William Baumgartner
Assistant Professor Of Medicine at University of Colorado Anschutz Medical Campus
Aurora, Colorado, United States
Summary
👤
Senior🎓
Top SchoolWilliam Baumgartner is an Assistant Professor of Medicine and computational bioscience researcher with 14 years of experience building reproducible, production-ready bioinformatics and clinical informatics systems. He combines deep expertise in biomedical NLP (concept recognition, relation extraction, transformers/BERT, LLMs) with semantic technologies and knowledge representation (ontologies, RDF/OWL, SPARQL, knowledge graphs) to enable interoperable EHR-driven observational research and computational phenotyping. He has led major projects such as NCATS Biomedical Translator’s text-mining provider and bridges symbolic AI with modern ML/AI workflows using CI/CD, Docker, and cloud platforms. Comfortable coding in Python, Java, R and SQL, he focuses on practical deployment and evaluation of NLP systems in clinical contexts. Based in Aurora, Colorado, he blends rigorous academic training (PhD, Computational Bioscience; MS/BS Johns Hopkins Biomedical Engineering) with hands-on software engineering to translate complex biomedical knowledge into usable, auditable systems.
15 years of coding experience
8 years of employment as a software developer
Doctor of Philosophy (Ph.D.), Computational Bioscience, Doctor of Philosophy (Ph.D.), Computational Bioscience at University of Colorado Anschutz Medical CampusJohns Hopkins University
Stackoverflow
1reputation
0reached
0answers
0questions
Github Skills (63)
biomedical-ontologies10
parsing10
natural-language-processing10
rdf10
uima10
json-api9
neo4j9
monarchinitiative9
biomedical9
owl9
text-mining9
translator8
continuous-integration8
api8
yaml8
Programming languages (14)
Github contributions (5)
UCDenver-ccp/file-conversion
Mar 2019 - Jul 2022
Conversion utility for various NLP-related file types
Contributions:7 releases, 12 PRs, 20 pushes in 3 years 4 months
nlppythonfile-typesconversionnatural-language-processing
UCDenver-ccp/ccp-nlp
Aug 2011 - Aug 2022
A library of NLP related code
Contributions:3 releases, 765 commits, 24 PRs in 11 years 2 months
natural-language-processing
Find and Hire Top DevelopersWe’ve analyzed the programming source code of over 60 million software developers on GitHub and scored them by 50,000 skills. Sign-up on Prog,AI to search for software developers.