William Baumgartner
Assistant Professor Of Medicine at University of Colorado Anschutz Medical Campus
Aurora, Colorado, United States
Summary
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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.
14 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
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Github Skills (90)
converting10
semantic-web10
shacl10
owl10
ontologies10
triplestore10
nlp10
uima10
annotate10
rdf10
sparql10
biomedical-ontologies10
linked-data10
parsing10
json-ld10
Programming languages (13)
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/translator-relation-extraction
Jun 2021 - Mar 2025
This repository catalogs manually annotated sentences, code, and models used to mine relations between ontology concepts from text.
Contributions:46 PRs, 358 pushes, 43 branches in 3 years 9 months
nlprelationslinked-datacatalogssentences
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