John Judkins
Ontologist at Pavati Solutions
United States
Summary
👤
Senior🎓
Top SchoolJohn Judkins is an ontologist with 11 years of experience building OBO Foundry- and Common Core-aligned ontologies to make biomedical data interoperable and computable. Currently at DeciSym.AI after five years creating ontology-driven applications at the University of Pennsylvania, he blends domain knowledge in bioinformatics and biomedical engineering with practical application development. His background includes graduate research and teaching roles in medical and engineering settings, giving him a strong foundation in both theory and implementation. He is skilled at translating complex biological concepts into reusable semantic models that support data integration and analysis. Based in Philadelphia, he brings a researcher’s rigor—evident from a 4.0 MS in Bioinformatics—combined with hands-on experience shipping ontology-enabled software. Colleagues value his ability to bridge lab, clinical, and engineering perspectives to produce auditable, standards-aligned knowledge resources.
11 years of coding experience
5 years of employment as a software developer
Master’s Degree Biomedical Engineering, Master’s Degree Biomedical Engineering at University of ArkansasChemical Engineering Biotechnology, Chemical Engineering Biotechnology at University of OklahomaMaster of Science - MS Bioinformatics, Master of Science - MS Bioinformatics at University of Arkansas at Little Rock
Github Skills (29)
ontology10
semantic-web10
bioinformatics10
owl10
agriculture9
webapp9
rdf8
text-mining8
monarchinitiative8
knowledge-graph8
knowledge-management8
geneontology8
anatomy8
semantics8
ecology8
Programming languages (8)
Github contributions (5)
VEuPathDB-ontology/OWLmaker
Feb 2019 - Jul 2021
Generate an .owl file from tabulated data
Contributions:1 review, 14 pushes, 1 branch in 2 years 5 months
pythonjsonldowlsemantic-web
VEuPathDB-ontology/VEuPathDB-ontology
Nov 2018 - Jan 2023
The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org).
Contributions:35 releases, 45 reviews, 885 commits in 4 years 2 months
obofoundry
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