Biomedical Information Extraction
113 items from caufieldjh/awesome-bioie ★468
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Disease Ontology disease-ontology.org
paper - An ontology of human diseases. Has cross-links to MeSH, ICD, NCI Thesaurus, SNOMED, and OMIM. Public domain. Available on GitHub and on the OBO Foundry.
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Columbia University Department of Biomedical Informatics dbmi.columbia.edu
Led by Drs. George Hripcsak and Noémie Elhadad.
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OHSUMED davis.wpi.edu
paper - 348,566 MEDLINE entries (title and sometimes abstract) from between 1987 and 1991. Includes MeSH labels. Primarily of historical significance.
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Coursera - Foundations of mining non-structured medical data coursera.org
About three hours worth of video lectures on working with medical data of various types and structures, including text and image data. Appears fairly high-level and intended for beginners.
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LLL corpora.informatik.hu-berlin.de
paper - 77 sentences from research articles about the bacterium Bacillus subtilis, annotated for protein–gene interactions (so, fairly close to PPI annotations). Additional information is here.
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IEPA corpora.informatik.hu-berlin.de
paper - 486 sentences from biomedical research abstracts annotated for pairs of co-occurring chemicals, including proteins (hence, PPI annotations).
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HPRD50 corpora.informatik.hu-berlin.de
paper - 50 scientific abstracts referenced by the Human Protein Reference Database, annotated for PPI.
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BioInfer corpora.informatik.hu-berlin.de
paper - 1,100 sentences from biomedical research abstracts annotated for relationships (including PPI), named entities, and syntactic dependencies. Additional information and download links are here.
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AIMed corpora.informatik.hu-berlin.de
paper - 225 MEDLINE abstracts annotated for PPI.
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Center for Computational Pharmacology NLP Group compbio.ucdenver.edu
based at University of Colorado, Denver and led by Larry Hunter - see their GitHub repos here.
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Columbia Open Health Data cohd.io
paper - A database of prevalence and co-occurrence frequencies of conditions, drugs, procedures, and patient demographics extracted from electronic health records. Does not include original record text.
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CLAMP clamp.uth.edu
paper - A natural language processing toolkit intended for use with the text in clinical reports. Check out their live demo first to see what it does. Usable at no cost for academic research.
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Boston Children's Hospital Natural Language Processing Laboratory childrenshospital.org
Led by Dr. Guergana Savova, formerly at Mayo Clinic and the Apache cTAKES project.
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Brown Center for Biomedical Informatics brown.edu
Based at Brown University and directed by Dr. Neil Sarkar, whose research group works on topics in clinical NLP and IE.
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brat brat.nlplab.org
paper - code - The brat rapid annotation tool. Supports producing text annotations visually, through the browser. Not subject specific; appropriate for many annotation projects. Visualization is based on that of the stav tool.
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VIB text mining and curation training bits.vib.be
This training workshop happenened in 2013 but the slides are still online.
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SPL-ADR-200db bionlp.nlm.nih.gov
paper - A pilot dataset containing standardised information, and annotations of occurence in text, about ~5,000 known adverse reactions for 200 FDA-approved drugs.
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Biolink biolink.github.io
code - A data model of biological entities. Provided as a YAML file.
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BioCreative VI CHEMPROT Corpus biocreative.bioinformatics.udel.edu
paper - >2,400 articles annotated with chemical-protein interactions of a variety of relation types. Requires registration.
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BioCreAtIvE V CDR Task Corpus (BC5CDR) biocreative.bioinformatics.udel.edu
paper - 1,500 articles (title and abstract) published in 2014 or later, annotated for 4,409 chemicals, 5,818 diseases and 3116 chemical–disease interactions. Requires registration.
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BioCreAtIvE workshop biocreative.bioinformatics.udel.edu
These workshops have been organized since 2004, with BioCreative VI happening February 2017 and the BioCreative/OHNLP Challenge held in 2018. See Datasets below.
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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.
