q EC Election Candidates – 2023 – ISB (Biocuration)

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.

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