optional and defaults to gzip (.gz). Returns a list or download key. Asynchronous.

Action

http://pubchem.ncbi.nlm.nih.gov/IDExchange

Input (Literal)

The input of this method is the argument IDExchange having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:InputListKey  s:string  1..1 
tns:Operation  tns:IDOperationType  1..1 
tns:OutputType  tns:PCIDType  1..1 
tns:OutputSourceName  s:string  0..1 
tns:OutputFormat  tns:IDOutputFormatType  1..1 
tns:ToWebEnv  s:string  0..1 
tns:eCompress  tns:CompressType  0..1 
Output (Literal)

The output of this method is the argument IDExchangeResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:ListKey  s:string  0..1 
tns:DownloadKey  s:string  0..1 

Method: InputAssay

Description

Specify 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.

Action

http://pubchem.ncbi.nlm.nih.gov/InputAssay

Input (Literal)

The input of this method is the argument InputAssay having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:AID  s:int  1..1 
tns:Columns  tns:AssayColumnsType  1..1 
tns:ListKeyTIDs  s:string  0..1 
tns:ListKeySCIDs  s:string  0..1 
tns:OutcomeFilter  tns:AssayOutcomeFilterType  0..1 
Output (Literal)

The output of this method is the argument InputAssayResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:AssayKey  s:string  1..1 

Method: InputEntrez

Description

Input an Entrez history key (db, query key, and WebEnv). Returns a list key. Synchronous.

Action

http://pubchem.ncbi.nlm.nih.gov/InputEntrez

Input (Literal)

The input of this method is the argument InputEntrez having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:EntrezKey  tns:EntrezKey  1..1 
Output (Literal)

The output of this method is the argument InputEntrezResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:ListKey  s:string  1..1 

Method: InputList

Description

Input a set of identifiers for a PubChem database, as an array of integers. Returns a list key. Synchronous.

Action

http://pubchem.ncbi.nlm.nih.gov/InputList

Input (Literal)

The input of this method is the argument InputList having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:ids  tns:ArrayOfInt  1..1 
tns:idType  tns:PCIDType  1..1 
Output (Literal)

The output of this method is the argument InputListResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:ListKey  s:string  1..1 

Method: InputListString

Description

Input a set of identifiers for a PubChem database, as an array of strings. Returns a list key. Synchronous.

Action

http://pubchem.ncbi.nlm.nih.gov/InputListString

Input (Literal)

The input of this method is the argument InputListString having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:strids  tns:ArrayOfString  1..1 
tns:idType  tns:PCIDType  1..1 
tns:SourceName  s:string  0..1 
Output (Literal)

The output of this method is the argument InputListStringResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:ListKey  s:string  1..1 

Method: InputListText

Description

Input 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.

Action

http://pubchem.ncbi.nlm.nih.gov/InputListText

Input (Literal)

The input of this method is the argument InputListText having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:ids  s:string  1..1 
tns:idType  tns:PCIDType  1..1 
Output (Literal)

The output of this method is the argument InputListTextResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:ListKey  s:string  1..1 

Method: InputStructure

Description

Input a chemical structure as a simple (one-line) string, either SMILES or InChI. Returns a structure key. Synchronous.

Action

http://pubchem.ncbi.nlm.nih.gov/InputStructure

Input (Literal)

The input of this method is the argument InputStructure having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:structure  s:string  1..1 
tns:format  tns:FormatType  1..1 
Output (Literal)

The output of this method is the argument InputStructureResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:StrKey  s:string  1..1 

Method: InputStructureBase64

Description

Input 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.

Action

http://pubchem.ncbi.nlm.nih.gov/InputStructureBase64

Input (Literal)

The input of this method is the argument InputStructureBase64 having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:structure  s:base64Binary  1..1 
tns:format  tns:FormatType  1..1 
Output (Literal)

The output of this method is the argument InputStructureBase64Response having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:StrKey  s:string  1..1 

Method: MFSearch

Description

Search 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.

Action

http://pubchem.ncbi.nlm.nih.gov/MFSearch

Input (Literal)

The input of this method is the argument MFSearch having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:MF  s:string  1..1 
tns:mfOptions  tns:MFSearchOptions  0..1 
tns:limits  tns:LimitsType  0..1 
Output (Literal)

The output of this method is the argument MFSearchResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:ListKey  s:string  1..1 

Method: ScoreMatrix

Description

Compute 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.

Action

http://pubchem.ncbi.nlm.nih.gov/ScoreMatrix

Input (Literal)

The input of this method is the argument ScoreMatrix having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:ListKey  s:string  1..1 
tns:SecondaryListKey  s:string  0..1 
tns:ScoreType  tns:ScoreTypeType  1..1 
tns:MatrixFormat  tns:MatrixFormatType  1..1 
tns:eCompress  tns:CompressType  0..1 
tns:N3DConformers  s:int  0..1 
tns:No3DParent  s:boolean  0..1 
Output (Literal)

The output of this method is the argument ScoreMatrixResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:DownloadKey  s:string  1..1 

Method: SimilaritySearch2D

Description

Search 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, or restricted to search only within a previous result set (given by a list key). Returns a list key. Asynchronous.

Action

http://pubchem.ncbi.nlm.nih.gov/SimilaritySearch2D

Input (Literal)

The input of this method is the argument SimilaritySearch2D having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:StrKey  s:string  1..1 
tns:simOptions  tns:SimilaritySearchOptions  1..1 
tns:limits  tns:LimitsType  0..1 
Output (Literal)

The output of this method is the argument SimilaritySearch2DResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:ListKey  s:string  1..1 

Method: Standardize

Description

Standardize the structure given by the structure key input, using the same algorithm PubChem uses to construct the Compound database. Returns a structure key. Asynchronous.

Action

http://pubchem.ncbi.nlm.nih.gov/Standardize

Input (Literal)

The input of this method is the argument Standardize having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:StrKey  s:string  1..1 
Output (Literal)

The output of this method is the argument StandardizeResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:StrKey  s:string  1..1 

Method: SubstructureSearch

Description

Search 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.

Action

http://pubchem.ncbi.nlm.nih.gov/SubstructureSearch

Input (Literal)

The input of this method is the argument SubstructureSearch having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:StrKey  s:string  1..1 
tns:ssOptions  tns:StructureSearchOptions  0..1 
tns:limits  tns:LimitsType  0..1 
Output (Literal)

The output of this method is the argument SubstructureSearchResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:ListKey  s:string  1..1 

Method: SuperstructureSearch

Description

Search 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.

Action

http://pubchem.ncbi.nlm.nih.gov/SuperstructureSearch

Input (Literal)

The input of this method is the argument SuperstructureSearch having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:StrKey  s:string  1..1 
tns:ssOptions  tns:StructureSearchOptions  0..1 
tns:limits  tns:LimitsType  0..1 
Output (Literal)

The output of this method is the argument SuperstructureSearchResponse having the structure defined by the following table.

Element  Type  Occurs 
    1..1 
tns:ListKey  s:string  1..1 

Complex Types: PUG SOAP

Complex Types
Name 
tns:AnyKeyType 
tns:ArrayOfInt 
tns:ArrayOfString 
tns:ArrayOfTargets 
tns:AssayDescriptionType 
tns:AssayTargetType 
tns:ColumnDescriptionType 
tns:DataBlobType 
tns:EntrezKey 
tns:IdentitySearchOptions 
tns:LimitsType 
tns:MFSearchOptions 
tns:SimilaritySearchOptions 
tns:StructureSearchOptions 
tns:TestedConcentrationType 

Complex Type: tns:AnyKeyType

Derived By

Restricting s:anyType

Content Model

Contains elements as defined in the following table.

Component  Type  Occurs 
    1..1 
tns:AnyKey  s:string  1..1 

Complex Type: tns:ArrayOfInt

Derived By

Restricting s:anyType

Content Model

Contains elements as defined in the following table.

Component  Type  Occurs 
    1..1 
tns:int  s:int  1..* 

Complex Type: tns:ArrayOfString

Derived By

Restricting s:anyType

Content Model

Contains elements as defined in the following table.

Component  Type  Occurs 
    1..1 
tns:string  s:string  1..* 

Complex Type: tns:ArrayOfTargets

Derived By

Restricting s:anyType

Content Model

Contains elements as defined in the following table.

Component  Type  Occurs 
    1..1 
tns:Target  tns:AssayTargetType  1..* 

Complex Type: tns:AssayDescriptionType

Derived By

Restricting s:anyType

Content Model

Contains elements as defined in the following table.

Component  Type  Occurs 
    1..1 
tns:Name  s:string  0..1 
tns:Description  tns:ArrayOfString  0..1 
tns:Protocol  tns:ArrayOfString  0..1 
tns:Comment  tns:ArrayOfString  0..1 
tns:NumberOfTIDs  s:int  1..1 
tns:HasScore  s:boolean  1..1 
tns:Method  s:string  0..1 
tns:Targets  tns:ArrayOfTargets  0..1 
tns:Version  s:int  0..1 
tns:Revision  s:int  0..1 
tns:LastDataChange  s:int  0..1 
tns:SIDCountAll  s:int  0..1 
tns:SIDCountActive  s:int  0..1 
tns:SIDCountInactive  s:int  0..1 
tns:SIDCountInconclusive  s:int  0..1 
tns:SIDCountUnspecified  s:int  0..1 
tns:SIDCountProbe  s:int  0..1 
tns:CIDCountAll  s:int  0..1 
tns:CIDCountActive  s:int  0..1 
tns:CIDCountInactive  s:int  0..1 
tns:CIDCountInconclusive  s:int  0..1 
tns:CIDCountUnspecified  s:int  0..1 
tns:CIDCountProbe  s:int  0..1 

Complex Type: tns:AssayTargetType

Derived By

Restricting s:anyType

Content Model

Contains elements as defined in the following table.

Component  Type  Occurs 
    1..1 
tns:gi  s:int  1..1 
tns:Name  s:string  0..1 

Complex Type: tns:ColumnDescriptionType

Derived By

Restricting s:anyType

Content Model

Contains elements as defined in the following table.

Component  Type  Occurs 
    1..1 
tns:Heading  tns:HeadingType  1..1 
tns:TID  s:int  0..1 
tns:Name  s:string  1..1 
tns:Description  tns:ArrayOfString  0..1 
tns:Type  s:string  1..1 
tns:Unit  s:string  0..1 
tns:TestedConcentration  tns:TestedConcentrationType  0..1 
tns:ActiveConcentration  s:boolean  0..1 

Complex Type: tns:DataBlobType

Derived By

Restricting s:anyType

Content Model

Contains elements as defined in the following table.

Component  Type  Occurs 
    1..1 
tns:Data  s:base64Binary  1..1 
tns:BlobFormat  tns:BlobFormatType  0..1 
tns:eCompress  tns:CompressType  0..1 

Complex Type: tns:EntrezKey

Derived By

Restricting s:anyType

Content Model

Contains elements as defined in the following table.

Component  Type  Occurs 
    1..1 
tns:db  s:string  1..1 
tns:key  s:string  1..1 
tns:webenv  s:string  1..1 

Complex Type: tns:IdentitySearchOptions

Derived By

Restricting s:anyType

Content Model

Contains elements as defined in the following table.

Component  Type  Occurs 
    1..1 
tns:eIdentity  tns:IdentityType  1..1 
tns:ToWebEnv  s:string  0..1 

Complex Type: tns:LimitsType

Derived By

Restricting s:anyType

Content Model

Contains elements as defined in the following table.

Component  Type  Occurs 
    1..1 
tns:seconds  s:int  0..1 
tns:maxRecords  s:int  0..1 
tns:ListKey  s:string  0..1 

Complex Type: tns:MFSearchOptions

Derived By

Restricting s:anyType

Content Model

Contains elements as defined in the following table.

Component  Type  Occurs 
    1..1 
tns:AllowOtherElements  s:boolean  1..1 
tns:ToWebEnv  s:string  0..1 

Complex Type: tns:SimilaritySearchOptions

Derived By

Restricting s:anyType

Content Model

Contains elements as defined in the following table.

Component  Type  Occurs 
    1..1 
tns:threshold  s:int  1..1 
tns:ToWebEnv  s:string  0..1 

Complex Type: tns:StructureSearchOptions

Derived By

Restricting s:anyType

Content Model

Contains elements as defined in the following table.

Component  Type  Occurs 
    1..1 
tns:MatchIsotopes  s:boolean  0..1 
tns:MatchCharges  s:boolean  0..1 
tns:MatchTautomers  s:boolean  0..1 
tns:RingsNotEmbedded  s:boolean  0..1 
tns:SingeDoubleBondsMatch  s:boolean  0..1 
tns:ChainsMatchRings  s:boolean  0..1 
tns:StripHydrogen  s:boolean  0..1 
tns:eStereo  tns:StereoType  0..1 
tns:ToWebEnv  s:string  0..1 

Complex Type: tns:TestedConcentrationType

Derived By

Restricting s:anyType

Content Model

Contains elements as defined in the following table.

Component  Type  Occurs 
    1..1 
tns:Concentration  s:double  1..1 
tns:Unit  s:string  1..1 

Simple Types: PUG SOAP

Simple Types
Name 
tns:AssayColumnsType 
tns:AssayFormatType 
tns:AssayOutcomeFilterType 
tns:BlobFormatType 
tns:CompressType 
tns:FormatType 
tns:HeadingType 
tns:IdentityType 
tns:IDOperationType 
tns:IDOutputFormatType 
tns:MatrixFormatType 
tns:PCIDType 
tns:ScoreTypeType 
tns:StatusType 
tns:StereoType 

Simple Type: tns:AssayColumnsType

Derived By

Restricting s:string

Enumeration
Value 
eAssayColumns_Complete 
eAssayColumns_Concise 
eAssayColumns_TIDs 

Simple Type: tns:AssayFormatType

Derived By

Restricting s:string

Enumeration
Value 
eAssayFormat_XML 
eAssayFormat_ASN_Text 
eAssayFormat_ASN_Binary 
eAssayFormat_CSV 

Simple Type: tns:AssayOutcomeFilterType

Derived By

Restricting s:string

Enumeration
Value 
eAssayOutcome_All 
eAssayOutcome_Inactive 
eAssayOutcome_Active 
eAssayOutcome_Inconclusive 
eAssayOutcome_Unspecified 

Simple Type: tns:BlobFormatType

Derived By

Restricting s:string

Enumeration
Value 
eBlobFormat_Unspecified 
eBlobFormat_ASNB 
eBlobFormat_ASNT 
eBlobFormat_XML 
eBlobFormat_SDF 
eBlobFormat_CSV 
eBlobFormat_Text 
eBlobFormat_HTML 
eBlobFormat_PNG 
eBlobFormat_Other 

Simple Type: tns:CompressType

Derived By

Restricting s:string

Enumeration
Value 
eCompress_None 
eCompress_GZip 
eCompress_BZip2 

Simple Type: tns:FormatType

Derived By

Restricting s:string

Enumeration
Value 
eFormat_ASNB 
eFormat_ASNT 
eFormat_XML 
eFormat_SDF 
eFormat_SMILES 
eFormat_InChI 
eFormat_Image 
eFormat_Thumbnail 

Simple Type: tns:HeadingType

Derived By

Restricting s:string

Enumeration
Value 
TID 
outcome 
score 

Simple Type: tns:IdentityType

Derived By

Restricting s:string

Enumeration
Value 
eIdentity_SameConnectivity 
eIdentity_AnyTautomer 
eIdentity_SameStereo 
eIdentity_SameIsotope 
eIdentity_SameStereoIsotope 
eIdentity_SameNonconflictStereo 
eIdentity_SameIsotopeNonconflictStereo 

Simple Type: tns:IDOperationType

Derived By

Restricting s:string

Enumeration
Value 
eIDOperation_Same 
eIDOperation_SameStereo 
eIDOperation_SameIsotope 
eIDOperation_SameConnectivity 
eIDOperation_SameParent 
eIDOperation_SameParentStereo 
eIDOperation_SameParentIsotope 
eIDOperation_SameParentConnectivity 
eIDOperation_Similar2D 
eIDOperation_Similar3D 

Simple Type: tns:IDOutputFormatType

Derived By

Restricting s:string

Enumeration
Value 
eIDOutputFormat_Entrez 
eIDOutputFormat_FileList 
eIDOutputFormat_FilePair 

Simple Type: tns:MatrixFormatType

Derived By

Restricting s:string

Enumeration
Value 
eMatrixFormat_CSV 
eMatrixFormat_IdIdScore 

Simple Type: tns:PCIDType

Derived By

Restricting s:string

Enumeration
Value 
eID_CID 
eID_SID 
eID_AID 
eID_TID 
eID_ConformerID 
eID_SourceID 
eID_InChI 
eID_InChIKey 

Simple Type: tns:ScoreTypeType

Derived By

Restricting s:string

Enumeration
Value 
eScoreType_Sim2DSubs 
eScoreType_ShapeOpt3D 
eScoreType_FeatureOpt3D 

Simple Type: tns:StatusType

Derived By

Restricting s:string

Enumeration
Value 
eStatus_Unknown 
eStatus_Success 
eStatus_ServerError 
eStatus_HitLimit 
eStatus_TimeLimit 
eStatus_InputError 
eStatus_DataError 
eStatus_Stopped 
eStatus_Running 
eStatus_Queued 

Simple Type: tns:StereoType

Derived By

Restricting s:string

Enumeration
Value 
eStereo_Ignore 
eStereo_Exact 
eStereo_Relative 
eStereo_NonConflicting