Biomedical Information Extraction
113 items from caufieldjh/awesome-bioie ★468
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BioC-BioGRID bioc.sourceforge.net
paper - 120 full text articles annotated for PPI and genetic interactions. Used in the BioCreative V BioC task.
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BioASQword2vec bioasq.org
paper - Qord embeddings derived from biomedical text (>10 million PubMed abstracts) using the popular word2vec tool.
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BioASQ bioasq.org
Challenges on biomedical semantic indexing and question answering. Challenges and workshops held annually since 2013.
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Mining Electronic Health Records (EHRs): A Survey arxiv.org
A review of the methods and philosophy behind mining electronic health records, including using them for adverse event detection. See Table 2 for a list of relevant papers as of mid-2017.
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AMIA amia.org
Many—but certainly not all—individuals studying biomedical informatics are members of the American Medical Informatics Association. AMIA publishes a journal, JAMIA (see below).
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SemEval workshop alt.qcri.org
Tasks and evaluations in computational semantic analysis. Tasks vary by year but frequently cover scientific and/or biomedical language, e.g. the SemEval-2019 Task 12 on Toponym Resolution in Scientific Papers.
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Biomedical Informatics on the Cloud: A Treasure Hunt for Advancing Cardiovascular Medicine ahajournals.org
An overview of how BioIE and bioinformatics workflows can be applied to questions in cardiovascular health and medicine research.
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ACM-BCB acm-bcb.org
The ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. Held annually since 2010.
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NAR academic.oup.com
Nucleic Acids Research. Has a broad biomolecular focus but is particularly notable for its annual database issue.
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JAMIA academic.oup.com
The Journal of the American Medical Informatics Association. Concerns "articles in the areas of clinical care, clinical research, translational science, implementation science, imaging, education, consumer health, public health, and policy".
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Database academic.oup.com
Its subtitle is "The Journal of Biological Databases and Curation". Open access.
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BioNLP ST 2013 datasets 2013.bionlp-st.org
data from six shared tasks, though some may not be easily accessible; try the CG task set (BioNLP2013CG) for extensive entity and event annotations.
