The community submission system

Our lightweight solution allows UniProt users to add publications and annotations to proteins of their interest, with a simple design and requiring minimal information, while providing options to contribute more details, and, most importantly, for acknowledging contributions. To develop such system, we adopted a user-centric approach, where a prototype was released to the community and feedback was collected through a survey to improve the design. The project homepage can be accessed at https://community.uniprot.org/bbsub/home.html and offers links to the submission system, the statistics, documentation, and code.

The submission process, described in Fig 1, starts with users and publication(s) to be added to one or more protein records. There are 2 access points, from the UniProt website or the community homepage (Fig 1, 1). To add one publication to a protein at a time, the “Add a publication” link in a UniProtKB entry page brings users to the submission page for such entry (Fig 1, 2a). Alternatively, a batch submission option is available from the homepage (https://community.uniprot.org/bbsub/batch.html) (Fig 1, 2b). ORCID identifiers are used for log in and contributor validation, as well as for credit attribution for community curation (Fig 1, 3). In the protein-centric submission case, the next step is to add the publication. The user has options to perform additional tasks, such as categorizing the publication into UniProt annotation topics and to input free text annotations related to protein/gene name, function, and disease (see sample form: https://community.uniprot.org/bbsub/sampleform.html) (Fig 1, 4a), whereas for submission in batch, the user would upload a file with multiple proteins, publications, and annotations (Fig 1, 4b). In both cases, submission triggers the review process (Fig 1, 5). Upon the reviewer’s approval, publications and annotations are publicly available on the submissions’ information page with ORCID and submitter’s name (https://community.uniprot.org/bbsub/bbsubinfo.html; Fig 1, 6) and will appear in the UniProt protein page under the “Community curation” link 24 to 48 h later (Fig 1, 7). Publications are also integrated into the UniProt bibliography in sync with the database release cycle (Fig 1, 8).

Download:

• PPT
  PowerPoint slide
• PNG
  larger image
• TIFF
  original image

Fig 1. Overview of the submission process.

https://doi.org/10.1371/journal.pbio.3001464.g001

There are multiple checkpoints in place both to help the user and for data integrity, including (a) automatic retrieval of publication title and authors via PubMed API, to confirm the publication of interest; (b) checking that the publication has not been already curated by UniProt for such protein; (c) checking data changes in the upcoming UniProt release (private), like obsoletion or merging of entries, and warning the user to choose an alternative entry; (d) checking submissions are updates versus a new annotation; and (e) helping with text editing with auto-correction capability, warnings for non-ASCII characters, and checking for valid email format. In terms of information content, a UniProt curator ensures that the publication is associated to the correct protein entry (organism and accession number) and that the information added is concise and appropriate. If any problem arises, the curator contacts the user for clarification via email.

Community participation and impact

The number of users and submissions have increased steadily since the inception of the system (UniProt Release 2019_08) (https://community.uniprot.org/bbsub/STATS.html). As of release 2021_03, a little more than half of the submissions provide annotations for unreviewed entries, whereas the rest offer updates for reviewed ones; roughly half of the contributions are done by students or researchers who are not authors on the submitted publications. Most importantly, the submissions add information to proteins from all superkingdoms and cover a variety of annotations topics, with majority related to Function, which is of high interest to UniProt. Regarding this last point, the community curation adds value to the UniProt entries. For example, it adds proper names to proteins annotated as uncharacterized in UniProt. Many offer functional information that is incorporated when publications are later curated by UniProt. For example, in release 2020_06, UniProtKB:Q8DPQ3 was an unreviewed entry with name “Uncharacterized protein” and lacking functional information (https://www.uniprot.org/uniprot/Q8DPQ3.txt?version=95); however, at the time, a community submitted publication added names (Pyrimidine nucleotidase A; PynA) and functional information to this entry (https://community.uniprot.org/bbsub/bbsubinfo.html?accession=Q8DPQ3). This publication and similar annotations were later incorporated when the entry was curated by UniProt (https://www.uniprot.org/uniprot/Q8DPQ3.txt?version=96). This and other representative examples (https://community.uniprot.org/bbsub/doc/public/uncharacterized_proteins.xlsx) show that the publications and annotations added by the community are relevant. The crowdsourcing effort also provides a number of annotations for unreviewed proteins, which can be retrieved in the information submission page, by selecting field “UniProt status” and “TrEMBL” in query box. In addition, the community submission system has enabled successful collaborations with research groups for improving annotations in defined research areas. Box 1 describes 2 of these examples.

Conclusions

Our system provides a solution for the scientific community to contribute their knowledge and enrich information for proteins in UniProt. Crowdsourcing the literature curation has been an asset both to UniProt and the users of the knowledgebase. Moreover, to cite your biocuration work, you can simply link to your public contributions using: https://community.uniprot.org/bbsub/bbsubinfo.html?ORCID=<ORCID>, where <ORCID> should be replaced with your ORCID.

Acknowledgments

UniProt Consortium: Alex Bateman, Maria-Jesus Martin, Sandra Orchard, Michele Magrane, Rahat Agivetova, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett, Ramona Britto, Borisas Bursteinas, Hema Bye-A-Jee, Ray Coetzee, Austra Cukura, Alan Da Silva, Paul Denny, Tunca Dogan, ThankGod Ebenezer, Jun Fan, Leyla Garcia Castro, Penelope Garmiri, George Georghiou, Leonardo Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Petteri Jokinen, Vishal Joshi, Dushyanth Jyothi, Antonia Lock, Rodrigo Lopez, Aurelien Luciani, Jie Luo, Yvonne Lussi, Alistair MacDougall, Fabio Madeira, Mahdi Mahmoudy, Manuela Menchi, Alok Mishra, Katie Moulang, Andrew Nightingale, Carla Susana Oliveira, Sangya Pundir, Guoying Qi, Shriya Raj, Daniel Rice, Milagros Rodriguez Lopez, Rabie Saidi, Joseph Sampson, Tony Sawford, Elena Speretta, Edward Turner, Nidhi Tyagi, Preethi Vasudev, Vladimir Volynkin, Kate Warner, Xavier Watkins, Rossana Zaru, and Hermann Zellner at the EMBL–European Bioinformatics Institute; Alan Bridge, Sylvain Poux, Nicole Redaschi, Lucila Aimo, Ghislaine Argoud-Puy, Andrea Auchincloss, Kristian Axelsen, Parit Bansal, Delphine Baratin, Marie-Claude Blatter, Jerven Bolleman, Emmanuel Boutet, Lionel Breuza, Cristina Casals-Casas, Edouard de Castro, Kamal Chikh Echioukh, Elisabeth Coudert, Beatrice Cuche, Mikael Doche, Dolnide Dornevil, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Sebastien Gehant, Vivienne Gerritsen, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Guillaume Keller, Arnaud Kerhornou, Vicente Lara, Philippe Le Mercier, Damien Lieberherr, Thierry Lombardot, Xavier Martin, Patrick Masson, Anne Morgat, Teresa Batista Neto, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Monica Pozzato, Manuela Pruess, Catherine Rivoire, Christian Sigrist, Karin Sonesson, Andre Stutz, Shyamala Sundaram, Michael Tognolli, and Laure Verbregue at the SIB Swiss Institute of Bioinformatics; Cathy H. Wu, Cecilia N. Arighi, Leslie Arminski, Chuming Chen, Yongxing Chen, John S. Garavelli, Hongzhan Huang, Kati Laiho, Peter McGarvey, Darren A. Natale, Karen Ross, C. R. Vinayaka, Qinghua Wang, Yuqi Wang, Lai-Su Yeh, and Jian Zhang at the Protein Information Resource.

We also would like to thank the UniProt users for their valuable contributions, especially Dr. Touz from Instituto Ferreyra, Córdoba, Argentina, and Dr. Pfeiffer from Max Planck Institute, Germany, who have contributed to the use cases indicated in this piece.

The content of this article is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.