InterPro 101.0

This is the code set in the InterPro API (https://www.ebi.ac.uk/interpro/api/) on 25th July 2024.

🌟 New Features

• matching entry in set by @gustavo-salazar in #146
• sort by in sets by @gustavo-salazar in #147
• Replacing _subset with _url in filter by DB requests by @gustavo-salazar in #151

🛠 Fixes/updates

• Pagination links to current API URL by @gustavo-salazar in #145
• Fix release notes by @matthiasblum in #153
• Exposing matching entry: f662107

Full Changelog: v1.15.0...v1.16.0

InterPro 100

This is the code set in the InterPro API (https://www.ebi.ac.uk/interpro/api/) on 30th May 2024.

🌟 New Features

• LLM-updated by @matthiasblum in #141
• Fixtures: descriptions as a list of objects by @matthiasblum in #143

🏡 Housekeeping

• Bump gunicorn from 20.1.0 to 22.0.0 by @dependabot in #139
• Bump tqdm from 4.64.0 to 4.66.3 by @dependabot in #140
• Bump pymysql from 1.0.2 to 1.1.1 by @dependabot in #142

Full Changelog: v1.14.0...v1.15.0

1.14.0

This is the code set in the InterPro API (https://www.ebi.ac.uk/interpro/api/) on 29 March 2024.

🌟 New Features

• Add granularity to counters to improve performances (#126)
• Expose the following new properties (#132):
  • Entries
    • is_llm: whether the entry has been generated using AI
    • is_reviewed_llm: if the entry has been generated using AI, whether a curator has reviewed and approved the entry
    • representative_structure: a "representative" PDB structure, i.e. a high-resolution structure whose sequence is significantly matched by the entry
  • Proteins
    • in_alphafold: whether the protein has a predicted structure in the AlphaFold database.

🏠 Housekeeping

• Upgrade Django from 3.2.20 to 3.2.24 (#119 and #127)
• Upgrade Elasticsearch from 7.3.0 to 8.12 (#130)
• Deprecate the following modifiers:
  • alignments for sets (#120)
  • related to RossettaFold models (#121 )
• Store LLM-generated and human-curated descriptions in the same MySQL column (#123)
• Improve performances of /taxonomy/uniprot/<tax-id>/entry/ and /proteome/uniprot/<proteome-id>/entry/ requests (#125 and #135)
• Update labels and external links of cross-references (#129 and #131)

Full Changelog: v1.13.0...v1.14.0

InterPro 97.0

This is the code set in the InterPro API (https://www.ebi.ac.uk/interpro/api/) on 9 November 2023.

🌟 New Features

• Return information for deleted signatures - #114
• Add support for text search using short names - #115
• Add AI-generated descriptions (Initially for Panther signatures) - #116
• Triage annotation suggestions between the InterPro and Pfam help desks - #117

Full Changelog: v1.12.0...v1.13.0

v1.12.0

This is the code set in the InterPro API (https://www.ebi.ac.uk/interpro/api/) on 14 September 2023.

🌟 New Features

• AntiFam families are now exposed as member database signatures (#111)
• We now use PDB chain sequences and matches on these sequences instead of relying on PDB-UniProt mappings (#112)

🏠 Housekeeping

• Django update (3.2.19 to 3.2.20)
• Remove references to ProDom (retired member database)

Full Changelog: v1.11.1...v1.12.0

v1.11.1

This is the code set in the live API https://www.ebi.ac.uk/interpro/api/ on 5th July 2023.

It includes the following changes:

🛠 Fixes

• The modifier has_model appends to the elastic query. but mistakingly was adding after sorting attributes were added, and therefore it was being ignored.

🏠 Housekeeping

• Dependencies update

Live on 10 May 2023

This is the code set in the live API https://www.ebi.ac.uk/interpro/api/ on 7th March 2023.

It includes the following changes:

🌟 New Features

• TIGRFAMs is now NCBIfam. The API will redirect any traffic to URLs with /tigrfams as DB in to the corresponding /ncbifam.
• Support to redirects from filters endpoints. e.g. /api/protein/uniprot/entry/tigrfams redirects to /api/protein/uniprot/entry/ncbifam
• Adding tests for the redirects.

🏠 Housekeeping

• Removing obsolete code dealing with dbcodes.
• Running black for code styling.

📃 Documentation

• Replacing usage of TIGRfams for NCBIfam.

Full Changelog: v1.10.0...v1.11.0

Live on 7 March 2023

This is the code set in the live API https://www.ebi.ac.uk/interpro/api/ on 7th March 2023.

It includes the following changes:

🌟 New Features

• Adding set_info in entry. e.g. https://www.ebi.ac.uk/interpro/api/entry/pfam/pf00001 contains "set_info": { "accession": "CL0192", "name": "GPCR_A" } #97
• Extending the logic of the cache to have a list of modifiers that won't be cached #101

🛠 Fixes

• Updates the version of Swagger to fix vulnerability #99

📃 Documentation

• Adding Examples of python scripts getting data from the API or from one of the ftp files ea51d05

Full Changelog: v1.9.0...v1.10.0

Live on on 15th Dec 2022

This is the code set in the live API https://www.ebi.ac.uk/interpro/api/ on 15th December 2022.

It includes the following changes:

🌟 New Features

• Extending the elastic manager sorting to multiple fields #96
• Using the above to order the list of alphafold models of an entry by is_fragment and alphafols_score
• Extending the subfamilies modifier to get the details of a single subfamily. #92

🛠 Fixes

• fixing an ordering bug when following the Next link and then the previous link: df7e2d0

Full Changelog: v1.8.0...v1.9.0

v1.8.0

This is the code set in the live API https://www.ebi.ac.uk/interpro/api/ on 13th October 2022.

It includes the following changes:

🌟 New Features

• Panther subfamilies are now grouped on the page of their associated family. Adds a modifier: subfamilies available in member DB accession endpoint. It allows listing the panther subfamilies. #89
• Funfam families are included in a similar way. But their detail can be retrieved as par of the other_features of a protein. #89
• The list of AlphaFold models associated with an Entry is now ordered by the average pLTTD score of the model #90
• Enable custom ordering of buckets in composite aggregations. #90

🛠 Fixes

• Some responses were cached when they shouldn't ([accession URL]?page_size=XX) 0dd90b5

🏡 Housekeeping

• Dependencies Updates

Full Changelog: v1.17.0...v1.18.0