# Auto-generated by scripts/export-rdf-data.mjs # Run: npm run rdf:export @prefix rdf: . @prefix rdfs: . @prefix xsd: . @prefix schema: . @prefix dcterms: . @prefix skos: . @prefix ec: . ec:citationCount "5"^^xsd:integer . ec:forPublication . ec:fromSnapshot . ec:publicationId "disjointness-llm-ISWC-2024" . rdf:type ec:CitationObservation . ec:citationCount "0"^^xsd:integer . ec:forPublication . ec:fromSnapshot . ec:publicationId "engineering-coliphages-2022" . rdf:type ec:CitationObservation . ec:citationCount "10"^^xsd:integer . ec:forPublication . ec:fromSnapshot . ec:publicationId "gardnerella-characterization-2021" . rdf:type ec:CitationObservation . ec:citationCount "3"^^xsd:integer . ec:forPublication . ec:fromSnapshot . ec:publicationId "genome-sharing-review-2026" . rdf:type ec:CitationObservation . ec:fromSnapshot . ec:publicationId "google-scholar" . rdf:type ec:CitationObservation . ec:citationCount "0"^^xsd:integer . ec:forPublication . ec:fromSnapshot . ec:publicationId "pengquin-eswc-2024" . rdf:type ec:CitationObservation . ec:citationCount "3"^^xsd:integer . ec:forPublication . ec:fromSnapshot . ec:publicationId "pm-pods-SWAT4HCLS-2024" . rdf:type ec:CitationObservation . ec:citationCount "0"^^xsd:integer . ec:forPublication . ec:fromSnapshot . ec:publicationId "TRIPLE-SWAT4HCLS-2024" . rdf:type ec:CitationObservation . ec:citationCount "6"^^xsd:integer . ec:forPublication . ec:fromSnapshot . ec:publicationId "urinary-coliphages-2023" . rdf:type ec:CitationObservation . ec:citationCount "0"^^xsd:integer . ec:forPublication . ec:fromSnapshot . ec:publicationId "vcf-to-rdf-rml-swat4hcls-2026" . rdf:type ec:CitationObservation . ec:forPublication . ec:fromSnapshot . ec:publicationId "vcf2rdf-SWAT4HCLS-2025" . rdf:type ec:CitationObservation . ec:citationCount "1"^^xsd:integer . ec:forPublication . ec:fromSnapshot . ec:publicationId "wikidata-sparql-ISWC-2025" . rdf:type ec:CitationObservation . dcterms:isPartOf . ec:filePath "/cv/artifacts/swat4hcls26-aibare-award-certificate.pdf" . ec:order "1"^^xsd:integer . rdf:type ec:CvArtifact . schema:name "AIbare Award Certificate" . schema:url . dcterms:isPartOf . ec:filePath "/cv/artifacts/isws24-best-paper-certificate.pdf" . ec:order "1"^^xsd:integer . rdf:type ec:CvArtifact . schema:name "Best Paper Certificate" . schema:url . dcterms:isPartOf . ec:filePath "/cv/artifacts/isws24-best-poster-certificate.pdf" . ec:order "1"^^xsd:integer . rdf:type ec:CvArtifact . schema:name "Best Poster Certificate" . schema:url . dcterms:isPartOf . ec:filePath "/cv/artifacts/isws24-participation-certificate.pdf" . ec:order "1"^^xsd:integer . rdf:type ec:CvArtifact . schema:name "Participation Certificate" . schema:url . dcterms:isPartOf . ec:icon "fa-envelope" . ec:order "1"^^xsd:integer . rdf:type ec:CvContact . rdf:value "elias.crum@ugent.be" . rdfs:label "Email" . schema:url . dcterms:isPartOf . ec:icon "fa-github" . ec:order "2"^^xsd:integer . rdf:type ec:CvContact . rdf:value "github.com/ecrum19" . rdfs:label "GitHub" . schema:url . dcterms:isPartOf . ec:icon "fa-linkedin" . ec:order "3"^^xsd:integer . rdf:type ec:CvContact . rdf:value "linkedin.com/in/elias-crum-413178142" . rdfs:label "LinkedIn" . schema:url . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "KNowledge on Web Scale (IDLab, UGent) / Digital Precision Health (VITO NV)" . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "Graduated with Bioinformatics Honors" . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "2"^^xsd:integer . ec:text "GPA: 4.00 / 4.00" . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "Double Major: Bioinformatics & Biology" . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "2"^^xsd:integer . ec:text "Minor: History" . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "3"^^xsd:integer . ec:text "GPA: 3.991 / 4.000" . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "Python, BASH, R, Java, JavaScript, TypeScript, SPARQL, SHACL, HTML, CSS, Vue, LaTeX" . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "BowTie2, Kallisto, Spades, FastANI, PATRIC, PHASTER, Anvi'o, ResFinder, BLAST+, Clustal Omega, and related tooling" . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "GitHub Actions, NGINX, Conda, Docker, Cytoscape" . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "SPARQL, RDF serialization, ontology definition, Solid" . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "English (native), Dutch (A1), French (A2)" . rdf:type ec:CvDetail . dcterms:isPartOf . ec:isInternal "true"^^xsd:boolean . ec:order "1"^^xsd:integer . ec:prefix "Details:" . ec:text "FWO Fellowship Record" . rdf:type ec:CvDetail . schema:url . dcterms:isPartOf . ec:isInternal "true"^^xsd:boolean . ec:order "1"^^xsd:integer . ec:prefix "Publication:" . ec:text "From VCF to RDF: RML-Based Conversion Approaches for the Semantic Representation of Variant Data" . rdf:type ec:CvDetail . schema:url . dcterms:isPartOf . ec:isInternal "true"^^xsd:boolean . ec:order "1"^^xsd:integer . ec:prefix "Slides:" . ec:text "ISWS 2024 Group Project Presentation" . rdf:type ec:CvDetail . schema:url . dcterms:isPartOf . ec:isInternal "true"^^xsd:boolean . ec:order "1"^^xsd:integer . ec:prefix "Poster:" . ec:text "ISWS 2024 Award-Winning Poster (PENGQUIN)" . rdf:type ec:CvDetail . schema:url . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "Developing framework for clinical genomic data storage, sharing, and querying." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "2"^^xsd:integer . ec:text "Implementation of the framework utilizes the Solid protocol." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "3"^^xsd:integer . ec:text "Experience with SPARQL, RDF, ODRL, Linked Data, decentralized querying, and ontology definition." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "Hosted by the Knowledge Representation Unit (KRU); worked directly with Jerven Bolleman, Tarcisio Mendes de Farias, Ana-Claudia Sima, and Vincent Emonet." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "2"^^xsd:integer . ec:text "Gained practical knowledge of public SPARQL endpoint maintenance." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "3"^^xsd:integer . ec:text "Developed Solid Cockpit to perform federated queries across public SPARQL endpoints and Solid pods containing research data, as part of the CHIST-ERA TRIPLE project." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "4"^^xsd:integer . ec:text "Funding: FWO Long Research Stay grant V416635N; project support through CHIST-ERA TRIPLE (CHIST-ERA-22-ORD-09)." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:isInternal "true"^^xsd:boolean . ec:order "5"^^xsd:integer . ec:prefix "Direct contribution to:" . ec:text "Does SPARQL federation work in the real world? A case study over large biological SPARQL endpoints (ISWC, Oct. 2026; accepted)" . rdf:type ec:CvDetail . schema:url . dcterms:isPartOf . ec:isInternal "true"^^xsd:boolean . ec:order "6"^^xsd:integer . ec:prefix "Direct contribution to:" . ec:text "Solid Cockpit: Data manager, privacy editor, and query facilitator for Solid pods (ESWC 2026 demo paper)" . rdf:type ec:CvDetail . schema:url . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "Identified and characterized novel, medically relevant bacteria and bacteriophage sequences." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "2"^^xsd:integer . ec:text "Master's thesis: Cataloguing Coliphages of the Human Urinary Microbiome." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "3"^^xsd:integer . ec:text "Experience with gene annotation and clustering, taxonomic classification screening, gene-similarity network production, genetic engineering and phage virulence augmentation." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:isInternal "true"^^xsd:boolean . ec:order "4"^^xsd:integer . ec:prefix "Publication:" . ec:text "10.1371/journal.pone.0283930" . rdf:type ec:CvDetail . schema:url . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "Performed independent research involving prokaryotic DNA sequencing, assembly, and analysis." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:isInternal "true"^^xsd:boolean . ec:order "2"^^xsd:integer . ec:prefix "Publication:" . ec:text "10.1128/mSphere.00154-21" . rdf:type ec:CvDetail . schema:url . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "Researched the variable resistance of strains of bladder E. coli to bacteriophage infection." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "2"^^xsd:integer . ec:text "Presented the outcomes of this work to the Stritch School of Medicine Microbiology and Immunology Department." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "3"^^xsd:integer . ec:text "Presented a poster at the Stritch School of Medicine annual St. Albert's Day Research Celebration." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "Taught two sections of Biology Lab I and II each semester, with 24 students per section." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "2"^^xsd:integer . ec:text "Designed and delivered lectures, assessed in-class exercises, and developed and evaluated quizzes and exams." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "3"^^xsd:integer . ec:text "Collaborated with colleagues and students to maximize student learning and growth." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "Directly assisted physician care of patients through patient intake charting, ordering tests, and other EPIC platform mediated physician logistical support." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "2"^^xsd:integer . ec:text "Interpreted and integrated medical charts to aid in the diagnosis and treatment of patients." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "3"^^xsd:integer . ec:text "Operated EPIC software for medical documentation." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "Trained incoming student tutors and supplementary instructors." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "2"^^xsd:integer . ec:text "Supervised peer leaders and provided constructive feedback on instruction." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "3"^^xsd:integer . ec:text "Led group discussions and presented during bi-weekly meetings of more than 100 tutors." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "Tutored and served as professor's assistant for Pre-calculus (MATH 117) and Organic Chemistry I and II (CHEM 223 and 224)." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "2"^^xsd:integer . ec:text "Attended lectures and aided professors with lessons for around 200 students." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "3"^^xsd:integer . ec:text "Hosted three tutoring sessions per week with an average attendance between 20 and 80 students." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "4"^^xsd:integer . ec:text "Tutored students in accelerated summer science courses including General Biology, Cell Biology, Genetics, General Chemistry, Organic Chemistry, Biochemistry, and Physics." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "Refereed intramural sports including flag football, soccer, and volleyball." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "2"^^xsd:integer . ec:text "Communicated with other officials and players to ensure a fair and enjoyable intramural atmosphere." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "3"^^xsd:integer . ec:text "Diffused conflicts arising during or after games." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "4"^^xsd:integer . ec:text "Earned Campus Recreation Employee of the Year for the 2017-2018 academic year." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "Participated in the 2024 International Semantic Web Summer School and related project activities." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "Coached underprivileged inner-city children in the fundamentals of skating and ice hockey." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "2"^^xsd:integer . ec:text "Taught, encouraged, and engaged with participants aged 8 to 15." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "Attended Loyola alumni events and communicated the student experience with Loyola alumni." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "2"^^xsd:integer . ec:text "Worked at a diverse array of Loyola-sponsored events and acted as a representative of the university." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "Volunteered in the emergency room on a weekly basis." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "2"^^xsd:integer . ec:text "Helped restock rooms, tend to patient needs, and assist medical professionals." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "Assisted in overseeing the afterschool homework program at Jordan Elementary for grades 3 and 4." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "2"^^xsd:integer . ec:text "Helped keep around 20 students focused while assisting with homework and occasional enrichment activities." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "1"^^xsd:integer . ec:text "Instructed underprivileged inner-city children in the fundamentals of skating and ice hockey." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:order "2"^^xsd:integer . ec:text "Assisted St. Paul Police officers with program coordination and participant organization." . rdf:type ec:CvDetail . dcterms:isPartOf . ec:dateText "Oct. 2023 - Present" . ec:hasDetail . ec:location "Gent, Belgium" . ec:order "1"^^xsd:integer . ec:organization "Ghent University" . ec:role "Doctor of Computer Science Engineering" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "Aug. 2020 - Aug. 2022" . ec:hasDetail . ec:hasDetail . ec:location "Chicago, IL, USA" . ec:order "2"^^xsd:integer . ec:organization "Loyola University Chicago" . ec:role "Master of Science (Bioinformatics)" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "Aug. 2017 - May 2021" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:location "Chicago, IL, USA" . ec:order "3"^^xsd:integer . ec:organization "Loyola University Chicago" . ec:role "Bachelor of Science" . rdf:type ec:CvItem . dcterms:isPartOf . ec:hasDetail . ec:order "1"^^xsd:integer . ec:role "Programming/Querying Languages" . rdf:type ec:CvItem . dcterms:isPartOf . ec:hasDetail . ec:order "2"^^xsd:integer . ec:role "Bioinformatics Tools" . rdf:type ec:CvItem . dcterms:isPartOf . ec:hasDetail . ec:order "3"^^xsd:integer . ec:role "Miscellaneous" . rdf:type ec:CvItem . dcterms:isPartOf . ec:hasDetail . ec:order "4"^^xsd:integer . ec:role "Semantic Web" . rdf:type ec:CvItem . dcterms:isPartOf . ec:hasDetail . ec:order "5"^^xsd:integer . ec:role "Languages" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "2024-28" . ec:group "Graduate Education" . ec:hasDetail . ec:location "Brussels, Belgium" . ec:order "1"^^xsd:integer . ec:organization "The Research Foundation - Flanders (FWO)" . ec:role "Strategic Basic PhD Fellowship Awardee" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "2026" . ec:group "Graduate Education" . ec:hasArtifact . ec:hasDetail . ec:location "Amsterdam, The Netherlands" . ec:order "2"^^xsd:integer . ec:organization "SWAT4HCLS 2026" . ec:role "AIbare Award" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "2024" . ec:group "Graduate Education" . ec:hasArtifact . ec:hasDetail . ec:location "Bertinoro, Italy" . ec:order "3"^^xsd:integer . ec:organization "International Semantic Web Summer School 2024" . ec:role "Best Paper (Group)" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "2024" . ec:group "Graduate Education" . ec:hasArtifact . ec:hasDetail . ec:location "Bertinoro, Italy" . ec:order "4"^^xsd:integer . ec:organization "International Semantic Web Summer School 2024" . ec:role "Best Poster (Individual)" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "2020-21" . ec:group "Pre-Graduate Education" . ec:location "Chicago, IL, USA" . ec:order "5"^^xsd:integer . ec:organization "Recipient of a research scholarship for the 2020-2021 school year" . ec:role "Mulcahy Research Fellowship Award" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "2017-21" . ec:group "Pre-Graduate Education" . ec:location "Chicago, IL, USA" . ec:order "6"^^xsd:integer . ec:organization "Eight-time Dean's List recipient" . ec:role "College of Arts and Sciences Dean's List Mention" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "2017-18" . ec:group "Pre-Graduate Education" . ec:location "Chicago, IL, USA" . ec:order "7"^^xsd:integer . ec:organization "Campus Recreation, Loyola University Chicago" . ec:role "Employee of the Year" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "2017-21" . ec:group "Pre-Graduate Education" . ec:location "Chicago, IL, USA" . ec:order "8"^^xsd:integer . ec:organization "College of Arts and Sciences, Loyola University Chicago" . ec:role "Presidential Scholarship Recipient" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "Oct. 2023 - Present" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:location "Ghent, Belgium" . ec:order "1"^^xsd:integer . ec:organization "Graduate Researcher, Ghent University & VITO NV" . ec:role "Ph.D. Candidate" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "Mar. - Apr. 2025 (2 months)" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:location "Lausanne, CH" . ec:order "2"^^xsd:integer . ec:organization "SIB Swiss Institute of Bioinformatics" . ec:role "Research Stay" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "Aug. 2020 - Aug. 2022" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:location "Chicago, IL, USA" . ec:order "3"^^xsd:integer . ec:organization "Master's Research, Loyola University Chicago (Putonti Lab)" . ec:role "Master's Researcher" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "Aug. 2019 - Aug. 2020" . ec:hasDetail . ec:hasDetail . ec:location "Chicago, IL, USA" . ec:order "4"^^xsd:integer . ec:organization "Undergraduate Research, Loyola University Chicago (Putonti Lab)" . ec:role "Undergraduate Researcher" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "May 2019 - Aug. 2019" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:location "Chicago, IL, USA" . ec:order "5"^^xsd:integer . ec:organization "Junior Researcher, Loyola Stritch School of Medicine (Wolfe Lab)" . ec:role "Junior Research Assistant" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "Aug. 2021 - May 2023" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:location "Chicago, IL, USA" . ec:order "1"^^xsd:integer . ec:organization "Department of Biology, Loyola University Chicago" . ec:role "Adjunct Professor of Biology" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "Nov. 2021 - Jan. 2023" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:location "Chicago, IL, USA" . ec:order "2"^^xsd:integer . ec:organization "Emergency Department, University of Chicago Medical Center" . ec:role "Medical Scribe" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "Nov. 2020 - May 2021" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:location "Chicago, IL, USA" . ec:order "3"^^xsd:integer . ec:organization "Tutoring Center, Loyola University Chicago" . ec:role "Training and Professional Development Committee Member" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "Jan. 2019 - May 2021" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:location "Chicago, IL, USA" . ec:order "4"^^xsd:integer . ec:organization "Tutoring Center, Loyola University Chicago" . ec:role "Supplementary Instructor (SI) and Group Tutor" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "Sept. 2017 - May 2019" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:location "Chicago, IL, USA" . ec:order "5"^^xsd:integer . ec:organization "Campus Recreation, Loyola University Chicago" . ec:role "Intramural Sports Official" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "2024" . ec:hasArtifact . ec:hasDetail . ec:location "Bertinoro, Italy" . ec:order "1"^^xsd:integer . ec:organization "International Semantic Web Summer School 2024" . ec:role "Participant" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "Oct. 2021 - Apr. 2023" . ec:hasDetail . ec:hasDetail . ec:location "Chicago, IL, USA" . ec:order "1"^^xsd:integer . ec:organization "Inner City Education (ICE) Program" . ec:role "Ice Hockey and Skating Coach" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "Aug. 2019 - May 2020" . ec:hasDetail . ec:hasDetail . ec:location "Chicago, IL, USA" . ec:order "2"^^xsd:integer . ec:organization "Alumni Relations, Loyola University Chicago" . ec:role "Student Alumni Ambassador" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "Oct. 2018 - Mar. 2020" . ec:hasDetail . ec:hasDetail . ec:location "Chicago, IL, USA" . ec:order "3"^^xsd:integer . ec:organization "AMITA St. Joseph's Hospital" . ec:role "Emergency Room Volunteer" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "Sept. 2019 - Mar. 2020" . ec:hasDetail . ec:hasDetail . ec:location "Chicago, IL, USA" . ec:order "4"^^xsd:integer . ec:organization "Loyola4Chicago - Jordan Elementary" . ec:role "Afterschool Program Tutor" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "Nov. 2015 - Mar. 2020" . ec:hasDetail . ec:hasDetail . ec:location "St. Paul, MN, USA" . ec:order "5"^^xsd:integer . ec:organization "St. Paul Police PAL - Learn to Skate Program" . ec:role "Assistant Skating Instructor" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "2019" . ec:location "Chicago, IL, USA" . ec:order "1"^^xsd:integer . ec:organization "Loyola University Chicago Chapter" . ec:role "Alpha Sigma Nu Jesuit Honors Society Inductee" . rdf:type ec:CvItem . dcterms:isPartOf . ec:dateText "2018" . ec:location "Chicago, IL, USA" . ec:order "2"^^xsd:integer . ec:organization "Epsilon Kappa Chapter, Loyola University Chicago" . ec:role "Delta Sigma Phi Fraternity" . rdf:type ec:CvItem . dcterms:isPartOf . ec:address "AA Tower, Floor 7, Technologiepark-Zwijnaarde 122, Gent 9052, Belgium" . ec:hasContact . ec:hasContact . ec:hasContact . ec:hasFocusTag . ec:hasFocusTag . ec:hasFocusTag . ec:hasFocusTag . ec:hasFocusTag . ec:hasFocusTag . ec:headline "Doctor of Computer Science Engineering PhD Candidate · Bioinformatician" . rdf:type ec:CvProfile . schema:name "Elias D. 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Flanders (FWO)" . rdfs:label "Funding Organization" . dcterms:isPartOf . ec:order "2"^^xsd:integer . rdf:type ec:FellowshipDetail . rdf:value "PhD Fellowship - Strategic Basic Research" . rdfs:label "Funding Scheme" . dcterms:isPartOf . ec:order "3"^^xsd:integer . rdf:type ec:FellowshipDetail . rdf:value "2024-2028" . rdfs:label "Period" . dcterms:isPartOf . ec:order "4"^^xsd:integer . rdf:type ec:FellowshipDetail . rdf:value "PENGQUIN (PErsoNal Genome QUery IN healthcare and clinical practice)" . rdfs:label "Project" . dcterms:isPartOf . ec:order "5"^^xsd:integer . rdf:type ec:FellowshipDetail . rdf:value "Ghent University (IDLab/KNoWS) and VITO NV" . rdfs:label "Host Institutions" . dcterms:identifier "fwo-phd-fellowship" . dcterms:isPartOf . ec:defenseSlidesUrl . ec:hasDefenseTalk . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:moreInfoUrl . ec:projectDescriptionPdfPath "/fellowship/FWO_Project_Description_EDC.pdf" . ec:projectDescriptionPdfUrl . ec:slug "fwo-phd-fellowship" . ec:subtitle "Strategic Basic Research Fellowship" . ec:summary "Doctoral fellowship supporting research on semantic-web and decentralized methods for privacy-aware personal genomic data management and querying." . rdf:type ec:Fellowship . schema:name "FWO PhD Fellowship" . dcterms:identifier "publication:disjointness-llm-ISWC-2024" . dcterms:isPartOf . ec:dateLabel "02 Dec 2024" . ec:linkLabel "Read publication" . ec:order "17"^^xsd:integer . ec:referencesEntity . ec:summary "Investigates how large language models can propose class disjointness axioms for ontologies, with validation on DBpedia and a workflow that preserves logical consistency while reducing manual effort." . ec:updateDate "2024-12-02"^^xsd:date . ec:updateType "Publication" . rdf:type ec:HomepageUpdate . schema:name "Enriching Ontologies with Disjointness Axioms using Large Language Models" . schema:url . dcterms:identifier "publication:engineering-coliphages-2022" . dcterms:isPartOf . ec:dateLabel "01 Sept 2022" . ec:linkLabel "Read publication" . ec:order "28"^^xsd:integer . ec:referencesEntity . ec:summary "Builds a large-scale catalog of urinary E. coli prophages and demonstrates induction plus engineering of temperate phages into obligately lytic variants for targeted lysis of non-native urinary strains." . ec:updateDate "2022-09-01"^^xsd:date . ec:updateType "Publication" . rdf:type ec:HomepageUpdate . schema:name "Cataloging and Engineering Temperate Coliphages of the Human Urinary Microbiome" . schema:url . dcterms:identifier "publication:gardnerella-characterization-2021" . dcterms:isPartOf . ec:dateLabel "12 May 2021" . ec:linkLabel "Read publication" . ec:order "29"^^xsd:integer . ec:referencesEntity . ec:summary "Compares urinary and vaginal Gardnerella genomes, identifying species-level structure and showing that whole-genome analysis is needed for reliable differentiation across groups in urogenital microbiota." . ec:updateDate "2021-05-12"^^xsd:date . ec:updateType "Publication" . rdf:type ec:HomepageUpdate . schema:name "Genome Investigation of Urinary Gardnerella Strains and Their Relationship to Isolates of the Vaginal Microbiota" . schema:url . dcterms:identifier "publication:genome-sharing-review-2026" . dcterms:isPartOf . ec:dateLabel "01 Jan 2026" . ec:linkLabel "Read publication" . ec:order "7"^^xsd:integer . ec:referencesEntity . ec:summary "Scoping review of how genomic sequence data is shared in clinical practice, surveying implementations, infrastructure, and guidance. Identifies key barriers to scalability and adoption, and proposes concrete steps toward more unified, scalable clinical genomic data sharing systems." . ec:updateDate "2026-01-01"^^xsd:date . ec:updateType "Publication" . rdf:type ec:HomepageUpdate . schema:name "Genomic sequence data sharing for clinical practice: A scoping review" . schema:url . dcterms:identifier "publication:genomic-variant-representation-rdf-preprint-2025" . dcterms:isPartOf . ec:dateLabel "24 Feb 2025" . ec:linkLabel "Read publication" . ec:order "16"^^xsd:integer . ec:referencesEntity . ec:summary "Reports initial BioHackathon results on aligning genomic variant RDF schemas identified at SWAT4HCLS 2025, with focus on improving interoperability and reuse of variant data for clinical applications." . ec:updateDate "2025-02-24"^^xsd:date . ec:updateType "Publication" . rdf:type ec:HomepageUpdate . schema:name "Variant representation in RDF" . schema:url . dcterms:identifier "publication:pengquin-eswc-2024" . dcterms:isPartOf . ec:dateLabel "26 May 2024" . ec:linkLabel "Read publication" . ec:order "22"^^xsd:integer . ec:referencesEntity . ec:summary "Presents the PENGQUIN PhD framework for privacy-preserving genomic data sharing and querying using Solid pods, RDF/Linked Data representations, policy attachments, and link-traversal querying." . ec:updateDate "2024-05-26"^^xsd:date . ec:updateType "Publication" . rdf:type ec:HomepageUpdate . schema:name "PErsoNal Genome QUery IN healthcare and clinical practice (PENGQUIN)" . schema:url . dcterms:identifier "publication:pm-pods-SWAT4HCLS-2024" . dcterms:isPartOf . ec:dateLabel "26 Feb 2024" . ec:linkLabel "Read publication" . ec:order "26"^^xsd:integer . ec:referencesEntity . ec:summary "Describes how Solid-based personal data pods can address privacy and data-sharing bottlenecks in genomic medicine by decentralizing storage and giving patients finer control over sensitive genomic data." . ec:updateDate "2024-02-26"^^xsd:date . ec:updateType "Publication" . rdf:type ec:HomepageUpdate . schema:name "Personalized medicine through personal data pods" . schema:url . dcterms:identifier "publication:real-world-federation-iswc-2026" . dcterms:isPartOf . ec:dateLabel "27 Oct 2026" . ec:linkLabel "Read publication" . ec:order "1"^^xsd:integer . ec:referencesEntity . ec:summary "Presents an 18-month longitudinal study of 67 real-world federated biological SPARQL queries over more than 20 public endpoints, and shows that a) execution success declines over time with very few queries functional by June 2026, b) current algorithmic federation approaches perform substantially worse than manual federation, and c) work is needed to assess how to enable federation over public endpoints in the age of the LLM." . ec:updateDate "2026-10-27"^^xsd:date . ec:updateType "Publication" . rdf:type ec:HomepageUpdate . schema:name "Does SPARQL federation work in the real world? A case study over large biological SPARQL endpoints" . schema:url . dcterms:identifier "publication:solid-cockpit-eswc-2026-demo" . dcterms:isPartOf . ec:dateLabel "01 Jun 2026" . ec:linkLabel "Read publication" . ec:order "3"^^xsd:integer . ec:referencesEntity . ec:summary "Presents Solid Cockpit, a browser-based interface for managing Solid Pods that integrates data management, privacy-aware permission workflows, and embedded SPARQL querying with result materialization." . ec:updateDate "2026-06-01"^^xsd:date . ec:updateType "Publication" . rdf:type ec:HomepageUpdate . schema:name "Solid Cockpit: Data manager, privacy editor, and query facilitator for Solid pods" . schema:url . dcterms:identifier "publication:TRIPLE-SWAT4HCLS-2024" . dcterms:isPartOf . ec:dateLabel "26 Feb 2024" . ec:linkLabel "Read publication" . ec:order "25"^^xsd:integer . ec:referencesEntity . ec:summary "Describes how Solid-based data pods can address privacy and data-sharing bottlenecks in academic research by allowing felxible sharing of sensitive research data and result/experimental data provenance." . ec:updateDate "2024-02-26"^^xsd:date . ec:updateType "Publication" . rdf:type ec:HomepageUpdate . schema:name "CHIST-ERA Triple: improving data interoperability and federation across RDF knowledge graphs and Solid Pods" . schema:url . dcterms:identifier "publication:urinary-coliphages-2023" . dcterms:isPartOf . ec:dateLabel "13 Apr 2023" . ec:linkLabel "Read publication" . ec:order "27"^^xsd:integer . ec:referencesEntity . ec:summary "Catalogs urinary E. coli phage diversity and shows that multiple urinary and non-urinary coliphages can lyse urinary E. coli strains, supporting a role for phages in shaping urobiome composition." . ec:updateDate "2023-04-13"^^xsd:date . ec:updateType "Publication" . rdf:type ec:HomepageUpdate . schema:name "Coliphages of the human urinary microbiota" . schema:url . dcterms:identifier "publication:vcf-to-rdf-rml-swat4hcls-2026" . dcterms:isPartOf . ec:dateLabel "24 Mar 2026" . ec:linkLabel "Read publication" . ec:order "6"^^xsd:integer . ec:referencesEntity . ec:summary "Presents an RML-based approach for converting VCF genomic variant files into RDF using established ontologies, targeting more interoperable, queryable, and privacy-aware variant data representation." . ec:updateDate "2026-03-24"^^xsd:date . ec:updateType "Publication" . rdf:type ec:HomepageUpdate . schema:name "From VCF to RDF: RML-Based Conversion Approaches for the Semantic Representation of Variant Data" . schema:url . dcterms:identifier "publication:vcf2rdf-SWAT4HCLS-2025" . dcterms:isPartOf . ec:dateLabel "24 Feb 2025" . ec:linkLabel "Read publication" . ec:order "15"^^xsd:integer . ec:referencesEntity . ec:summary "Introduces a framework for converting VCF genomic variant files into RDF, combining a comprehensive ontology, storage-efficient HDT serialization, and alignment with clinical metadata schemas to improve interoperability, data linking, querying, and semantic interpretability." . ec:updateDate "2025-02-24"^^xsd:date . ec:updateType "Publication" . rdf:type ec:HomepageUpdate . schema:name "Semantifying Genomic Variant Data: VCF to RDF Conversion Framework" . schema:url . dcterms:identifier "publication:wikidata-sparql-ISWC-2025" . dcterms:isPartOf . ec:dateLabel "02 Nov 2025" . ec:linkLabel "Read publication" . ec:order "9"^^xsd:integer . ec:referencesEntity . ec:summary "Client-side query federation can automatically combine data across the newly split Wikidata SPARQL endpoints, reducing the need for manual source annotations in queries while remaining feasible for queries that stay within client resource limits." . ec:updateDate "2025-11-02"^^xsd:date . ec:updateType "Publication" . rdf:type ec:HomepageUpdate . schema:name "Observations on automated client-side query federation over Wikidata SPARQL endpoints" . schema:url . dcterms:identifier "talk:18m-vito-internal-jury" . dcterms:isPartOf . ec:dateLabel "20 Nov 2025" . ec:linkLabel "View talk" . ec:order "8"^^xsd:integer . ec:referencesEntity . ec:summary "Internal PhD milestone review covering completed work, validation status, and the next research phase." . ec:updateDate "2025-11-20"^^xsd:date . ec:updateType "Talk" . rdf:type ec:HomepageUpdate . schema:name "18-Month Internal VITO PhD Jury" . schema:url . dcterms:identifier "talk:dph-day-talk" . dcterms:isPartOf . ec:dateLabel "10 Oct 2025" . ec:linkLabel "View talk" . ec:order "10"^^xsd:integer . ec:referencesEntity . ec:summary "Presented progress on decentralized clinical-genomics workflows and interoperability priorities in precision health." . ec:updateDate "2025-10-10"^^xsd:date . ec:updateType "Talk" . rdf:type ec:HomepageUpdate . schema:name "Digital Precision Health Day" . schema:url . dcterms:identifier "talk:edc-knows-26" . dcterms:isPartOf . ec:dateLabel "31 Mar 2026" . ec:linkLabel "View talk" . ec:order "5"^^xsd:integer . ec:referencesEntity . ec:summary "KNoWS Day presentation outlining how semantic representations can improve genomic-data interoperability, privacy-aware access control, and federated querying in healthcare settings." . ec:updateDate "2026-03-31"^^xsd:date . ec:updateType "Talk" . rdf:type ec:HomepageUpdate . schema:name "Genomic Data, Healthcare, and the Semantic Web" . schema:url . dcterms:identifier "talk:eswc-phdsymp-pangquin" . dcterms:isPartOf . ec:dateLabel "28 May 2024" . ec:linkLabel "View talk" . ec:order "21"^^xsd:integer . ec:referencesEntity . ec:summary "PhD symposium talk on the PENGQUIN research agenda for decentralized and policy-aware genomic data use." . ec:updateDate "2024-05-28"^^xsd:date . ec:updateType "Talk" . rdf:type ec:HomepageUpdate . schema:name "ESWC - PhD Symposium" . schema:url . dcterms:identifier "talk:fwo-interview" . dcterms:isPartOf . ec:dateLabel "05 Sept 2024" . ec:linkLabel "View talk" . ec:order "19"^^xsd:integer . ec:referencesEntity . ec:summary "Funding interview pitch describing the PENGQUIN PhD vision, feasibility, and expected impact." . ec:updateDate "2024-09-05"^^xsd:date . ec:updateType "Talk" . rdf:type ec:HomepageUpdate . schema:name "FWO Interview" . schema:url . dcterms:identifier "talk:isws-group-project-presentation" . dcterms:isPartOf . ec:dateLabel "15 Jun 2024" . ec:linkLabel "View talk" . ec:order "20"^^xsd:integer . ec:referencesEntity . ec:summary "Final group project presentation from ISWS 2024 highlighting design choices and implementation outcomes." . ec:updateDate "2024-06-15"^^xsd:date . ec:updateType "Talk" . rdf:type ec:HomepageUpdate . schema:name "International Semantic Web Summer School (ISWS) 2024: Group Project" . schema:url . dcterms:identifier "talk:metabolinkai" . dcterms:isPartOf . ec:dateLabel "08 Oct 2026" . ec:linkLabel "View talk" . ec:order "2"^^xsd:integer . ec:referencesEntity . ec:summary "Invited MetaboLinkAI presentation connecting the PENGQUIN PhD project with real-world SPARQL federation, the Ontology Companion Generator, and semantic representation of genomic variant data." . ec:updateDate "2026-10-08"^^xsd:date . ec:updateType "Talk" . rdf:type ec:HomepageUpdate . schema:name "MetaboLinkAI: From personal genomes to federated queries" . schema:url . dcterms:identifier "talk:sib-researchstay-reflection" . dcterms:isPartOf . ec:dateLabel "15 May 2025" . ec:linkLabel "View talk" . ec:order "11"^^xsd:integer . ec:referencesEntity . ec:summary "Reflected on outcomes from the SIB research stay, including technical gains and collaboration opportunities." . ec:updateDate "2025-05-15"^^xsd:date . ec:updateType "Talk" . rdf:type ec:HomepageUpdate . schema:name "SIB Research Stay Reflection" . schema:url . dcterms:identifier "talk:sib-vital-it-talk" . dcterms:isPartOf . ec:dateLabel "04 Apr 2025" . ec:linkLabel "View talk" . ec:order "13"^^xsd:integer . ec:referencesEntity . ec:summary "Reviewed client-side federated SPARQL strategies for combining private Solid pod data with public knowledge graphs." . ec:updateDate "2025-04-04"^^xsd:date . ec:updateType "Talk" . rdf:type ec:HomepageUpdate . schema:name "SIB Vital-IT" . schema:url . dcterms:identifier "talk:solid-intro-triple-consortium" . dcterms:isPartOf . ec:dateLabel "10 Oct 2024" . ec:linkLabel "View talk" . ec:order "18"^^xsd:integer . ec:referencesEntity . ec:summary "Introductory consortium session on Solid concepts, architecture, and relevance to TRIPLE project goals." . ec:updateDate "2024-10-10"^^xsd:date . ec:updateType "Talk" . rdf:type ec:HomepageUpdate . schema:name "TRIPLE Consortium: Intro to Solid" . schema:url . dcterms:identifier "talk:solidsymp-genomepods" . dcterms:isPartOf . ec:dateLabel "02 Apr 2024" . ec:linkLabel "View talk" . ec:order "23"^^xsd:integer . ec:referencesEntity . ec:summary "Explored how Solid pods can host and govern personal genomic data for privacy-preserving analytics." . ec:updateDate "2024-04-02"^^xsd:date . ec:updateType "Talk" . rdf:type ec:HomepageUpdate . schema:name "Solid Symposium" . schema:url . dcterms:identifier "talk:sosy2026" . dcterms:isPartOf . ec:dateLabel "30 Apr 2026" . ec:linkLabel "View talk" . ec:order "4"^^xsd:integer . ec:referencesEntity . ec:summary "Demonstration of Solid Cockpit as a unified web interface for Solid Pods, integrating data management, privacy and access-control editing, notification support, and in-browser SPARQL data discovery." . ec:updateDate "2026-04-30"^^xsd:date . ec:updateType "Talk" . rdf:type ec:HomepageUpdate . schema:name "Solid Cockpit" . schema:url . dcterms:identifier "talk:sphn-pengquin-talk" . dcterms:isPartOf . ec:dateLabel "29 Apr 2025" . ec:linkLabel "View talk" . ec:order "12"^^xsd:integer . ec:referencesEntity . ec:summary "Introduced the PENGQUIN approach for privacy-aware clinical genomics integration using RDF and decentralized data pods." . ec:updateDate "2025-04-29"^^xsd:date . ec:updateType "Talk" . rdf:type ec:HomepageUpdate . schema:name "Swiss Public Health Network (SPHN)" . schema:url . dcterms:identifier "talk:swissprot-talk" . dcterms:isPartOf . ec:dateLabel "25 Mar 2025" . ec:linkLabel "View talk" . ec:order "14"^^xsd:integer . ec:referencesEntity . ec:summary "Presented semantic integration opportunities between curated protein resources and decentralized query workflows." . ec:updateDate "2025-03-25"^^xsd:date . ec:updateType "Talk" . rdf:type ec:HomepageUpdate . schema:name "SIB / SwissProt" . schema:url . dcterms:identifier "talk:ugent-genomics-talk" . dcterms:isPartOf . ec:dateLabel "04 Mar 2024" . ec:linkLabel "View talk" . ec:order "24"^^xsd:integer . ec:referencesEntity . ec:summary "Foundational genomics overview tailored to computer science researchers entering health-data domains." . ec:updateDate "2024-03-04"^^xsd:date . ec:updateType "Talk" . rdf:type ec:HomepageUpdate . schema:name "KNoWS: An Intro to Genomics for Computer Scientists" . schema:url . dcterms:identifier "e-i-xchange24-poster-edc" . dcterms:isPartOf . ec:abstract "This poster frames the core PENGQUIN research challenge around making personal genomic data more interoperable and usable without giving up privacy protections. It highlights engineering work on storing genomic data in Solid pods, managing access and privacy constraints, representing variant data as RDF, linking genomic and health information, and supporting both single-pod and multi-pod querying workflows. The poster positions these tasks as a practical semantic-web response to current barriers in clinical genomics data use." . ec:audienceExpertise "Interdisciplinary attendees interested in applied data sharing, privacy-aware web technologies, and translational genomics." . ec:displayDate "2024-10-05"^^xsd:date . ec:displayDateDetailedLabel "Saturday, 05 October 2024" . ec:displayDateLabel "05/10/2024" . ec:filePath "/talks/posters/E(i)xchange24_Poster_EDC.pdf" . ec:goal "Introduce the broader PENGQUIN research agenda and show how semantic-web technologies can support privacy-aware genomic data management and querying." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:hasVenueTag . ec:summary "Poster overview of the PENGQUIN research direction, focusing on privacy-aware storage, RDF representation, and distributed querying for personal genomic data." . rdf:type ec:Poster . schema:name "PENGQUIN: Personal Genome Query in Healthcare and Clinical Practice" . schema:url . dcterms:identifier "edc-poster-isws2024-award-winner" . dcterms:isPartOf . ec:abstract "This poster presents the motivating research questions behind PENGQUIN, centered on using semantic-web technologies to support genomic data use in healthcare and clinical practice. It identifies major technical challenges such as governance, privacy granularity, data formatting, RDF conversion, data linkage, and scalable querying. The poster also outlines the engineering work needed to store genomic data in Solid pods, manage privacy-aware access, represent variant data in RDF, and support querying across one or many patient-controlled data pods." . ec:audienceExpertise "Semantic-web students, trainees, and researchers with interest in applying linked-data methods to sensitive biomedical data." . ec:displayDate "2024-06-15"^^xsd:date . ec:displayDateDetailedLabel "Saturday, 15 June 2024" . ec:displayDateLabel "15/06/2024" . ec:filePath "/talks/posters/EDC_Poster_ISWS2024(award_winner).pdf" . ec:goal "Communicate the PENGQUIN research vision clearly to a semantic-web training audience and motivate the main technical work packages." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:hasVenueTag . ec:summary "Award-winning poster introducing the PENGQUIN research problem space around personal genomic data storage, privacy, semantic representation, and distributed querying." . rdf:type ec:Poster . schema:name "PENGQUIN: Personal Genome Query in Healthcare and Clinical Practice" . schema:url . dcterms:identifier "eswc-2026-print" . dcterms:isPartOf . ec:abstract "This poster presents Solid Cockpit as a client-side web interface designed to reduce the practical complexity of working with Solid Pods. It integrates key workflows for uploading and organizing data, managing access and privacy controls, and querying resources through SPARQL in a single environment, while preserving a decentralized architecture. The approach emphasizes usability for non-expert users without removing advanced capabilities needed for semantic data workflows." . ec:audienceExpertise "Semantic web and decentralized data researchers interested in practical interfaces for privacy-aware Solid ecosystems." . ec:displayDate "2026-06-01"^^xsd:date . ec:displayDateDetailedLabel "Monday, 01 June 2026" . ec:displayDateLabel "30/04/2026" . ec:filePath "/talks/posters/eswc_2026_print.pdf" . ec:goal "Communicate the Solid Cockpit architecture, usability focus, and privacy-aware data interaction model for decentralized Solid Pod workflows." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasRelatedResource . ec:hasRelatedResource . ec:hasRelatedResource . ec:hasRelatedResource . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:hasVenueTag . ec:isPosterForTalk . ec:relatedSoftware . ec:summary "Poster overview of Solid Cockpit, a unified user interface for Solid Pods that combines data management, privacy control, notifications, and semantic querying." . rdf:type ec:Poster . schema:name "Solid Cockpit - ESWC 2026 Poster" . schema:url . dcterms:identifier "eswc-24-poster-edc" . dcterms:isPartOf . ec:abstract "This ESWC poster presents PENGQUIN as a patient-centric semantic-web approach to handling personal genomic data in healthcare settings. It highlights challenges in governance, privacy granularity, data formatting, RDF conversion, data linkage, and querying performance, then sketches a solution space built around Solid pods, RDF representations, and link-traversal querying. The poster also introduces a patient-centric storage model that connects genomic data, health data, and controlled access pathways across distributed resources." . ec:audienceExpertise "Semantic-web researchers and technically oriented conference attendees familiar with linked-data, web architecture, and knowledge graph methods." . ec:displayDate "2024-05-28"^^xsd:date . ec:displayDateDetailedLabel "Tuesday, 28 May 2024" . ec:displayDateLabel "28/05/2024" . ec:filePath "/talks/posters/ESWC_24_Poster_EDC.pdf" . ec:goal "Summarize the PENGQUIN PhD direction for the semantic-web research community and position its main technical challenges and solution strategy." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:hasVenueTag . ec:isPosterForTalk . ec:summary "Conference poster summarizing the PENGQUIN approach for privacy-aware genomic data storage, RDF conversion, and patient-centric query workflows." . rdf:type ec:Poster . schema:name "PENGQUIN: Personal Genome Query in Healthcare and Clinical Practice" . schema:url . dcterms:identifier "swat4hcls-2025" . dcterms:isPartOf . ec:abstract "This poster argues that VCF files remain difficult to integrate, query, and interpret semantically in their native form, then presents a conversion framework based on RDF to address those limitations. It introduces a VCF-focused ontology, an HDT-backed storage strategy, and the use of the RDF Mapping Language (RML) to express a reusable conversion pipeline that is not locked into a single hard-coded script. The poster also positions the work relative to existing VCF-to-RDF approaches and emphasizes future directions around ontology publication and pharmacogenomic data linkage." . ec:audienceExpertise "Semantic-web researchers, bioinformaticians, and genomics data practitioners interested in semantically interoperable variant data." . ec:displayDate "2025-02-24"^^xsd:date . ec:displayDateDetailedLabel "Monday, 24 February 2025" . ec:displayDateLabel "24/02/2025" . ec:filePath "/talks/posters/swat4hcls_2025.pdf" . ec:goal "Show that a richer semantic representation of VCF data can improve interoperability, data linking, and downstream genomic data use." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:hasVenueTag . ec:relatedSoftware . ec:relatedSoftware . ec:summary "Poster presenting a framework for semantically converting VCF genomic variant data into RDF using a dedicated ontology, HDT-based storage, and reusable mapping specifications." . rdf:type ec:Poster . schema:name "Semantifying Genomic Variant Data: VCF to RDF Conversion Framework" . schema:url . dcterms:identifier "swat4hcls-2026" . dcterms:isPartOf . ec:abstract "This poster introduces an RML-based approach for representing Variant Call Format (VCF) data in RDF in a way that preserves both the structural richness of VCF and compatibility with established semantic technologies. It frames the main challenges of VCF conversion around structural irregularity, weak semantics, limited interoperability, and constrained access-control patterns, then positions an RDF-based representation as a response. The proposed approach emphasizes complete file representation, explicit provenance and structure at header, record, and call levels, and ontology alignment with established genomic vocabularies such as SO, FALDO, and GENO. It also highlights the role of RML and RMLStreamer in expressing reusable declarative mappings that can scale to larger datasets." . ec:audienceExpertise "Semantic web researchers, bioinformaticians, and life-science data practitioners interested in genomic data interoperability and FAIR representation." . ec:displayDate "2026-03-24"^^xsd:date . ec:displayDateDetailedLabel "Tuesday, 24 March 2026" . ec:displayDateLabel "24/03/2026" . ec:filePath "/talks/posters/swat4hcls_2026.pdf" . ec:goal "Demonstrate that VCF-to-RDF conversion using declarative RML mappings is feasible and useful for interoperable, machine-actionable genomic variant data workflows." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:hasVenueTag . ec:relatedSoftware . ec:relatedSoftware . ec:summary "Poster presenting an RML-based method for converting full VCF variant files into RDF with stronger structure, provenance, interoperability, and privacy-aware semantics." . rdf:type ec:Poster . schema:name "SWAT4HCLS 2026 Poster: From VCF to RDF" . schema:url . dcterms:identifier "swat4hcls-24-poster-edc" . dcterms:isPartOf . ec:abstract "This poster examines how personal data pods could support more scalable and privacy-aware personalized medicine workflows. It motivates the need for a patient-centric approach by pointing to data duplication, poor transparency, limited sharing, and fragmented control in current institution-centric systems. The poster then frames the main research and engineering challenges around governance, consent, privacy granularity, data linkage, and querying performance, while presenting a unified framework for giving patients more direct control over sensitive genome data." . ec:audienceExpertise "Life-science and semantic-web researchers interested in privacy, interoperability, and data infrastructure for personalized medicine." . ec:displayDate "2024-02-26"^^xsd:date . ec:displayDateDetailedLabel "Monday, 26 February 2024" . ec:displayDateLabel "26/02/2024" . ec:filePath "/talks/posters/SWAT4HCLS_24_poster_EDC.pdf" . ec:goal "Present a patient-centric storage and access model for genomic medicine and clarify the key technical barriers to making it practical." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:hasVenueTag . ec:summary "Poster describing how patient-controlled data pods could improve privacy, transparency, and data sharing for genomic medicine workflows." . rdf:type ec:Poster . schema:name "Personalized Medicine Through Personal Data Pods" . schema:url . dcterms:identifier "google-scholar" . ec:profileVariant "scholar" . rdf:type ec:ExternalProfile . schema:name "Google Scholar" . schema:url . dcterms:identifier "orcid" . ec:profileVariant "orcid" . rdf:type ec:ExternalProfile . schema:name "ORCID" . schema:url . dcterms:identifier "research-portal" . ec:profileVariant "research-portal" . rdf:type ec:ExternalProfile . schema:name "Research Portal" . schema:url . dcterms:identifier "semantic-scholar" . ec:profileVariant "semantic" . rdf:type ec:ExternalProfile . schema:name "Semantic Scholar" . schema:url . dcterms:isPartOf . ec:order "1"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "Workshop Paper" . rdfs:label "Publication Type" . dcterms:isPartOf . ec:order "2"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "International 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dcterms:isPartOf . ec:order "5"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "Accepted" . rdfs:label "Status" . dcterms:isPartOf . ec:order "6"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "SPARQL Querying, Federated Querying, Real-World Querying, SPARQL Endpoints" . rdfs:label "Keywords" . dcterms:isPartOf . ec:order "7"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "Federated Query Results Explorer" . rdfs:label "Related Software" . schema:url . dcterms:isPartOf . ec:order "8"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "fed-survey-results" . rdfs:label "Companion Results Website" . schema:url . dcterms:isPartOf . ec:order "9"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "Not yet available" . rdfs:label "DOI" . dcterms:isPartOf . ec:order "1"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "Demo Paper (Conference Paper)" . rdfs:label "Publication Type" . dcterms:isPartOf . ec:order "2"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "European Semantic Web Conference (ESWC) 2026" . rdfs:label "Conference" . dcterms:isPartOf . ec:order "3"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "Dubrovnik, Croatia" . rdfs:label "Location" . dcterms:isPartOf . ec:order "4"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "2026-06-01" . rdfs:label "Date" . dcterms:isPartOf . ec:order "5"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "Solid Cockpit" . rdfs:label "Related Software" . schema:url . dcterms:isPartOf . ec:order "6"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "Solid Cockpit live demo" . rdfs:label "Demo Link" . schema:url . dcterms:isPartOf . ec:order "7"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "Not yet available" . rdfs:label "DOI" . dcterms:isPartOf . ec:order "8"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "Not yet available" . rdfs:label "Web Version" . dcterms:isPartOf . ec:order "1"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "Conference Paper" . rdfs:label "Publication Type" . dcterms:isPartOf . ec:order "2"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "SWAT4HCLS" . rdfs:label "Conference" . dcterms:isPartOf . ec:order "3"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "2024-02-26" . rdfs:label "Date" . dcterms:isPartOf . ec:order "4"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "CEUR paper PDF" . rdfs:label "Full Text" . schema:url . dcterms:isPartOf . ec:order "1"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "Journal Article" . rdfs:label "Publication Type" . dcterms:isPartOf . ec:order "2"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "PLOS ONE" . rdfs:label "Journal" . dcterms:isPartOf . ec:order "3"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "2023-04-13" . rdfs:label "Date" . dcterms:isPartOf . ec:order "4"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "10.1371/journal.pone.0283930" . 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dcterms:isPartOf . ec:order "1"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "Workshop Paper" . rdfs:label "Publication Type" . dcterms:isPartOf . ec:order "2"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "International Semantic Web Conference (ISWC)" . rdfs:label "Conference" . dcterms:isPartOf . ec:order "3"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "2025-11-02" . rdfs:label "Date" . dcterms:isPartOf . ec:order "4"^^xsd:integer . rdf:type ec:PublicationDetail . rdf:value "CEUR paper PDF" . rdfs:label "Full Text" . schema:url . ec:forPublication . ec:linksTalk . ec:order "1"^^xsd:integer . rdf:type ec:PublicationPresentationLink . schema:name "Presentation (PhD Symposium - ESWC 2024)" . ec:filePath "/talks/posters/ESWC_24_Poster_EDC.pdf" . ec:forPublication . ec:order "2"^^xsd:integer . rdf:type ec:PublicationPresentationLink . schema:name "Poster (PhD Symposium - ESWC 2024)" . schema:url . ec:filePath "/talks/posters/SWAT4HCLS_24_poster_EDC.pdf" . ec:forPublication . ec:order "1"^^xsd:integer . rdf:type ec:PublicationPresentationLink . schema:name "Poster (SWAT4HCLS 2024)" . schema:url . ec:forPublication . ec:linksTalk . ec:order "1"^^xsd:integer . rdf:type ec:PublicationPresentationLink . schema:name "Presentation (Solid Symposium 2026)" . ec:filePath "/talks/posters/eswc_2026_print.pdf" . ec:forPublication . ec:order "2"^^xsd:integer . rdf:type ec:PublicationPresentationLink . schema:name "Poster (ESWC 2026)" . schema:url . ec:filePath "/talks/posters/swat4hcls_2026.pdf" . ec:forPublication . ec:order "1"^^xsd:integer . rdf:type ec:PublicationPresentationLink . schema:name "Poster (SWAT4HCLS 2026)" . schema:url . ec:filePath "/talks/posters/swat4hcls_2025.pdf" . ec:forPublication . ec:order "1"^^xsd:integer . rdf:type ec:PublicationPresentationLink . schema:name "Poster (SWAT4HCLS 2025)" . schema:url . dcterms:identifier "disjointness-llm-ISWC-2024" . dcterms:isPartOf . ec:abstract "Ontologies often lack explicit disjointness declarations between classes, despite their usefulness for sophisticated reasoning and consistency checking in Knowledge Graphs. In this study, we explore the potential of Large Language Models (LLMs) to enrich ontologies by identifying and asserting class disjointness axioms. Our approach aims at leveraging the implicit knowledge embedded in LLMs, using prompt engineering to elicit this knowledge for classifying ontological disjointness. We validate our methodology on the DBpedia ontology, focusing on open-source LLMs. Our findings suggest that LLMs, when guided by effective prompt strategies, can reliably identify disjoint class relationships, thus streamlining the process of ontology completion without extensive manual input. For comprehensive disjointness enrichment, we propose a process that takes logical relationships between disjointness and subclass statements into account in order to maintain satisfiability and reduce the number of calls to the LLM. This work provides a foundation for future applications of LLMs in automated ontology enhancement and offers insights into optimizing LLM performance through strategic prompt design. Our code is publicly available on GitHub at https://github.com/n28div/llm-disjointness." . ec:authors "E. Crum, A. De Santis, M. Ovide, J. Pan, A. Pisu, N. Lazzari, S. Rudolph" . ec:bibtex "@misc{disjointness_LLM_2024,\n title={Enriching Ontologies with Disjointness Axioms using Large Language Models}, \n author={Elias Crum and Antonio De Santis and Manon Ovide and Jiaxin Pan and Alessia Pisu and Nicolas Lazzari and Sebastian Rudolph},\n year={2024},\n eprint={2410.03235},\n archivePrefix={arXiv},\n primaryClass={cs.AI},\n url={https://ceur-ws.org/Vol-3853/paper1.pdf}, \n urldate={2026-03-05},\n}" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasPublicationTypeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:publicationYear "2024"^^xsd:gYear . ec:sortDate "2024-12-02"^^xsd:date . ec:summary "Investigates how large language models can propose class disjointness axioms for ontologies, with validation on DBpedia and a workflow that preserves logical consistency while reducing manual effort." . ec:venue "International Semantic Web Conference (ISWC) 2024 (KBC-LM'24 workshop)" . rdf:type ec:Publication . schema:name "Enriching Ontologies with Disjointness Axioms using Large Language Models" . schema:url . dcterms:identifier "engineering-coliphages-2022" . dcterms:isPartOf . ec:abstract "In the US, around 60% of females will be diagnosed with a Urinary Tract Infection (UTI) in their lifetime, and Escherichia coli is the most implicated etiological agent in UTIs. Despite its frequent association with lower urinary tract symptoms, recent studies have found that the urinary microbiome (UMB), the viral, bacterial, and fungal resident members of the urinary tract, of healthy females can also consist of E. coli. While most research has focused on the bacterial constituents of the UMB, bacteriophages, viruses that infect bacteria, are far more abundant. Bacteriophages (phages) of other human microbiomes have been shown to play a significant role in shaping the bacterial community dynamics. While a handful of E. coli infecting phages (coliphages) have been characterized, little is known about the diversity of coliphages of the human UMB or their role within this microbial community. Of the known types of phages in nature, temperate phages have complex, broad impacts on bacterial populations and therefore, community dynamics, through both lytic and lysogenic means. One such widely studied impact is lysogenic conversion, the alteration of host phenotype by the infection and integration of a temperate phage. Lysogenic conversion has the potential to offer a host bacterium human-relevant phenotypes including antibiotic resistance or virulence factor production. Since it has been shown that UMB phages can exhibit host ranges broader than just their native host, phages could be facilitating the horizontal gene transfer of potentially harmful genes within the human UMB. Despite the threat posed by UMB temperate phages, little work has been done characterizing their integrated form, prophages, in UMB E. coli. Additionally, the ability of these phages to be induced form their native host, then infect and integrate into a non-native host has not been shown previously by phages of the human UMB. Here I present a two-part study into (i) the diversity of E. coli prophages within the human UMB and (ii) the ability of UMB temperate coliphages to be induced from a native host, engineered to be obligately lytic to then infect and lyse a non-native UMB host. First, 3,177 predicted intact prophages were identified from 961 urinary E. coli genome assemblies by the prophage predicting tool PHASTER. Prophages were pervasive; 95% of the strains contained at least one intact prophage (average >3 prophages per genome assembly). Furthermore, ~50% of these predicted prophages did not share significant sequence similarity to characterized phages, thus likely representing novel phages. Some predicted prophage sequences contained antibiotic resistance and virulence genes, but these genes were not common among the prophage sequences. Investigation of the predicted prophages’ integrase gene suggests that the UMB coliphages share common attachment sites for integration in the E. coli chromosome. Collectively, this study provides the first catalog of urinary E. coli temperate phages. Next, predicted intact prophages were induced from urinary E. coli strains using biologically relevant pH conditions. The induced phages were identified using PCR with primers designed based on the PHASTER sequence predictions. One of these induced prophages was then engineered from temperate to obligately lytic through the removal of its integrase gene sequence, and the host range of this engineered phage (d700) and its ancestral strain (i700) was assessed. d700 was able to lyse one strain of UMB E. coli that i700 was not suggesting that i700 infected and lysogenized the bacterium. This study shows that there is substantial diversity in UMB E. coli prophages and shows that some temperate coliphages can be induced, engineered to be obligately lytic, and lyse non-native hosts." . ec:authors "E. Crum" . ec:bibtex "@mastersthesis{crum2022cataloging,\n title={Cataloging and Engineering Temperate Coliphages of the Human Urinary Microbiome},\n author={Crum, Elias},\n school={Loyola University Chicago},\n year={2022},\n url={https://ecommons.luc.edu/luc_theses/4434/}\n urldate={2026-03-05},\n}" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasPublicationTypeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:publicationYear "2022"^^xsd:gYear . ec:sortDate "2022-09-01"^^xsd:date . ec:summary "Builds a large-scale catalog of urinary E. coli prophages and demonstrates induction plus engineering of temperate phages into obligately lytic variants for targeted lysis of non-native urinary strains." . ec:venue "Loyola University Chicago (Master's Thesis)" . rdf:type ec:Publication . schema:name "Cataloging and Engineering Temperate Coliphages of the Human Urinary Microbiome" . schema:url . dcterms:identifier "gardnerella-characterization-2021" . dcterms:isPartOf . ec:abstract "Gardnerella is a frequent member of the urogenital microbiota. Given the association between Gardnerella vaginalis and bacterial vaginosis (BV), significant efforts have been focused on characterizing this species in the vaginal microbiota. However, Gardnerella also is a frequent member of the urinary microbiota. In an effort to characterize the bacterial species of the urinary microbiota, we present here 10 genomes of urinary Gardnerella isolates from women with and without lower urinary tract symptoms. These genomes complement those of 22 urinary Gardnerella strains previously isolated and sequenced by our team. We included these genomes in a comparative genome analysis of all publicly available Gardnerella genomes, which include 33 urinary isolates, 78 vaginal isolates, and 2 other isolates. While once this genus was thought to consist of a single species, recent comparative genome analyses have revealed 3 new species and an additional 9 groups within Gardnerella. Based upon our analysis, we suggest a new group for the species. We also find that distinction between these Gardnerella species/groups is possible only when considering the core or whole-genome sequence, as neither the sialidase nor vaginolysin genes are sufficient for distinguishing between species/groups despite their clinical importance. In contrast to the vaginal microbiota, we found that only five Gardnerella species/groups have been detected within the lower urinary tract. Although we found no association between a particular Gardnerella species/group(s) and urinary symptoms, further sequencing of urinary Gardnerella isolates is needed for both comprehensive taxonomic characterization and etiological classification of Gardnerella in the urinary tract." . ec:authors "C. Putonti, K. Thomas-White, E. Crum, E. E. Hilt, T. K. Price, A. J. Wolfe" . ec:bibtex "@article{putonti2021genome,\n title={Genome Investigation of Urinary Gardnerella Strains and Their Relationship to Isolates of the Vaginal Microbiota},\n author={Putonti, Catherine and Thomas-White, Krystal and Crum, Elias and Hilt, Evann E. and Price, Travis K. and Wolfe, Alan J.},\n journal={mSphere},\n volume={6},\n number={3},\n pages={e00154-21},\n year={2021},\n doi={10.1128/mSphere.00154-21},\n}" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasPublicationTypeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:publicationYear "2021"^^xsd:gYear . ec:sortDate "2021-05-12"^^xsd:date . ec:summary "Compares urinary and vaginal Gardnerella genomes, identifying species-level structure and showing that whole-genome analysis is needed for reliable differentiation across groups in urogenital microbiota." . ec:venue "mSphere 6(3), e00154-21" . rdf:type ec:Publication . schema:name "Genome Investigation of Urinary Gardnerella Strains and Their Relationship to Isolates of the Vaginal Microbiota" . schema:url . dcterms:identifier "genome-sharing-review-2026" . dcterms:isPartOf . ec:abstract "A key barrier to scaling genomic medicine is sharing patient genomic data. This study assesses current genomic data sharing approaches, infrastructure, and guidelines, while incorporating insights from national initiatives and industry to ensure broad relevance. We aim to provide a foundation for dialogue by highlighting current challenges and barriers while promoting actionable standards and future points of emphasis. Our analysis uses Arksey & O’Malley’s scoping review framework to survey peer-reviewed articles, gray literature, national genomics initiatives, and corporate strategies to address four questions revolving around what genome data sharing approaches exist in: 1. Clinical-care, 2. Research, 3. National genome initiatives, and 4. Corporations. We identified 55 studies, separated them into groups, and determined 7 core components of an implementable technology. Notably, the studies included 15 clinical genome sharing implementations, 9 research-focused frameworks, and 13 ethical/legal guidelines. We also analyzed 57 active national genome initiatives and 20 major genomics companies. We found implementations for clinical genomic data sharing exist, yet scalability and widespread adoption remain limited. We identify scalability, clinical versus research-grade infrastructure requirements, and genomic medicine maturity as main challenges to overcome and suggest 4 steps that will encourage a unified path forward. Our discussion aims to facilitate discourse and catalyze future genomic data sharing system innovation." . ec:authors "E. Crum, R. Taelman, B. Buelens, G. Ertaylan" . ec:bibtex "@article{crum_genomesharingrev_2025,\n author = {Crum, Elias and Taelman, Ruben and Buelens, Bart and Ertaylan, Gokhan},\n title = {Genomic sequence data sharing for clinical practice: A scoping review},\n month = jan,\n journal = {Computers in Biology and Medicine},\n volume = {200},\n pages = {111335},\n year = {2026},\n issn = {0010-4825},\n doi = {https://doi.org/10.1016/j.compbiomed.2025.111335},\n }" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasPublicationTypeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:publicationYear "2026"^^xsd:gYear . ec:relatedSoftware . ec:sortDate "2026-01-01"^^xsd:date . ec:summary "Scoping review of how genomic sequence data is shared in clinical practice, surveying implementations, infrastructure, and guidance. Identifies key barriers to scalability and adoption, and proposes concrete steps toward more unified, scalable clinical genomic data sharing systems." . ec:venue "Computers in Biology and Medicine" . rdf:type ec:Publication . schema:name "Genomic sequence data sharing for clinical practice: A scoping review" . schema:url . dcterms:identifier "genomic-variant-representation-rdf-preprint-2025" . dcterms:isPartOf . ec:abstract "During the International SWAT4HCLS conference held on 24-27th February 2025 in Barcelona (Spain), we detected an emerging number of novel RDF models to represent variant information in genomic datasets potentially hindering data reuse. We tackled the question how semantic representations can enhance the interoperability of variant data for clinical applications. Here we report our initial results on genomic variant schema alignment." . ec:authors "N. Queralt-Rosinach, A. J. Kellmann, A. Bodrug-Schepers, A. Gaignard, E. Crum, P. Larmande, A. Waagmeester, J. Bolleman" . ec:bibtex "@misc{crum2025genomicvariantrdf,\n title={Variant representation in RDF},\n author={Queralt-Rosinach, Nuria and Kellmann, Alexander Jonathan and Bodrug-Schepers, Alexandrina and Gaignard, Alban and Crum, Elias and Larmande, Pierre and Waagmeester, Andra and Bolleman, Jerven},\n year={2025},\n month={feb},\n note={BioHackrXiv preprint associated with SWAT4HCLS BioHackathon 2025},\n doi={10.37044/osf.io/jazsb_v1},\n url={https://doi.org/10.37044/osf.io/jazsb_v1},\n}" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasPublicationTypeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:paperPdfPath "/publications/papers/variant-representation-in-rdf.pdf" . ec:publicationYear "2025"^^xsd:gYear . ec:relatedSoftware . ec:relatedSoftware . ec:sortDate "2025-02-24"^^xsd:date . ec:summary "Reports initial BioHackathon results on aligning genomic variant RDF schemas identified at SWAT4HCLS 2025, with focus on improving interoperability and reuse of variant data for clinical applications." . ec:venue "BioHackrXiv" . rdf:type ec:Publication . schema:name "Variant representation in RDF" . schema:url . schema:url . dcterms:identifier "pengquin-eswc-2024-paper" . ec:hasPresentationLink . ec:hasPresentationLink . ec:isResolved "false"^^xsd:boolean . ec:relatedTalk . rdf:type ec:PublicationReference . dcterms:identifier "pengquin-eswc-2024" . dcterms:isPartOf . ec:abstract "Medical care is in the process of becoming increasingly personalized through the use of patient genetic information. At present, data useful for clinical care, including genetic data, is commonly diffuse, organized arbitrarily, and stored in data silos. Thus, unstructured organization, high costs for data storage and generation, and tight privacy restrictions pose serious challenges to scaling personalized clinical strategies. I propose an early stage Ph.D. that aims to improve the connectedness and shareability of genomic data storage(s), while preserving data privacy, to decrease the costs of using patient genome data in clinical practice. In this pursuit, I will integrate various domains of semantic web research into a novel, holistic framework designed for use in clinical practice. Specifically, I will (a) store patient data using Solid pods, (b) represent personal genome sequence data in RDF as Linked Data, (c) attach policies to stored data, and (d) query data through link traversal queries." . ec:authors "E. Crum" . ec:bibtex "@inproceedings{crum2024pengquin,\n title={PErsoNal Genome QUery IN healthcare and clinical practice (PENGQUIN)},\n author={Crum, Elias},\n booktitle={European Semantic Web Conference 2024 Satellite Events},\n year={2024},\n publisher=\"Springer Nature Switzerland\",\n isbn=\"978-3-031-78955-7\"\n doi={10.1007/978-3-031-78955-7_3},\n}" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasPublicationTypeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:publicationYear "2024"^^xsd:gYear . ec:sortDate "2024-05-26"^^xsd:date . ec:summary "Presents the PENGQUIN PhD framework for privacy-preserving genomic data sharing and querying using Solid pods, RDF/Linked Data representations, policy attachments, and link-traversal querying." . ec:venue "European Semantic Web Conference (ESWC) 2024" . rdf:type ec:Publication . schema:name "PErsoNal Genome QUery IN healthcare and clinical practice (PENGQUIN)" . schema:url . dcterms:identifier "pm-pods-SWAT4HCLS-2024" . dcterms:isPartOf . ec:abstract "Medical care is in the process of becoming increasingly personalized through the use of patient genetic information. Meanwhile, privacy concerns regarding collection and storage of sensitive personal genome sequence data have encouraged public debate and legal regulation. Here we identify two fundamental challenges associated with privacy and shareability of genomic data storage (s) and propose the use of Solid pods to address these challenges. We establish that personal data pods using Solid specifications can enable decentralized storage, increased patient control over their data, and support of Linked Data formats, which when combined, could offer solutions to challenges currently restricting personalized medicine in practice." . ec:authors "E. Crum, R. Taelman, B. Buelens, G. Ertaylan, R. Verborgh" . ec:bibtex "@inproceedings{crum2024pmpods,\n title={Personalized medicine through personal data pods},\n author={Crum, Elias and Taelman, Ruben and Buelens, Bart and Ertaylan, Gokhan and Verborgh, Ruben},\n booktitle={Proceedings of the 15th International SWAT4HCLS Conference},\n year={2024},\n url={https://ceur-ws.org/Vol-3890/paper-25.pdf}\n urldate={2026-03-05},\n}" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasPresentationLink . ec:hasPublicationTypeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:publicationYear "2024"^^xsd:gYear . ec:sortDate "2024-02-26"^^xsd:date . ec:summary "Describes how Solid-based personal data pods can address privacy and data-sharing bottlenecks in genomic medicine by decentralizing storage and giving patients finer control over sensitive genomic data." . ec:venue "Proceedings of the 15th International SWAT4HCLS Conference (CEUR Workshop Proceedings)" . rdf:type ec:Publication . schema:name "Personalized medicine through personal data pods" . schema:url . dcterms:identifier "real-world-federation-iswc-2026" . dcterms:isPartOf . ec:abstract "Federated SPARQL querying theoretically enables data integration over distributed knowledge sources without requiring centralized data replication. In practice, federated SPARQL querying can be performed manually (i.e., the user provides SERVICE clauses that specify targets for operations) or algorithmically (i.e., an adaptive approach for automatic source assignment for operations). To date, most evaluations of SPARQL federation, both manual and algorithmic, are conducted under controlled benchmark conditions and say relatively little about how federation behaves against public endpoints in everyday use. We present a longitudinal study that executes 67 real-world federated SPARQL queries that target over 20 widely-used, large public SPARQL endpoints, using both manual and algorithmic federation approaches, at four different time points between Spring 2025 and Spring 2026. The federated queries were obtained from users of these endpoints and the majority represent complex, biologically relevant questions. We found that the current state-of-the-art algorithmic federation approaches perform substantially worse than manual approaches across all time points, and in most cases encounter errors when executing the queries tested. We also found that query execution success decreased over the time points tested for both manual and automatic methods. These findings are framed from both user and endpoint-maintainer perspectives to encourage collaborative, community-driven improvements for users and data source maintainers alike." . ec:authors "E. Crum, B.-E. Tam, J. Hanski, A.-C. Sima, T. Mendes de Farias, J. Bolleman, R. Taelman" . ec:bibtex "@inproceedings{crum2026realworldfederation,\n title={Does SPARQL federation work in the real world? A case study over large biological SPARQL endpoints},\n author={Crum, Elias and Tam, Bryan-Elliott and Hanski, Jonni and Sima, Ana-Claudia and Mendes de Farias, Tarcisio and Bolleman, Jerven and Taelman, Ruben},\n booktitle={International Semantic Web Conference (ISWC) 2026},\n address={Bari, Italy},\n month={oct},\n year={2026},\n note={Accepted conference paper},\n}" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasPublicationTypeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:paperPdfPath "/publications/papers/iswc-2026-real-world-federation-paper.pdf" . ec:publicationYear "2026"^^xsd:gYear . ec:relatedSoftware . ec:sortDate "2026-10-27"^^xsd:date . ec:summary "Presents an 18-month longitudinal study of 67 real-world federated biological SPARQL queries over more than 20 public endpoints, and shows that a) execution success declines over time with very few queries functional by June 2026, b) current algorithmic federation approaches perform substantially worse than manual federation, and c) work is needed to assess how to enable federation over public endpoints in the age of the LLM." . ec:venue "International Semantic Web Conference (ISWC) 2026" . rdf:type ec:Publication . schema:name "Does SPARQL federation work in the real world? A case study over large biological SPARQL endpoints" . schema:url . dcterms:identifier "solid-cockpit-eswc-2026-demo" . dcterms:isPartOf . ec:abstract "Solid enables decentralized, user-controlled personal data management, but practical Pod interaction remains difficult because existing interfaces typically cover only isolated workflow fragments. This demo paper presents Solid Cockpit, a browser-based system that unifies Pod data management, visual privacy control, and semantic querying in one interface. In addition to CRUD-style Pod interaction, the system supports auditable permission-change notifications and Pod-native storage of query results through draft technical specifications. The application is positioned against related Solid systems and demonstrates how privacy-transparent sharing and query workflows can be operationalized for broader Solid usage." . ec:authors "E. Crum, B. Buelens, G. Ertaylan, R. Taelman" . ec:bibtex "@inproceedings{crum2026solidcockpitdemo,\n title={Solid Cockpit: Data manager, privacy editor, and query facilitator for Solid pods},\n author={Crum, Elias and Buelens, Bart and Ertaylan, Gokhan and Taelman, Ruben},\n booktitle={European Semantic Web Conference (ESWC) 2026},\n address={Dubrovnik, Croatia},\n year={2026},\n note={Demo paper},\n}" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasPresentationLink . ec:hasPresentationLink . ec:hasPublicationTypeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:paperPdfPath "/publications/papers/eswc-2026-demo-paper.pdf" . ec:publicationYear "2026"^^xsd:gYear . ec:relatedSoftware . ec:relatedTalk . ec:sortDate "2026-06-01"^^xsd:date . ec:summary "Presents Solid Cockpit, a browser-based interface for managing Solid Pods that integrates data management, privacy-aware permission workflows, and embedded SPARQL querying with result materialization." . ec:venue "European Semantic Web Conference (ESWC) 2026" . rdf:type ec:Publication . schema:name "Solid Cockpit: Data manager, privacy editor, and query facilitator for Solid pods" . schema:url . dcterms:identifier "TRIPLE-SWAT4HCLS-2024" . dcterms:isPartOf . ec:abstract "The TRIPLE project, a collaborative effort between the SIB Swiss Institute of Bioinformatics, the University of Ghent and the IOCB Prague, aims to boost the (re) usability of existing knowledge graph resources and improve software tools for RDF data access, documentation and data model visualization. In addition, TRIPLE will increase interoperability between existing public SPARQL endpoints and private data stored in Solid Pods, thus creating an ecosystem of research data that can be seamlessly integrated through efficient and expressive federated SPARQL queries." . ec:authors "J. Bolleman, E. Crum, I. Dragan, J. Galgonek, M. Ibberson, T. Mendes de Farias, M. Moos, M. Pagni, R. Taelman, J. Vondrášek, A. C. Sima" . ec:bibtex "@inproceedings{bolleman2024triple,\n title={CHIST-ERA Triple: improving data interoperability and federation across RDF knowledge graphs and Solid Pods},\n author={Bolleman, Jerven and Crum, Elias and Dragan, Iulian and Galgonek, Jakub and Ibberson, Mark and Mendes de Farias, Tarcisio and Moos, Marek and Pagni, Marco and Taelman, Ruben and Vondrášek, Jiří and Sima, Ana Claudia},\n booktitle={Proceedings of the 15th International SWAT4HCLS Conference},\n year={2024},\n url={https://ceur-ws.org/Vol-3890/paper-28.pdf}\n urldate={2026-03-05},\n}" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasPublicationTypeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:publicationYear "2024"^^xsd:gYear . ec:sortDate "2024-02-26"^^xsd:date . ec:summary "Describes how Solid-based data pods can address privacy and data-sharing bottlenecks in academic research by allowing felxible sharing of sensitive research data and result/experimental data provenance." . ec:venue "Proceedings of the 15th International SWAT4HCLS Conference (CEUR Workshop Proceedings)" . rdf:type ec:Publication . schema:name "CHIST-ERA Triple: improving data interoperability and federation across RDF knowledge graphs and Solid Pods" . schema:url . dcterms:identifier "urinary-coliphages-2023" . dcterms:isPartOf . ec:abstract "Due to its frequent association with urinary tract infections (UTIs), Escherichia coli is the best characterized constituent of the urinary microbiota (urobiome). However, uropathogenic E. coli is just one member of the urobiome. In addition to bacterial constituents, the urobiome of both healthy and symptomatic individuals is home to a diverse population of bacterial viruses (bacteriophages). A prior investigation found that most bacterial species in the urobiome are lysogens, harboring one or more phages integrated into their genome (prophages). Many of these prophages are temperate phages, capable of entering the lytic cycle and thus lysing their bacterial host. This transition from the lysogenic to lytic life cycle can impact the bacterial diversity of the urobiome. While many phages that infect E. coli (coliphages) have been studied for decades in the laboratory setting, the coliphages within the urobiome have yet to be cataloged. Here, we investigated the diversity of urinary coliphages by first identifying prophages in all publicly available urinary E. coli genomes. We detected 3,038 intact prophage sequences, representative of 1,542 unique phages. These phages include both novel species as well as species also found within the gut microbiota. Ten temperate phages were isolated from urinary E. coli strains included in our analysis, and we assessed their ability to infect and lyse urinary E. coli strains. We also included in these host range assays other urinary coliphages and laboratory coliphages. The temperate phages and other urinary coliphages were successful in lysing urinary E. coli strains. We also observed that coliphages from non-urinary sources were most efficient in killing urinary E. coli strains. The two phages, T2 and N4, were capable of lysing 83.5% (n = 86) of strains isolated from females with UTI symptoms. In conclusion, our study finds a diverse community of coliphages in the urobiome, many of which are predicted to be temperate phages, ten of which were confirmed here. Their ability to infect and lyse urinary E. coli strains suggests that urinary coliphages may play a role in modulating the E. coli strain diversity of the urobiome." . ec:authors "E. Crum, Z. Merchant, A. Ene, T. Miller-Ensminger, G. Johnson, A. J. Wolfe, C. Putonti" . ec:bibtex "@article{crum2023coliphages,\n title={Coliphages of the human urinary microbiota},\n author={Crum, Elias and Merchant, Zubia and Ene, Adriana and Miller-Ensminger, Taylor and Johnson, Genevieve and Wolfe, Alan J. and Putonti, Catherine},\n journal={PLOS ONE},\n volume={18},\n number={4},\n pages={e0283930},\n year={2023},\n doi={10.1371/journal.pone.0283930},\n}" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasPublicationTypeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:publicationYear "2023"^^xsd:gYear . ec:sortDate "2023-04-13"^^xsd:date . ec:summary "Catalogs urinary E. coli phage diversity and shows that multiple urinary and non-urinary coliphages can lyse urinary E. coli strains, supporting a role for phages in shaping urobiome composition." . ec:venue "PLoS ONE 18(4), e0283930" . rdf:type ec:Publication . schema:name "Coliphages of the human urinary microbiota" . schema:url . dcterms:identifier "vcf-to-rdf-rml-swat4hcls-2026" . dcterms:isPartOf . ec:abstract "Representing Variant Call Format (VCF) data using the Resource Description Framework (RDF) offers benefits in interoperability, integration with other biomedical datasets, and selective privacy protections. Due to complexities of the data represented in VCF files, conversion of VCF to RDF poses challenges, especially concerning complex, heterogeneous data fields. Here, we propose converting VCF files to serialized RDF using the RML mapping language and established genomic data ontologies. Such a methodology will demonstrate the feasibility of an RML-based approach and inform a more FAIR, machine-actionable representation strategy for representing VCF data that is compatible with semantic data privacy policies and useful in both clinical and academic domains." . ec:authors "E. Crum, B. Buelens, G. Ertaylan, R. Taelman" . ec:bibtex "@inproceedings{crum2026vcf2rdfposter,\n title={From VCF to RDF: RML-Based Conversion Approaches for the Semantic Representation of Variant Data},\n author={Crum, Elias and Buelens, Bart and Ertaylan, Gokhan and Taelman, Ruben},\n booktitle={SWAT4HCLS 2026: Bridging Life Sciences and Technology},\n year={2026},\n month={mar},\n address={Amsterdam, Netherlands},\n note={Poster paper},\n}" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasPresentationLink . ec:hasPublicationTypeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:paperPdfPath "/publications/papers/swat4hcls-2026-poster-paper.pdf" . ec:publicationYear "2026"^^xsd:gYear . ec:relatedSoftware . ec:relatedSoftware . ec:sortDate "2026-03-24"^^xsd:date . ec:summary "Presents an RML-based approach for converting VCF genomic variant files into RDF using established ontologies, targeting more interoperable, queryable, and privacy-aware variant data representation." . ec:venue "SWAT4HCLS 2026" . rdf:type ec:Publication . schema:name "From VCF to RDF: RML-Based Conversion Approaches for the Semantic Representation of Variant Data" . schema:url . dcterms:identifier "vcf2rdf-SWAT4HCLS-2025" . dcterms:isPartOf . ec:abstract "Variant Call Format (VCF) files, the standard for representing patient genomic variant data, face limitations in interoperability, data linking, querying, and semantic interpretability. We propose a framework for converting VCF data into semantic data using the Resource Description Framework (RDF) to address these limitations. Our approach includes a comprehensive ontology, a storage-efficient RDF representation using Header Dictionary Triples (HDT), and integration with clinical metadata schemas like that proposed by SPHN. Our framework and the representation of VCF data semantically will contribute to greater integration, scalability, and usability of these genomic variant data in both genomic medicine and research." . ec:authors "E. Crum, R. Taelman, B. Buelens, G. Ertaylan, R. Verborgh" . ec:bibtex "@inproceedings{crum2025semantifying,\n title={Semantifying Genomic Variant Data: VCF to RDF Conversion Framework},\n author={Crum, Elias and Taelman, Ruben and Buelens, Bart and Ertaylan, Gokhan and Verborgh, Ruben},\n booktitle={Proceedings of the 16th International SWAT4HCLS Conference},\n address={Barcelona, Spain},\n month={feb},\n year={2025},\n}" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasPresentationLink . ec:hasPublicationTypeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:paperPdfPath "/publications/papers/swat4hcls-2025-vcf-to-rdf-paper.pdf" . ec:publicationYear "2025"^^xsd:gYear . ec:relatedSoftware . ec:relatedSoftware . ec:sortDate "2025-02-24"^^xsd:date . ec:summary "Introduces a framework for converting VCF genomic variant files into RDF, combining a comprehensive ontology, storage-efficient HDT serialization, and alignment with clinical metadata schemas to improve interoperability, data linking, querying, and semantic interpretability." . ec:venue "Proceedings of the 16th International SWAT4HCLS Conference (CEUR Workshop Proceedings)" . rdf:type ec:Publication . schema:name "Semantifying Genomic Variant Data: VCF to RDF Conversion Framework" . schema:url . dcterms:identifier "wikidata-sparql-ISWC-2025" . dcterms:isPartOf . ec:abstract "The recent Wikidata graph split divided a previously singular SPARQL endpoint into two distinct ones, breaking existing queries that depend on the combined data from these endpoints. To accommodate this graph split, instructions for manual source assignment have been provided. However, the proposed solution of manual source annotations within the queries themselves, through the use of SPARQL SERVICE clauses, not only imposes additional work on users of these endpoints, but also assumes prior knowledge of which data come from which endpoint, and how they should be combined. Potential future graph splits would result in this manual source assignment having to be done again. Within this work, we employ client-side query federation over the two Wikidata endpoints, using state-of-the-art source assignment approaches for query operations, to demonstrate the feasibility and challenges of automated federation as an alternative to manual source assignment. Through our experiments, we show how client-side federation can offer a viable alternative to manual source assignment for certain queries, where the amount of data to process remains within client-side resource limits, and provided no custom behaviour is attached to standard SPARQL operations. Future work will be needed to address the trade-offs between network request counts and client-side data processing, to be able to execute queries that access large amounts of data from multiple sources." . ec:authors "J. Hanski, E. Crum, R. Taelman" . ec:bibtex "@misc{federation_wikidata_2025,\n title={Observations on automated client-side query federation over Wikidata SPARQL endpoints}, \n author={Jonni Hanski and Elias Crum and Ruben Taelman},\n year={2025},\n url={https://wikidataworkshop.github.io/2025/papers/paper5.pdf}, \n urldate={2026-03-05},\n}" . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasPublicationTypeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:publicationYear "2025"^^xsd:gYear . ec:sortDate "2025-11-02"^^xsd:date . ec:summary "Client-side query federation can automatically combine data across the newly split Wikidata SPARQL endpoints, reducing the need for manual source annotations in queries while remaining feasible for queries that stay within client resource limits." . ec:venue "International Semantic Web Conference (ISWC) 2025 (WikiData workshop)" . rdf:type ec:Publication . schema:name "Observations on automated client-side query federation over Wikidata SPARQL endpoints" . schema:url . rdf:type ec:RelatedResource . schema:name "Demo Video" . schema:url . rdf:type ec:RelatedResource . schema:name "Related Software" . schema:url . rdf:type ec:RelatedResource . schema:name "Related Publication" . schema:url . rdf:type ec:RelatedResource . schema:name "Related Talk" . schema:url . rdf:type ec:RelatedResource . schema:name "MetaboLinkAI" . schema:url . rdf:type ec:RelatedResource . schema:name "Related Software" . schema:url . rdf:type ec:RelatedResource . schema:name "Related Publication" . schema:url . rdf:type ec:RelatedResource . schema:name "MetaboLinkAI" . schema:url . rdf:type ec:RelatedResource . schema:name "Related Software" . schema:url . rdf:type ec:RelatedResource . schema:name "Related Publication" . schema:url . dcterms:isPartOf . dcterms:modified "2026-05-04T07:20:41.484Z"^^xsd:dateTime . rdf:type ec:ScholarCitationSnapshot . dcterms:isPartOf . ec:order "1"^^xsd:integer . rdf:type ec:SoftwareDetail . rdf:value "ontology-companion-generator on npm" . rdfs:label "Package Registry" . schema:url . dcterms:isPartOf . ec:order "1"^^xsd:integer . rdf:type ec:SoftwareDetail . rdf:value "https://w3id.org/vcf-core/vocab#" . rdfs:label "Namespace" . schema:url . dcterms:isPartOf . ec:order "2"^^xsd:integer . rdf:type ec:SoftwareDetail . rdf:value "v2.0.0" . rdfs:label "Version" . schema:url . dcterms:isPartOf . ec:order "3"^^xsd:integer . rdf:type ec:SoftwareDetail . rdf:value "Renamed from VCF-RDFizer Vocabulary; 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It is intended to make the experimental findings easier to inspect, revisit, and communicate beyond the static paper." . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:purpose "Experimental Results Exploration" . ec:relatedPublication . ec:softwareType "Companion Website" . ec:summary "Interactive results website for exploring longitudinal federation experiments over real-world biological SPARQL endpoints." . ec:webUrl . ec:year "2026" . rdf:type ec:Software . schema:name "Federated Query Results Explorer" . schema:url . dcterms:identifier "genome-sharing-paper-webpage" . dcterms:isPartOf . ec:description "This repository contains the companion website that displays national genomic initiative data. It is meant to make the review outputs easier to revisit and communicate beyond the PDF publication itself." . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:latestRelease . ec:purpose "Public Data Resource" . ec:relatedPublication . ec:repositoryUrl . ec:softwareType "Companion Website" . ec:summary "Supporting website for the genomic sequence data sharing scoping review paper, intended to make national genome initiative data easier to browse, revisit, and update in the future." . ec:year "2026" . rdf:type ec:Software . schema:codeRepository . schema:name "Genome Sharing Paper Webpage" . schema:url . dcterms:identifier "ldp-permissions-notifications-specification" . dcterms:isPartOf . ec:description "This work establishes guidelines for linked data privacy permission handling and notification semantics for Linked Data Platform resources. It is a standard to be used by developers for use in the broader ecosystem of interoperable linked-data infrastructure design." . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:latestRelease . ec:purpose "Standards Design" . ec:repositoryUrl . ec:softwareType "Technical Specification Draft" . ec:summary "Permissions and notification semantics technical specification for Linked Data Platform resources." . ec:year "Ongoing" . rdf:type ec:Software . schema:codeRepository . schema:name "LDP Permissions Notifications Specification" . schema:url . dcterms:identifier "ontology-companion-generator" . dcterms:isPartOf . ec:description "Ontology Companion Generator is a tool for automatically generating a companion website for an ontology directly from the ontology's home GitHub repository. It runs as an npm package and can produce GitHub Pages-ready outputs for ontology exploration, visualization, and documentation, while allowing extensive customization through a configuration file." . ec:hasDetail . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:latestRelease . ec:purpose "Ontology Documentation Generation" . ec:repositoryUrl . ec:softwareType "Ontology Documentation Tool" . ec:summary "An npm-based generator that creates GitHub Pages companions for exploring, visualizing, and documenting ontologies with configurable output." . ec:webUrl . ec:year "2026" . rdf:type ec:Software . schema:codeRepository . schema:name "Ontology Companion Generator" . schema:url . dcterms:identifier "qr-code-generator" . dcterms:isPartOf . ec:description "A utility project for quickly creating QR codes for links and references in research-facing assets such as conference posters, presentation slides, and supporting documentation." . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:latestRelease . ec:purpose "Research Communication" . ec:repositoryUrl . ec:softwareType "Utility Tool" . ec:summary "Lightweight generator for producing QR codes that can be reused in posters, slides, and project materials." . ec:year "2026" . rdf:type ec:Software . schema:codeRepository . schema:name "QR Code Generator" . schema:url . dcterms:identifier "solid-cockpit" . dcterms:isPartOf . ec:description "Solid Cockpit is a browser-based interface for managing Solid Pod data, editing permissions, handling notifications, and executing SPARQL queries. It also supports materializing query results for reuse." . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:latestRelease . ec:purpose "Interface for Solid Pod Interaction" . ec:relatedPoster . ec:relatedPublication . ec:relatedTalk . ec:repositoryUrl . ec:softwareType "Web Application" . ec:summary "Web application for interacting with Solid Pod resources in an integrated, user-friendly interface." . ec:year "Ongoing" . rdf:type ec:Software . schema:codeRepository . schema:name "Solid Cockpit" . schema:url . dcterms:identifier "sparql-view-materialization-containers" . dcterms:isPartOf . ec:description "This technical specification outlines materialization of SPARQL query records into a containerized environment so they can be easily reproduced, executed, and used as a cache for future query executions. 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It includes SHACL shapes and provides expanded and condensed representations for genotype data at different cohort scales." . ec:hasDetail . ec:hasDetail . ec:hasDetail . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:latestRelease . ec:purpose "VCF Semantic Modeling" . ec:relatedPoster . ec:relatedPoster . ec:relatedPublication . ec:relatedPublication . ec:relatedPublication . ec:repositoryUrl . ec:softwareType "Semantic Vocabulary and SHACL Shapes" . ec:summary "Vocabulary and SHACL shapes for representing the logical VCF 4.5 model in RDF." . ec:webUrl . ec:year "2026" . rdf:type ec:Software . schema:codeRepository . schema:name "VCF-Core Vocabulary" . schema:url . dcterms:identifier "vcf-rdfizer" . dcterms:isPartOf . ec:description "VCF-RDFizer converts genomic variant data into RDF using the RML mapping language and the RMLStreamer conversion engine. It uses the VCF Core Vocabulary as a converter-independent semantic model while offering compression options to reduce the effects of semantic inflation." . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:latestRelease . ec:purpose "RDF Data Conversion" . ec:relatedPoster . ec:relatedPoster . ec:relatedPublication . ec:relatedPublication . ec:relatedPublication . ec:repositoryUrl . ec:softwareType "RDF Conversion Tool" . ec:summary "A CLI tool for converting genomic variant data from VCF into RDF, supporting semantically interoperable downstream workflows." . ec:year "2026" . rdf:type ec:Software . schema:codeRepository . schema:name "VCF-RDFizer" . schema:url . dcterms:identifier "vord" . dcterms:isPartOf . ec:description "This repository provides the VoRD vocabulary as a semantic resource intended for exploration, visualization, and documentation. It fits the same companion-resource pattern as other ontology-facing sites in the project and supports clearer inspection of vocabulary structure and intended usage." . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:latestRelease . ec:purpose "Semantic Vocabulary Reference" . ec:repositoryUrl . ec:softwareType "Semantic Vocabulary" . ec:summary "Semantic vocabulary resource for documenting and exploring VoRD in a browsable, companion-style format." . ec:year "2026" . rdf:type ec:Software . schema:codeRepository . schema:name "Vocabulary of Restrictive Datasets (VoRD)" . schema:url . ec:isDeclaredOption "false"^^xsd:boolean . ec:isDeclaredOption "true"^^xsd:boolean . ec:tagKind "audience-group" . rdf:type ec:Tag . skos:prefLabel "Bioinformaticians" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "audience-group" . rdf:type ec:Tag . skos:prefLabel "Biologists" . ec:isDeclaredOption "false"^^xsd:boolean . ec:isDeclaredOption "true"^^xsd:boolean . ec:tagKind "audience-group" 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skos:prefLabel "Notifications" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "topic" . rdf:type ec:Tag . rdf:type ec:TopicTag . skos:prefLabel "Ontology Engineering" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "topic" . rdf:type ec:Tag . rdf:type ec:TopicTag . skos:prefLabel "Ontology Tooling" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "topic" . rdf:type ec:Tag . rdf:type ec:TopicTag . skos:prefLabel "Permissions" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "topic" . rdf:type ec:Tag . rdf:type ec:TopicTag . skos:prefLabel "Personalized Medicine" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "topic" . rdf:type ec:Tag . rdf:type ec:TopicTag . skos:prefLabel "RDF" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "topic" . rdf:type ec:Tag . rdf:type ec:TopicTag . skos:prefLabel "Research Communication" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "topic" . rdf:type ec:Tag . rdf:type ec:TopicTag . skos:prefLabel "Semantic Querying" . ec:isDeclaredOption "false"^^xsd:boolean . ec:isDeclaredOption "true"^^xsd:boolean . ec:tagKind "topic" . rdf:type ec:Tag . rdf:type ec:TopicTag . skos:prefLabel "Semantic Web" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "topic" . rdf:type ec:Tag . rdf:type ec:TopicTag . skos:prefLabel "SHACL" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "topic" . rdf:type ec:Tag . rdf:type ec:TopicTag . skos:prefLabel "Solid" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "topic" . rdf:type ec:Tag . rdf:type ec:TopicTag . skos:prefLabel "SPARQL" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "topic" . rdf:type ec:Tag . rdf:type ec:TopicTag . skos:prefLabel "SPARQL Federation" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "topic" . rdf:type ec:Tag . rdf:type ec:TopicTag . skos:prefLabel "Taxonomy" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "topic" . rdf:type ec:Tag . rdf:type ec:TopicTag . skos:prefLabel "Utilities" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "topic" . rdf:type ec:Tag . rdf:type ec:TopicTag . skos:prefLabel "VCF" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "topic" . rdf:type ec:Tag . rdf:type ec:TopicTag . skos:prefLabel "View Materialization" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "topic" . rdf:type ec:Tag . rdf:type ec:TopicTag . skos:prefLabel "Web Application" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "topic" . rdf:type ec:Tag . rdf:type ec:TopicTag . skos:prefLabel "Website" . ec:isDeclaredOption "false"^^xsd:boolean . ec:isDeclaredOption "true"^^xsd:boolean . ec:tagKind "venue" . rdf:type ec:Tag . rdf:type ec:VenueTag . skos:prefLabel "Conference" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "venue" . rdf:type ec:Tag . rdf:type ec:VenueTag . skos:prefLabel "Consortium Meeting" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "venue" . rdf:type ec:Tag . rdf:type ec:VenueTag . skos:prefLabel "E(I)Xchange" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "venue" . rdf:type ec:Tag . rdf:type ec:VenueTag . skos:prefLabel "ESWC" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "venue" . rdf:type ec:Tag . rdf:type ec:VenueTag . skos:prefLabel "Fellowship Interview" . ec:isDeclaredOption "false"^^xsd:boolean . ec:isDeclaredOption "true"^^xsd:boolean . ec:tagKind "venue" . rdf:type ec:Tag . rdf:type ec:VenueTag . skos:prefLabel "Internal Meeting" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "venue" . rdf:type ec:Tag . rdf:type ec:VenueTag . skos:prefLabel "Invited Talk" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "venue" . rdf:type ec:Tag . rdf:type ec:VenueTag . skos:prefLabel "ISWC" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "venue" . rdf:type ec:Tag . rdf:type ec:VenueTag . skos:prefLabel "ISWS" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "venue" . rdf:type ec:Tag . rdf:type ec:VenueTag . skos:prefLabel "KBC-LM'24 workshop at ISWC 2024" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "venue" . rdf:type ec:Tag . rdf:type ec:VenueTag . skos:prefLabel "KNoWS Day" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "venue" . rdf:type ec:Tag . rdf:type ec:VenueTag . skos:prefLabel "MetaboLinkAI" . ec:isDeclaredOption "false"^^xsd:boolean . ec:isDeclaredOption "true"^^xsd:boolean . ec:tagKind "venue" . rdf:type ec:Tag . rdf:type ec:VenueTag . skos:prefLabel "Non-Academic Event" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "venue" . rdf:type ec:Tag . rdf:type ec:VenueTag . skos:prefLabel "Research Stay Presentation" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "venue" . rdf:type ec:Tag . rdf:type ec:VenueTag . skos:prefLabel "Solid Symposium" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "venue" . rdf:type ec:Tag . rdf:type ec:VenueTag . skos:prefLabel "Summer School" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "venue" . rdf:type ec:Tag . rdf:type ec:VenueTag . skos:prefLabel "SWAT4HCLS" . ec:isDeclaredOption "false"^^xsd:boolean . ec:isDeclaredOption "true"^^xsd:boolean . ec:tagKind "venue" . rdf:type ec:Tag . rdf:type ec:VenueTag . skos:prefLabel "Symposium" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "venue" . rdf:type ec:Tag . rdf:type ec:VenueTag . skos:prefLabel "Virtual Meeting" . ec:isDeclaredOption "false"^^xsd:boolean . ec:tagKind "venue" . rdf:type ec:Tag . rdf:type ec:VenueTag . skos:prefLabel "WikiData workshop at ISWC 2025" . ec:abstract "This internal jury talk presented a structured review of progress against the first 18 months of the PhD trajectory. I summarized technical deliverables, empirical observations, and unresolved methodological risks across modeling, querying, and integration work packages. The presentation concluded with a revised execution plan for the next phase based on committee feedback and project constraints." . ec:audienceExpertise "Internal PhD jury members and supervisors with expertise in data science, semantic technologies, and digital health." . ec:audienceSizeApprox "4"^^xsd:integer . ec:date "2025-11-20"^^xsd:date . ec:description "Internal PhD milestone review covering completed work, validation status, and the next research phase." . ec:durationMinutes "10"^^xsd:integer . ec:forTalk . ec:goal "Provide a rigorous progress assessment and align the next-phase plan with internal supervision priorities." . ec:hasAudienceGroupTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:summary "Internal PhD milestone review covering completed work, validation status, and the next research phase." . rdf:type ec:TalkMetadata . schema:name "18-Month Internal VITO PhD Jury" . ec:abstract "This talk summarized ongoing research toward robust data interoperability for precision health applications using semantic web technologies. I highlighted progress across data representation, policy-aware sharing, and cross-source query workflows, with emphasis on clinical utility. The session connected technical decisions to broader implementation constraints in multidisciplinary healthcare environments." . ec:audienceExpertise "Precision health researchers, clinicians collaborating with data teams, and applied data scientists." . ec:audienceSizeApprox "30"^^xsd:integer . ec:date "2025-10-10"^^xsd:date . ec:description "Presented progress on decentralized clinical-genomics workflows and interoperability priorities in precision health." . ec:durationMinutes "20"^^xsd:integer . ec:forTalk . ec:goal "Communicate practical progress and roadmap priorities for applying semantic technologies in digital precision health settings." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:summary "Presented progress on decentralized clinical-genomics workflows and interoperability priorities in precision health." . rdf:type ec:TalkMetadata . schema:name "Digital Precision Health Day" . ec:abstract "An overview of genomic medicine and the principal barriers limiting broader genomic data use in healthcare was presented, grounded in findings from a recent scoping review. Semantic representation was then proposed as a response to several of these challenges by supporting richer data linkages, more granular privacy and access-control definitions, and future federated querying capabilities across distributed resources. The conversion layer required to enable such workflows was introduced through a tool and accompanying semantic vocabulary for translating genomic variant data from VCF into RDF. The presentation concluded by framing my PhD as the unifying research program connecting this completed work to the next stages of investigation into linkage, privacy-aware data use, and federated query workflows for genomic data." . ec:audienceExpertise "Semantic web researchers with interests in data spaces, semantic querying, and knowledge representation." . ec:audienceSizeApprox "30"^^xsd:integer . ec:date "2026-03-31"^^xsd:date . ec:description "KNoWS Day presentation outlining how semantic representations can improve genomic-data interoperability, privacy-aware access control, and federated querying in healthcare settings." . ec:durationMinutes "10"^^xsd:integer . ec:forTalk . ec:goal "Show how semantic representation and policy-aware querying can make genomic data more usable, interoperable, and privacy-conscious in healthcare." . ec:hasAudienceGroupTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:hasVenueTag . ec:summary "KNoWS Day presentation outlining how semantic representations can improve genomic-data interoperability, privacy-aware access control, and federated querying in healthcare settings." . rdf:type ec:TalkMetadata . schema:name "Genomic Data, Healthcare, and the Semantic Web" . ec:abstract "This PhD symposium presentation outlined the end-to-end PENGQUIN research framework, from RDF representation of genomic data to policy-constrained decentralized querying. I detailed the central research questions, methodological plan, and validation strategy across realistic data-sharing scenarios. Feedback from the symposium was incorporated into subsequent prioritization of federation, policy modeling, and interoperability tasks." . ec:audienceExpertise "Semantic web researchers, PhD supervisors, and conference participants focused on the semantic web." . ec:audienceSizeApprox "50"^^xsd:integer . ec:date "2024-05-28"^^xsd:date . ec:description "PhD symposium talk on the PENGQUIN research agenda for decentralized and policy-aware genomic data use." . ec:durationMinutes "15"^^xsd:integer . ec:forTalk . ec:goal "Present and validate my PhD research roadmap for the semantic web research community." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:summary "PhD symposium talk on the PENGQUIN research agenda for decentralized and policy-aware genomic data use." . rdf:type ec:TalkMetadata . schema:name "ESWC - PhD Symposium" . ec:abstract "In this interview presentation, I introduced the research motivation, technical novelty, and staged execution plan for the PENGQUIN project. The talk emphasized risk management, measurable milestones, and expected contributions to privacy-aware genomic data interoperability. I also framed the anticipated scientific and translational impact for both semantic-web and health-data communities." . ec:audienceExpertise "12-member interdisciplinary research-funding jury from academia and industry with backgrounds in data science, biomedicine, and policy-maker backgrounds." . ec:audienceSizeApprox "20"^^xsd:integer . ec:date "2024-09-05"^^xsd:date . ec:description "Funding interview pitch describing the PENGQUIN PhD vision, feasibility, and expected impact." . ec:durationMinutes "10"^^xsd:integer . ec:forTalk . ec:goal "Convince the funding panel of the scientific relevance, technical feasibility, and societal value of the proposed PhD project." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:summary "Funding interview pitch describing the PENGQUIN PhD vision, feasibility, and expected impact." . rdf:type ec:TalkMetadata . schema:name "FWO Interview" . ec:abstract "This project presentation described a collaborative semantic-web prototype developed during ISWS 2024. We documented the problem framing, data-model choices, and implementation architecture, then reflected on evaluation outcomes and limitations. The talk emphasized team-based design trade-offs and lessons that transfer to larger linked-data projects." . ec:audienceExpertise "Semantic web students, early-stage researchers, and instructors with mixed theoretical and applied semantic web backgrounds." . ec:audienceSizeApprox "60"^^xsd:integer . ec:date "2024-06-15"^^xsd:date . ec:description "Final group project presentation from ISWS 2024 highlighting design choices and implementation outcomes." . ec:durationMinutes "15"^^xsd:integer . ec:forTalk . ec:goal "Summarize project outcomes and demonstrate the reasoning behind key technical choices made during the summer school project." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:summary "Final group project presentation from ISWS 2024 highlighting design choices and implementation outcomes." . rdf:type ec:TalkMetadata . schema:name "International Semantic Web Summer School (ISWS) 2024: Group Project" . ec:abstract "This invited presentation for a MetaboLinkAI virtual meeting connects four strands of work on making life-science data more usable. It introduces PENGQUIN and its approach to privacy-aware storage, linking, and querying of personal genomic data, then examines SPARQL federation across real public endpoints. It also presents the Ontology Companion Generator for producing browsable ontology documentation and the conversion of VCF genomic variant files into linked, queryable RDF." . ec:audienceExpertise "An interdisciplinary life-science audience interested in semantic data integration and querying." . ec:audienceSizeApprox "9"^^xsd:integer . ec:audienceSizeEstimate "Approx. 8–10 attendees" . ec:date "2026-10-08"^^xsd:date . ec:description "Invited MetaboLinkAI presentation connecting the PENGQUIN PhD project with real-world SPARQL federation, the Ontology Companion Generator, and semantic representation of genomic variant data." . ec:durationMinutes "90"^^xsd:integer . ec:forTalk . ec:goal "Share how semantic web methods and practical tooling can support interoperable, privacy-aware life-science data and federated querying." . ec:hasAudienceGroupTag . ec:hasRelatedResource . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:hasVenueTag . ec:hasVenueTag . ec:summary "Invited MetaboLinkAI presentation connecting the PENGQUIN PhD project with real-world SPARQL federation, the Ontology Companion Generator, and semantic representation of genomic variant data." . rdf:type ec:TalkMetadata . schema:embedUrl . schema:name "MetaboLinkAI: From personal genomes to federated queries" . ec:abstract "This reflection talk synthesized the primary outcomes of a focused research stay, including prototype results, methodological lessons, and areas for follow-up collaboration. I discussed what approaches translated well into practice and what bottlenecks remained when integrating decentralized data and federation tooling. The presentation also mapped concrete next steps into the broader PhD research timeline." . ec:audienceExpertise "UGent ID-Lab researchers and colleagues." . ec:audienceSizeApprox "20"^^xsd:integer . ec:date "2025-05-15"^^xsd:date . ec:description "Reflected on outcomes from the SIB research stay, including technical gains and collaboration opportunities." . ec:durationMinutes "30"^^xsd:integer . ec:forTalk . ec:goal "Translate research-stay outcomes into actionable follow-up work and shared priorities with host collaborators." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:summary "Reflected on outcomes from the SIB research stay, including technical gains and collaboration opportunities." . rdf:type ec:TalkMetadata . schema:name "SIB Research Stay Reflection" . ec:abstract "The presentation examined practical query federation patterns for bioinformatics workflows that combine protected, patient-centric data with public linked data sources. I compared source-selection behavior, execution trade-offs, and endpoint characteristics observed in prototype evaluations. The discussion focused on where decentralized querying currently works well and where optimization work is still needed for production-scale workloads." . ec:audienceExpertise "Bioinformatics infrastructure engineers, computational biologists, and semantic data platform developers." . ec:audienceSizeApprox "30"^^xsd:integer . ec:date "2025-04-04"^^xsd:date . ec:description "Reviewed client-side federated SPARQL strategies for combining private Solid pod data with public knowledge graphs." . ec:durationMinutes "45"^^xsd:integer . ec:forTalk . ec:goal "Evaluate realistic federation strategies for combining Solid data and public RDF endpoints in genomics-adjacent analyses." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:summary "Reviewed client-side federated SPARQL strategies for combining private Solid pod data with public knowledge graphs." . rdf:type ec:TalkMetadata . schema:name "SIB Vital-IT" . ec:abstract "This consortium talk provided an implementation-oriented introduction to Solid, with focus on identity, access control, and decentralized data interoperability. I connected Solid primitives to TRIPLE project objectives around federation and reusable data infrastructures. The session included concrete examples of how Solid-based resources can integrate with existing RDF and SPARQL workflows." . ec:audienceExpertise "Consortium researchers and developers spanning semantic web, bioinformatics, and database engineering." . ec:audienceSizeApprox "12"^^xsd:integer . ec:date "2024-10-10"^^xsd:date . ec:description "Introductory consortium session on Solid concepts, architecture, and relevance to TRIPLE project goals." . ec:durationMinutes "20"^^xsd:integer . ec:forTalk . ec:goal "Build shared understanding of Solid fundamentals and position them within consortium-level technical planning." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:summary "Introductory consortium session on Solid concepts, architecture, and relevance to TRIPLE project goals." . rdf:type ec:TalkMetadata . schema:name "TRIPLE Consortium: Intro to Solid" . ec:abstract "The talk introduced a Solid-based approach for storing and sharing personal genomic data with stronger user control over access and policy constraints. I showed how this approach can interoperate with linked-data standards to support fine-grained querying and selective disclosure. The session also covered practical barriers to adoption, including policy complexity and execution-performance considerations." . ec:audienceExpertise "Solid ecosystem contributors, web standards practitioners, and researchers in decentralized data systems." . ec:audienceSizeApprox "90"^^xsd:integer . ec:date "2024-04-02"^^xsd:date . ec:description "Explored how Solid pods can host and govern personal genomic data for privacy-preserving analytics." . ec:durationMinutes "15"^^xsd:integer . ec:forTalk . ec:goal "Show that Solid-compatible data pods can provide a practical foundation for controlled genomic data access workflows." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:summary "Explored how Solid pods can host and govern personal genomic data for privacy-preserving analytics." . rdf:type ec:TalkMetadata . schema:name "Solid Symposium" . ec:abstract "Solid Pods provide decentralized, user-controlled data storage with fine-grained privacy controls, but practical usage still presents a steep learning curve for users unfamiliar with RDF and web-server concepts. This work introduces Solid Cockpit, a web-based interface designed to lower that barrier by bringing core Solid workflows into a single environment. The application supports uploading and organizing Pod data, modifying privacy and access permissions, and querying connected resources, while maintaining a fully client-side architecture through the Inrupt Solid-Client SDK. The system also incorporates linked-data privacy notification and SPARQL result-materialization specifications to improve workflow transparency and reusable query outcomes. Together, these capabilities position Solid Cockpit as a practical bridge between Solid’s decentralized architecture and everyday user interaction needs." . ec:audienceExpertise "Semantic web and decentralized-data researchers evaluating practical user interfaces for privacy-aware Solid ecosystem workflows." . ec:audienceSizeApprox "25"^^xsd:integer . ec:date "2026-04-30"^^xsd:date . ec:description "Demonstration of Solid Cockpit as a unified web interface for Solid Pods, integrating data management, privacy and access-control editing, notification support, and in-browser SPARQL data discovery." . ec:durationMinutes "5"^^xsd:integer . ec:forTalk . ec:goal "Show that a single, user-oriented interface can make decentralized Solid Pod workflows substantially more accessible without sacrificing privacy-aware controls or query capabilities." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasRelatedResource . ec:hasRelatedResource . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:hasVenueTag . ec:summary "Demonstration of Solid Cockpit as a unified web interface for Solid Pods, integrating data management, privacy and access-control editing, notification support, and in-browser SPARQL data discovery." . rdf:type ec:TalkMetadata . schema:embedUrl . schema:name "Solid Cockpit" . ec:abstract "This talk presented an architectural approach for representing and querying patient-level genomic information across distributed systems while preserving privacy constraints. I outlined how RDF modeling choices, policy-aware access patterns, and federated querying can be combined in practical workflows relevant to translational medicine. The session also discussed trade-offs between interoperability, query performance, and governance requirements in public-health contexts." . ec:audienceExpertise "Public health informatics researchers, biomedical data integration specialists, and semantic web practitioners." . ec:audienceSizeApprox "10"^^xsd:integer . ec:date "2025-04-29"^^xsd:date . ec:description "Introduced the PENGQUIN approach for privacy-aware clinical genomics integration using RDF and decentralized data pods." . ec:durationMinutes "45"^^xsd:integer . ec:forTalk . ec:goal "Demonstrate how semantic modeling plus decentralized infrastructure can support interoperable and privacy-aware genomic data sharing." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:summary "Introduced the PENGQUIN approach for privacy-aware clinical genomics integration using RDF and decentralized data pods." . rdf:type ec:TalkMetadata . schema:name "Swiss Public Health Network (SPHN)" . ec:abstract "This presentation examined how curated protein knowledge resources can be linked more effectively with distributed semantic data workflows. I discussed interoperability opportunities at the schema, identifier, and query orchestration levels, along with caveats around curation assumptions and endpoint behavior. The talk emphasized practical pathways for incremental integration rather than disruptive platform changes." . ec:audienceExpertise "Bioinformatics database curators, SPARQL endpoint knowledge graph maintainers, and biological knowledge representation researchers." . ec:audienceSizeApprox "25"^^xsd:integer . ec:date "2025-03-25"^^xsd:date . ec:description "Presented semantic integration opportunities between curated protein resources and decentralized query workflows." . ec:durationMinutes "45"^^xsd:integer . ec:forTalk . ec:goal "Identify realistic integration points between curated bioinformatics resources and decentralized semantic querying approaches." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:summary "Presented semantic integration opportunities between curated protein resources and decentralized query workflows." . rdf:type ec:TalkMetadata . schema:name "SIB / SwissProt" . ec:abstract "This talk introduced genomics concepts most relevant to computational audiences, including sequencing outputs, variant interpretation, and common data structures used in analysis pipelines. I mapped these foundations to challenges in representation, interoperability, and reproducibility that are central to modern data engineering. The session served as a bridge from domain fundamentals to semantic and decentralized research directions." . ec:audienceExpertise "Semantic web / computer science colleagues and researchers with limited prior exposure to biology and/or genomics." . ec:audienceSizeApprox "20"^^xsd:integer . ec:date "2024-03-04"^^xsd:date . ec:description "Foundational genomics overview tailored to computer science researchers entering health-data domains." . ec:durationMinutes "60"^^xsd:integer . ec:forTalk . ec:goal "Provide a domain foundation that enables computer scientists to contribute effectively to genomics data problems." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:summary "Foundational genomics overview tailored to computer science researchers entering health-data domains." . rdf:type ec:TalkMetadata . schema:name "KNoWS: An Intro to Genomics for Computer Scientists" . dcterms:identifier "18m-vito-internal-jury" . dcterms:isPartOf . ec:audienceExpertise "Internal PhD jury members and supervisors with expertise in data science, semantic technologies, and digital health." . ec:audienceSizeApprox "4"^^xsd:integer . ec:audienceSizeCategory "Small" . ec:audienceSizeEstimate "Approx. 4 attendees" . ec:description "This internal jury talk presented a structured review of progress against the first 18 months of the PhD trajectory. I summarized technical deliverables, empirical observations, and unresolved methodological risks across modeling, querying, and integration work packages. The presentation concluded with a revised execution plan for the next phase based on committee feedback and project constraints." . ec:displayDate "2025-11-20"^^xsd:date . ec:displayDateLabel "20/11/2025" . ec:durationCategory "Short" . ec:durationMinutes "10"^^xsd:integer . ec:goal "Provide a rigorous progress assessment and align the next-phase plan with internal supervision priorities." . ec:hasAudienceGroupTag . ec:hasAudienceSizeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:slidePath "/talks/slides/18m-vito-internal-jury.pdf" . ec:sourceDate "2025-11-20"^^xsd:date . ec:sourceDateLabel "20/11/2025" . ec:sourceFile "EDC-18m-VITO-Jury.pdf" . ec:sourceTitle "EDC 18m VITO Jury" . ec:summary "Internal PhD milestone review covering completed work, validation status, and the next research phase." . rdf:type ec:Talk . schema:encodingFormat "application/pdf" . schema:name "18-Month Internal VITO PhD Jury" . schema:url . dcterms:identifier "dph-day-talk" . dcterms:isPartOf . ec:audienceExpertise "Precision health researchers, clinicians collaborating with data teams, and applied data scientists." . ec:audienceSizeApprox "30"^^xsd:integer . ec:audienceSizeCategory "Medium" . ec:audienceSizeEstimate "Approx. 30 attendees" . ec:description "This talk summarized ongoing research toward robust data interoperability for precision health applications using semantic web technologies. I highlighted progress across data representation, policy-aware sharing, and cross-source query workflows, with emphasis on clinical utility. The session connected technical decisions to broader implementation constraints in multidisciplinary healthcare environments." . ec:displayDate "2025-10-10"^^xsd:date . ec:displayDateLabel "10/10/2025" . ec:durationCategory "Medium" . ec:durationMinutes "20"^^xsd:integer . ec:goal "Communicate practical progress and roadmap priorities for applying semantic technologies in digital precision health settings." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceSizeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:slidePath "/talks/slides/dph-day-talk.pdf" . ec:sourceDate "2025-10-10"^^xsd:date . ec:sourceDateLabel "10/10/2025" . ec:sourceFile "EDC-DPH-25.pdf" . ec:sourceTitle "EDC DPH 25" . ec:summary "Presented progress on decentralized clinical-genomics workflows and interoperability priorities in precision health." . rdf:type ec:Talk . schema:encodingFormat "application/pdf" . schema:name "Digital Precision Health Day" . schema:url . dcterms:identifier "edc-knows-26" . dcterms:isPartOf . ec:audienceExpertise "Semantic web researchers with interests in data spaces, semantic querying, and knowledge representation." . ec:audienceSizeApprox "30"^^xsd:integer . ec:audienceSizeCategory "Medium" . ec:audienceSizeEstimate "Approx. 30 attendees" . ec:description "An overview of genomic medicine and the principal barriers limiting broader genomic data use in healthcare was presented, grounded in findings from a recent scoping review. Semantic representation was then proposed as a response to several of these challenges by supporting richer data linkages, more granular privacy and access-control definitions, and future federated querying capabilities across distributed resources. The conversion layer required to enable such workflows was introduced through a tool and accompanying semantic vocabulary for translating genomic variant data from VCF into RDF. The presentation concluded by framing my PhD as the unifying research program connecting this completed work to the next stages of investigation into linkage, privacy-aware data use, and federated query workflows for genomic data." . ec:displayDate "2026-03-31"^^xsd:date . ec:displayDateLabel "31/03/2026" . ec:durationCategory "Short" . ec:durationMinutes "10"^^xsd:integer . ec:goal "Show how semantic representation and policy-aware querying can make genomic data more usable, interoperable, and privacy-conscious in healthcare." . ec:hasAudienceGroupTag . ec:hasAudienceSizeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:hasVenueTag . ec:slidePath "/talks/slides/edc-knows-26.pdf" . ec:sourceDate "2026-03-31"^^xsd:date . ec:sourceDateLabel "31/03/2026" . ec:sourceFile "EDC-KNoWS-26.pdf" . ec:sourceTitle "EDC KNoWS 26" . ec:summary "KNoWS Day presentation outlining how semantic representations can improve genomic-data interoperability, privacy-aware access control, and federated querying in healthcare settings." . rdf:type ec:Talk . schema:encodingFormat "application/pdf" . schema:name "Genomic Data, Healthcare, and the Semantic Web" . schema:url . dcterms:identifier "eswc-phdsymp-pangquin" . dcterms:isPartOf . ec:audienceExpertise "Semantic web researchers, PhD supervisors, and conference participants focused on the semantic web." . ec:audienceSizeApprox "50"^^xsd:integer . ec:audienceSizeCategory "Medium" . ec:audienceSizeEstimate "Approx. 50 attendees" . ec:description "This PhD symposium presentation outlined the end-to-end PENGQUIN research framework, from RDF representation of genomic data to policy-constrained decentralized querying. I detailed the central research questions, methodological plan, and validation strategy across realistic data-sharing scenarios. Feedback from the symposium was incorporated into subsequent prioritization of federation, policy modeling, and interoperability tasks." . ec:displayDate "2024-05-28"^^xsd:date . ec:displayDateLabel "28/05/2024" . ec:durationCategory "Short" . ec:durationMinutes "15"^^xsd:integer . ec:goal "Present and validate my PhD research roadmap for the semantic web research community." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceSizeTag . ec:hasPoster . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:posterPath "/talks/posters/ESWC_24_Poster_EDC.pdf" . ec:posterTitle "ESWC 24 Poster EDC" . ec:relatedPublication . ec:slidePath "/talks/slides/eswc-phdsymp-pangquin.pdf" . ec:sourceDate "2024-05-28"^^xsd:date . ec:sourceDateLabel "28/05/2024" . ec:sourceFile "PENGQUIN_ESWC_2024.pdf" . ec:sourceTitle "PENGQUIN ESWC 2024" . ec:summary "PhD symposium talk on the PENGQUIN research agenda for decentralized and policy-aware genomic data use." . rdf:type ec:Talk . schema:encodingFormat "application/pdf" . schema:name "ESWC - PhD Symposium" . schema:url . dcterms:identifier "fwo-interview" . dcterms:isPartOf . ec:audienceExpertise "12-member interdisciplinary research-funding jury from academia and industry with backgrounds in data science, biomedicine, and policy-maker backgrounds." . ec:audienceSizeApprox "20"^^xsd:integer . ec:audienceSizeCategory "Small" . ec:audienceSizeEstimate "Approx. 20 attendees" . ec:description "In this interview presentation, I introduced the research motivation, technical novelty, and staged execution plan for the PENGQUIN project. The talk emphasized risk management, measurable milestones, and expected contributions to privacy-aware genomic data interoperability. I also framed the anticipated scientific and translational impact for both semantic-web and health-data communities." . ec:displayDate "2024-09-05"^^xsd:date . ec:displayDateLabel "05/09/2024" . ec:durationCategory "Short" . ec:durationMinutes "10"^^xsd:integer . ec:goal "Convince the funding panel of the scientific relevance, technical feasibility, and societal value of the proposed PhD project." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceSizeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:relatedFellowship . ec:slidePath "/talks/slides/fwo-interview.pdf" . ec:sourceDate "2024-09-05"^^xsd:date . ec:sourceDateLabel "05/09/2024" . ec:sourceFile "FWO24_Pitch_EDC(official).pdf" . ec:sourceTitle "FWO24 Pitch EDC(Official)" . ec:summary "Funding interview pitch describing the PENGQUIN PhD vision, feasibility, and expected impact." . rdf:type ec:Talk . schema:encodingFormat "application/pdf" . schema:name "FWO Interview" . schema:url . dcterms:identifier "isws-group-project-presentation" . dcterms:isPartOf . ec:audienceExpertise "Semantic web students, early-stage researchers, and instructors with mixed theoretical and applied semantic web backgrounds." . ec:audienceSizeApprox "60"^^xsd:integer . ec:audienceSizeCategory "Medium" . ec:audienceSizeEstimate "Approx. 60 attendees" . ec:description "This project presentation described a collaborative semantic-web prototype developed during ISWS 2024. We documented the problem framing, data-model choices, and implementation architecture, then reflected on evaluation outcomes and limitations. The talk emphasized team-based design trade-offs and lessons that transfer to larger linked-data projects." . ec:displayDate "2024-06-15"^^xsd:date . ec:displayDateLabel "15/06/2024" . ec:durationCategory "Short" . ec:durationMinutes "15"^^xsd:integer . ec:goal "Summarize project outcomes and demonstrate the reasoning behind key technical choices made during the summer school project." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceSizeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:slidePath "/talks/slides/isws-group-project-presentation.pdf" . ec:sourceDate "2024-06-15"^^xsd:date . ec:sourceDateLabel "15/06/2024" . ec:sourceFile "ISWS2024_Slytherin_Presentation.pdf" . ec:sourceTitle "ISWS2024 Slytherin Presentation" . ec:summary "Final group project presentation from ISWS 2024 highlighting design choices and implementation outcomes." . rdf:type ec:Talk . schema:encodingFormat "application/pdf" . schema:name "International Semantic Web Summer School (ISWS) 2024: Group Project" . schema:url . dcterms:identifier "metabolinkai" . dcterms:isPartOf . ec:audienceExpertise "An interdisciplinary life-science audience interested in semantic data integration and querying." . ec:audienceSizeApprox "9"^^xsd:integer . ec:audienceSizeCategory "Small" . ec:audienceSizeEstimate "Approx. 8–10 attendees" . ec:description "This invited presentation for a MetaboLinkAI virtual meeting connects four strands of work on making life-science data more usable. It introduces PENGQUIN and its approach to privacy-aware storage, linking, and querying of personal genomic data, then examines SPARQL federation across real public endpoints. It also presents the Ontology Companion Generator for producing browsable ontology documentation and the conversion of VCF genomic variant files into linked, queryable RDF." . ec:displayDate "2026-10-08"^^xsd:date . ec:displayDateLabel "08/10/2026" . ec:durationCategory "Long" . ec:durationMinutes "90"^^xsd:integer . ec:goal "Share how semantic web methods and practical tooling can support interoperable, privacy-aware life-science data and federated querying." . ec:hasAudienceGroupTag . ec:hasAudienceSizeTag . ec:hasRelatedResource . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:hasVenueTag . ec:hasVenueTag . ec:slidePath "https://ecrum19.github.io/MetaboLinkAI-Slides/" . ec:sourceDate "2026-10-08"^^xsd:date . ec:sourceDateLabel "08/10/2026" . ec:sourceFile "https://ecrum19.github.io/MetaboLinkAI-Slides/" . ec:sourceTitle "From personal genomes to federated queries" . ec:summary "Invited MetaboLinkAI presentation connecting the PENGQUIN PhD project with real-world SPARQL federation, the Ontology Companion Generator, and semantic representation of genomic variant data." . rdf:type ec:Talk . schema:embedUrl . schema:encodingFormat "text/html" . schema:name "MetaboLinkAI: From personal genomes to federated queries" . schema:url . dcterms:identifier "sib-researchstay-reflection" . dcterms:isPartOf . ec:audienceExpertise "UGent ID-Lab researchers and colleagues." . ec:audienceSizeApprox "20"^^xsd:integer . ec:audienceSizeCategory "Small" . ec:audienceSizeEstimate "Approx. 20 attendees" . ec:description "This reflection talk synthesized the primary outcomes of a focused research stay, including prototype results, methodological lessons, and areas for follow-up collaboration. I discussed what approaches translated well into practice and what bottlenecks remained when integrating decentralized data and federation tooling. The presentation also mapped concrete next steps into the broader PhD research timeline." . ec:displayDate "2025-05-15"^^xsd:date . ec:displayDateLabel "15/05/2025" . ec:durationCategory "Medium" . ec:durationMinutes "30"^^xsd:integer . ec:goal "Translate research-stay outcomes into actionable follow-up work and shared priorities with host collaborators." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceSizeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:slidePath "/talks/slides/sib-researchstay-reflection.pdf" . ec:sourceDate "2025-05-15"^^xsd:date . ec:sourceDateLabel "15/05/2025" . ec:sourceFile "SIB-ReflectionUGent.pdf" . ec:sourceTitle "SIB ReflectionUGent" . ec:summary "Reflected on outcomes from the SIB research stay, including technical gains and collaboration opportunities." . rdf:type ec:Talk . schema:encodingFormat "application/pdf" . schema:name "SIB Research Stay Reflection" . schema:url . dcterms:identifier "sib-vital-it-talk" . dcterms:isPartOf . ec:audienceExpertise "Bioinformatics infrastructure engineers, computational biologists, and semantic data platform developers." . ec:audienceSizeApprox "30"^^xsd:integer . ec:audienceSizeCategory "Medium" . ec:audienceSizeEstimate "Approx. 30 attendees" . ec:description "The presentation examined practical query federation patterns for bioinformatics workflows that combine protected, patient-centric data with public linked data sources. I compared source-selection behavior, execution trade-offs, and endpoint characteristics observed in prototype evaluations. The discussion focused on where decentralized querying currently works well and where optimization work is still needed for production-scale workloads." . ec:displayDate "2025-04-04"^^xsd:date . ec:displayDateLabel "04/04/2025" . ec:durationCategory "Medium" . ec:durationMinutes "45"^^xsd:integer . ec:goal "Evaluate realistic federation strategies for combining Solid data and public RDF endpoints in genomics-adjacent analyses." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceSizeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:slidePath "/talks/slides/sib-vital-it-talk.pdf" . ec:sourceDate "2025-04-04"^^xsd:date . ec:sourceDateLabel "04/04/2025" . ec:sourceFile "Vital-IT-EDC-040425.pdf" . ec:sourceTitle "Vital IT EDC 040425" . ec:summary "Reviewed client-side federated SPARQL strategies for combining private Solid pod data with public knowledge graphs." . rdf:type ec:Talk . schema:encodingFormat "application/pdf" . schema:name "SIB Vital-IT" . schema:url . dcterms:identifier "solid-intro-triple-consortium" . dcterms:isPartOf . ec:audienceExpertise "Consortium researchers and developers spanning semantic web, bioinformatics, and database engineering." . ec:audienceSizeApprox "12"^^xsd:integer . ec:audienceSizeCategory "Small" . ec:audienceSizeEstimate "Approx. 12 attendees" . ec:description "This consortium talk provided an implementation-oriented introduction to Solid, with focus on identity, access control, and decentralized data interoperability. I connected Solid primitives to TRIPLE project objectives around federation and reusable data infrastructures. The session included concrete examples of how Solid-based resources can integrate with existing RDF and SPARQL workflows." . ec:displayDate "2024-10-10"^^xsd:date . ec:displayDateLabel "10/10/2024" . ec:durationCategory "Medium" . ec:durationMinutes "20"^^xsd:integer . ec:goal "Build shared understanding of Solid fundamentals and position them within consortium-level technical planning." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceSizeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:slidePath "/talks/slides/solid-intro-triple-consortium.pdf" . ec:sourceDate "2024-10-10"^^xsd:date . ec:sourceDateLabel "10/10/2024" . ec:sourceFile "Solid_intro_TRIPLE.pdf" . ec:sourceTitle "Solid Intro TRIPLE" . ec:summary "Introductory consortium session on Solid concepts, architecture, and relevance to TRIPLE project goals." . rdf:type ec:Talk . schema:encodingFormat "application/pdf" . schema:name "TRIPLE Consortium: Intro to Solid" . schema:url . dcterms:identifier "solidsymp-genomepods" . dcterms:isPartOf . ec:audienceExpertise "Solid ecosystem contributors, web standards practitioners, and researchers in decentralized data systems." . ec:audienceSizeApprox "90"^^xsd:integer . ec:audienceSizeCategory "Large" . ec:audienceSizeEstimate "Approx. 90 attendees" . ec:description "The talk introduced a Solid-based approach for storing and sharing personal genomic data with stronger user control over access and policy constraints. I showed how this approach can interoperate with linked-data standards to support fine-grained querying and selective disclosure. The session also covered practical barriers to adoption, including policy complexity and execution-performance considerations." . ec:displayDate "2024-04-02"^^xsd:date . ec:displayDateLabel "02/04/2024" . ec:durationCategory "Short" . ec:durationMinutes "15"^^xsd:integer . ec:goal "Show that Solid-compatible data pods can provide a practical foundation for controlled genomic data access workflows." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceSizeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:slidePath "/talks/slides/solidsymp-genomepods.pdf" . ec:sourceDate "2024-04-02"^^xsd:date . ec:sourceDateLabel "02/04/2024" . ec:sourceFile "SolidSymp2024_EDC.pdf" . ec:sourceTitle "SolidSymp2024 EDC" . ec:summary "Explored how Solid pods can host and govern personal genomic data for privacy-preserving analytics." . rdf:type ec:Talk . schema:encodingFormat "application/pdf" . schema:name "Solid Symposium" . schema:url . dcterms:identifier "sosy2026" . dcterms:isPartOf . ec:audienceExpertise "Semantic web and decentralized-data researchers evaluating practical user interfaces for privacy-aware Solid ecosystem workflows." . ec:audienceSizeApprox "25"^^xsd:integer . ec:audienceSizeCategory "Small" . ec:audienceSizeEstimate "Approx. 25 attendees" . ec:description "Solid Pods provide decentralized, user-controlled data storage with fine-grained privacy controls, but practical usage still presents a steep learning curve for users unfamiliar with RDF and web-server concepts. This work introduces Solid Cockpit, a web-based interface designed to lower that barrier by bringing core Solid workflows into a single environment. The application supports uploading and organizing Pod data, modifying privacy and access permissions, and querying connected resources, while maintaining a fully client-side architecture through the Inrupt Solid-Client SDK. The system also incorporates linked-data privacy notification and SPARQL result-materialization specifications to improve workflow transparency and reusable query outcomes. Together, these capabilities position Solid Cockpit as a practical bridge between Solid’s decentralized architecture and everyday user interaction needs." . ec:displayDate "2026-04-30"^^xsd:date . ec:displayDateLabel "30/04/2026" . ec:durationCategory "Short" . ec:durationMinutes "5"^^xsd:integer . ec:goal "Show that a single, user-oriented interface can make decentralized Solid Pod workflows substantially more accessible without sacrificing privacy-aware controls or query capabilities." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceSizeTag . ec:hasPoster . ec:hasRelatedResource . ec:hasRelatedResource . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:hasVenueTag . ec:posterPath "/talks/posters/eswc_2026_print.pdf" . ec:posterTitle "Eswc 2026 Print" . ec:relatedPublication . ec:relatedSoftware . ec:slidePath "/talks/slides/sosy2026.pdf" . ec:sourceDate "2026-04-30"^^xsd:date . ec:sourceDateLabel "30/04/2026" . ec:sourceFile "SoSy2026.pdf" . ec:sourceTitle "SoSy2026" . ec:summary "Demonstration of Solid Cockpit as a unified web interface for Solid Pods, integrating data management, privacy and access-control editing, notification support, and in-browser SPARQL data discovery." . rdf:type ec:Talk . schema:embedUrl . schema:encodingFormat "application/pdf" . schema:name "Solid Cockpit" . schema:url . dcterms:identifier "sphn-pengquin-talk" . dcterms:isPartOf . ec:audienceExpertise "Public health informatics researchers, biomedical data integration specialists, and semantic web practitioners." . ec:audienceSizeApprox "10"^^xsd:integer . ec:audienceSizeCategory "Small" . ec:audienceSizeEstimate "Approx. 10 attendees" . ec:description "This talk presented an architectural approach for representing and querying patient-level genomic information across distributed systems while preserving privacy constraints. I outlined how RDF modeling choices, policy-aware access patterns, and federated querying can be combined in practical workflows relevant to translational medicine. The session also discussed trade-offs between interoperability, query performance, and governance requirements in public-health contexts." . ec:displayDate "2025-04-29"^^xsd:date . ec:displayDateLabel "29/04/2025" . ec:durationCategory "Medium" . ec:durationMinutes "45"^^xsd:integer . ec:goal "Demonstrate how semantic modeling plus decentralized infrastructure can support interoperable and privacy-aware genomic data sharing." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceSizeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:slidePath "/talks/slides/sphn-pengquin-talk.pdf" . ec:sourceDate "2025-04-29"^^xsd:date . ec:sourceDateLabel "29/04/2025" . ec:sourceFile "SPHN-290425.pdf" . ec:sourceTitle "SPHN 290425" . ec:summary "Introduced the PENGQUIN approach for privacy-aware clinical genomics integration using RDF and decentralized data pods." . rdf:type ec:Talk . schema:encodingFormat "application/pdf" . schema:name "Swiss Public Health Network (SPHN)" . schema:url . dcterms:identifier "swissprot-talk" . dcterms:isPartOf . ec:audienceExpertise "Bioinformatics database curators, SPARQL endpoint knowledge graph maintainers, and biological knowledge representation researchers." . ec:audienceSizeApprox "25"^^xsd:integer . ec:audienceSizeCategory "Small" . ec:audienceSizeEstimate "Approx. 25 attendees" . ec:description "This presentation examined how curated protein knowledge resources can be linked more effectively with distributed semantic data workflows. I discussed interoperability opportunities at the schema, identifier, and query orchestration levels, along with caveats around curation assumptions and endpoint behavior. The talk emphasized practical pathways for incremental integration rather than disruptive platform changes." . ec:displayDate "2025-03-25"^^xsd:date . ec:displayDateLabel "25/03/2025" . ec:durationCategory "Medium" . ec:durationMinutes "45"^^xsd:integer . ec:goal "Identify realistic integration points between curated bioinformatics resources and decentralized semantic querying approaches." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceSizeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:slidePath "/talks/slides/swissprot-talk.pdf" . ec:sourceDate "2025-03-25"^^xsd:date . ec:sourceDateLabel "25/03/2025" . ec:sourceFile "SwissProt.pdf" . ec:sourceTitle "SwissProt" . ec:summary "Presented semantic integration opportunities between curated protein resources and decentralized query workflows." . rdf:type ec:Talk . schema:encodingFormat "application/pdf" . schema:name "SIB / SwissProt" . schema:url . dcterms:identifier "ugent-genomics-talk" . dcterms:isPartOf . ec:audienceExpertise "Semantic web / computer science colleagues and researchers with limited prior exposure to biology and/or genomics." . ec:audienceSizeApprox "20"^^xsd:integer . ec:audienceSizeCategory "Small" . ec:audienceSizeEstimate "Approx. 20 attendees" . ec:description "This talk introduced genomics concepts most relevant to computational audiences, including sequencing outputs, variant interpretation, and common data structures used in analysis pipelines. I mapped these foundations to challenges in representation, interoperability, and reproducibility that are central to modern data engineering. The session served as a bridge from domain fundamentals to semantic and decentralized research directions." . ec:displayDate "2024-03-04"^^xsd:date . ec:displayDateLabel "04/03/2024" . ec:durationCategory "Long" . ec:durationMinutes "60"^^xsd:integer . ec:goal "Provide a domain foundation that enables computer scientists to contribute effectively to genomics data problems." . ec:hasAudienceGroupTag . ec:hasAudienceGroupTag . ec:hasAudienceSizeTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasTopicTag . ec:hasVenueTag . ec:slidePath "/talks/slides/ugent-genomics-talk.pdf" . ec:sourceDate "2024-03-04"^^xsd:date . ec:sourceDateLabel "04/03/2024" . ec:sourceFile "UGent_PENGQUIN_Intro.pdf" . ec:sourceTitle "UGent PENGQUIN Intro" . ec:summary "Foundational genomics overview tailored to computer science researchers entering health-data domains." . rdf:type ec:Talk . schema:encodingFormat "application/pdf" . schema:name "KNoWS: An Intro to Genomics for Computer Scientists" . schema:url .