2022 EC election

The election of four members of the International Society for Biocuration Executive Committee (ISB EC) will be held from September 26 – October 03, 2022.

Emails will be sent to current members on 26th September. Only current members, as of 20 September 2022, 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 six candidates for agreeing to stand for election to the Executive Committee (EC). The ISB success is reliant on many ISB volunteers, including those on the EC.

Stephen Piccolo, Associate Professor

Brigham Young University, USA

I am a principal investigator at an institution that is focused primarily on undergraduate education. However, I also supervise graduate students. My research touches on four primary areas: 1) analysis of genomic and transcriptomic data, 2) using machine-learning to predict patient outcomes, 3) building software tools that make it easier for non-computational biologists to work with biological data, and 4) curating publicly available, transcriptomic datasets (and accompanying metadata). Regarding the latter areas, I am particularly interested on methodologies for restructuring, standardizing, and annotating datasets (a huge unmet need for public datasets). In terms of service activities, I have been on conference organizing committees, reviewed lots of papers and some grants, and have led academic committees at my university.

Although I am not a biocurator in the traditional sense, I am passionate about curating publicly available biological data and making it easier for researchers to navigate the world of publicly available data. My lab is building tools and methodologies that aim to improve this process. In addition, we have published papers that describe curated versions of transcriptomic data. One of these, in particular, has been highly used (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944). I could be wrong, but it seems that this type of work is less emphasized in the ISB community than other types of work. I see myself as being a reliable contributor to committee-based work. I am a listener more than a speaker, but I am willing to speak up when needed. I am willing to do whatever types of tasks would be most helpful. I have Web-development skills and have worked with WordPress, though I am definitely not an expert. Depending on the needs, I might be able to help in that area.

I have no conflicts of interest or competing commitments to declare.

Marc Gillespie, Vice Provost

Reactome, USA

I am currently the Vice Provost for Graduate Education, Clinical Operations and Research, and Assessment serves as a senior staff member in the Office of the Provost at St. John’s University Queens, USA. I earned my doctorate in Oncological Sciences from the University of Utah in 1998 and was a research fellow at Memorial Sloan Kettering Cancer Center. I am a molecular biologist, bioinformaticist, and toxicologist, leading a research group working in pharmacogenomic biomarker discovery. I have published research papers on topics including molecular toxicology RNA biology, and SARS-CoV-2 pathway curation and am an Adjunct Professor in the Department of Biochemistry and Molecular Pharmacology at the NYU Langone Health New York University Grossman School of Medicine, and a Biocurator and Editor on the Reactome project, an open-source, open-access, manually curated, and peer-reviewed biological pathway database supported by the National Institutes of Health, European Molecular Biology Laboratory, and Ontario Institute of Cancer Research. I joined St. John’s faculty in the Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, in 2000.

Since starting at Reactome in 2003 I have learned, lead, explored, and pushed biocuration alongside a fantastic team of curators, developers, researchers, and leaders. My experience with the field has developed in parallel with the ISB itself. Quite frankly, I think we [biocurators] should all be interested in some aspect of the ISB, from the Executive Committee, to planning meetings and involving ourselves in education and research. Throughout my career I have been lucky to spend much more time listening than speaking. As a Vice Provost, I spend a great deal of my time listening to different constituencies all of which are interested in the success of the venture, but may have other ideas as to how to improve. I think that the ISB like many organizations needs responsive leadership that can listen, lead, and succeed. That is what I bring to the committee.

No conflicts of interest.

Raul Rodriguez-Esteban, Senior Principal Scientist, Swiss Resident

Roche Pharmaceuticals, Switzerland

Raul Rodriguez-Esteban is Senior Principal Scientist at Roche Pharmaceuticals in Basel, Switzerland, where he works on text mining workflows and biocuration of text mining results for applications in pharmaceutical R&D such as pharmacovigilance, target discovery and patient-reported outcomes. Previously, he worked in the Scientific Knowledge Discovery group at Boehringer Ingelheim and at the Knowledge Mining and Representation group at Pfizer Global R&D. He completed his PhD in automatic curation of text mining results at the laboratory of Andrey Rzhetsky at Columbia University. He was a winner of the Bio-IT World Innovative Practices Award in 2020.

My work is at the intersection of biocuration and text mining. Because the outcome of text mining applications almost always requires manual curation, I am versed both in the curation of text mining results and in automatic strategies to reduce curation burden. The main work of my doctoral thesis centered on the reduction of curation workload and was published under the title “Imitating manual curation of text-mined facts in biomedicine.” Later, I summarized my thinking on curation trade-offs in resource-constrained curation efforts in my publication “Biocuration with insufficient resources and fixed timelines.” Throughout the rest of my published work, curation has had an important role, paired with the use of text mining workflows. This reflects my everyday work in a pharmaceutical company. I believe I could bring this experience to the ISB EC, particularly from the perspective of an industry setting with evolving needs. As member of the ISB EC, I would promote the cross-pollination of traditional manual curation and semi-automatic curation approaches. Additionally, my daily work covers a broad scope of text sources, from patents, to full-text articles, to EHRs and to social media posts. For the analysis of the latter, I led a team that won the Bio-IT World Innovative Practices Award in 2020. Because of my experience, I would see of particular interest to highlight and promote work that focuses beyond the most traditional text sources for biocuration, which present their particular set of challenges. (Additionally, as encouraged to be reported in the announcement, I have programming and web development skills.)

I am an employee of the pharmaceutical company F. Hoffmann-La Roche Ltd. I am editorial board member of the journal BMC Digital Health.

Ruth Lovering, Biocuration Professor 

University College London (UCL), UK

I have been participating in the annotation of the human genome for over 20 years at UCL with a focus on the manual Gene Ontology (GO) annotation of human genes. I am in an unusual position, of having created a small annotation group, within a university environment, with a focus on the annotation of genes that contribute to human disease. My biocuration experience started at the HUGO Gene Nomenclature Committee (HGNC), following 12 years of bench genetic research studying Drosophila and then human immune genes. Although, not working within a large curation group or bioinformatics institute, I have very close links with EMBL-EBI, the GO and the IMEx Consortia. A few years ago I was promoted to Professorial Research Fellow, possibly one of the first biocurators to be awarded this title, weirdly, I felt like this was recognition not just for my work but also recognition of the importance of the work contributed by all biocurators.

I can confirm that I have no affiliation or relationship that prevents me from performing duties as a member of the Executive Committee of the International Society for Biocuration, should I be elected. I am a member of International Society for Biocuration (ISB) and British Atherosclerosis Society neither of which would provide a conflict of interest. I understand that I must contact both the ISB and the Nomination Committee if a conflict exists or arises during my service.

Tarcisio Mendes de Farias, Computational biologist, Swiss Resident

SIB Swiss Institute of Bioinformatics, Switzerland

Dr Tarcisio Mendes de Farias is a computer scientist and engineer specialized in data and knowledge management, working as a computational biologist at the SIB Swiss Institute of Bioinformatics. Previously, he worked, first, as a R&D engineer in the French company Active3D, a subsidiary of Sopra Steria, and second as R&D product manager in the Dassault Systemes company. Via SIB, he was also a data integration and interoperability consultant for BASF, a leading company in the crop protection industry. He is currently working on academic and industry research projects involving data management applied to biological and biomedical data (e.g., orthology, gene expression, protein, cancer biomarker databases). His recent works in data management comprise the design and development of knowledge graphs and ontologies, natural language processing, and methods for data integration and interoperability among biological data sources. A full list of his scientific publications is available at https://purl.org/tarcisio/scholar.

Motivations: the ISB has been an important endeavor to promote the biocuration field. As a computational biologist at the Swiss Institute of Bioinformatics, I see all great work accomplished by ISB so far and fostered scientific collaborations in the past decades as consolidated opportunities to bring biocuration to the next level. That is, a more and more biocurator-center approach in order to help and facilitate the biocurators’ job and the consumers (e.g., researchers) of the curated data, information. Experiences with biocuration, intersections: I have been working in multiple projects in academia and industry involving data integration and semantic interoperability in biology (e.g., Bgee and OMA databases) and biomedicine (e.g., OncoMX database) that includes creating and maintaining standards. Among them, as an ontologist, I led the development of the second version of Orthology Ontology under the umbrella of the Quest for Orthologs community (see https://questfororthologs.org/standards). For your information, I had the occasion to participate in the Biocuration 2018 (Shanghai) and 2019 (Cambridge) conferences. Areas with ISB to see developed: with the increased amount of data and information to handle/process, biocurators urge the need for better tools and best research practices (e.g., access to FAIR data) that will ease and improve their high-quality work, for instance, better computer-assisted solutions. Therefore, as an ISB executive committee member I will stress the fact that we need to promote an interdisciplinary community engagement towards an approach where computer-aided solutions are adapted and serve biocurators (not the opposite!) to boost and enhance their work.

No conflicts of interest.

Susan Bello, Senior Scientific Curator

Mouse Genome Informatics, USA

I have been a curator for Mouse Genome Informatics for over 18 years. While my background was in oceanography and toxicology, I translated that experience into mouse phenotypes. I began by concentrating on curation of phenotypes and alleles developing an understanding of nomenclature standards and use of ontologies.  Over time, I moved into work on ontology development for the Mammalian Phenotype and Human Disease Ontologies. I’ve also been involved with website development, including the creation of the Human – Mouse: Disease Connection portal at MGI. With the advent of the Alliance of Genome Resources I worked as part of a team on the integration and harmonization of allele, phenotype and disease curation across species. This project has lately moved into the development of LinkML models to support curation needs across a wide range of species.

I have been a member of the ISB since 2009 and am running for a position on the ISB Executive Committee because I believe in the mission of the society and want to contribute to expanding the influence and reach of the society. I am interested in helping with the outreach and educational work of the society. I am interested in working to develop and improve the availability of training materials on the fundamentals and principles of biocuration. Increasing the visibility of the work of biocurators and improving the broader communities understanding of the importance of and value added by the work of biocurators will hopefully increase support for biocuration. I was a conference co-chair for the 2020 and 2021 Biocuration meetings, adapting the workshops planned for the 2020 meeting to a virtual format and developing the first virtual full meeting in 2021. I would like to bring what I’ve learned from these experiences to the work done by the EC.

No conflicts of interest.