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List of works by William Baumgartner

A Framework for Automated Construction of Heterogeneous Large-Scale Biomedical Knowledge Graphs

scientific article published on 2 May 2020

A UIMA wrapper for the NCBO annotator

scientific article

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

scientific article

An open-source framework for large-scale, flexible evaluation of biomedical text mining systems

scientific article

BioLemmatizer: a lemmatization tool for morphological processing of biomedical text

scientific article

Biomedical discovery acceleration, with applications to craniofacial development

scientific article published in March 2009

CaGE: cardiac gene expression knowledgebase.

scientific article

Concept annotation in the CRAFT corpus

scientific article

Concept recognition as a machine translation problem

scientific article published on 17 December 2021

Concept recognition for extracting protein interaction relations from biomedical text

scientific article published on September 2008

Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles

scientific article

Coreference resolution improves extraction of Biological Expression Language statements from texts

scientific article published on 03 July 2016

Corpus refactoring: a feasibility study

scientific article

Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies.

scientific article

Exploring species-based strategies for gene normalization.

scientific article

Gold-standard ontology-based anatomical annotation in the CRAFT Corpus

article

HIGH-PRECISION BIOLOGICAL EVENT EXTRACTION: EFFECTS OF SYSTEM AND OF DATA.

scientific article

High-precision biological event extraction with a concept recognizer

scientific article published in 2009

Improving precision in concept normalization

scientific article published in January 2018

Improving protein function prediction methods with integrated literature data

scientific article

Introducing meta-services for biomedical information extraction

scientific article published on September 2008

KaBOB: ontology-based semantic integration of biomedical databases

scientific article

Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters

scientific article (publication date: 26 February 2014)

Manual curation is not sufficient for annotation of genomic databases

scientific article

Mining Protein-Protein Interactions from GeneRIFs with OpenDMAP

article

MutationFinder: a high-performance system for extracting point mutation mentions from text

scientific article

OWL-NETS: Transforming OWL Representations for Improved Network Inference.

scientific article published in January 2018

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

scientific article

Overview of BioCreative II gene mention recognition

scientific article published on September 2008

Rapid pattern development for concept recognition systems: application to point mutations

scientific article published in December 2007

Refactoring corpora

Refactoring corpora

Software testing and the naturally occurring data assumption in natural language processing

article

Sublanguage Corpus Analysis Toolkit: A tool for assessing the representativeness and sublanguage characteristics of corpora

SuperCAT: The (New and Improved) Corpus Analysis Toolkit

article published in 2016

U-Compare: share and compare text mining tools with UIMA

scientific article

Visualization and Language Processing for Supporting Analysis across the Biomedical Literature

scholarly article by Carsten Görg et al published 2010 in Lecture Notes in Computer Science

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