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Mapping lists of IDs in ChEMBL



In order to facilitate the mapping of identifiers in ChEMBL, we have developed a new type of search in the ChEMBL Interface. Now, it is possible to enter a list of ChEMBL IDs and see a list of the corresponding entities. Here is an example:

1. Open the ChEMBL Interface, on the main search bar, click on 'Advanced Search':


2. Click on the 'Search by IDs' tab:



3. Select the source entity of the IDs and the destination entity that you want to map to:

4. Enter the identifiers, you can either paste them, or select a file to upload. When you paste IDs, by default it tries to detect the separator. You can also select from a list of separators to force a specific one:

Alternatively, you can upload a file, the file can be compressed in GZIP and ZIP formats, this makes the transfer of the file to the ChEMBL servers faster. Examples of the files that can be uploaded to the search by IDs can be found here.

5. Click on the search button:

6. You will be redirected to a search results page, you can see the status of the process while the ids are being mapped:
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7. When the process is finished, the 'Summary' tab will be enabled, you can see details such as how many terms where recognised, how many matched in ChEMBL and how many IDs were found to be downgraded, among other details:

8. Below the description of the steps, you will see the results of your search:


Currently, users can do the following mappings:
  • From Molecule ChEMBL IDs to ChEMBL Molecules.
  • From Target ChEMBL IDs to ChEMBL Targets.
However, we plan to implement more kinds of mappings, such as:
  • From Assay ChEMBL IDs to ChEMBL Assays.
  • From Document ChEMBL IDs to ChEMBL Document.
  • From Cell Line ChEMBL IDs to ChEMBL Cell Lines.
  • From Molecule ChEMBL IDs to ChEMBL Drugs.
  • From Tissue ChEMBL IDs to ChEMBL Tissues.
  • From UniProt IDs to ChEMBL Compounds.
  • From Smiles to ChEMBL Compounds.
Currently, you can enter up to 200k IDs. We are working on improving this restriction.
Remember that if you have any questions, you can contact us at chembl-help@ebi.ac.uk.

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