Jerven T. Bolleman

Most-cited papers

1. UniProt: the Universal Protein Knowledgebase in 2023

   A. Bateman, M. Martin, S. Orchard, M. Magrane +110 more

   2022Nucleic Acids Res.6,464 citations Open access

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2. UniProt: the universal protein knowledgebase in 2021

   A. Bateman, M. Martin, S. Orchard, M. Magrane +129 more

   2020Nucleic Acids Res.5,834 citations Open access

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3. UniProt: the Universal Protein Knowledgebase in 2025

   Alex Bateman, M. Martin, Sandra Orchard, M. Magrane +95 more

   2024Nucleic Acids Research2,546 citations Open access

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4. UniProt: A hub for protein information

   A. Bateman, M. Martin, C. O'Donovan, M. Magrane +124 more

   20152,435 citations

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5. Activities at the Universal Protein Resource (UniProt)

   R. Apweiler, A. Bateman, M. Martin, C. O'Donovan +130 more

   2013Nucleic Acids Res.1,813 citations Open access

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6. The Universal Protein Resource (UniProt) in 2010

   R. Apweiler, M. Martin, C. O'Donovan, M. Magrane +130 more

   2009Nucleic Acids Res.1,205 citations Open access

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7. Ongoing and future developments at the Universal Protein Resource

   A. Morgat, R. Apweiler, M. Martin, C. O'Donovan +122 more

   2010Nucleic Acids Res.704 citations Open access

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8. Annotation of biologically relevant ligands in UniProtKB using ChEBI

   E. Coudert, S. Gehant, E. de Castro, Monica Pozzato +109 more

   2022bioRxiv292 citations Open access

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9. The EBI RDF platform: linked open data for the life sciences

   S. Jupp, J. Malone, Jerven T. Bolleman, Marco Brandizi +12 more

   2014Bioinform.246 citations Open access

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10. Interoperability and FAIRness through a novel combination of Web technologies

    M. Wilkinson, R. Verborgh, Luiz Olavo Bonino da Silva Santos, Tim Clark +12 more

    2017PeerJ Preprints99 citations Open access

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11. Enzyme annotation in UniProtKB using Rhea

    A. Morgat, T. Lombardot, E. Coudert, K. Axelsen +13 more

    2019bioRxiv97 citations Open access

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12. Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search

    D. Alocci, J. Mariethoz, O. Horlacher, Jerven T. Bolleman +2 more

    2015PLoS ONE73 citations Open access

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13. UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase

    Alistair MacDougall, V. Volynkin, R. Saidi, D. Poggioli +27 more

    2020Bioinform.64 citations Open access

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14. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

    Toshiaki Katayama, M. Wilkinson, K. Aoki-Kinoshita, Shuichi Kawashima +81 more

    2014Journal of Biomedical Semantics58 citations Open access

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15. Genetic variations and diseases in UniProtKB/Swiss-Prot: The ins and outs of expert manual curation

    M. Famiglietti, A. Estreicher, A. Gos, Jerven T. Bolleman +7 more

    2014Human Mutation50 citations Open access

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16. LLM-based SPARQL Query Generation from Natural Language over Federated Knowledge Graphs

    Vincent Emonet, Jerven T. Bolleman, S. Duvaud, T. M. de Farias +1 more

    2024HGAIS@ISWC44 citations

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17. Introducing glycomics data into the Semantic Web

    K. Aoki-Kinoshita, Jerven T. Bolleman, Matthew P. Campbell, S. Kawano +13 more

    2013Journal of Biomedical Semantics41 citations Open access

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18. BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data

    Hongyan Wu, Toyofumi Fujiwara, Yasunori Yamamoto, Jerven T. Bolleman +1 more

    2014Journal of Biomedical Semantics39 citations Open access

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19. FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation

    Jerven T. Bolleman, C. Mungall, F. Strozzi, J. Baran +7 more

    2014Journal of Biomedical Semantics34 citations Open access

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20. The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

    Toshiaki Katayama, Mark D. Wilkinson, G. Micklem, Shuichi Kawashima +62 more

    2013Journal of Biomedical Semantics31 citations Open access

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21. SwissBioPics—an interactive library of cell images for the visualization of subcellular location data

    Philippe le Mercier, Jerven T. Bolleman, E. de Castro, E. Gasteiger +12 more

    2022Database J. Biol. Databases Curation19 citations Open access

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22. FAIR adoption, assessment and challenges at UniProt

    L. García, Jerven T. Bolleman, S. Gehant, N. Redaschi +2 more

    2019Scientific Data18 citations Open access

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23. Dataset Descriptions: HCLS Community Profile

    A. Gray, J. Baran, M. S. Marshall, M. Dumontier +27 more

    201518 citations

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24. The SIB Swiss Institute of Bioinformatics Semantic Web of data

    Adrian Amos Parit Delphine Frederic Jerven Alan Frédéric Altenhoff Bairoch Bansal Baratin Bastian Bolleman*, A. Altenhoff, A. Bairoch, Parit Bansal +35 more

    2023Nucleic Acids Research15 citations Open access

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25. SPARQL-enabled identifier conversion with Identifiers.org

    Sarala M. Wimalaratne, Jerven T. Bolleman, N. Juty, Toshiaki Katayama +5 more

    2015Bioinform.12 citations Open access

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26. Provenance and evidence in UniProtKB

    Jerven T. Bolleman, A. Gateau, S. Gehant, N. Redaschi

    2010Workshop on Semantic Web Applications and Tools for Life Sciences10 citations

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27. HAMAP as SPARQL rules—A portable annotation pipeline for genomes and proteomes

    Jerven T. Bolleman, E. de Castro, D. Baratin, S. Gehant +10 more

    2020GigaScience9 citations Open access

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28. UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase

    Alistair MacDougall, V. Volynkin, R. Saidi, D. Poggioli +26 more

    2020Bioinform.8 citations Open access

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29. A large collection of bioinformatics question–query pairs over federated knowledge graphs: methodology and applications

    Jerven T. Bolleman, Vincent Emonet, A. Altenhoff, A. Bairoch +13 more

    2024GigaScience7 citations Open access

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30. Catching Inconsistencies with the Semantic Web: A Biocuration Case Study

    Jerven T. Bolleman, S. Gehant, N. Redaschi

    2012Workshop on Semantic Web Applications and Tools for Life Sciences6 citations

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31. BioHackathon 2015: Semantics of data for life sciences and reproducible research

    R. Vos, Toshiaki Katayama, H. Mishima, S. Kawano +73 more

    2020F1000Research5 citations Open access

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32. Navigating in vitro bioactivity data by investigating available resources using model compounds

    S. Ilmjarv, Fiona Augsburger, Jerven T. Bolleman, R. Liechti +5 more

    2019Scientific Data4 citations Open access

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33. Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB

    M. Feuermann, E. Boutet, A. Morgat, K. Axelsen +14 more

    2021Metabolites3 citations Open access

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34. Data validation and schema interoperability

    L. García-Castro, Jerven T. Bolleman, M. Dumontier, S. Jupp +5 more

    20202 citations Open access

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35. Treating Query Graphs As Connecting Trees Mapping SPARQL Queries to FHIR API

    E. Prud'hommeaux, Jerven T. Bolleman, Claude J. Nanjo

    2025SWAT4HCLS0 citations

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36. Assessment of metadata descriptors of AI-ready datasets

    Jerven T. Bolleman, Leyla Jael Castro, Alban Gaignard, Agoritsa Kalampaliki +8 more

    2025SWAT4HCLS0 citations

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37. Developers Workshop

    Ruben Taelman, Jindrich Mynarz, Jerven T. Bolleman

    2025International Conference on Semantic Systems0 citations

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38. CHIST-ERA Triple: improving data interoperability and federation across RDF knowledge graphs and Solid Pods

    Jerven T. Bolleman, Elias Crum, I. Dragan, Jakub Galgonek +7 more

    2024SWAT4HCLS0 citations

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39. FAIR Service Descriptions: enriching life science SPARQL endpoints

    Jerven T. Bolleman, A. Bridge, N. Redaschi

    2024SWAT4HCLS0 citations

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40. Making expert curated knowledge graphs FAIR

    Jerven T. Bolleman, A. Bridge, N. Redaschi, UniProt Consortium

    2023SWAT4HCLS0 citations

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41. UniProt, ChEBI and IDSM Sachem: exploring biologically relevant ligands

    S. Gehant, E. Coudert, A. Morgat, Jerven T. Bolleman +3 more

    2023SWAT4HCLS0 citations

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42. SwissBioPics – an interactive library of cell images for the visualization of subcellular location data

    Parit Bansal, P. Le Mercier, Jerven T. Bolleman, E. de Castro +12 more

    20200 citations Open access

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43. BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

    Toshiaki Katayama, Shuichi Kawashima, G. Micklem, S. Kawano +72 more

    2019F1000Research0 citations Open access

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44. Enhanced enzyme annotation in UniProtKB using Rhea

    K. Axelsen, A. Morgat, T. Lombardot, E. Coudert +7 more

    20190 citations Open access

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45. SemanticGenomeGraphs

    Simon Heumos, Jerven T. Bolleman

    2019SWAT4HCLS0 citations

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46. HAMAP as SPARQL: annotate all your proteins

    Jerven T. Bolleman, E. de Castro, D. Baratin, S. Gehant +10 more

    20190 citations Open access

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47. HAMAP rules as SPARQL A portable annotation pipeline for genomes and proteomes

    Jerven T. Bolleman, E. de Castro, D. Baratin, S. Gehant +10 more

    2019bioRxiv0 citations Open access

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48. Rhea, an expert curated resource of biochemical reactions for enzyme annotation and genome-scale metabolic modeling

    A. Morgat, T. Lombardot, K. Axelsen, L. Aimo +8 more

    20190 citations Open access

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49. A Microbial metabolism resource for Systems Biology: Shared semantic standards for reference data types (ELIXIR Implementation Study Deliverable Report)

    Jerven T. Bolleman, T. Lombardot, N. Redaschi, M. Pagni +1 more

    20180 citations Open access

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50. The 3rd DBCLS BioHackathon : Improving life science with semantic web technologies

    Toshiaki Katayama, M. Wilkinson, G. Micklem, Shuichi Kawashima +62 more

    20130 citations

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