PUG SOAP Web Service Reference
Contents
Methods: PUG SOAP
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 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 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. |
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 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 |
Description
Given a list key, prepare for download a file containing those records in the selected format. See the web download service documentation 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 |
---|---|---|
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1..1 | |
tns:DownloadKey | s:string | 0..1 |
tns:DataBlob | tns:DataBlobType | 0..1 |
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 |
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..* |
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 |
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 |
---|---|---|
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1..1 | |
tns:url | s:string | 1..1 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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
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 |
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..* |
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..* |
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..* |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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
Derived By
Restricting s:string
Enumeration
Value |
---|
eAssayColumns_Complete |
eAssayColumns_Concise |
eAssayColumns_TIDs |
Derived By
Restricting s:string
Enumeration
Value |
---|
eAssayFormat_XML |
eAssayFormat_ASN_Text |
eAssayFormat_ASN_Binary |
eAssayFormat_CSV |
Derived By
Restricting s:string
Enumeration
Value |
---|
eAssayOutcome_All |
eAssayOutcome_Inactive |
eAssayOutcome_Active |
eAssayOutcome_Inconclusive |
eAssayOutcome_Unspecified |
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 |
Derived By
Restricting s:string
Enumeration
Value |
---|
eCompress_None |
eCompress_GZip |
eCompress_BZip2 |
Derived By
Restricting s:string
Enumeration
Value |
---|
eFormat_ASNB |
eFormat_ASNT |
eFormat_XML |
eFormat_SDF |
eFormat_SMILES |
eFormat_InChI |
eFormat_Image |
eFormat_Thumbnail |
Derived By
Restricting s:string
Enumeration
Value |
---|
TID |
outcome |
score |
Derived By
Restricting s:string
Enumeration
Value |
---|
eIdentity_SameConnectivity |
eIdentity_AnyTautomer |
eIdentity_SameStereo |
eIdentity_SameIsotope |
eIdentity_SameStereoIsotope |
eIdentity_SameNonconflictStereo |
eIdentity_SameIsotopeNonconflictStereo |
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 |
Derived By
Restricting s:string
Enumeration
Value |
---|
eIDOutputFormat_Entrez |
eIDOutputFormat_FileList |
eIDOutputFormat_FilePair |
Derived By
Restricting s:string
Enumeration
Value |
---|
eMatrixFormat_CSV |
eMatrixFormat_IdIdScore |
Derived By
Restricting s:string
Enumeration
Value |
---|
eID_CID |
eID_SID |
eID_AID |
eID_TID |
eID_ConformerID |
eID_SourceID |
eID_InChI |
eID_InChIKey |
Derived By
Restricting s:string
Enumeration
Value |
---|
eScoreType_Sim2DSubs |
eScoreType_ShapeOpt3D |
eScoreType_FeatureOpt3D |
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 |
Derived By
Restricting s:string
Enumeration
Value |
---|
eStereo_Ignore |
eStereo_Exact |
eStereo_Relative |
eStereo_NonConflicting |