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PubChem Identifier Exchange Service Help

This document describes how to use the PubChem Identifier Exchange web service, which can be found at the URL:

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

The input IDs are converted into CIDs, which is called input CIDs.  The CIDs that satisfy the condition specified by the selected operation type are retrieved. We called these CIDs, output CIDs. The output CIDs are then converted into the ID type specified by the user and written into a file or Entrez history.

Requests are processed in the order received. All requests are kept private; without your unique 64-bit key, nobody else can see what structures you have submitted.

Steps to identifier exchange:

1) Select an input format and give the ID list:

Registry ID: External registry ID list.

CID: Compound ID list.

SID: Substance ID list.

InChI: InChI string list.

InChIKey: InChIKey string list.

Synonyms: Synonym string list.

The ID list could be provided by a string, a text file, or Entrez history. If Registry ID is selected, the DSN (Data Source Name) should also be provided.

2) Select an operation type:

Same CID: Same CIDs as input CIDs.

Same, Stereochemistry: CIDs that have same stereo centers as input CIDs.

Same, Isotopes: CIDs that have the same isotopes as input CIDs.

Same, Connectivity: CIDs that have the same connectivity as input CIDs.

Same parent: CIDs that have the same parents as input CIDs.

Same parent, Stereochemistry: CIDs that have the same stereo centers and parents as input CIDs.

Same parent, Isotopes: CIDs that have the same isotopes and parents as input CIDs.  

Same parent, Connectivity: CIDs that have the same connectivity and parents as input CIDs.

Similar 2D Compound: CIDs that have the similar 2D compound as input CIDs.

Similar 3D Conformer: CIDs that have the similar 3D comformer as input CIDs.

3) Select an output type:

Registry ID: External registry ID list.

CID: Compound ID list.

SID: Substance ID list.

InChI: InChI string list.

InChIKey: InChIKey string list.

 If Registry ID is selected, the DSN (Data Source Name) should also be provided.

4) Select an output method:

Entrez History (SID or CID only): The result is saved into Entrez history. Registry IDs will be converted into SIDs.

Single column showing unique results: The result file has the output IDs only. Duplicate IDs are removed.

Two column file showing input-output correspondence: The result file includes both input and output IDs.  

5) Select a compression method for result file:

None: No compression.

Gzip: Gzip (.gz) compression, the default.

Bzip2: Bzip2 (.bz2) (.bz2) compression.

6) Select a action:

Submit Job: Begin the computation. You will be taken to a self-refreshing waiting page while your request is queued on NCBI's servers. When done, the URL of the final result file is displayed. Use this URL to download the results to your computer. The result can also be saved into Entrez history.

Save Job: Save the XML specification of this request, mainly for use with PubChem's PUG service. If Entrez history is used for input ID, instead of save a webenv value that might be expired soon, the full input ID list is retrieved from Entrez history and saved. If Entrez history is selected for output method, single-column file method will be used instead.

Load Job: Load and submit a saved XML job file.

Clear Form: Clear the form.

 


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