Biomedical Information Extraction
113 items from caufieldjh/awesome-bioie ★468
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Capturing the Patient's Perspective: a Review of Advances in Natural Language Processing of Health-Related Text ncbi.nlm.nih.gov
A 2017 review of natural language processing methods applied to information extraction in health records and social media text. An important note from this review: "One of the main challenges in the field is the availability of data that can be shared and which can be used by…
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NCBI Disease Corpus ncbi.nlm.nih.gov
paper - A corpus of 793 biomedical abstracts annotated with names of diseases and related concepts from MeSH and OMIM.
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Scientific Data nature.com
An open-access Springer Nature journal publishing "descriptions of scientifically valuable datasets, and research that advances the sharing and reuse of scientific data".
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National Centre for Text Mining (NaCTeM) nactem.ac.uk
Based at the University of Manchester and led by Prof. Sophia Ananiadou, NaCTeM is concerned with text mining in general but has a particular focus on biomedical applications.
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Monarch Initiative monarchinitiative.org
A joint effort between groups at Oregon State University, Oregon Health & Science University, Lawrence Berkeley National Lab, The Jackson Laboratory, and several others, seeking to "integrate biological information using semantics, and present it in a novel way, leveraging…
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MIMIC-III mimic.physionet.org
paper - Deidentified health data from ~60,000 intensive care unit admissions. Requires completion of an online training course (CITI training) and acceptance of a data use agreement prior to use.
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MIMIC-IV mimic-iv.mit.edu
An update to MIMIC-III's multimodal patient data, now covering more recent years of admissions, plus a new data structure, emergency department records, and links to MIMIC-CXR images.
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PubMedBERT microsoft.github.io
paper - A BERT model trained from scratch on PubMed, with versions trained on abstracts+full texts and on abstracts alone.
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Med7 medium.com
paper - code - a Python package and model (for use with spaCy) for doing NER with medication-related concepts.
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Mayo Clinic's clinical natural language processing program mayo.edu
Several groups at Mayo Clinic have made major contributions to BioIE (for example, the Apache cTAKES platform) over the past 20 years.
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Biomedical Literature Mining link.springer.com
A (non-free) volume of Methods in Molecular Biology from 2014. Chapters covers introductory principles in text mining, applications in the biological sciences, and potential for use in clinical or medical safety scenarios.
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Demner-Fushman group at NLM lhncbc.nlm.nih.gov
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SPECIALIST Lexicon lexsrv3.nlm.nih.gov
paper - A general English lexicon that includes many biomedical terms. Updated yearly since 1994 and still updated as of 2019. Part of UMLS but does not require UTS account to download.
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eHealth-KD knowledge-learning.github.io
Challenges for encouraging "development of software technologies to automatically extract a large variety of knowledge from eHealth documents written in the Spanish Language". Previously held as part of TASS, an annual workshop for semantic analysis in Spanish.
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Undiscovered Public Knowledge jstor.org
(paywalled) and Rediscovering Don Swanson: the Past, Present and Future of Literature-Based Discovery.
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Getting Started in Text Mining journals.plos.org
A brief introduction to bio-text mining from Cohen and Hunter. More than ten years old but still quite relevant. See also an earlier paper by the same authors.
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JensenLab text mining exercises jensenlab.org
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JensenLab jensenlab.org
Based at the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen, Denmark.
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ISMB iscb.org
The International Conference on Intelligent Systems for Molecular Biology is an annual conference hosted by the International Society for Computational Biology since 1993. Much of its focus has concerned bioinformatics and computational biology without an explicit clinical…
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IMIA imia-medinfo.org
The International Medical Informatics Association. Publishes the IMIA Yearbook of Medical Informatics.
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BIBM ieeebibm.org
The IEEE International Conference on Bioinformatics and Biomedicine.
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Flair embeddings from PubMed github.com
A language model available through the Flair framework and embedding method. Trained over a 5% sample of PubMed abstracts until 2015, or > 1.2 million abstracts in total.
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BioRED ftp.ncbi.nlm.nih.gov
paper - a set of >6.5K biomedical relation annotations, plus labels for novel findings.
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BioWordVec figshare.com
paper - code - Word embeddings derived from biomedical text (>27 million PubMed titles and abstracts), including subword embedding model based on MeSH.
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eICU Collaborative Research Database eicu-crd.mit.edu
paper - a database of observations from more than 200 thousand intensive care unit admissions, with consistent structure. Requires registration, training course completion, and data use agreement.
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On the Dangers of Stochastic Parrots: Can Language Models Be Too Big? 🦜 dx.doi.org
a frequently referenced but still relevant work concerning the roles, applications, and risks of language models.
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Large language models in healthcare: A comprehensive benchmark dx.doi.org
a statistical and human evaluation of sixteen different LLMs applied to medical language tasks.
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Assessing the research landscape and clinical utility of large language models: a scoping review doi.org
a high-level review of LLM applications in medicine as of March 2024.
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Ethical and regulatory challenges of large language models in medicine doi.org
a review of ethical issues arising from applications of LLMs in biomedicine.
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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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