By Nicole Vasilevsky and Sabrina Toro
The ISB hosted the second session for the Virtual Biocuration Conference on June 15, 2021. The session, chaired by Peter Uetz, Ph.D. from the Virginia Commonwealth University, focused on career paths and projections in Biocuration and hosted three panelists: Pankaj Jaiswal, Ph.D, Professor in Plant Genomics at Oregon State University (OSU) in Corvallis, Oregon; Tanya Berardini, Ph.D co-founder and Chief Scientific Officer at Phoenix Bioinformatics in Newark, California; and Nicola Mulder, Ph.D, Professor of Computational Biology at the University of Cape Town in South Africa. The session recording is available here.
Panelist paths in Biocuration
Dr. Tanya Berardini entered the biocuration field after completing a Ph.D. and a post-doc when she joined the Arabidopsis Information Resource (TAIR) as a curator. When TAIR underwent a funding crisis after many years of serving the plant genome community, Dr. Berardini and her colleagues founded the non-profit Phoenix Bioinformatics which developed a sustainable model to support the TAIR database through subscriptions and has subsequently expanded into assisting other databases and resources to address funding issues, through subscription and membership models. Dr. Beradini’s career path is unique, as she initially performed database curation for a single resource, TAIR, and now also works in an entrepreneurial position. She has learned various aspects about running a business (such as Human Resources, insurance requirements, contract negotiation), as well as curation in additional domains outside of plant biology. Dr. Beradini noted that her detailed-oriented curation skills and experience with databases were very transferable to the business world.
Dr. Pankaj Jaiswal’s work on sequencing plant molecules (his initial training was in biochemistry and plant molecular biology) prompted his interest in bioinformatics analyses and genome biology curation. He currently runs a wet lab (“on the bench”) and a dry lab (“at the computer”) at OSU in the Comparative Plant Genomics department. Dr. Jaiswal leads the curation efforts for the Gramene database and the Planteome projects, which require the creation of ontologies for the standardization of plant characteristics such as gene function, phenotypes, pathways, and gene expression. Dr. Jaiswal started curating during his basic science training as he read papers learned about specific subjects and synthesized information to address biological questions. His efforts to facilitate the synthesis of information and ease of interpretation, search, and access, included networking with peers, including Gene Ontology and Model Organism Database curators, and brought him to the field of biocuration. Dr. Jaiswal currently trains his students, post-docs, and researchers to apply data standards and learn the curation process to build upon the foundations laid by the biocuration community.
Dr. Nicola Mulder holds a Ph.D. from the University of Cape Town in South Africa, where she did basic science research and studied molecular biology of infectious diseases, which ultimately led her to bioinformatics. She became a curator at European Bioinformatics Institute (EBI), first at SwissProt, then as part of the InterPro project, which she went on to lead. Dr. Mulder currently leads the Pan African Bioinformatics Network for the Human Heredity and Health in Africa (H3Africa) in Cape Town, which supports bioinformatics and genomic analysis in Africa. Her team brought together a global community of experts, including clinicians, biocurators, and ontologists, which led to the development of the Sickle Cell Disease Ontology (SCDO) in response to the need to standardize information around Sickle Cell Disease, and the Hearing Impairment Ontology. Dr. Mulder and her team’s curation efforts include standardizing phenotype data for research cohorts and curating genomic data for African relevance, such as curating single nucleotide polymorphism (SNPs) from African populations and curating diseases that are relevant to Africans.
Becoming a Biocurator
The field of biocuration is still relatively new and small; colleges and universities do not typically offer a degree in biocuration. Therefore, the path to becoming a biocurator rarely follows a straightforward trajectory like many other fields, as many biocurators are subject matter experts in various subdomains of biology who completed a Ph.D. in a biological area or have a background in some aspect of computer science or semantic technologies, and have an interest in standardizing data. Our panelists shared some suggestions for those interested in joining the field:
- Draw on your area of expertise: Most databases focus on specific subject areas and expert community contributions (such as contribution to open biomedical ontologies, and all of the OBO Foundry ontologies) are always needed, welcomed, and greatly appreciated. If you notice missing information or content in a database, reach out and share your knowledge.
- As a researcher, curate your data before it is published: Work with the databases to make sure your data is prepared in a proper format for completeness and efficiency before you publish. Dr. Berardini mentioned that over 10,000 labs work on Arabidopsis, creating a massive backlog of papers to curate. Structuring data before and at the time of publication dramatically assists with the curation process.
- Volunteer at databases: If you have expertise in a particular field, contact the databases directly to discuss opportunities to contribute. Volunteering can be beneficial to build your experience, provide contributions to biocuration efforts, and provide networking opportunities within the community. In addition, volunteering can reveal whether the field is right for you. Biocuration requires a particular personality, including attention to detail and a desire to organize. While some people derive extreme satisfaction from it, others can find it quite tedious. Dr. Berardini noted, “if through volunteering, you find biocuration brings you joy, this is the right career for you.”
- Participate in hackathons, data jamborees, biomedical competitions: these events bring together researchers across various career stages, from junior biologists to practicing clinicians, and are opportunities to network, build your CV, and contribute to impactful work. Examples are biomedical competitions like Dream Challenges, and hackathons, data jamborees, face-to-face meetings, and online events hosted by Dr. Mulder to facilitate community curation of H3Africa projects.
- Do as much training as you can: Courses are available, such as massively open online courses (MOOCs), college courses, and the newer Post-Graduate Certificate in Biocuration offered by the University of Cambridge.
- Build your skill set: Search for job advertisements to determine what qualifications are needed, and work towards enhancing your skill set and competencies that meet job requirements. As an outcome of the Careers in Biocuration Workshop at the Biocuration 2018 conference, we created a generic position description for a biocuration profession, which is available here.
Biocuration career opportunities
A lot of opportunities exist in the biocuration field: biocuration in academia, which may entail biocuration for grant-funded database projects and ontology development, such as the work of Dr. Jaiswal; community-based bioinformatics and curation projects, such as those led by Dr. Mulder; and biocuration in a non-profit business setting, as Dr. Berardini’s work at Phoenix Bioinformatics. Biocuration opportunities are also available in the industry as companies are recognizing the importance of curating and standardizing data (for example, standardizing clinical trial data), in government agencies; and even as independent consultants
The skills gained as biocurators, such as attention to detail, the ability to take in and synthesize data, and computational skills, are very valuable and can be translated to different areas, such as other areas of science or technologies.
Biocuration is a growing field and we anticipate that, as the amount of biological data being generated increases, so will the demand for curators. The ISB aims to promote the field and support our community through offering dissemination of job openings (see regular posts on our website here.), training opportunities, and networking. The ISB also promotes collaborations and exchanges between biocuration groups and offers funding for exchange fellowships. This fellowship will fund members to visit another laboratory or organization for training or knowledge sharing; more information is available here.
Researchers have the opportunity to better structure their datasets, share their data in repositories, and better structure the content that they publish, however, they are often unaware of the career opportunities in biocuration. We have not only an opportunity to promote the biocuration field, but also the responsibility to train the future generations, provide knowledge transfer, and have succession plans for those coming up after us.