Making expert curated knowledge graphs FAIR
Jerven Bolleman1 , Alan Bridge1,* , Nicole Redaschi1 and UniProt Consortium1,2,3,4
1
  Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211 Geneva 4, Switzerland
2
  European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK
3
  Protein Information Resource (PIR), Georgetown University Medical Center, 3300 Whitehaven Street, NW, Suite 1200,
Washington, DC 20007, USA
4
  Protein Information Resource (PIR), University of Delaware, 15 Innovation Way, Suite 205, Newark, DE 19711, USA


                                         Abstract
                                        To address the users’ need to combine knowledge from different expert curated resources, the biocuration
                                        community is heavily invested in the standardization of knowledge with shared ontologies and, more
                                        recently, in the representation of data in the form of knowledge graphs (KGs). To easily integrate
                                        data from, or query data across, different KGs it is necessary to also standardize the form in which
                                        they are published. The W3C standards RDF/OWL and SPARQL were created to address this need
                                        and enable the creation of a Semantic Web. Here we describe the use of these standards to publish
                                        public SPARQL endpoints for resources such as UniProt, Rhea and SwissLipids and RDF allowing private
                                        SPARQL endpoints on premise and in clouds (e.g. AWS, Oracle). At more than 110 distinct billion triples
                                        - RDF statements - UniProt is the largest freely available KG. UniProt and other SPARQL endpoints
                                        support complex analytical queries and inferences that go beyond queries through graph-based machine
                                        learning and other approaches. They integrate - federate - expert curated knowledge of protein function
                                        with biological and biochemical data from other KGs available in RDF or OWL like the Gene Ontology
                                        (functions), Bgee (expression patterns), OMA (orthology), and IDSM (chemical structures). They also
                                        serve as APIs to enhance website data display and data mining capabilities - for example to select and
                                        enrich SwissBioPics images to visualize subcellular location data, or to perform chemical similarity and
                                        chemical substructure search with IDSM directly in Rhea.

                                         Keywords
                                         protein, UniProt, SPARQL, Rhea, SwissLipds, lipids, reaction




1. Funding & acknowledgements
This work was supported by the National Eye Institute (NEI), National Human Genome Research
Institute (NHGRI), National Heart, Lung, and Blood Institute (NHLBI), National Institute on
Aging (NIA), National Institute of Allergy and Infectious Diseases (NIAID), National Institute of
Diabetes and Digestive and Kidney Diseases (NIDDK), National Institute of General Medical
Sciences (NIGMS), National Institute of Mental Health (NIMH), and National Cancer Institute
(NCI) of the National Institutes of Health (NIH) under grant U24HG007822. Additional support
for the EMBL-EBI’s involvement in UniProt comes from European Molecular Biology Labo-

SWAT4HCLS 2023
*
 Corresponding author.
$ jerven.bolleman@sib.swiss (J. Bolleman); alan.bridge@sib.swiss (A. Bridge); nicole.redaschi@sib.swiss
(N. Redaschi)
 0000-0002-7449-1266 (J. Bolleman); 0000-0003-2148-9135 (A. Bridge); 0000-0001-8890-2268 (N. Redaschi)
                                       © 2023 Copyright for this paper by its authors. Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0).
                                       CEUR Workshop Proceedings (CEUR-WS.org)
    CEUR
                  http://ceur-ws.org
    Workshop      ISSN 1613-0073
    Proceedings
ratory (EMBL) core funds, the Alzheimer’s Research UK (ARUK) grant ARUK-NAS2017A-1,
the Biotechnology and Biological Sciences Research Council (BBSRC) [BB/T010541/1] and
Open Targets. UniProt activities at the SIB are additionally supported by the Swiss Federal
Government through the State Secretariat for Education, Research and Innovation SERI. PIR’s
UniProt activities are also supported by the NIH grants R01GM080646, G08LM010720, and
P20GM103446, and the National Science Foundation (NSF) grant DBI-1062520.