Demo Data from EDBT 2026 / reviewers in the wild / expert
Sangya Pundir
dblp:155/3974
· DBLP profile ↗
3ranked-venue papers
0as first author
1since 2021 · last 2023
0000-0003-4526-6833ORCID · corroborated
Domains — the database's venue-derived domains; a paper can count in several
Applied, interdisciplinary, general and emerging computing · 3 · 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
biological data visualization |
0.3 | 1 | 2017 | ProtVista: visualization of protein sequence annotations · Bioinform. 2017 |
Bioinformatics and computational biology › biological database
protein database |
0.1 | 1 | 2017 | ProtVista: visualization of protein sequence annotations · Bioinform. 2017 |
Methods — techniques the papers use, named apart from their topics
ontology-based annotation · 0.7SPARQL querying · 0.7javascript · 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. | 84 |
| 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. | 3 |
| 2014 | Ten Simple Rules for Running Interactive WorkshopsabstractDo you have a difficult problem to solve? Are you writing a grant proposal involving several stakeholders? Do you want to gather user feedback on a resource, tool, or service? Or perhaps you need to improve a process or way of working in a team? To address problems such as these, we recommend holding an interactive workshop. We find that the dynamic nature of such workshops encourages creative thought and can quickly yield ideas and solutions [1].
Our ten simple rules aim to empower you to design and lead your own successful interactive workshops. We define an “interactive workshop” as a structured set of facilitated activities for groups of participants who work together to explore a problem and its solutions, over a specific period of time, in one location. Participants can be users, potential users, team members, customers, or stakeholders. Figure 1 shows a typical layout; note if you have five or fewer participants, consider having just one group.
Figure 1
Example room layout for an interactive workshop.
An interactive workshop is distinct from a standard meeting because it aims to stimulate creativity through collaborative working. A meeting, in contrast, usually involves planning and reporting work with attendees sharing their individual points; it does not involve group activities “live” in the meeting. Also, meetings may be an hour or less, whereas the minimum time needed for an interactive workshop is 2–3 hours.
We also do not include training workshops, talks, or seminars in our definition, because from our experience they tend to comprise lectures and tutorials, not brainstorming activities. However, it could be possible to have an interactive workshop session as part of a longer training course. Katrina Pavelin, Sangya Pundir, Jennifer A. Cham |
PLoS Comput. Biol. | 2 |