- Course overview
- Search within this course
- What is UniProt?
- Where does the data come from?
- Why do we need UniProt?
- When to use UniProt
- Quiz: Check your learning I
- How to access and navigate UniProt
- How to search UniProt
- Annotation score
- Quiz: Check your learning II
- Exploring a UniProtKB entry
- How to get data from UniProt
- How to submit data to UniProt
- When to use UniProt: guided examples
- Exercise: finding entries with 3D structures
- Exercise: mapping other database identifiers to UniProt
- Summary
- Get help and support on UniProt
- References
- Next steps
- Your feedback
All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.
Batch retrieval & ID mapping
You can use the ‘ID Mapping’ feature to download UniProt entries corresponding to a list of UniProt accessions. You can also use this feature to convert database identifiers from UniProt to external databases or vice versa.
Batch retrieval of UniProtKB entries
Try it for yourself….
1. Click on ‘ID Mapping’ in the header bar.
2. Provide your list of UniProtKB identifiers in the box. You can separate the identifiers by a whitespace (space, tab, new line) or by a comma. You may also upload an input file from your machine.
3. For the default batch download of UniProtKB entries, leave the ‘From’ and ‘To’ dropdowns on their default selection of ‘UniProtKB’ and click on the ‘Map IDs’ button.
You get a results page where you can further filter the results, edit the table columns to add or remove information and download the information in various formats. The results of this job will stay on the Tools dashboard for 7 days.
Converting UniProt identifiers to external identifiers (or vice versa)
Try it for yourself…
Let’s assume that we have a list of RefSeq identifiers that we would like to convert to UniProtKB identifiers.
1. Click on ‘ID Mapping’ in the header bar.
2. Provide your list of RefSeq identifiers in the box. You can separate the identifiers by a whitespace (space, tab, new line) or by a comma. You can also upload an input file from your machine using the link provided (Figure 57 – interactive image). If you want to try the exercise but do not have a set of RefSeq identifiers, you can use the following: NP_009225.1, NP_001012300.1, NP_001310232.1
3. Select the ‘From’ database as ‘RefSeq Protein’ and the ‘To’ database as ‘UniProtKB’ (default selection). As you will see from the ‘From’ and ‘To’ dropdowns, you can convert various types of identifiers to UniProtKB and vice versa.
You will get a results page with your converted identifiers ready for download.
Figure 57 Converting RefSeq identifiers to UniProtKB identifiers. This is an interactive image where you can carry out the ID mapping exercise.