UniProt - the ultimate colleague on your biological research team!

 

How many members do you have on your team and have you ever considered UniProt as one of them? 

UniProt is a suite of open access protein databases, accessed by 9 million unique visitors a year, but how much money does it save you?

Our contribution to the scientific community and wider economy has now been analysed in a case study by CSIL, as part of the EU-funded project PathOS. This study investigated the cost-benefit of open data resources, and an analysis of UniProt’s impact between the years of 2017 and 2023 has been published.

What are the main costs of maintaining UniProt?
Across our three consortia sites, EMBL-EBI, SIB, PIR, we have office space, equipment, consumables and publication costs. But our main outgoings (70%) are salaries for our teams of expert biocurators and software developers. Cost to a user is measured in time spent providing valuable voluntary knowledge contributions. 49% of our users visit weekly and 26% daily.

What are the benefits to using UniProt?
The immediate benefits for users are significant time savings. UniProt integrates data from over 180 cross-reference databases, combines it with expert manually curated sequence and protein data, then puts it all in one place, in a standardized format. This saves users time because they don’t have to navigate between multiple resources or download data in different formats. Additionally users do not have to sift through numerous scientific publications to understand the current cutting edge research available for a given protein. It also helps streamline research and analysis pipelines by providing centralized ready-to-use data. 

Long-term benefits are measured in publications and patents that mention UniProt, indicating the wider impact on scientific knowledge advancement and technological development. Over a period of 7 years over 15,200 publications and over 183,000 patents cited or referenced UniProt. Many of these patents go on to be referenced by subsequent patents spanning a number of biotechnology and health innovation fields. Economic benefits have also been seen in the number of start-up companies that rely on UniProt data for their business model.

Demonstrating the value of UniProt

• Each user gains a net benefit from UniProt of up to €5,475 and saves 219 hours a year.
• Users say that our main strength ‘is the ability to integrate protein sequences identified in the literature with an extensive body of functional information’. This is facilitated by incredibly passionate teams of expert biocurators and software developers that ensure data is curated into the database reliably, and presented in a consistent and easily accessible manner.
• Users agree ‘that there is no alternative offering the same breadth of knowledge, quality and level of integration as UniProt’. 
• Overall users say: ‘UniProt plays a crucial role in accelerating scientific research and innovation in various forms, thereby facilitating the creation of new knowledge.’
• In total UniProt provides a benefit of between €373-565 million per year to its community of scientific users.

Learn more about the details of how UniProt supports research and innovation by reading the full report: Measuring the value and impact of open science

Links to associated articles

ELIXIR - https://elixir-europe.org/news/UniProt-CBA

SIB -  https://www.sib.swiss/news/uniprot-user-benefits-up-to-39-times-higher-than-operational-costs

PathOS - https://pathos-project.eu/open-science-value-costs-and-benefits-for-whom-how-to-support-informed-investment-decisions

The UniProt team would like to take the opportunity to thank our funders, collaborators and users for their time, support and contributions to the database. UniProt is a key part of the  EMBL-EBI, SIB Swiss Institute of Bioinformatics and the Protein Information Resource (PIR)  and ELIXIR

infrastructure. Our main funders are EMBL, The State Secretariat for Education, Research and Innovation SERI (Switzerland), and NIH (USA). We are one of ELIXIR’s Core Data Resources, and two of our three partners, EMBL-EBI and SIB, are ELIXIR Nodes. The findings of this study will support efforts to advocate for long-term funding for critical biodata resources.

Capturing the Diversity of Life - Reorganizing the Protein Space in UniProtKB

 

Advances in genome sequencing technology means that large-scale efforts such as the Earth Biogenome project and the Darwin Tree of Life are aiming to produce high-quality reference genomes for individual species, to capture the biodiversity of our planet. Each of these genomes will translate to complete set of proteins for that species. To enable UniProt to present this wealth of data to our users, we are making significant improvements to our data content.

 

Upcoming changes in our selection of Reference Proteomes

 

In release 2025_04 (currently scheduled 27th August 2025), we will deploy a new Reference Proteome selection pipeline to improve the representation of species biodiversity in the UniProt Knowledgebase (UniProtKB). From release 2026_01 onwards (currently scheduled 25th February 2026), we will restrict the protein space in UniProtKB to those sequences which are part of a Reference Proteome in addition to the expert reviewed UniProtKB/Swiss-Prot section, and also unreviewed entries associated with experimental Gene Ontology annotations or additional biologically important data such as a 3D structure.

 

What is a Reference Proteome?

A proteome is the set of all translated proteins from a genome assembly. For each species, we generally use an automatic pipeline to select one proteome as the Reference Proteome - the proteome that we believe is the best representative of the proteins encoded by that species (for example, the Reference Proteome for Drosophila simulans is UP000000304 as it provides the best coverage of the protein space for the species). In addition, proteomes of well-studied model organisms and other proteomes of interest for biomedical and biotechnological research may be selected as Reference Proteomes by UniProt curators.

 

Is every sequenced proteome currently in UniProtKB?

No. While we currently include many proteomes that are not Reference Proteomes in UniProtKB, we already exclude many others, for example those which are of poor quality or where the species is already over-represented in UniProtKB.

 

Why are we reorganizing the protein space in UniProtKB?

Submissions of genomes to hubs such as the International Nucleotide Sequence Database Collaboration (INSDC) have grown due to the rapid increase in sequencing capabilities, resulting in a large influx of proteomes into UniProtKB. Our new pipeline will provide a much better representation of the biodiversity of life and coverage of the sequence space and improve user experience when searching and selecting the best proteome for their research work. It will also allow us to improve our functional annotation of the proteins in these proteomes in order to provide an enhanced understanding of these species.

 

Figure 1 - Growth of UniProtKB entries throughout the years

 

What is going to happen over the next few months?

In release 2025_04, we will deploy the new pipeline that will improve our selection of Reference Proteomes for cellular organisms (more details below), and we will align our viral Reference Proteomes to the set of exemplar genomes from the International Committee on Taxonomy of Viruses (ICTV). Additionally, we will start the process of removing proteins from non-Reference Proteomes from UniProtKB. In the first stage (2025_04), this includes proteins from taxonomically unclassified organisms. In release 2026_01 we will remove the remainder of proteins from non-Reference Proteomes from UniProtKB.

 

 

How does the new pipeline work?

The new pipeline to select Reference Proteomes has been designed to select the proteome that best represents the protein space of a species using a clustering system based on MMseqs2 [1] to select one or a few, proteomes for each species. It only analyzes high quality proteomes from species with a recognized taxonomy and a formal scientific name. Problematic proteomes, such as proteomes from contaminated genomes, for example, are excluded from the analysis.

 

MMseqs2 is used to cluster first proteins, then proteomes:

1. Protein clusters: firstly, it clusters similar proteins from different proteomes of the same species. The more proteins a proteome has in different clusters, the more likely it is to be selected as a reference.

2. Proteome clusters: secondly, it calculates how similar the proteomes of the same species are, based on the number of protein clusters shared between any two proteomes. Proteomes are clustered together if they share 50% or more protein clusters.

 

Figure 2 - Diagram of the Reference Proteome selection pipeline

 

This new pipeline will select at least one Reference Proteome for every sequenced species for inclusion in UniProtKB, ensuring a broad representation of the Tree of Life. It may select more than one  Reference Proteome for species with a high genomic diversity. To keep the set of Reference Proteomes stable, but not static, between UniProt releases the pipeline preferably selects the most complete proteome (as determined by BUSCO [2]) and will only replace an existing Reference Proteome when a new one is published which is of significantly higher quality.

 

How big a change will this make to UniProtKB?

The changes in UniProt, between release 2025_04 and 2026_01, will result in a change in the content and size of the database. The number of Reference Proteomes will increase by 36% (reflecting a 34% increase on species covered), while the number of proteins in UniProtKB can be decreased by 43%

 

What do I do if the proteome I am working on is no longer in UniProtKB?

All proteomes that are not selected as Reference Proteomes by the new pipeline will be available through UniParc. When you search for such proteomes in the Proteomes portal, you will be directed to UniParc to access your protein set. The UniParc FASTA header format for proteomes will be improved to show the protein and gene names, and database identifiers, of the underlying genome records from EMBL, Ensembl or RefSeq.

 

If the annotation provided by UniProtKB is particularly important to your work, or your organism is actively worked on by a research community, but has not been selected as a Reference Proteome, please Contact us and we will consider promoting it to Reference Proteome status. The list of proteomes that will be deprecated by release 2026-01 is available on our FTP site.

 

 

[1] MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets | Nature Biotechnology

[2] BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes | Molecular Biology and Evolution | Oxford Academic

 

 

 

Proteome help page: https://www.uniprot.org/help/proteome

MMseqs2 GitHub: https://github.com/soedinglab/MMseqs2