Pfam website decommission

After more than 20 years of good and faithful service, we have decided to retire the Pfam website. Do not worry though, we are still planning to do Pfam releases and the data will still be available. 

As you can imagine this wasn’t an easy decision, and be sure it wasn’t taken lightly. The Pfam website codebase was first released over 20 years ago, and although it has been updated from time to time, some of its core functionality still dates back to its origins. There is a lot of technical debt in its current state and it is only becoming harder to maintain. 

Currently, on every release, we are taking more time generating data exclusively related to the website than the core data of Pfam: its alignments, and models. Additionally, our team size doesn’t have the capacity to execute all the release procedures for Pfam on a consistent basis.

Retiring the website will allow us to focus our efforts on producing the core of Pfam. The plan then is to leave the deployment and visualisation tasks to the InterPro website. InterPro was redesigned in recent years, using up to date technologies, including a modern framework (React).

The Pfam data and different viewing features are already available on the InterPro website. For example, searching for a Pfam accession (e.g. PF05093) using the InterPro search by text will allow you to reach the corresponding Pfam entry page, where the menu on the left hand-side gives access to different datasets related to the entry, as shown in the figure below.

Example of Pfam entry page in the InterPro website (PF05093)

The correspondence between the Pfam menu and InterPro menu is given in the table below.

Pfam website tab	InterPro website tab
Summary	Overview
Clan	Available in Overview, Set
Domain organisation	Domain Architectures
Alignments	Alignment
HMM logo	Signature
Trees	Taxonomy (tree icon)
Curation & model	Curation
Species	Taxonomy
Structures	Structures
AlphaFold structures	AlphaFold
trRosetta	RoseTTAFold

You can also browse through the different Pfam families and clans (called Set in InterPro) using the InterPro Browse feature.

The Overview tab of the Set pages in InterPro, the different members of the set (nodes) and the relationship between each other (lines) are displayed in a graph (it corresponds to the Relationship tab in the Pfam website). The size of the nodes is proportional to the number of proteins in the Pfam entry. The graph can be customised to display the Pfam Accession, short name and/or name. Other tabs include Entries (equivalent to the Members section in the Summary tab in Pfam), Proteins, Structures, Taxonomy (equivalent to the Species tab in Pfam), Proteomes and alignments. Additionally, the Proteins tab in InterPro lists all the proteins matched by the different Pfam entries included in a set.

We are aware that not all of the Pfam users are familiar with the InterPro website interface, hence the decommission will be progressive through multiple months, starting from October 5th 2022. On October 5th, we will start redirecting the traffic from Pfam (pfam.xfam.org) to InterPro (www.ebi.ac.uk/interpro). The Pfam website will be available at pfam-legacy.xfam.org until January 2023, when it will be decommissioned. We are also going to organise a webinar to show you where to find the Pfam annotations in InterPro, so stay tuned and check our twitter accounts (@PfamDB/@InterProDB) to register.

If you have any requests, feedback or suggestions on ways to improve Pfam data visualisation in InterPro please contact us through the InterPro helpdesk.

Written by Typhaine Paysan-Lafosse.