Citation: Wang Y, Wang Q, Huang H, Huang W, Chen Y, McGarvey PB, et al. (2021) A crowdsourcing open platform for literature curation in UniProt. PLoS Biol 19(12): e3001464. https://doi.org/10.1371/journal.pbio.3001464
Published: December 6, 2021
Copyright: © 2021 Wang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was funded by the National Institutes of Health (https://www.nih.gov, ROR: https://ror.org/01cwqze88) under Award Number U24HG007822 (YW, QW, HH, YC, PBM, CHW, CNA). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
UniProt is a public source of protein sequence and function information. It includes proteins from the entire tree of life, serving a wide user community across diverse fields. The UniProt knowledgebase (UniProtKB) contains protein information derived by expert curation (Swiss-Prot section) and automated annotation (TrEMBL section) . Expert curation involves a critical review of the experimental data from the literature and interpretation of the results from sequence analysis tools . Currently, the UniProtKB contains over 220 million protein entries (Release 2021_03). Proteins from most organisms are unreviewed and only annotated via automatic annotation. This is due in part to a lack of direct experimental data available and a limited curation task force. Still, there is a significant number of proteins with some level of characterization or new information, awaiting annotation from the literature. Many UniProt users are highly engaged and motivated in providing feedback about entries in the database, especially when data are missing or an update is needed as UniProtKB is a highly valued resource and critical to their work. Users have vested interest that the knowledgebase is comprehensively annotated.
Engaging the research community in helping support curation or directly curating a resource has been an ongoing and evolving effort by many biological knowledge resources [3–5]. Here, we present a novel crowdsourcing community annotation system that enables researchers to quickly add annotations from the literature to UniProtKB protein entries. As opposed to past feedback options, this mechanism provides a systematic solution for community input, with a fast turnaround for presenting the added information to the community, and uses ORCID (https://orcid.org/) for authentication and acknowledgment of the contributions.
There are many reasons to contribute. As an expert on a given subject area, you are up-to-date with the literature and know what information is missing for a protein of interest. Thus, you can play an important and active role in improving the database and helping scale up curation. An improved database better supports the entire research ecosystem and moves science forward. To link a publication to a UniProt entry, you do not have to be its author, but to understand the content. In return, you get recognition for the biocuration work you do, you can cite it, and add it to your research portfolio.
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).
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.
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.
Box 1. Collaborations—Success stories
Here are 2 illustrative examples of users who are actively providing valuable annotations to unreviewed entries for specific taxonomic groups.
- Annotation of Giardia intestinalis protein. G. intestinalis is a eukaryotic parasite that causes giardiasis, with diarrhea and stomach cramps as main symptoms (https://www.cdc.gov/parasites/giardia/index.html). A search in UniProt (release 2021_03) with the query taxonomy “Giardia ” retrieved 43,668 and 66 unreviewed and reviewed Giardia protein entries, respectively. A search in PubMed (accessed on June 30, 2021) with query terms “giardia AND (intestinalis or lamblia or duodenalis) AND “Amino Acids, Peptides, and Proteins”[MESH]” retrieved 1,825 articles, suggesting that a significant number of potentially relevant publications could be added to Giardia protein entries. Thus, Dr. Touz (Instituto Ferreyra, Cordoba, Argentina), an expert on Giardia, has helped in this task by contributing annotations and contacting other experts in the community. So far, over 50 unreviewed entries now have publications and annotations.
- Annotation of Haloarchaeal proteins. Halophilic archaea are unique microorganisms adapted to survive under high salt conditions, and biomolecules produced by them may possess unusual properties, thus they are of high interest in the biotechnology field . Dr. Pfeiffer (Max Planck Institute, Germany) has actively provided feedback to UniProt on the annotation of prokaryotic proteins. Since the community annotation functionality started, he has now contributed over 250 submissions, especially adding publications and annotation to proteins from haloarchaeal genomes while developing a strategy for curation of their corresponding genomes [7,8].
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.
- 1. Consortium UniProt. UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D480–9. pmid:33237286
- 2. Poux S, Arighi CN, Magrane M, Bateman A, Wei CH, Lu Z, et al. On expert curation and scalability: UniProtKB/Swiss-Prot as a case study. Bioinformatics. 2017 Nov 1;33(21):3454–60. pmid:29036270
- 3. Lock A, Harris MA, Rutherford K, Hayles J, Wood V. Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications. Database (Oxford). 2020 Jan 1;2020. pmid:32353878
- 4. Arnaboldi V, Raciti D, Van Auken K, Chan JN, Müller H-M, Sternberg PW. Text mining meets community curation: a newly designed curation platform to improve author experience and participation at WormBase. Database (Oxford). 2020 Jan 1;2020. pmid:32185395
- 5. Viteri G, Matthews L, Varusai T, Gillespie M, Milacic M, Cook J, et al. Reactome and ORCID-fine-grained credit attribution for community curation. Database (Oxford). 2019 Jan 1;2019. pmid:31802127
- 6. Singh A, Singh AK. Haloarchaea: worth exploring for their biotechnological potential. Biotechnol Lett. 2017 Dec;39(12):1793–800. pmid:28900776
- 7. Pfeiffer F, Oesterhelt D. A manual curation strategy to improve genome annotation: application to a set of haloarchael genomes. Life (Basel). 2015 Jun 2;5(2):1427–44. pmid:26042526
- 8. Pfeiffer F, Dyall-Smith M. Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea. Genes [Internet]. 2021;12(7). Available from: https://www.mdpi.com/2073-4425/12/7/963. pmid:34202810