Demo Data from VLDB 2026 / reviewers in the wild / expert
James D. Stephenson
dblp:254/3426
· DBLP profile ↗
2ranked-venue papers
1as first author
1since 2021 · last 2023
0000-0002-6427-5703ORCID · reported
Domains — the database's venue-derived domains; a paper can count in several
Applied, interdisciplinary, general and emerging computing · 2 · 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 3 heaviest of 4, 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
genomics |
0.4 | 1 | 2019 | VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations · Bioinform. 2019 |
Bioinformatics and computational biology › genome annotation
genomic variant annotation |
0.4 | 1 | 2019 | VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations · Bioinform. 2019 |
Methods — techniques the papers use, named apart from their topics
ontology-based annotation · 0.7SPARQL querying · 0.7web tool · 0.4
| 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. | 92 |
| 2019 | VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotationsabstractMOTIVATION: Understanding the protein structural context and patterning on proteins of genomic variants can help to separate benign from pathogenic variants and reveal molecular consequences. However, mapping genomic coordinates to protein structures is non-trivial, complicated by alternative splicing and transcript evidence. RESULTS: Here we present VarMap, a web tool for mapping a list of chromosome coordinates to canonical UniProt sequences and associated protein 3D structures, including validation checks, and annotating them with structural information. AVAILABILITY AND IMPLEMENTATION: https://www.ebi.ac.uk/thornton-srv/databases/VarMap. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. James D. Stephenson, Roman A. Laskowski, Andrew Nightingale, Matthew E. Hurles, Janet M. Thornton |
Bioinform. | 1 |