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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.
SMILES: SMILES
string list.
Synonyms: Synonym
string list.
The input list can be provided by text, a file, or Entrez history. Registry IDs, SIDs, CIDs, InChIKey, and SMILES can be separated by white space, comma, tab, or carriage return, however InChI and Synonyms should be separated by tab or carriage return only. If Registry IDs are provided, the Registry Source Name must 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.
Parent
CID: Parent CIDs of input CIDs.
Component
CID: CIDs that are individual components (covalent units) of input CIDs.
Mixture
CID: CIDs that contain input CIDs as components (individual covalent units).
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.
SMILES: SMILES
string list.
Synonyms: Synonym
string list.
IUPAC Names: IUPAC Name
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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