Held on September 2, 2022, the Biocuration Careers Workshop was the third and final installment of the International Society for Biocuration (ISB) virtual conferences in 2022. The workshop’s aim was to determine ways that ISB can assist Biocurators with career progression. 

Organized and led by Nicole Vasilevsky, Lead Biocurator at the University of Colorado Anschutz Medical Campus, the workshop was facilitated by four field experts: Mohammad Hosseini, Kristi Holmes, Mary Ann Tuli, and Randi Vita.

To set the stage, the diverse set of job titles and roles collected as part of the 2020-2021 ISB survey were presented, as well as current job openings on the ISB website were discussed. One of the key ways the ISB helps biocurators in finding a new position is by posting job openings in the biocuration field. However, the job titles and descriptions of these positions can vary a great deal, which can be confusing for hiring managers and problematic for junior biocurators or those updating their resumes and looking to change positions. 

Biocurators face some unique challenges with tracking our contributions to science. While it is not unusual for some biocurators to successfully work in their field without being a co-author of peer-reviewed articles, some biocurators might not always receive their due credit; making career advancement difficult, especially in academic settings where publications are viewed as the main proof of success. Mohammad Hosseini of Northwestern University presented Contributor Roles, an innovation developed to describe individual contributions to research. By providing a standard list of roles to specify individual contributions to publications, Contributor Roles enhance the transparency and consistency about the reporting of conducted tasks, and accordingly, improve the attribution of credit and responsibilities. The CRediT taxonomy is the most widely adopted Contributor Role schema, offering 14 standard roles, one of which is Data Curation, defined as: “Management activities to annotate (produce metadata), scrub data and maintain research data (including software code, where it is necessary for interpreting the data itself) for initial use and later re-use” (NISO 2022). The Contributor Role Ontology (CRO) is an extension of CRediT to highlight individual contributions to research. Although CRO provides more granularity with ten specific data roles (e.g., data aggregation, data integration, data modeling, data quality assurance), the biocurator roles are not similarly detailed. Mohammad also illustrated how publications with datasets stored in public repositories often do not adequately attribute the associated data processing efforts conducted by biocurators. Clarifying these roles can improve future attribution of credit and responsibilities.

Kristi Holmes, professor of Preventive Medicine and the director of Galter Health Sciences Library at Northwestern University shared ways to track scholarly products, including the traditional metrics that are typically captured on a CV, as well as other research products. By highlighting roles that biocurators play in pushing data-driven research forward, she highlighted the importance of tracking and assigning credit to biocurators in terms of understanding the work that is required to drive research, and ways those contributions can be described more accurately using a narrative approach.

Randi Vita from the La Jolla Institute for Immunology described the generic job description for a biocurator that was drafted as part of a previous ISB workshop in 2018, illustrating how diverse these positions can be. She stressed how different specialized skills are valuable to these positions and hiring managers, but are often overlooked when job candidates are polishing their CVs.

Understanding the wide range of roles that biocurators play in research projects and programs is critical to understand research process itself. The workshop facilitated a brief exploration of relevant topics such as standardization of job titles to support biocurators’ career progression, especially in academic settings wherein contributions are quantified and necessary for promotion, as well as novel and relevant credit and attribution for biocurators. Moving forward, the ISB could provide an excellent platform to advocate for more accurate and encompassing biocurator roles. 

Help us continue this discussion and inform future activities:

1. The ISB would like to collect titles and qualifications, metrics and accomplishments for different career levels: https://bit.ly/3PvP9uu 

2. Weigh in on future workshop ideas: 
   • How do you get a job as a curator? 
   • How do you write your resume/CV? 
   • How do you write a job description for a curator?

3. Answer the study question: Are biocurator positions hard to fill? Could we get stats on how long biocuration jobs are open? 

Email: isb@biocurator.org

By Federica Quaglia

The fourth and final session of the ISB2021 14^th annual conference (virtual) took place on October 5^th, 2021, featuring the Annual General Meeting (i), a Panel Discussion on Strategic Planning with former ISB Executive Committee (EC) members (ii), talks from the Biocuration Awards recipients in 2021 (iii) and a Poster Session (iv).

During the Annual General Meeting, Nicole Vasilevsky, chair of the ISB EC, talked about the current status of ISB and the future directions of the Society. Four invited Panelists joined the Panel Discussion on Strategic Planning: Pascale Gaudet, Mike Cherry, Andrew Su and Monica Munoz-Torres, all of them being former members of the Executive of ISB. Finally, talks from the recipients of this year’s Biocuration Awards were presented: Amos Bairoch (2021 Exceptional Contribution to Biocuration Award) and Anne Niknejad (2021 Biocuration Award).

A Poster Session was carried out in gather.town, on a dedicated space entirely set up for the ISB, and followed by a social hour for ISB members and conference participants to interact and exchange ideas.

Annual General Meeting

The talk – led by the ISB EC Chair Nicole Vasilevsky – started with an overview of the current ISB Executive Committee, composed by nine members, that in 2020-2021 included Nicole Vasilevsky, (USA, Chair), Ruth Lovering (UK, Secretary), Robin Haw (Canada, Treasurer), Rama Balakrishnan (USA), Frederic Bastian (Switzerland), Jane Lomax (UK), Randi Vita (USA), Mary Ann Tuli (UK), and Sandra Orchard (UK). Three members, Sandra, Frederic and Jane, concluded their mandate in the ISB EC, while Mary Ann was re-elected along with three newly elected ISB members for the 2021-2024 term: Federica Quaglia, Sushma Naitani and Parul Gupta. 

The ISB EC work in the past year included also the activities of several subcommittees, composed by ISB EC members and external members too: 

• Outreach and Training (Chair: Randi Vita) 
• IT infrastructure (Chair: Ruth Lovering) 
• Fellowships and Awards (Chair: Frederic Bastian) 
• Conference coordination (Co-chair: Rama Balakrishnan, Sue Bello) 
• Elections (Officer: Petra Fey)
• Equity, Diversity and Inclusion

The ISB was founded in 2009, and since then the main goals of the society have been to promote the work of biocurators and encourage best practices in biocuration, and to foster communications and connections amongst the members. To this end, there are formal memberships in the society – currently including 232 members – although anybody in the community is welcome to participate in most of the activities. Relevant information on how to join the society (https://www.biocuration.org/membership/membership-levels/) and on the benefits associated with the ISB membership (https://www.biocuration.org/membership/join-isb/) can be found on the website.

A report of ISB finances for the last year, 2020, shows that we have collected over 7000 CHF – the society is based in Switzerland – and the expenditures include sponsorships and some administrative fees and taxes while currently operating on a balance of over 121.000 CHF. The ISB offers travel fellowships, funds attendees to join our conferences (when meeting in person), but also funds micro-grants and various proposals including smaller gatherings for curators to meet and work together, e.g. to visit another group and learn about new techniques or workflows. For members of the ISB we offer a discount on the publications in our affiliated journal, Database: The Journal of Biological Databases and Curation (https://academic.oup.com/database). To promote the work of our members in the society and in the field of biocuration we have a mailing list and a quarterly newsletter – organized by Mary-Ann Tuli – to communicate and disseminate information to our community of over 700 members. Finally, the ISB Twitter account (https://twitter.com/biocurator) actively advertises news related to the society and to the biocuration field.
There are also two dedicated ISB awards that we offer yearly, the exceptional contribution to biocuration award and the biocuration career award, the recipients this year being Amos Bairoch and Anne Niknejad.

In an effort to assess the work of biocurators the ISB sent out a survey during the last year, that shed light on biocuration-related work positions, satisfaction, work environment, leadership levels and scholarly products. Highlights are shown below and the results of the survey are available here.

The survey had over 130 respondents – 74% out of them are women and 25% men. Interestingly, the majority of respondents have been in the field for over 10 years (62%), suggesting their satisfaction and identifying biocuration as a stable career choice. For what concerns salary range of biocurators, half of respondents (54.2%) earns between 50 and 100k a year in US dollars. Further inquiring on the the work environment highlighted some flexibility in the work schedule (identified as flexibility during regular business hours) for 62% biocurators, while 30% are actually able to choose their own working hours. Among the biocurators involved in the survey, 84% are satisfied with their job, with their work environment (79%), professional success (62%) and career progression (56%) – people are overall highly satisfied – with under half of respondents (49.65%) that have also been promoted during their career. In terms of leadership opportunities, we were able to identify four main areas of leadership for biocurators, namely manuscript drafting and publication (82%), project leading (72%), staff management (47%) and writing grants applications (38%), pointing up to the involvement of biocurators in managerial positions and further supporting the high rate of satisfaction in biocuration careers. Finally, the survey identified the five main types of scholarly products generated by biocurators, i.e. curated datasets (87%), publications (41%), talks at conferences (15%), softwares (12%) and codes (6%), identifying a need for ways that could increase the articles published by biocurators.

Panel Discussion on Strategic Planning with former EC committee members at the Biocuration2021 virtual conference

The Panel Discussion on Strategic Planning was joined by former members of the Executive Committee of ISB, Pascale Gaudet, Mike Cherry, Andrew Su and Monica Munoz-Torres.

• Andrew Su: Professor at Scripps Research. Representative projects include the Gene Wiki, and BioThings Explorer. He served on the ISB from 2016-2019.
• Mike Cherry: Professor of Genetics at Stanford University. He oversees the Saccharomyces Genome Database. As well, he is involved in ENCODE (Encyclopedia of DNA elements), Gene Ontology Consortium, Alliance of Genome Resources, RegulomeDB, and Lattice: Human Cell Atlas. He served on the ISB from 2010-2016 and acted as chair from 2015-2016.
• Pascale Gaudet: Senior Project Manager in the Swiss-Prot group of the SIB Swiss Institute of Bioinformatics. Project Manager of the Gene Ontology project. She is a founding member of the ISB and acted as Chair of the ISB Executive Committee from 2009 to 2013.
• Monica Munoz-Torres: Associate Research Professor in the Center for Health Artificial Intelligence at the University of Colorado Anschutz Medical Campus. Director of Operations for the Center for Cancer Data Harmonization (for NIH/NCI) and Program Director for the Phenomics First Resource (an NHGRI CEGS) and the Monarch Initiative. She served on the ISB Executive Committee from 2012 through 2017, as Secretary in 2012-2016 and as Chair in 2016-2017.

The discussion started with the panelists’ reflections on the very beginning of the ISB and on how those dreams and hopes became reality over the years, while continuously looking at the future of biocuration and at new ways to improve our profession by serving in the Society.

The ISB has a well-established central role in fostering and building connections among the members, in first place thanks to the meetings that took place over the years and now including additional venues that facilitate our interactions, such as a mailing list, newsletter, our Twitter account and a dedicated Slack workspace. Awards and microgrants have also played a crucial role in raising awareness on the centrality of biocuration careers inside the scientific community and in supporting knowledge-exchange between biocurators from different groups. It is fundamental to reach a better appreciation of biocuration as a means to advance scientific research by making research data shareable and accessible in a standardized format, especially at the level of funding agencies. These topics have a particular relevance when paired with the advancements in machine learning and artificial intelligence: these indeed can not replace expert literature curation, vice versa machines can be supported by biocurators via the use of carefully curated high quality annotations.

Over the years following its foundations, the ISB has been growing to be more inclusive and diverse and focused on developing and implementing a code of professional conduct. The introduction of several subcommittees, composed not only of EC members but of the greater ISB members too, raised the opportunity to increase the ability to volunteer in the activities of the ISB. The society is now also exploring new ways to cover a variety of professional experiences by engaging biocurators in poorly-represented geographical areas and by welcoming graduate students, by considering introduction of  a dedicated “students section”.

Our society also benefited from the efforts of the ISB EC back in 2008, with the establishment of a dedicated journal, Database: The Journal of Biological Databases and Curation (https://academic.oup.com/database). This peer-reviewed journal is now at the forefront in the publication of biocuration-related articles, providing also a 20% discount on publication fees to members of the ISB. The existence of a specific journal for biocuration positively affected our field – it was usually hard to publish in traditional scientific journals – and provided our community with a specific venue to publish our research work. It is worth considering the option to provide microgrants to cover publication costs in Database, in those situations where a restricted access to funding prevents the submission of manuscripts to a scientific journal. Finally, an additional option would be considering the micropublication system, where no publication cost is involved while still allowing to make research data public (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5836261/, https://www.micropublication.org/).  

Although a result of the ongoing global pandemic, this year’s virtual conference overall received great feedback as it has been more accessible by allowing everyone to attend, even those who could not afford to travel e.g. due to family commitments. It was therefore proposed to keep on maintaining some virtual events even once the restrictions related to the pandemic will be lifted and the conference will resume in presence.

Finally, panelists unanimously agreed on the relevance of the ISB in supporting and promoting career development for biocurators, with a great starting point being the establishment of formal training opportunities and professional certificates that did not previously exist in the field. At the same time, creating, maintaining and sharing FAIR training materials (Goblet, ELIXIR TeSS) should be even more supported and pursued, while also providing dedicated learning sessions where to present them. 

All these directions will play a crucial role in our job security and will make room for professional development of biocuration careers, actively supported by the International Society for Biocuration.

By Nicole Vasilevsky

At the third session of the Virtual Biocuration Conference on August 17, 2021, Sushma Naithani, Associate Professor Senior Research & Lead Biocurator for Plant Reactome at Oregon State University led a Workshop on Addressing Implicit or Unconscious Bias organized by the Equity, Diversity, and Inclusion (EDI) committee of the International Society for Biocuration (ISB). Three invited panelists joined the discussion: Laurie Goodman, Publishing Director, GigaScience Press, Yasmin Alam-Faruque, Senior Biocurator at Healx, and Varsha Khodiyar, Data Curation Manager at Springer Nature. The session recording is available here.

The discussion started with a recap of Picture A Scientist, a documentary film that was screened by the ISB EDI in March 2021 (and is currently available on Netflix). 

Impact of ‘Picture A Scientist’ 

Picture of Scientist is a documentary that follows three women in different scientific careers: Jane Willenbring, a geologist who faced unrelenting harassment during a once-in-a-lifetime opportunity performing fieldwork in Antarctica; Nancy Hopkins, a biologist who documented concrete evidence of discrimination against women in allocating lab space at her institution, and Raychelle Burks, a chemist who has to contend with a hostile work environment as she progressed through her career. The primary consensus from our panel in response to the movie was a feeling of empathy, commiseration, and a recognition that we still need to fight for equity for women in science.

Our panelists called for the need to do more to recognize and acknowledge gender discrimination as well as other forms of unconscious biases that persist in the scientific field. They recognized unique challenges for women, people of color, immigrant scientists, etc. Opportunities to progress in science, particularly in academia, can be very limited without a Ph.D. If someone experiences issues in their lab during their early-career training, it can be really difficult to start over. In addition, training can be very specialized and limited. They called out the need for better strategies to aid scientists-in-training and junior scientists when their progress is impeded. These kinds of challenges may not exist in other male-dominated fields like law, where there are opportunities to move between firms.

For those who are dependent on employment visas from immigration offices, they may feel less empowered to take action or speak up when their immigration status is linked to their employment. In addition, the need for recommendations from previous employers may impact our sense of empowerment to take action against inappropriate workplace situations. We all need to stand up and take action when we see discrimination and inappropriate actions. We need to be allies and support each other. However, the problem with implicit bias is that many well-intentioned folks are not aware of their own biases and how it contributes to the environment of scientific institutions, fraternities and societies. Thus, we also need clear institutional guidelines, support for training the scientist in soft skills, and addressing the implicit bias for resolving the issues related to EDI. 

Our panelists brainstormed some strategies and mechanisms to address some of these problems.

• Education and training
  • Regular education and training sessions, such as unconscious bias training are helpful to provide the most up-to-date information.
  • Tests are available that can give insight on your own potential implicit biases, such as https://implicit.harvard.edu/implicit/takeatest.html
• Institutions have the responsibility opportunity to aid in reporting of harassment and discrimination
  • Most institutions over a certain size have a Human Resources (HR) department and mechanisms to report harassment or inequity.
  • For example, the company Healx conducts regular surveys to understand employee engagement and satisfaction in the workplace. The survey includes questions around equity, diversity, and inclusion, and provides a platform for employees to anonymously report any inequality/harassment issues they may have encountered. 
  • When new students and employees are onboarded, they should be informed about processes for reporting issues to HR.
• Mentorship 
  • Money talks: if women are awarded large grants earlier in their career, this may significantly help their career trajectory.
  • More established biocurators have the opportunity to help train women on how to write good grants.
  • Including women and other scientists, who are marginalized, in formal and informal collaborations, and various professional groups will help to achieve inclusion and diversity of the STEM.    
• Defund offenders
  • Institutions and funding agencies should implement policies to take away positions and/or grant funding from people who are guilty of harassment or discrimination.

Opportunity for the ISB: Define our job titles

The panelists pointed out that standardization of job titles could help with career progression. The ISB has an opportunity to help define standardized job titles across the ranks. For example, what does a starting position look like, and what qualifications does a more advanced biocurator typically have? What is the difference between a Lead Biocurator and a Senior Biocurator? Our recent survey revealed that the majority of respondents (62%) have been in their position for 10 years or more, but only about half (49.6%) of the biocurators who responded have been promoted since they started their career in biocuration.

Job titles for biocurators vary widely and there is a lack of standardized names and titles for the biocuration positions. The field of biocuration has existed for approximately 20 years, yet there is not a widespread understanding of what a biocurator does and what a typical career progression should look like.

Based on results from a recent survey that was conducted by the EDI Subcommittee, ISB community members reported 24 unique job titles as outlined in the table below. Of note, most respondents identified as (bio)curators, but some respondents distinguished their title as a Scientific curator or Scientific Database curator, emphasizing the need for standardization of the job titles. 

A generic biocuration position description is available on the ISB website here, which was created as an outcome of the Careers in Biocuration Workshop at the Biocuration 2018 conference in Shanghai, China. This could be used as a starting point for further definitions and standardization of position descriptions.

We need better data

As scientists, we recognize the need for concrete data and evidence to back up assertions and stimulate change. There is a call for the ISB to collect data from the biocuration community to address key questions such as:

• Are women being paid less than men?
• What is the gender breakdown of the membership of the ISB?
• What percentage of women obtain grant funding compared to men?
• Is there evidence of gender or racial discrimination in the biocuration community?
• Are biocurators progressing in their career at the same rate as other types of scientists?

A previously published report on ‘Gender Balance at the International Society for Biocuration Annual Conferences’ is available here (https://zenodo.org/record/3541014#.YUpRJtNKh59). 

Conclusion

The EDI Subcommittee was formed as an outcome of the inaugural Equity, Diversity, and Inclusion workshop at the last in-person Biocuration conference in Cambridge, UK in 2019. This is a volunteer-run committee with members from the ISB Executive Committee and community members. Anyone is welcome to join and all contributions are valued and appreciated. We are extremely grateful to the workshop organizers, Sushma Naithani for moderating this session, and a huge thanks to our panelists, Laurie Goodman, Yasmin Alam-Faruque, and Varsha Khodiyar for their insightful perspectives and for assisting us in thinking about these important issues.

More Information

Join us: Email us at: intosocbio@gmail.com to inquire about joining the EDI Subcommittee

Equity, Diversity, and Inclusion Subcommittee website: https://www.biocuration.org/equity-diversity-and-inclusion-committee/

Slack: https://isbedicommittee.slack.com/archives/CKENH257H

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. 

By: Nicole Vasilevsky and Jane Lomax

Like all in-person gatherings in this past year, the annual International Society for Biocuration conference went virtual in 2021. At the inaugural session on April 13, 2021, a group of panelists discussed ‘the future of biocuration’. The panel was moderated by Rama Balakrishnan, who has served on the ISB Executive Committee since 2017, and is the co-chair (along with Susan Bello from the Jackson Laboratory) of the Biocuration2021 conference. Rama was joined by four panelists from various roles in academia and industry to discuss what is in store for our community. The recording is available here.

What is curation: Distilling knowledge from information

Rama initiated the discussion with the fundamental and relevant question, ‘what does the word curation mean to you?’ Working in the biocuration field, many curators can probably relate to this question, a question that is frequently asked by people who are outside this field. The role of a curator at a museum, for example, may be more familiar, but biocuration is a less well-understood field. Rama, who has held varying roles as a curator (academic and industry), tried to get after how the actual task of curation may differ amongst us. Sandra Orchard, from EBI shared a classical definition of ‘turning unstructured data into structured searchable data’, but recognized this is not always true as, whilst some curation tasks involve making data more structured, text-minable and machine-readable, the outcome of data curation does not always result in completely structured data. Carol Bult from MGI defined curation as “applying semantic standards to ensure data findability and aggregation.” 

Coming from the industry perspective, both Kambiz Karimi (Myriad Women’s Health) and James Malone (SciBite) agreed. Curation involved meaning-based capture and structuring of content using controlled vocabularies. Data curation can also include data cleaning, which is often a pre-curation task. Curation can help improve and enrich data interpretability and ultimately add value. It allows for enhanced search, querying, semantic integration and meta-analysis. 

How can we ensure quality?

Given that the panelists all agreed on a high level definition of curation, Rama then asked about ensuring data quality. What does good quality mean and what are metrics to assess quality? Different quality control (QC) and quality assurance (QA) processes apply, depending on the type of curation that is being done, whether you are curating tax forms (as James did in a summer job long ago) or curating the mouse biology literature. Some processes that were discussed by Carol and others  included intercurator checks, crowdsourcing feedback from downstream users, practices to ensure collaboration, regression testing to ensure continuity and consistency across datasets. Sandra pointed out that curators cannot be all things to everything, and stressed the importance of specialist databases with curators who are domain experts who can take the first pass at the curation, and build re-processing pipelines or scoring mechanisms to export high quality subsets to other data resources.

James and Rama noted how detecting outliers can assist with quality checks. However, it may not always be easy to detect the outliers without the expert knowledge in a specific area. For example, Rama curates patient data at Genentech, and once came across a data reporting a patient had a 100℃ fever (rather than 100℉), which was easy to spot as an error. However, in a more complicated clinical use case, detecting erroneous data points may not be so obvious and require more specialized knowledge.

Kambiz shared that Myriad has several QC approaches, including a peer review process, a spot checking program to have curators spot check each other’s work and a quality check process that compares their classification to previous classifications from the community. 

Sandra also noted the importance of researchers collaborating with curators prior to publication. She shared an anecdote where an author published a paper with an erroneous dataset, a simple mistake where a row in a spreadsheet had been accidentally deleted, causing nonsensical results. The curator picked this up and contacted the author, who was able to correct it, but this speaks to the importance of pre-submitting data to the database before publication and the important role a curator can play with the research community. 

Opportunities with Machine Learning and Automation 

While a lot of biocuration is done manually, more and more processes and workflow are being automated, with text mining, machine learning (ML), natural language processing (NLP) and AI.  The panel was asked their opinion on how AI and ML will affect the work of biocurators? Sandra assured us that machine learning will enhance our work, but is not concerned that it will replace human curation. Data is too messy, the literature is too unstructured, and human review and curation is going to be needed in the foreseeable future. James echoed her sentiments in saying, “[Machine Learning] will become an assistant, it will not replace subject matter experts who are biologists, scientists, curators. It will play a role in helping us.” James sees it as an opportunity for biocuration, where we should work to exploit advances in deep learning, noting the importance of biocuration is more pronounced now than ever. We can train AI to aid in biocuration and we can work together. In addition, quality Machine Learning/AI requires training sets that have been human-curated, and the advances of these technologies will require more curators; this is a new opportunity for this community. Carol agreed, but brought up the point that there may be the perception that these technologies are advanced to the point where curators can be replaced. This is causing challenges with funding for biocuration due to the notion that machine learning can do all or most of what human curators do. While machine learning can assist with making biocuration scalable, we need to do better as a community at communicating how these things interrelate and feed off each other.

“Biocuration has never been more valuable than it is now and yet under appreciated.” It’s something the Society can help us tackle: this perception and articulate how manual and machine learning biocuration can go hand and hand. – Carol Bult

Approaching authors

An audience member inquired whether database curators approached authors for clarification about their published data, and whether authors were responsive. Kambiz shared that they did approach authors when there was ambiguity with the content or data in an article. Sandra concurred, and alluded to the challenge with time dependencies; if a paper was recently published (1 year – 18 months ago), they frequently got a response. If a paper is over 3 years old, in general, they were less likely to get a reply, as the first author may have moved on and the PI is unfamiliar with the details of the data. 

This may speak to an opportunity to better train researchers in becoming familiar with curation methods and standards, to allow for unambiguous reporting in their publications. Requirements to share data at the time of publication will also help address this need.

Getting the journals involved

This led to the next question about working with the journals to publish data in a more structured way. Carol has had some experience working with journals in the mouse community, who are careful about publishing mouse names with the accepted terminology and nomenclature. She did mention that sometimes there is push back as to whether the recommended standard is the accepted standard, and whether this is going to evolve or change in the future. We all may be familiar with the situation below.

This is an opportunity for a systematic community approach, the ISB should promote standards adoption to the journals.

Sandra pointed out that a challenge with approaching journals to use our standards, is the sheer number of journals. A more targeted approach may be more appropriate. For example, the proteomics community was successful in getting a restricted number of journals in their field to require data sharing to ProteomeXchange (http://www.proteomexchange.org/) prior to publication.

Sandra also recommended that we first talk amongst ourselves as a community and define our needs, and what standards to adopt and promote, and then approach the journals.

The elephant in the room: Funding

In recent years, NIH funding has decreased to various databases. How do we sustain our own careers, and train the next generation of curators? 

Kambiz felt it is easier to justify the need for curation due to the regulatory aspect of his industry. Even if there are NLP based processes to extract gene to disease relationships,  manual review will always be needed. He foresees  automated processes will assist with manual curation going forward.

Carol emphasized that we need to promote how important curation is to data science. Data science is recognized as an important field, therefore we should frame curation within its role in data science. We have to be better about explaining return on investment in curation – what can we do when data is curated, and we wouldn’t be able to do, if it wasn’t? She pointed out that the reality that biocuration is considered infrastructure, which is largely ignored, until it is broken. As a Society, can we demonstrate the impact that biocuration has on advancing data science?

Sandra reiterated that we need to make ourselves more visible, we need people outside the community to understand what we do. We need to work together as a community efficiently to not duplicate efforts, we need to align on standards, use specialist databases for initial analysis and data cleaning, and use the baseline resources like accession numbers, and show good examples of good curation.

Continue the conversation on Slack.

Do you have topics you’d like to discuss in a future panel, or suggested speakers? Please let us know (intsocbio@gmail.com).