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.

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 standardsknowledge 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.

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.