Vivienne Baillie Gerritsen

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3ranked-venue papers

1as first author

1since 2021 · last 2023

—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 3 · 1 first-author · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing

2 papers

Bioinformatics and computational biology · 100%

Topics — the 2 heaviest of 3, each with the papers that count most for it

Topic	Weight	Papers	Last	Evidence papers
Bioinformatics and computational biology › protein analysis › protein bioinformatics protein annotation	0.7	1	2023	Annotation of biologically relevant ligands in UniProtKB using ChEBI · Bioinform. 2023
Bioinformatics and computational biology bioinformatics infrastructure	0.4	1	2020	The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences · Bioinform. 2020

Methods — techniques the papers use, named apart from their topics

ontology-based annotation · 0.7SPARQL querying · 0.7

Year	Publication	Venue	Position
2023	Annotation of biologically relevant ligands in UniProtKB using ChEBI abstract MOTIVATION: To provide high quality, computationally tractable annotation of binding sites for biologically relevant (cognate) ligands in UniProtKB using the chemical ontology ChEBI (Chemical Entities of Biological Interest), to better support efforts to study and predict functionally relevant interactions between protein sequences and structures and small molecule ligands. RESULTS: We structured the data model for cognate ligand binding site annotations in UniProtKB and performed a complete reannotation of all cognate ligand binding sites using stable unique identifiers from ChEBI, which we now use as the reference vocabulary for all such annotations. We developed improved search and query facilities for cognate ligands in the UniProt website, REST API and SPARQL endpoint that leverage the chemical structure data, nomenclature and classification that ChEBI provides. AVAILABILITY AND IMPLEMENTATION: Binding site annotations for cognate ligands described using ChEBI are available for UniProtKB protein sequence records in several formats (text, XML and RDF) and are freely available to query and download through the UniProt website (www.uniprot.org), REST API (www.uniprot.org/help/api), SPARQL endpoint (sparql.uniprot.org/) and FTP site (https://ftp.uniprot.org/pub/databases/uniprot/). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Elisabeth Coudert, Sebastien Gehant, Edouard De Castro, Monica Pozzato, Delphine Baratin, Teresa Batista Neto, Christian J. A. Sigrist, Nicole Redaschi, Alan J. Bridge, Lucila Aimo, Ghislaine Argoud-Puy, Andrea H. Auchincloss, Kristian B. Axelsen, Parit Bansal, Marie-Claude Blatter, Jerven T. Bolleman, Emmanuel Boutet, Lionel Breuza, Blanca Cabrera Gil, Cristina Casals-Casas, Kamal Chikh Echioukh, Béatrice A. Cuche, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Pascale Gaudet, Vivienne Baillie Gerritsen, Arnaud Gos, Nadine Gruaz-Gumowski, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Arnaud Kerhornou, Philippe Le Mercier, Damien Lieberherr, Patrick Masson, Anne Morgat, Venkatesh Muthukrishnan, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Sylvain Poux, Manuela Pruess, Catherine Rivoire, Karin Sonesson, Shyamala Sundaram, Alex Bateman, Maria Jesus Martin, Sandra E. Orchard, Michele Magrane, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett, Ramona Britto, Hema Bye-A-Jee, Austra Cukura, Paul Denny 0002, Tunca Dogan, Thankgod Ebenezer, Penelope Garmiri, Leonardo Jose da Costa Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Vishal Joshi, Dushyanth Jyothi, Swaathi Kandasamy, Antonia Lock, Aurelien Luciani, Marija Lugaric, Yvonne Lussi, Alistair MacDougall, Fábio Madeira, Mahdi Mahmoudy, Alok Mishra 0004, Katie Moulang, Andrew Nightingale, Sangya Pundir, Guoying Qi, Shriya Raj, Pedro Raposo, Daniel Rice, Rabie Saidi, Elena Speretta, James D. Stephenson, Prabhat Totoo, Edward Turner, Nidhi Tyagi, Preethi Vasudev, Kate Warner, Xavier Watkins, Rossana Zaru, Hermann Zellner, Cathy H. Wu, Cecilia N. Arighi, Leslie Arminski, Chuming Chen, Yongxing Chen, Hongzhan Huang, Kati Laiho, Peter B. McGarvey, Darren A. Natale, Karen E. Ross, C. R. Vinayaka, Qinghua Wang 0003	Bioinform.	28
2020	The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences abstract SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Rachel Drysdale, Charles E. Cook, Robert Petryszak, Vivienne Baillie Gerritsen, Mary Barlow, Elisabeth Gasteiger, Franziska Gruhl, Jerry Lanfear, Rodrigo Lopez, Nicole Redaschi, Heinz Stockinger, Daniel Teixeira, Aravind Venkatesan, Alex Bateman, Alan J. Bridge, Guy Cochrane, Robert D. Finn, Frank Oliver Glöckner, Marc Hanauer, Thomas M. Keane, Luana Licata, Per Oksvold, Sandra E. Orchard, Christine A. Orengo, Helen E. Parkinson, Bengt Persson, Pablo Porras, Jordi Rambla De Argila, Ana Rath, Charlotte Rodwell, Ugis Sarkans, Dietmar Schomburg, Ian Sillitoe, J. Dylan Spalding, Mathias Uhlen, Sameer Velankar, Juan Antonio Vizcaíno, Kalle von Feilitzen, Christian von Mering, Andy Yates, Niklas Blomberg, Christine Durinx, Johanna R. McEntyre	Bioinform.	4
2019	Bioinformatics on a national scale: an example from Switzerland abstract Switzerland has been a pioneer in the field of bioinformatics since the early 1980s. As time passed, the need for one entity to gather and represent bioinformatics on a national scale was felt and, in 1998, the SIB Swiss Institute of Bioinformatics was created. Hence, 2018 marks the Institute's 20th anniversary. Today, the Institute federates 65 research and service groups across the country-whose activity domains range from genomics, proteomics, medicine and health to structural biology, systems biology, phylogeny and evolution-and a group whose sole task is dedicated to training. The Institute hosts 12 competence centres that provide bioinformatics and biocuration expertise to life scientists across the country. SIB sensed early on that the wealth of data produced by modern technologies in medicine and the growing self-awareness of patients was about to revolutionize the way medical data are considered. In 2012, it created a Clinical Bioinformatics group to address the issue of personalized health, thus working towards a more global approach to patient management, and more targeted and effective therapies. In this respect, SIB has a major role in the Swiss Personalized Health Network to make patient-related data available to research throughout the country. The uniqueness of the Institute's governance structure has also inspired the structure of other European life science organizations, notably ELIXIR. Vivienne Baillie Gerritsen, Patricia M. Palagi, Christine Durinx	Briefings Bioinform.	1