The 1st session of ISB2022 Biocuration Virtual Conference will take place on Thursday, April 7th 2022 at 8 – 10.30 am PT / 11 – 1.30 pm ET / 4 – 6.30 pm BST / 5 – 7.30 pm CET.
Check out the panelists and speakers of our 1st session here!
The 15th Annual Biocuration Conference (ISB2022) will be virtual in 2022.
Click here to know more about the the three sessions of ISB2022, featuring talks and workshops that will take place starting April 2022.
By Federica Quaglia
The fourth and final session of the ISB2021 14th annual conference (virtual) took place on October 5th, 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.
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:
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.
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.
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.
We are pleased to announce the newly elected members of the ISB Executive Committee (EC).
Mary Ann Tuli was re-elected for another term (from 2021-2024).
Federica was one of the key organizers of the ISB Virtual Conference in 2021. Sushma Naithani is also a member of the ISB Equity, Diversity, and Inclusion Committee and chaired the EDI workshop at the Session 3 virtual session.
The new committee will start on November 01, 2021. We are thrilled to have these new members on the EC and look forward to their contributions.
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).
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.
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.
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:
A previously published report on ‘Gender Balance at the International Society for Biocuration Annual Conferences’ is available here (https://zenodo.org/record/3541014#.YUpRJtNKh59).
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.
Join us: Email us at: email@example.com to inquire about joining the EDI Subcommittee
Equity, Diversity, and Inclusion Subcommittee website: https://www.biocuration.org/equity-diversity-and-inclusion-committee/
The election of the new International Society for Biocuration Executive Committee (ISB EC) will be held from September 27 – October 04, 2021.
Candidates for 2021 election:
Mary Ann Tuli, BGI-Hong Kong
Federica Quaglia, University of Padova, Italy
Caio Cesar de Carvalho, University of Nevada – Reno
Sushma Naithani, Oregon State University
Parul Gupta, Oregon State University
Please click the links on each candidate’s name for their bio and their motivations or running for the EC.
4 positions on the Executive Committee are up for election in 2021/2022. These positions are currently held by Mary Ann Tuli, Frederic Bastian, Jane Lomax, and Sandra Orchard. Mary Ann, Frederic, and Jane can re-stand for election. (The current ISB EC members are here.)
2021 Election Timeline:
*Note – please note that if you do not receive the email please contact us at firstname.lastname@example.org
Anne Niknejad, University of Lausanne and SIB Swiss Institute of Bioinformatics was unanimously selected for the Biocuration Career Award.
AnneNiknejad is an exceptional biocurator who has worked for over 10 years on the development of resources and vocabularies for the description of anatomical ontologies. She is playing a key role in curation of expression data, of anatomical and developmental ontologies, as lead curator for the Bgee project in Marc Robinson-Rechavi’s group in Lausanne. Anne’s contribution to anatomical homology has been essential to provide a large coverage of anatomical homology in a curated and structured manner originally in vHOG and since 2012 directly using Uberon (http://uberon.github.io). Anne combines the capture of knowledge from textbooks of anatomy, development and zoology, with scientific literature which spans evolutionary developmental biology (Evo-Devo), paleontology, systematics, zoology and recently single-cell atlases. By creating the ontology relations of homology, Anne extracts new knowledge from these disparate sources. She also participated in the development of mechanisms to handle the contradictions which emerge from new results or differences in interpretation between reports. This homology annotation work is critical to the future success of Bgee, but also of other projects relying on comparisons between species which map to anatomy, such as the Monarch Initiative. Anne’s knowledge is not limited to anatomy and she contributed to annotations in other resources: she curated lipid structures in SwissLipids (PMID:25943471) and enzyme reactions in Rhea (PMID: 30272209).
Thank you to the Award Committee:
It is our great pleasure to announce the recipient of the 2021 Exceptional Contribution to Biocuration Award:
Prof. Amos Bairoch, University of Geneva and SIB Swiss Institute of Bioinformatics.
Amos created the Swiss-Prot knowledgebase in 1986, which rapidly became the gold standard for proteins in terms of biocuration. Nobody, except Michael Ashburner, contributed more to the biocuration field. Amos was definitively the most accurate and productive biocurator in Swiss-Prot. In 2002, he co-founded UniProt, the universal protein resource, and Swiss-Prot became UniProtKB/Swiss-Prot, the expertly curated section of UniProtKB. UniProt is the reference resource in the field of proteins: it is accessed by hundreds of thousands of users each month and is cited in tens of thousands of publications. UniProt is an Elixir core data resource. In 2009, Amos left UniProt and co-founded NextProt, a knowledge platform on human proteins, which constitutes the reference knowledgebase for human protein annotation in the context of HUPO Human Proteome Project (HPP). Last but not least, he created Cellosaurus, a knowledge resource on cell lines, which attempts to document all cell lines used in biomedical research. Cellosaurus is now considered as the reference for cell lines in biology and is an Elixir core data resource. Amos is also co-founder of the SIB Swiss Institute of Bioinformatics and of the ExPASy Bioformatics portal. But it is impossible to list all his contributions.
Congratulations to Amos!
Thank you to the Award Committee:
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.
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.
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:
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.