Biomedical Information Extraction
113 items from caufieldjh/awesome-bioie ★468
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Comparative Toxicogenomics Database ctdbase.org
paper - A database of manually curated associations between chemicals, gene products, phenotypes, diseases, and environmental exposures. Useful for assembling ontologies of the related concepts, such as types of chemicals.
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Biopython biopython.org
paper - code - Python tools primarily intended for bioinformatics and computational molecular biology purposes, but also a convenient way to obtain data, including documents/abstracts from PubMed (see Chapter 9 of the documentation).
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Apache cTAKES ctakes.apache.org
paper - code - A system for processing the text in electronic medical records. Widely used and open source.
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Zaklab zaklab.org
Group led by Dr. Isaac Kohane at Harvard Medical School's Department of Biomedical Informatics (Dr. Kohane is also a steward of the n2c2 (formerly i2b2) datasets - see Datasets below).
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Word Sense Disambiguation (WSD) wsd.nlm.nih.gov
paper - 203 ambiguous words and 37,888 automatically extracted instances of their use in biomedical research publications. Requires UTS account.
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BioUML wiki.biouml.org
paper - An architecture for biomedical data analysis, integration, and visualization. Conceptually based on the visual modeling language UML.
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TurkuNLP turkunlp.org
Based at the University of Turku and concerned with NLP in general with a focus on BioNLP and clinical applications.
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EHR DREAM Challenge synapse.org
Held along with several other more bioinformatics-focused challenges, this challenge opened in October 2019 and focuses on using electronic health record data to predict patient mortality. Uses a synthetic data set rather than real EHR contents.
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BioCreAtIvE 1 sourceforge.net
paper - 15,000 sentences (10,000 training and 5,000 test) annotated for protein and gene names. 1,000 full text biomedical research articles annotated with protein names and Gene Ontology terms.
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UMLS Semantic Network semanticnetwork.nlm.nih.gov
paper - Lists of 133 semantic types and 54 semantic relationships covering biomedical concepts and vocabulary. Is the Metathesaurus too complex for your needs? Try this. Does not require UTS account to download.
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This paper from Hongfang Liu's group at Mayo Clinic sciencedirect.com
demonstrates how text embeddings trained on biomedical or clinical text can, but don't always, perform better on biomedical natural language processing tasks. That being said, pre-trained embeddings may be appropriate for your needs, especially as training domain-specific…
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Clinical information extraction applications: A literature review sciencedirect.com
A review of clinical IE papers published as of September 2016. From Mayo Clinic group (see below).
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Literature Based Discovery: Models, methods, and trends sciencedirect.com
A review of Literature Based Discovery (LBD), or the philosophy that meaningful connections may be found between seemingly unrelated scientific literature.
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JBI sciencedirect.com
The Journal of Biomedical Informatics. Not open access by default, though it does have an open-access "X" version.
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UTHealth Houston Biomedical Natural Language Processing Lab sbmi.uth.edu
Based in the University of Texas Health Science Center at Houston, School of Biomedical Informatics and led by Dr. Hua Xu.
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BioScope rgai.inf.u-szeged.hu
paper - a corpus of sentences from medical and biological documents, annotated for negation, speculation, and linguistic scope.
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PSB psb.stanford.edu
The Pacific Symposium on Biocomputing.
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n2c2 (formerly i2b2) Data portal.dbmi.hms.harvard.edu
The Department of Biomedical Informatics (DBMI) at Harvard Medical School manages data for the National NLP Clinical Challenges and the Informatics for Integrating Biology and the Bedside challenges running since 2006. They require registration before access and use. Datasets…
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MIMIC-CXR physionet.org
The MIMIC Chest X-Ray database. Contains more than 377,000 radiographic images and accompanying free-text radiology reports. As with MIMIC-III, requires acceptance of a data use agreement.
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MedTator ohnlp.github.io
paper - code - An annotation tool designed to have minimal dependencies.
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VCU Natural Language Processing Lab nlp.cs.vcu.edu
Based at Virginia Commonwealth University and led by Dr. Bridget McInnes.
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RxNorm nlm.nih.gov
paper - Normalized names for clinical drugs and drug packs, with combined ingredients, strengths, and form, and assigned types from the Semantic Network (see below). Released monthly.
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UMLS Knowledge Sources nlm.nih.gov
reference manual - A large and comprehensive collection of biomedical terminology and identifiers, as well as accompanying tools and scripts. Depending on your purposes, the single file MRCONSO.RRF may be sufficient, as this file contains unique identifiers and names for all…
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UMLS Metathesaurus nlm.nih.gov
paper - Mappings between >3.8 million concepts, 14 million concept names, and >200 sources of biomedical vocabulary and identifiers. It's big. It may help to prepare a subset of the Metathesaurus with the MetamorphoSys installation tool but we're still talking about ~30 Gb of…
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Clinical Questions Collection nlm.nih.gov
also known as CQC or the Iowa collection, these are several thousand questions posed by physicians during office visits along with the associated answers.
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PubTator Central ncbi.nlm.nih.gov
paper - A web platform that identifies five different types of biomedical concepts in PubMed articles and PubMed Central full texts. The full annotation sets are downloadable (see Annotated Text Data below).
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TaggerOne ncbi.nlm.nih.gov
paper - Performs concept normalization (see also DNorm above). Can be trained for specific concept types and can perform NER independent of other normalization functions.
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DNorm ncbi.nlm.nih.gov
paper - A method for disease normalization, i.e., linking mentions of disease names and acronyms to unique concept identifiers. Downloadable version includes the NCBI Disease Corpus and BC5CDR (see Annotated Text Data below).
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BioNLP group at NCBI ncbi.nlm.nih.gov
Develops improvements to biomedical literature search and curation (e.g., through PubMed), led by Dr. Zhiyong Lu.
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PubMed Central Open Access Subset ncbi.nlm.nih.gov
A set of PubMed Central articles usable under licenses other than traditional copyright, though the exact licenses vary by publication and source. Articles are available as PDF and XML.
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