Demo Data from EDBT 2026 / reviewers in the wild / expert
Xavier Watkins
dblp:122/2323
· DBLP profile ↗
3ranked-venue papers
1as first author
1since 2021 · last 2023
0000-0001-9327-5887ORCID · corroborated
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
3 papers |
Bioinformatics and computational biology · 100% | |
| Databases, data mining, and information retrieval
1 paper |
Data integration and cleaning · 50% Query processing and optimization · 50% |
Topics — the 5 heaviest of 7, 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
biological data visualization |
0.3 | 1 | 2017 | ProtVista: visualization of protein sequence annotations · Bioinform. 2017 |
Bioinformatics and computational biology › data integration
biological data integration |
0.1 | 1 | 2012 | InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data · Bioinform. 2012 |
Bioinformatics and computational biology › biological database
protein database |
0.1 | 1 | 2017 | ProtVista: visualization of protein sequence annotations · Bioinform. 2017 |
Data integration and cleaning
heterogeneous data integration |
0.0 | 1 | 2012 | InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data · Bioinform. 2012 |
Methods — techniques the papers use, named apart from their topics
ontology-based annotation · 0.7SPARQL querying · 0.7web services · 0.3javascript · 0.3
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2023 | Annotation of biologically relevant ligands in UniProtKB using ChEBIabstractMOTIVATION: 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. | 98 |
| 2017 | ProtVista: visualization of protein sequence annotationsabstractSUMMARY: ProtVista is a comprehensive visualization tool for the graphical representation of protein sequence features in the UniProt Knowledgebase, experimental proteomics and variation public datasets. The complexity and relationships in this wealth of data pose a challenge in interpretation. Integrative visualization approaches such as provided by ProtVista are thus essential for researchers to understand the data and, for instance, discover patterns affecting function and disease associations. AVAILABILITY AND IMPLEMENTATION: ProtVista is a JavaScript component released as an open source project under the Apache 2 License. Documentation and source code are available at http://ebi-uniprot.github.io/ProtVista/ . CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Xavier Watkins, Leyla Jael Castro, Sangya Pundir, Maria Jesus Martin |
Bioinform. | 1 |
| 2012 | InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological dataabstractSUMMARY: InterMine is an open-source data warehouse system that facilitates the building of databases with complex data integration requirements and a need for a fast customizable query facility. Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for easy integration of new data types. The analysis tools include a flexible query builder, genomic region search and a library of 'widgets' performing various statistical analyses. The results can be exported in many commonly used formats. InterMine is a fully extensible framework where developers can add new tools and functionality. Additionally, there is a comprehensive set of web services, for which client libraries are provided in five commonly used programming languages. AVAILABILITY: Freely available from http://www.intermine.org under the LGPL license. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Richard N. Smith, Jelena Aleksic, Daniela Butano, Adrian Carr, Sergio Contrino, Fengyuan Hu, Mike Lyne, Rachel Lyne, Alex Kalderimis, Kim Rutherford, Radek Stepan, Julie M. Sullivan, Matthew Wakeling, Xavier Watkins, Gos Micklem |
Bioinform. | 14 |