Category: The ISB

Announcement for the 2024 Annual General Meeting (AGM)

The International Society for Biocuration (ISB) will hold its Annual General Meeting (AGM) on Tuesday, October 29th, 2024 along with presentations by our two biocurator career award winners, Sushma Naithani and Maria Victoria Nugnes.

Time:

  • 3:00–5:00 pm CET (Central European)
  • 2:00–4:00 pm GMT (British)
  • 10:00 am–12:00 pm EST (Eastern)
  • 8:00–10:00 am PST (Pacific)

Note that daylight savings begins in Europe/UK on October 27th, 2024 and daylight savings begins on November 3rd, 2024 in the USA, so there’s a slightly different offset than usual. All canonical times for this event are based on European time!

Please fill out this form to register to attend by Monday, October 28th, 2024 to receive the meeting link: https://forms.gle/hr9H6z2MKAYC84haA.

Schedule (in CET):

  • 3:00pm Sue Bello: ISB Annual General Meeting
  • 3:30pm Open for questions and suggestions from attendees
  • 3:45pm Maria Victoria Nugnes, winner of the Early Career Award
  • 4:10pm Sushma Naithani, winner of the Advanced Career Award

This meeting will be recorded, by attending the meeting you are agreeing to be recorded. The recording will be available on the ISB website after the meeting.

Announcement for winners of “Excellence in Biocuration Awards 2024”

The International Society for Biocuration (ISB) would like to congratulate the recipients of the 2024 Excellence in Biocuration Early and Advanced Career awards:

  • Early – Maria Victoria Nugnes from the University of Padova
  • Advanced – Sushma Naithani from Oregon State University

Thank you to the Award Subcommittee:

Parul Gupta 

Sue Bello

Sara Chuguransky

Thank you to all the ISB members who participated in the voting.

EC Election Candidates – 2023

The election of five members of the International Society for Biocuration Executive Committee (ISB EC) will be held from September 26 – October 03, 2023.

Emails will be sent to current members on 26th September. Only current members, as of 20 September 2023, who receive this email will be allowed to vote. Please note that if you are an ISB member and do not receive the email please contact us at isb@biocurator.org.

We thank all of the following nine candidates for agreeing to stand for election to the Executive Committee (EC). Information about the candidates standing for election to the Executive Committee (EC) is available below:

Sara Chuguransky

InterPro/Pfam Biocurator

Sequence Family Resources, EMBL-EBI, Hinxton (Cambridge), England

I studied biochemistry and did my PhD in Diabetes, bone disease and alendronate treatment, using animal models and cell cultures, along with cytology techniques to evaluate different conditions and effects of bone loss/maintenance in this disease, in the National University of La Plata (UNLP), Argentina. Then I changed the topic in my postdoctoral position at the LiDeB (Research and Development of Bioactives Laboratory) also at the UNLP, Argentina, working in drug repurposing epilepsy treatment, especially refractory epilepsy. I also made collaborations in drug repurposing studies for tropical neglected diseases projects such as malaria, Chagas’ disease and Leishmania. During this time, I came to the EBI as a REFRACT secondee, a Marie Slowdowska-Curie project which involves European and Latin-American institutions for research internships, to improve and expand the coverage of repetitive proteins. From January 2020, I’m a Pfam/InterPro biocurator at the EMBL-EBI, as part of the Sequence Families Team lead by Alex Bateman, where we maintain and check that information from InterPro member databases is up-to-date and accurate, increasing the protein universe coverage integrating new models and updating the current ones. As a Pfam curator, I create new models to fill in the gaps in protein sequences, we improve the existing ones as well as check and increase the grouping of these models into superfamilies. I am also involved in delivering training as part of EBI courses, workshops, and webinars (for example Structural Bioinformatics course, Bioinformatics resources for Protein Biology course, UniAndes and UCR Bioinformatics training course (Colombia), webinars at the EBI, etc).

For the past three years, I’ve been working in biocuration, a job that I really enjoy as it is interesting and challenging. I’ve been learning a lot as it is dynamic, involving tasks which make me expand my knowledge to cover several aspects of the biology to understand predictions and provide accurate and up-to-date information based on current knowledge. This role also gives me the opportunity of interacting with many other database members and attending to conferences and meetings where I met members from a wide range of resources to expand our network which is great to understand users and databases’ requirements, leading to improvement of our services. A clear example of this is the Gene Ontology Consortium, with which we keep a fluent and usual contact. Based on these interactions, we received valuable feedback to make Pfam and InterPro more accessible and useful for researchers and the biocuration community.

 I am a new member of ISB and relatively new in the biocuration field, so I believe that crosslinks with other members, establishing a fluent communication and interaction will enhance our strengths and make it easier for all of us, to improve our services for the good of the community. The biocuration role is not the most visible one, so promoting participation of people from different places in the world and databases, along with promotion of events, conferences and jobs would be great to support us, since our role is critical for the understanding and giving the biological sense to bioinformatic tools, to expand and assist the development of different areas, from agriculture to human diseases and treatments, bacterial system, etc. I’m enthusiastic and open to change and evolution in the field, being confident that networking and exchanges between the biocuration community members is key for improvement and expansion of all services, supporting each other for a common objective.

To the ISB, as an EC member, I can bring the commitment of promoting activities and events within the organisation to increase and promote members participation and networking. I can take care of administrative task related to organisation and promotion of events, grants applications or workshops, as well as helping with email monitoring and maintaining the website. I have used WordPress before, when we make posts/protein focus articles in InterPro, although I don’t have experience in PHP/HTML/CSS or development skills. I’m keen to learn about ISB dynamics and function, and to support the biocuration community to make it more interactive.

No conflicts of interest.

Marc E. Gillespie

Professor, Biocurator, Vice Provost

Reactome & St. John’s University, NY  USA

I am a Senior Vice Provost at St. John’s University in Queens, NY USA and a biocurator on the Reactome Project (reactome.org). I received a BA in zoology from the University of Vermont in 1989 and worked as a lab technician at Cold Spring Harbor Laboratory and New York University Medical Center. I was lucky enough to get into the University of Utah’s Molecular Biology Program and received my PhD in 1998. My post-doctoral fellowship was done at Memorial Sloan Kettering’s Sloan Kettering Institute in NYC, working in x-ray crystallography. I originally trained as a molecular biologist focused on protein biochemistry, transitioning to genomics, proteomics, toxicology, bioinformatics, and eventually biocuration. My work in biocuration began when I joined the Reactome Team in 2003, a fantastic group and time to start in biocuration, alongside running my own lab focused on toxicogenomics. As with many groups the Reactome curators grew with the biocuration field, inventing methods and practices as we moved along. I have continued to work within the biocuration community, meeting many of you along the way. During the pandemic I had the fortune to work with the COVID-19 Disease Mapping Group and helped lead our disease curation efforts on a new more pressing front. Despite administrative pressures I continue to curate and look forward to new opportunities to contribute.

My interest in joining the ISB leadership started with the 2014 Biocuration meeting. Along with Francis Ouellette and Robin Haw I had the chance to co-chair the 2014 Biocuration meeting in Toronto, CA, at a time when the ISB was growing. The diversity of the members and attendees at biocuration meetings is the strength and a challenge for the society. Working across platforms and fields during the pandemic reminded me again that biocuration is a big tent encompassing many different fields. Professionally (outside of my biocuration role) I work in these cross seams regularly. I believe that the need for biocuration will grow, and that the field needs leadership that can bring the benefits of the society to an expanding group of stakeholders, many of whom work in a curation role, but don’t know that the ISB is here to help them grow professionally. At a time when FAIR principles and appreciation and attribution of the work that biocurators do is growing we need clear and straightforward support for expanding the ranks of the society, I am very interested in expanding and defining the practicalities and benefits that ISB membership can bring. I think we must explore what other societies and fields we should be aligning with. The value of the ISB hinges on the support and resources that it provides new, mid-career, and experienced biocurators.

No conflicts of interest.

Charles Tapley Hoyt

Senior Scientist

Gyori Lab for Computational Biomedicine, Northeastern University, Boston, MA, USA

Dr. Charles Tapley Hoyt received his Ph.D. in Computational Life Sciences from the University of Bonn. His research interests cover the interface of biocuration, knowledge graphs, and machine learning with systems biology, networks biology, and drug discovery. He currently works remotely from Germany as a Senior Scientist in the Gyori Lab for Computational Biomedicine at Northeastern University. He is an advocate of open source software, reproducibility, and open science. His open source projects such as PyBEL and PyKEEN are used by several academic and industrial groups.

My work in biocuration supplements my primary interests in translational science and drug discovery. To this end, I am the primary curator and developer of several community datasets and databases such as the Bioregistry and Biomappings. I make frequent small contributions to other curated resources and promote the concept of the Drive-By Curation. I am also active in the development of community standards such as the Simple Standard for Sharing Ontology Mappings (SSSOM) and the Biological Expression Language (BEL) as well as participating in the OBO Foundry community. From proximity to many of its members, I joined the ISB during the pandemic, quickly became involved in the planning of the 2022 virtual and 2023 in-person conferences, and was later awarded the 2023 Excellence in Biocuration Early Career Award. Throughout these experiences, I have developed many meaningful professional and personal connections.

There are two grand issues within the ISB and the wider biocuration community that I believe joining the ISB Executive Committee will help address. The first issue is to improve the outreach of the ISB further than the typical nexus around North American, British, and Swiss research institutes. This issue became apparent to me during my service as the Biocuration 2023 co-chair as we were ineffective at identifying and communicating to researchers outside of this bubble and there were no institutional tools available from the ISB to help. I would like to use my time on the ISB EC to develop such tools. The second issue is to promote the longevity and sustainability of curated resources. The ISB is enriched with members who provide key resources to the community, which in turn pose the highest risk with respect to longevity and sustainability. Therefore, I envision the ISB as an excellent platform through which to educate and enable progress towards these lofty goals. This might be accomplished through workshops, development of societal guidelines, partnerships with publishers, etc. Following my time as the Biocuration 2023 co-chair, I have the less grand goal to better support future Biocuration conference organizers, both in terms of preparing additional material as well as donation of my time. While I have already volunteered in this capacity for the Biocuration 2024 conference in India, I believe that I can better serve in that role as a liaison to the ISB EC.

No conflicts of interest.

Luana Licata

Assistant Professor and MINT database coordinator 

Department of Biology, Tor Vergata University of Rome, Rome, Italy

I work as Assistant Professor in the Department of Biology at the Tor Vergata University of Rome, Italy and I am the scientific coordinator of MINT, the Molecular INTeraction database (ELIXIR Core Data Resources). I have been working for over 16 years both as a curator and a team coordinator of MINT and I am directly involved in the curation of SIGNOR, a database that collects experimental verified causal relationships between biological entities. I have collaborated with other research groups in the development, organisation and/or curation of several Bioinformatics Resources such as, virusMINT, Complex Portal, DISNOR, CancerGeneNet. I am involved in the development of PSI-MI standards and controlled vocabularies (Molecular Interaction Ontology of the Proteomics Standard Initiative) to enable the exchange and integration of molecular interaction data and I am the Ontology coordinator of the HUPO Proteomics Standards Initiative (PSI), Molecular Interaction group.

I am a member of ELIXIR Italy Training Team which has the aim to produce quality training in bioinformatics in order to achieve excellence in life science research. I am also a trainer in Bioinformatics courses on Network Biology, Bioinformatics tools to study protein-protein interactions and Use of Standards, Controlled Vocabularies and Ontologies. I have experience in organising biocuration meetings and I am a member of the International Society of Biocuration (ISB) and I am a member of the Steering committee ELIXIR Biocuration Focus Group.

Since 2018, I am a member of the International Society of Biocuration (ISB), I am also a member of the ELIXIR Biocuration Focus Group Steering committee. I had been involved in several biocuration activities and I have experience in organising biocuration meetings. I would like to bring my experience to support ISB to promote biocuration activities and jobs in academia and industry (particularly needed in Italy) via, for example, high quality training  and University courses. I am also interested in identifying biocurator literature support tools to improve the quality of work.

No conflicts of interest.

Frederique Lisacek

Group Leader

Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, CH

PhD in Computer Science (Artificial Intelligence) from the University Pierre & Marie Curie, Paris, France in 1984. From 1985 to 1998, held research positions in biology labs in France, Japan and Australia working on knowledge representation and predictive methods based on sequence analysis. Successively worked in two biotech companies leading projects on knowledge management and mining in Proteome Systems Ltd in Sydney, Australia (1999-2000) and in Geneva Bioinformatics (GeneBio) S.A, Switzerland (2001-2005). Joined the SIB Swiss Institute of Bioinformatics in the Proteome Informatics Group in 2006. Manages the group since 2008 driving knowledge discovery projects in proteomics and glycomics. Specialised in glycoinformatics since 2010.

Having been recruited in Geneva by Amos Bairoch  in 2001, I need not explain how familiar I have been with biocuration and its evolution over the past decades. My input has been steady over that period but not in the forefront; it encompasses contributions to text mining methods, ontology definition and database development. Since 2010, I have specialised in glycoscience a source of many bioinformatics challenges, somehow a niche research topic though slowly but surely expanding. Our issues span data standardisation, formalisation, and curation. Our community struggles to produce reliable computational solutions for we need to handle the sparsity and the heterogeneity of glycodata.

Chairing the scientific committee of Biocuration23 gave me the opportunity to take a broader view on data curation and interact more extensively with a diversity of biocurators. It also occurred to me more clearly that dissemination and reinforcement of biocuration requires constant and long-term effort. The team spirit that I shared with the Biocuration23 committees has convinced me that I could partake in pursuing the needed constructive endeavours within the Executive Committee. I could simply contribute my experience and energy.

No conflicts of interest.

Saurabh Raghuvanshi

Professor

Department of Plant Molecular Biology, University of Delhi South Campus, Benito juarez road, New Delhi-110021, India

With a background in plant molecular biology I had ventured in plant genomics and bioinformatics. I concentrated on doing pioneering work in establishing the genome level data analytics expertise at national level by working in the rice genome project, which was the first genome sequencing project of India. This was followed by the first microbial genome (mycobacterium indicus pranii) and several EST sequencing projects. Also actively participated in the Rice Annotation Project (RAP) jamboree (meeting in Tsukuba, Japan). Subsequently, as a proof of concept, our group developed data digitization models for experimental data from published research articles. These models use an organized multi-tiered schema of ontologies to digitize data from over 150 different experimental techniques. Continuing further towards increasing the national level competence, I worked as the project lead to establish the first life science data center in India i.e. the Indian Biological Data Center (ibdc.rcb.res.in).

On the other hand our group also works extensively on global miRNA mediated regulatory schemas with a combination of molecular biology and data analytics techniques.

We are further venturing towards developing AI/ML based dynamic regulatory models for miRNA mediated regulatory networks as well as developing predictive models to aid precision breeding.

The capacity to integrated various biological data sets is critical to generate knowledge and understand any organism at the ‘systems’ level. Globally, extensive efforts are done to develop systems that can integrate curate and analyze biological data sets. I would like to create emphasis on methods and schemas that will enable complete and semantic digitization of all types of experimental data sets. Currently, only a portion of the published experimental data is in a computer discoverable format. Even if it is digitized, due to lack of uniformity over thousands of experimental technique the data requires lot of manual intervention (curation) to make it discoverable and be integrated in semantic fashion. Unless all published experimental data is (i.e. every data point) is made discoverable from all aspects that it represents we will continue to struggle to achieve ‘systems’ level understanding.

I would also like to continue my efforts to strengthen the field of data analytics and biocuration in India. It needs to be much better organized and strengthened so that the national capacity can also contribute to the global efforts to understand organisms and ecosystems at ‘Systems’ level. To this end I have been making efforts at various levels. I have introduced an ‘open-elective’ masters program on ‘Data Analytics and Biocuration’ at Delhi University. Further, started a series of National workshops entitled ‘National Symposium on Database Development and Biocuration’ (http://genomeindia.org/nsddb). The establishment of the Indian Biological Data Center (https://ibdc.rcb.res.in) is a major milestone to this end. Subsequently, hosting the 17th Annual International Biocuration Conference in India for the first time would prove to be very beneficial in consolidating efforts at national level as well as generating an organic connect with the international community.

No conflicts of interest.

Leonore Reiser

Principal Biocuration Scientist

Phoenix Bioinformatics

I received my PhD in Plant Biology from UC Berkeley under the supervision of Dr Robert Fischer and completed a post doc in Plant Genetics under the supervision of Dr Sarah Hake. After completing my post doc I joined the staff of the Arabidopsis Information Resource (TAIR). As one of the founding curators I helped with the design of the database and UI for this database that serves a global community.  I was part of the initial effort to integrate plants into the Gene Ontology and early integration leading to the Plant Ontology. I spent about a decade working  on DEI programs in science at the Carnegie Institution of Science, the Molecular Sciences Institute and UC Berkeley while still maintaining my connection to TAIR as an occasional consulting curator. I returned to TAIR full time 8 years ago and continue to work primarily in the area of literature curation. I also serve as a co-PI on the AgBioData RCN and as a managing editor for the Arabidopsis section of microPublication.

My primary motivation is to increase representation of plant sciences within the ISB and promote more interactions/collaborations with plant biocurators and DBs. Many of the goals of our AgBioData RCN are relevant to biological databases in general (FAIRificaiton of data, definition of metadata and data standards, education and database sustainability.)

I serve as a managing editor for microPublication Biology, I am a co-PI of the AgBioData RCN and serve on several of the working groups. I am a full time curator for TAIR and a working mother.

TBK Reddy

Genomic Standards Group Lead

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

As a resolute and passionate member of our esteemed society, I consistently demonstrated an unwavering commitment to the field of biocuration, including building and maintaining biological databases over the last 20+ years, enhancing scientific data quality, metadata standards and accessibility.
For the last 12 years I have been leading the Genomic Standards Group at the DOE Joint Genome Institute and maintaining Genomes OnLine Database (GOLD), a metadata management system for genome and metagenome projects from around the world. We develop and apply metadata standards, controlled vocabularies, standardized naming for metagenome samples and promote its use in the research community. We ensure the data we put in the public domain adheres to the standards and train students in metadata curation.

Starting with my postdoctoral project to run initial annotation of Dictyostelium discoideum genome and find analogs of human disease-causing genes in early 2001, I continued working in the biocuration field till date. My work and experience at the Mouse Genome Informatics (The Jackson Laboratory 2003-2008), Tuberculosis Database (Stanford School of Medicine 2008-2011) and GOLD (DOE Joint Genome Institute 2011 – current) provided me an opportunity to work on different aspects of biocuration as well as in the design and development of biological databases by interfacing between biologists, biocurators and software developers. In my role as a Scientific Data Curator, I have been responsible for the meticulous curation of complex biological data, ensuring accuracy, consistency, and compliance with established standards. Collaborating closely with multidisciplinary teams, I have spearheaded efforts to enhance data sharing and accessibility, bridging the gap between researchers and valuable information resources. I often describe my role as a translator of English to English at biological databases, to ensure clear communication between biologists, biocurators and software developers to get things done in an efficient manner.

I not only did hands on data curation, developed SOPs, trained career biocurators as well as high school and undergraduate student interns. With a deep-rooted passion for advancing the field of biocuration, I have contributed significantly to the development and implementation of innovative strategies that foster data integrity and dissemination.

My ability to connect with individuals from diverse backgrounds and disciplines makes me an ideal candidate for Executive Committee Member.
 
By serving on the Executive Committee of the ISB, I am dedicated to driving the organization’s mission to enhance the practice of biocuration globally. Through collaborative initiatives, strategic planning, and thought leadership, I am committed to elevating the role of biocuration in scientific research and discovery.

I plan to continue promoting training the next generation of Biocurators as well as promoting biocuration as a career choice. I will be a steadfast advocate for the interests of our members and a proactive contributor to shaping the future of biocuration to strengthen the foundation of our society and pave the way for continued progress and excellence in the field of biocuration.

No conflicts of interest.

Peter Uetz

Associate Professor

Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA

While I was a graduate student at EMBL (Heidelberg, 1993-1997) I witnessed the internet and the web pop into our lives. Although I was trained as a molecular biologist (sequencing a gene as a master’s student and studying protein function as a grad student), I have always been interested in biodiversity research. So, I took the opportunity and started the “EMBL Reptile Database” (now without the “EMBL” part) and later the Microbial Protein interaction database, still curating the former after nearly 30 years.

Officially, my lab has studied protein function until about 2020, mainly protein interaction networks, but after obtaining tenure I gave up the wet-lab work and now mostly work on taxonomic data (although I still teach a lab class on functional genomics).

Biocuration is a critical but undervalued part of the biomedical sciences. We need to strengthen its role in science and society at large, given the critical importance of data. I have had various roles and positions, ranging from database curator, citizen science advocate (e.g. iNaturalist), teacher, and meeting co-organizer (ISB, various herpetological societies), so I think I am in a good position to help develop ISB further. I also believe that my experience with a broad range of topics, from basic science to medical applications will help (I have had the genomes of most of my family members sequenced, after all 🙂

No conflicts of interest.

Annual General Meeting October 18, 2023

The slides, minutes and recording of this meeting can be found here.

You are invited to a virtual Annual General Meeting of the International Society for Biocuration on Wednesday, 18 October. The meeting will include presentations by our two biocurator career award winners, Nico Matentzoglu and Charlie Hoyt.

Time: 5 pm CET / 4 pm BST / 8 am PT / 11 pm ET

Please fill out this form to register to attend and receive the zoom meeting link. NOTE this meeting will be recorded, by attending the meeting you are agreeing to be recorded. The recording will be available on the ISB website after the meeting.

Program (CET times)

5.00pm Ruth Lovering (ISB EC Chair): ISB Annual General Meeting 

5:30pm Open for questions and suggestions from attendees

5:45pm Nico Matentzoglu, Excellence in Biocuration, Advanced Career Award

Presentation title: Closing the gap between effective Biocuration and meaningful ontology evolution

6:10pm Charlie Hoyt, Excellence in Biocuration, Early Career Award

Presentation title: Democratizing Biocuration, or, How I Learned to Love the Drive-by Curation

Presentation Abstracts

Nico Matentzoglu, Excellence in Biocuration, Advanced Career Award

Presentation title: Closing the gap between effective Biocuration and meaningful ontology evolution

Effective Biocuration is dependent on controlled
vocabularies such as biomedical ontologies. From the perspective of
biocurators, it is of central importance to get new terms integrated into the
ontology as soon as they are needed. From the perspective of the users who want
to exploit the ontology for analysing their data, however, it is key that the
integrated term is carefully curated into the ontological structure, which is
difficult and time-consuming. This provides a dilemma for ontology developers
who, on the one side, are expected to respond quickly to curation requests, but
on the other side are tasked to provide a reliable resource for the community.
In this talk, I will describe a strategy based on change languages, design
patterns and templates that could be used to “outsource” some of the ontology
curation to biocurators, thereby creating a drastically reduced effort and
subsequently much tighter turnaround time for new (and changed) term requests.
I will discuss the importance of such community contributions to open ontology
projects and hope to convince the biocuration community to engage more closely
with the ontology curation process.

Charlie Hoyt, Excellence in Biocuration, Early Career Award

Presentation title: Democratizing Biocuration, or, How I Learned to Love the Drive-by Curation

Abstract: The increasing reliance of artificial intelligence applications in biomedicine on reliable structured data, metadata, and knowledge accentuates the need for effective, sustainable biocuration. While there has been a historical disconnect between such consumers and biocurators, the looming paradigm shift towards the open code, open data, and open infrastructure (O3) principles presents an opportunity to engage and empower consumers to contribute to the maintenance and ongoing development of the resources they use. In this talk, I will reflect on how biocuration became an important facet of my job as a systems and networks biologist interested in translational research as I became more aware of the importance of data quality and provenance. Notably, I will highlight the concept of the drive-by curation and how it fits into a more community-oriented future vision for biocuration.

Highlights from Biocuration Careers Workshop

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 
  1. 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?
  1. 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

Excellence in curation – Early Career Award Nominees

Voting will be from 26th July to 25th August 2022

Four biocurators have been nominated for this award. As an ISB member you are invited to vote for one of the nominees described below. If you are an ISB member and did not receive an invite, please send an email to: isb@biocurator.org.

The winner of the Early Career Award will be awarded a prize of 500CHF and will give a 15 minute talk at a virtual ISB conference. In addition, they will have agreed to give their name, bio and photograph included on the ISB website, newsletter (circulated via the ISB distribution list) and twitter account.

Lauren Chan, Oregon State University, Corvallis, OR, USA.

Lauren Chan is a Nutrition PhD Candidate with three years of experience in biomedical ontologies under the supervision of Melissa Haendel. Lauren’s educational background is focused in nutrition and dietetics, which she leverages in her work focused on investigating nutrition and environmental exposure impacts on disease. Lauren is a regular contributor to a variety of OBO Foundry ontologies including the Food Ontology, Compositional Dietary Nutrition Ontology, and Mondo Disease Ontology. Her work has been integral for quality improvement of existing ontology content, as well as creation of essential hierarchies focused on nutrition and environmental exposures.

Lauren is a lead curator for the Environmental Conditions, Treatments, and Exposures Ontology (ECTO) She conducts this effort as a part of the Monarch Initiative, and she is working towards integration of exposure content with disease and phenotype information within the Monarch knowledge graph. She is also a passionate collaborator, working with multiple international, interdisciplinary teams on curation projects.

Lauren is an active member of a variety of biocuration community efforts, including serving as a Program Committee Member for ICBO 2021, and as a Coordinating Team Member for the 2021 and 2022 Integrated Food Ontology Workshops (IFOW). Her commitment to learning and the dissemination of knowledge benefits the biocuration community, and also individuals in the nutrition community who are eager to harness opportunities using biomedical ontologies.

While she is still early in her career, it is evident that Lauren has and will continue making meaningful impacts to the biocuration field and exposure sciences.

  • Chan, L., Thessen, A., Duncan, W. D., Matentzoglu, N., Schmitt, C., Grondin, C., Vasilevsky, N., McMurry, J., Robinson, P., Mungall, C. J., & Haendel, M. (2022). The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): Connecting Toxicology and Exposure to Human Health and Beyond. https://doi.org/10.5281/zenodo.6360645 (submitted for the ICBO 2022 conference and proceedings).
  • Chan, L., Vasilevsky, N., Thessen, A., Matentzoglu, N., Duncan, W., Mungall, C., & Haendel, M. (2021). A semantic model leveraging pattern-based ontology terms to bridge environmental exposures and health outcomes. CEUR Worshop Proceedings. This paper was presented at ICBO 2021 and published in the 2021 ICBO Conference Proceedings.
  • Andrés-Hernández, L., Blumberg, K., Walls, R. L., Dooley, D., Mauleon, R., Lange, M., Weber, M., Chan, L., Malik, A., Møller, A., Ireland, J., Segovia, L., Zhang, X., Burton-Freeman, B., Magelli, P., Schriever, A., Forester, S. M., Liu, L., & King, G. J. (2022). Establishing a Common Nutritional Vocabulary – From Food Production to Diet. Frontiers in Nutrition, 9. https://doi.org/10.3389/fnut.2022.928837
  • Chan, L., Vasilevsky, N., Thessen, A., McMurry, J., & Haendel, M. (2021). The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research. Database: The Journal of Biological Databases and Curation, 2021. https://doi.org/10.1093/database/baab003
  • Dooley, D., Andrés-Hernández, L., Bordea, S., Carmody, L., Cavalieri, D., Chan, L., Castellano-Escuder, P., Lachat, C., Mougin, F., Vitali, F., Yang, C., Weber, M., Kucuk McGinty, H., & Lange, M. (2021). OBO Foundry Food Ontology Interconnectivity. CEUR Workshop Proceedings.

Shirin Saverimuttu, SciBite Limited, Cambridge, UK.

Shirin started her biocurator career with a MSc project at University College London (UCL) in 2019 and then as a Gene Ontology (GO) biocurator at UCL. In addition to her biocurator role, Shirin supervised the next cohort of MSc students, checked their annotations, and provided them useful and supportive feedback. During this time, Shirin identified the need for a decision tree to support more consistent annotation of microRNAs and was involved in developing this resource.

Shirin is quick to grasp scientific concepts and the variety of different projects she has undertaken demonstrates her ability to apply herself.  During her time at UCL she was awarded a COST grant to exchange ideas about microRNA annotation with Dr Panni, in Italy. Additionally, she has worked as both an intern and scientific curator at EMBL-EBI for the PGS and GWAS Catalogs and is now at SciBite.

Having only been in SciBite for 7 months, Shirin has quickly understood the complexities of the role and the software required to perform her tasks. She has worked on tricky customer projects with patience and confidence. Shirin is keen to take on new challenges and has a great attention to detail in her work and often volunteers to undertake tasks that are tedious or unpopular. Shirin participated in the UK local Biocuration Conference “FAIR” workshop in May 2022 and presented a clear and knowledgeable talk on how SciBite creates FAIR data.

Although Shirin is an early career biocurator, she is already showing a maturity in her attitude to her work and will continue to grow and be an asset to the biocuration community.

  • Talk presented by SCC Saverimuttu at the “FAIR Data and Ontologies in Industry” workshop at the UK-local Biocuration Conference in May 2022, Wellcome Genome Campus, Hinxton: “FAIR at SciBite”.
  • Saverimuttu SCC, Kramarz B, Rodríguez-López M, Garmiri P, Attrill H, Thurlow KE, Makris M, de Miranda Pinheiro S, Orchard S, Lovering RC. Gene Ontology curation of the blood-brain barrier to improve the analysis of Alzheimer’s and other neurological diseases. Database (Oxford). 2021 Oct 26;2021:baab067. PMID: 34697638.
  • Kramarz B, Huntley RP, Rodríguez-López M, Roncaglia P, Saverimuttu SCC, Parkinson H, Bandopadhyay R, Martin MJ, Orchard S, Hooper NM, Brough D, Lovering RC. Gene Ontology Curation of Neuroinflammation Biology Improves the Interpretation of Alzheimer’s Disease Gene Expression Data. J Alzheimers Dis. 2020;75(4):1417-1435. PMID: 32417785.
  • Gene Ontology Consortium, The Gene Ontology resource: enriching a GOld mine, Nucleic Acids Research, 2021, 49(D1), D325-D334. PMID:33290552.
  • Poster presented by Shirin Saverimuttu at the CompBioMed conference 2019, London: Saverimuttu SCC, Kramarz B, Lovering RC. “Describing the role of microRNAs in Alzheimer’s disease using a bioinformatic approach”.

Mahima Vedi, Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA.

My career as a biocurator started at the Rat Genome Database (RGD) in 2020. I have a Ph.D. in Pharmacology and Toxicology, and my educational background helped me learn how to read scientific literature and capture important details. Following a comprehensive mentorship with senior curators, I now play an essential role in conducting data curation into the RGD database for genes to disease, phenotype, gene function, biological process, cellular component, pathways and interactions, and drug/chemical interactions. This is in addition to rat strain disease and phenotype association curation. This rigorous manual literature review and curated data input is the foundation for building the RGD dataset. However, arguably my most crucial role at RGD is in community outreach by handling RGD social media accounts and presenting research work at different scientific conferences. In the past two years, I’ve presented posters and oral presentations at the GLBio-21, Rat Genomics and CTC meeting-21, Virtual Research Week at MCW-21, and Swine in Biomedical Research Conference-22 for RGD.

  • Vedi M, Nalabolu HS, Lin CW, Hoffman MJ, Smith JR, Brodie K, De Pons JL, Demos WM, Gibson AC, Hayman GT, Hill ML, Kaldunski ML, Lamers L, Laulederkind SJF, Thorat K, Thota J, Tutaj M, Tutaj MA, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses. Genetics. 2022 Apr 4;220(4):iyac005. doi: 10.1093/genetics/iyac005. PMID: 35380657; PMCID: PMC8982048
  • Kaldunski ML, Smith JR, Hayman GT, Brodie K, De Pons JL, Demos WM, Gibson AC, Hill ML, Hoffman MJ, Lamers L, Laulederkind SJF, Nalabolu HS, Thorat K, Thota J, Tutaj M, Tutaj MA, Vedi M, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. The Rat Genome Database (RGD) facilitates genomic and phenotypic data integration across multiple species for biomedical research. Mamm Genome. 2022 Mar;33(1):66-80. doi: 10.1007/s00335-021-09932-x. Epub 2021 Nov 5. PMID: 34741192; PMCID: PMC8570235
  • Gene Ontology Consortium, The Gene Ontology resource: enriching a GOld mine, Nucleic Acids Research, 2021, 49(D1), D325-D334. https://doi.org/10.1093/nar/gkaa1113
  • Vedi M, Sabina EP. Assessment of hepatoprotective and nephroprotective potential of withaferin A on bromobenzene-induced injury in Swiss albino mice: possible involvement of mitochondrial dysfunction and inflammation. Cell Biol Toxicol. 2016 Oct;32(5):373-90. doi: 10.1007/s10565-016-9340-2. Epub 2016 Jun 1. PMID: 27250656

Samuel Rund, Center for Research Computing, University of Notre Dame, IN, USA.

Dr. Rund is one of several VectorBase staff members who facilitate the biocuration of international arbovector bioinformatic and ecoinformatic  data, assist and mentor data donors, and instruct end users of new features and datasets in VectorBase in person and via webinar. More generally Dr. Rund has helped develop minimal information standards on depositing arthropod disease vector occurrence records, and through talks and symposium organizing encouraged the deposition of data. 

  • Rund, S.S.C., Moise, I.K., Beier, J.C.,Martinez, M.E. ** (2019). Rescuing troves of data to tackle emerging mosquito-borne diseases. Journal of the American Mosquito Control Association. 35:75-83.
  • Giraldo-Calderón GI, Harb OS, Kelly SA, Rund SSC, Roos DS, McDowell MA. (2021) VectorBase.org updates: bioinformatic resources for invertebrate vectors of human pathogens and related organisms. Current opinion in insect science. Dec 3.
  •  Rund, S.S.C. et al. (2019)MIReAD, a minimum information standard for reporting arthropod abundance data.  Nature Scientific Data. 6:40
  • (Magazine article) Lord, C., Bayer, B., Carlson, D., Rogers, A., Smith, R., Rund, S.S.C.  The collection and public dissemination of mosquito abundance data: Perspectives and options. (2019) WingBeats.
  •  “The collection and public dissemination of mosquito abundance data: Perspectives and options.” American Mosquito Control Association annual meeting. San Diego. Co-organizer. February 2017.

1st UK-local Biocuration Conference Travel Fellowship Applications

The International Society for Biocuration and the 1st UK-local Biocuration Conference invite current ISB members to apply for Travel Fellowships to attend this year’s conference at the Wellcome Genome Centre, Hinxton.

Apply for Travel Fellowship here

Details

We are pleased to provide current ISB members with a travel fellowship opportunity. We intend to support up to 2 applicants. Students and junior curators are encouraged to apply. Selections will be prioritized by financial need.

Please note that applying for a fellowship does not guarantee that you will receive funding.

Awards

Each award will be issued as reimbursement for up to £500 per fellowship depending on the costs of your registration and travel (e.g. hotel, flight, and ground transportation). 

  1. ISB Travel Fellows must be able to cover their own conference registration fees and travel cost before attending the conference. ISB Travel Fellows will then submit receipts to request a reimbursement from ISB. Save your receipts! 
  2. A traveller’s check, or a bank transfer for up to £500 – depending on your registration and travel costs – will be arranged for ISB Travel Fellows.
  3. The Biocuration Travel Fellowships Committee will advise you on how to receive these funds as reimbursement at the end of the conference.

Requirements and Procedures

Each applicant for a travel fellowship must satisfy the following conditions:

  1. The applicant must be an active ISB member.
  2. The applicant must have been selected for a poster or oral presentation at the 1st UK-local Biocuration Conference.
  3. Only the presenting author from a multi-author abstract may apply for a fellowship.
  4. The applicant must submit an accompanying letter explaining why they are requesting travel funds and how they envision that attending the Biocuration Conference will benefit their career.

Application Deadline: application form must be submitted on or before 16th March 2022.

Submit an abstract – Before submitting your travel fellowship application

A condition of the award is that a successful applicant agrees to provide a photograph of themselves and a brief summary of the work they presented and their experience of the conference. The photograph and extracts from their summary will be made public on the ISB website and circulated by email to the ISB distribution list.  

Notification of award will be sent via email by 20th March 2022 and announced on the ISB website after acceptance of the award.

If the event is cancelled – full registration fee refunds will be issued. However, please ensure that any bookings you make for accommodation and travel are fully refundable, as it is possible that this meeting will be cancelled at the last minute. The organisers will not cover any financial losses due to cancellations.

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