Recipient of the 2023 Excellence in Biocuration Early Career Award

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

Charles Tapley Hoyt, Laboratory of Systems Pharmacology Harvard Medical School, MA, USA

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.

Nico Matentzoglu – Recipient of the 2023 Excellence in Biocuration Advanced Career Award

Closing the gap between effective Biocuration and meaningful ontology evolution

Nico Matentzoglu, Monarch Initiative, Semanticly, Greece

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. 

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.

Announcement for 2023 winners of “Excellence in Biocuration Awards”

We are pleased to announce winners of “Excellence in Biocuration Award” for the year 2023 in two categories:

Charlie is in 3/4 profile playing a guitar with his mouth open singing into a mic with an orange covering. He is wearing a black t-shirt and orange slacks.

Early Career Award – Charles Tapley Hoyt, Laboratory of Systems Pharmacology Harvard Medical School, MA, USA

Charlie has been so amazingly busy in such a short amount of time. He is a Research Fellow at Harvard Medical School and the primary curator, developer, and maintainer of several community datasets and databases.These include Bioregistry, which promotes standardization of prefixes, CURIEs, and URIs when used to reference entities/concepts in the life sciences. He contributes to Biomappings, which provides mappings between named biological entities. He created Chemical Roles Graph, which curates mechanistic relations between small molecules and biological processes, pathways, and diseases in an ontological framework. He is a frequent contributor to other curated datasets, and promotes the concept of the Drive-by Curation and of progressive governance models to enable community curation and strengthen project sustainability.

Charlie actively contributes to community efforts; he is an active member of the OBO Foundry ontology community, focusing on promoting standardization of semantics, better curation and coding practices through continuous integration/continuous development and social workflows, promotes more granular attribution and explicit/transparent licensing to better enable reuse.

He contributes to standards development including the SSSOM standard, a simple standard for sharing ontology mappings that includes explicit semantics and provenance, and is a member of Biological Expression Language (BEL), a domain-specific language for representing causal, correlative, and associative relationships between biomedical entities as well as their associated contextual and provenance annotations.

He has mentored a large number of students at the Institute for Algorithms and Scientific Computing (SCAI) and is frequently available to lend support to public projects such as PyBEL and PyKEEN.

Charlie is actively engaged in the Biocuration community and co-chaired the most recent Biocuration 2023 conference in Padova, Italy and participated in the organizing committee of the Virtual Biocuration 2022 Conference. His charisma, enthusiasm and energy are invaluable to our community. His enthusiasm and energy are rare and he deserves to be celebrated.

Advanced Career Award – Nicolas Matentzoglu, Monarch Initiative, Semanticly, Greece

The head and shoulders of Nico appear in front of a background of blue sky and green trees. Nico is wearing a dark blue shirt.

Nico is celebrated in the bio-ontology and biocuration community as a passionate promoter of open science and a champion of curators and ontology editors. He generously shares his extensive knowledge of semantic and ontology engineering, and works tirelessly to drive complex collaborations involving many different stakeholders.

Nico co-leads the OBO Academy, which brings together extensive yet highly accessible training material on ontologies and related topics through collaboratively authored online material as well as curated seminars, tutorials, and courses. This material has been used extensively by many curators to help them master everything from ontology development to writing queries to retrieve biological data.

Thanks to Nico’s vision and technical oversight, the Ontology Development Kit (ODK) has enabled the editors of dozens of bio-ontologies to utilize powerful automated workflows for maintaining, QC-ing, and releasing their products with ease. The ODK has had a huge positive impact on ontology standardization.

Nico leads the development of the widely used Simple Standard for Sharing Ontological Mappings (SSSOM), involving years of painstaking standards work, driving consensus on key design and modeling issues. He also led the efforts to unify multiple phenotype ontologies (Mammalian (MP), Zebrafish (ZP), Human (HPO), Ontology of Biological Attributes (OBA) through common design patterns.

Nico has recruited and encouraged a diverse range of contributors (researchers, government officials, clinicians as well as ontology developers) to grow and unite our community, promote open science, and provide mentorship. He is the ultimate team player and demonstrates unwavering positive energy and dedication to our community.

Thank you to the Award subcommittee:

  • Nicole Vasilevsky
  • Parul Gupta
  • Susan Bello
  • Ruth Lovering

Many thanks to the ISB members for voting!

Pascale Gaudet and Sandra Orchard – Recipients of the 2023 Exceptional Contribution to Biocuration Award

It is our great pleasure to announce the recipients of the 2023 Exceptional Contribution to Biocuration Award, the voting this year resulted in a tie and thus we have two recipients:

Pascale Gaudet, Swiss Institute of Bioinformatics, Switzerland

Pascale Gaudet has worked in the biocuration field for over 19 years first at DictyBase and more recently NextProt and the Gene Ontology Consortium. Pascale is currently the GO Project Manager and oversees all editorial content. She has worked continually not only to improve the Gene Ontology structure and formalization, but also has driven the project to produce high quality phylogenetically inferred GO annotation using the PAINT annotation system. The PAINT annotations are much more specific than existing annotation from automated sources, because they can be refined on a family-by-family and even gene-by-gene basis. This system is now providing over 3.5 million annotation in the GOA annotation database.

Pascale is working constantly to refine legacy and dormant annotations across the ontology, and with multiple collaborating groups to refine the both ontology and annotation to ensure that both are fit for purpose. She is driving the coordination of overhauls in many areas of GO ontology including multi-species processes, transcription, chromatin remodeling, tacking each are with insight and attention to detail but never failing to see the bigger picture. She has been key to the communication between different interested groups and manages the numerous discussions with efficiency. This is work that almost every bench biologist depends on to some degree, but is largely unrecognized because it depends on thousands of incremental tasks that are not usually attributed or described in publications.

Sandra Orchard, EBI, Hinxton, Cambridge, UK

Sandra has worked tirelessly for the biocuration community for over 20 years. She is currently the Team Leader for Protein Function Content at UniProt (https://www.uniprot.org), and is therefore responsible for a major part of probably the most used biological database in the world. In this role, she also maintains two other key interfaces: the Complex Portal (https://www.ebi.ac.uk/complexportal) and the Enzyme Portal (https://www.ebi.ac.uk/enzymeportal/). Previously, Sandra led the IntAct molecular interaction database (https://www.ebi.ac.uk/intact) and managed the IMEx consortium of collaborating interaction databases. She has also been key in establishing standards within the proteomics community, and has made significant contributions to the InterPro database and the Gene Ontology. Sandra has always been a strong proponent of FAIR principles, education and the biocuration community: she has chaired and/or contributed to numerous biocuration-related committees; she established the first formal educational qualification in biocuration (PgCert at the University of Cambridge); and she has been a long-time supporter of the ISB, serving as treasurer from 2015-2018 and chair from 2018-2020. Sandra has published ~200 papers on biocuration methods, standards and databases, which serves as a measure of her impact and importance both to the biocuration community as well as to the researchers who depend on the many resources to which she has contributed.

Congratulations Pascale and Sandra!

Thank you to the Awards Committee:

  • Nicole Vasilevsky
  • Parul Gupta
  • Susan Bello
  • Ruth Lovering

Many thanks to ISB members for voting!

Posted in Uncategorized

2023 Travel Grant Awardees

Travel Grant Awardees – 16th Annual International Biocuration Conference

The ISB are pleased to award fellowships to the following six members to attend the forthcoming ISB conference. These grants help cover travel expenses associated with attending the conference e.g. accommodation, flights and ground transportation.

Congratulations to you all!

Yukie Akune is a postdoctoral bioinformatician in the Glycosciences Laboratory at Imperial College, London, UK directed by Professor Ten Feizi and Dr Yan Liu. Dr Akune and her collaborators at the Complex Carbohydrate Research Center in Atlanta, Georgia have developed the Carbohydrate micro-Array Analysis and Reporting Tool (CarbArrayART), for storing, processing and presenting glycan array data, as well as data submission to the international GlyGen glycan microarray repository that has been developed with her input. She is committed to establishing data-mining systemsin the field of glycan recognition including definitions of parameters for curation and annotation of published glycan microarray dataon diverse glycan-recognition systems in health and disease.
Shasank Sekhar Swain (post-doctoral researcher, Regional Medical Center (ICMR), Bhubaneswar, India) introduced a novel ‘hybrid drug’ concept using chemical conjugationbetween phytochemicals and clinically inactive or obsolete drugs during his doctoral research work. Currently, he is working on developing a greater number of potential hybrid drug candidates against bacteria, mycobacteria, cancer, etc. As an early-career research scientist in bioinformatics, he uses widely available computer-aided drug discovery platforms and bioinformatics tools to select the most drug-able hybrid drugs prior to synthesis and clinical experiments in order to reduce the resources and costs associated with traditional hit-and-trial drug discovery methods.
Dominik Martinat is a PhD student at the Department of Physical Chemistry of Palacky University in Olomouc, Czech Republic. The focus of his study is an integration of biomedical databases. The main project he participates in is MolMeDB (Molecules On Membrane Database).
Anna Spackova, is a PhD student at Palacky University in Olomouc, Czech Republic, Department of Physical Chemistry. Anna is also a bioinformatician and her research involves mainly tools connected to protein structure especially to protein tunnels, that link the surface with active sites of the protein. Her main focus is the the MOLEonline tool together with the ChannelsDB database.
Nishad Thalhath is a doctoral candidate in Information Science and a member of the Metadata Laboratory at the School of Library, Media and Information Studies, University of Tsukuba, Japan.His research interests include metadata standards, knowledge graphs, and (meta)data interoperability. Before becoming a doctoral student, he worked as a developer, engineer and consultant in various IT and ITES projects. He currently works as a part-time researcher in the Laboratory for Large-Scale Biomedical Data Technology, RIKEN Center for Integrative Medical Sciences, Japan, where he develops and manages the metadata and integration systems for omics data.
Karina Martinez, is a graduate student in the Bioinformatics and Molecular Biochemistry MS program at The George Washington University in Washington, DC and is a member of the GlyGen data management team. She is working on curating glycan expression levels in the presence and absence of disease from the literature. She expects this effort to result in a set of publicly available datasets designed for bioinformatic and machine learning applications. She is also working in the biomarker curation space to create a comprehensive dataset of glycan biomarkers which will present new opportunities for data mining.

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

Announcement for winners of “Excellence in Biocuration Awards”

We are pleased to announce winners of “Excellence in Biocuration Award” for the year 2022 in two categories:

Early Career Award – Shirin Saverimuttu, SciBite Limited, Wellcome Genome Campus Hinxton, Cambridge, UK

Shirin started her biocuration career in 2019 at University College London (UCL) as a Gene Ontology biocurator. As a biocurator at UCL, she focussed on the curation of microRNAs and helped to develop a resource for more consistent annotation of microRNAs. During this time, she helped master students with their annotation projects. After being awarded a COST grant she spent a week in Italy with Dr Panni, Università della Calabria, where she exchanged information about microRNA annotation. In late 2020, Shirin joined the Polygenic Score (PGS) Catalog at EMBL-EBI as an intern biocurator and got trained to identify suitable PGS publications and extract polygenic scores from them, along with relevant metadata, for inclusion in the PGS Catalog. Later, she continued to work as a full time biocurator for both the PGS Catalog and GWAS Catalog at EMBL-EBI. Since 2021, Shirin has been working at SciBite as a scientific curator. At SciBite, she is involved in developing ontologies for customers as well as updating SciBite’s pre-existing vocabularies. Shirin enjoys working as a biocurator and would like to thank the ISB community for this recognition.

Advanced Career Award – Antonia Lock, European Bioinformatics Institute, Hinxton, Cambridge, UK

Following a PhD in molecular biology, Antonia started her career as a curator at the PomBase database in 2011. From 2016, she split her time to work with the drug discovery company Healx. From 2020, she started working full time biocurator at UniProt. Antonia has enjoyed being part of a varied range of projects over her career from curating model and pathogenic organisms to human, drugs, and diseases, developing new procedures, encouraging community data submissions, and problem-solving data display and software specification. Antonia is proud to have developed standards to describe metadata for genome-wide HTP data sets, mapped controlled vocabularies to ontologies, and done ground-work curation for a genetic disorder with drugs currently in clinical trial. In all her roles she has promoted the efficient use of curated data by training users, students, and novice curators.

Thank you to the Award subcommittee:

  • Parul Gupta (Chair)
  • Ruth Lovering
  • Randi Vita
  • Caio Cesar De Carvalho
  • Rama Balakrishnan

          Many Thanks to ISB members for voting!

          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.

          Search by Categories