William A. Baumgartner Jr.

According to our database1, William A. Baumgartner Jr. authored at least 40 papers between 2005 and 2023.

Collaborative distances:



In proceedings 
PhD thesis 


On csauthors.net:


Reproducible variability: assessing investigator discordance across 9 research teams attempting to reproduce the same observational study.
J. Am. Medical Informatics Assoc., April, 2023

Ontologizing health systems data at scale: making translational discovery a reality.
npj Digit. Medicine, 2023

An Open-Source Knowledge Graph Ecosystem for the Life Sciences.
CoRR, 2023

Ontologizing Health Systems Data at Scale: Making Translational Discovery a Reality.
CoRR, 2022

Knowledge-Driven Mechanistic Enrichment of the Preeclampsia Ignorome.
CoRR, 2022

Concept recognition as a machine translation problem.
BMC Bioinform., 2021

CRAFT Shared Tasks 2019 Overview - Integrated Structure, Semantics, and Coreference.
Proceedings of The 5th Workshop on BioNLP Open Shared Tasks, 2019

OWL-NETS: Transforming OWL representations for improved network inference.
Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

Improving precision in concept normalization.
Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles.
BMC Bioinform., 2017

Gold-standard ontology-based anatomical annotation in the CRAFT Corpus.
Database J. Biol. Databases Curation, 2017

Coreference resolution improves extraction of Biological Expression Language statements from texts.
Database J. Biol. Databases Curation, 2016

SuperCAT: The (New and Improved) Corpus Analysis Toolkit.
Proceedings of the Tenth International Conference on Language Resources and Evaluation LREC 2016, 2016

KaBOB: ontology-based semantic integration of biomedical databases.
BMC Bioinform., 2015

Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters.
BMC Bioinform., 2014

Sublanguage Corpus Analysis Toolkit: A tool for assessing the representativeness and sublanguage characteristics of corpora.
Proceedings of the Ninth International Conference on Language Resources and Evaluation, 2014

Closure Properties of Bulgarian Clinical Text.
Proceedings of the Recent Advances in Natural Language Processing, 2013

A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools.
BMC Bioinform., 2012

Concept annotation in the CRAFT corpus.
BMC Bioinform., 2012

BioLemmatizer: a lemmatization tool for morphological processing of biomedical text.
J. Biomed. Semant., 2012

High-Precision Biological Event Extraction: Effects of System and of Data.
Comput. Intell., 2011

Fast and simple semantic class assignment for biomedical text.
Proceedings of the 2011 Workshop on Biomedical Natural Language Processing, 2011

Exploring Species-Based Strategies for Gene Normalization.
IEEE ACM Trans. Comput. Biol. Bioinform., 2010

A UIMA wrapper for the NCBO annotator.
Bioinform., 2010

Test Suite Design for Biomedical Ontology Concept Recognition Systems.
Proceedings of the International Conference on Language Resources and Evaluation, 2010

Visualization and Language Processing for Supporting Analysis across the Biomedical Literature.
Proceedings of the Knowledge-Based and Intelligent Information and Engineering Systems, 2010

Biomedical Discovery Acceleration, with Applications to Craniofacial Development.
PLoS Comput. Biol., 2009

U-Compare: share and compare text mining tools with UIMA.
Bioinform., 2009

High-precision biological event extraction with a concept recognizer.
Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, BioNLP@HLT-NAACL 2009, 2009

OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression.
BMC Bioinform., 2008

Improving protein function prediction methods with integrated literature data.
BMC Bioinform., 2008

Mining Protein-Protein Interactions from GeneRIFs with OpenDMAP.
Proceedings of the Linking Literature, Information, and Knowledge for Biology, 2008

Software Testing and the Naturally Occurring Data Assumption in Natural Language Processing.
Proceedings of the Software Engineering, 2008

Rapid Pattern Development for Concept Recognition Systems: Application to Point mutations.
J. Bioinform. Comput. Biol., 2007

MutationFinder: a high-performance system for extracting point mutation mentions from text.
Bioinform., 2007

Manual curation is not sufficient for annotation of genomic databases.
Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

Concept Recognition, Information Retrieval, and Machine Learning in Genomics Question-Answering.
Proceedings of the Fifteenth Text REtrieval Conference, 2006

Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies.
Proceedings of the Biocomputing 2006, 2006

Refactoring Corpora.
Proceedings of the Workshop on Linking Natural Language and Biology, 2006

Concept Recognition and the TREC Genomics Tasks.
Proceedings of the Fourteenth Text REtrieval Conference, 2005