What is BioIE? It includes any effort to extract structured information from unstructured (or, at least inconsistently structured) biological, clinical, or other biomedical data. The data source is often some collection of text documents written in technical language. If the resulting information is verifiable and consistent across sources, we may then consider it knowledge. Extracting information and producing knowledge from bio data requires adaptations upon methods developed for other types of unstructured data.
BioIE has undergone massive changes since the introduction of language models like BERT and the more recently created Large Language Models (LLMs; e.g., GPT-3/4, LLAMA2/3, Gemini, etc).
Resources included here are preferentially those available at no monetary cost and limited license requirements. Methods and datasets should be publicly accessible and actively maintained.
See also awesome-nlp, awesome-biology and Awesome-Bioinformatics.
Please read the contribution guidelines before contributing. Please add your favourite resource by raising a pull request.
Journals and Events
The interdisciplinary nature of BioIE means researchers in this space may share their findings and tools in a variety of ways. They may publish papers in journals, as is common in the biomedical and life sciences. They may publish conference papers and, upon acceptance, give a poster and/or oral presentation at an event; this is common practice in computer science and engineering fields. Conference papers are often published in collections of proceedings. Preprint publication is an increasingly popular and institutionally-accepted way to publish findings as well. Surrounding these formal, written products are the ideas of open science, open data, and open source: the code, data, and software BioIE researchers develop are valuable resources to the community.
Journals
For preprints, try arXiv, especially the subjects Computation and Language (cs.CL) and Information Retrieval (cs.IR); bioRxiv; or medRxiv, especially the Health Informatics subject area.
- Database - Its subtitle is "The Journal of Biological Databases and Curation". Open access.
- NAR - Nucleic Acids Research. Has a broad biomolecular focus but is particularly notable for its annual database issue.
- JAMIA - 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".
- JBI - The Journal of Biomedical Informatics. Not open access by default, though it does have an open-access "X" version.
- Scientific Data - An open-access Springer Nature journal publishing "descriptions of scientifically valuable datasets, and research that advances the sharing and reuse of scientific data".
Conferences and Other Events
- ACM-BCB - The ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. Held annually since 2010.
- BIBM - The IEEE International Conference on Bioinformatics and Biomedicine.
- ISMB - 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 focus, though it has included an increasing amount of text mining content (e.g., the 2019 meeting included a full-day special session on Text Mining for Biology and Healthcare). The meeting is combined with that of the European Conference on Computational Biology (ECCB) on odd-numbered years.
- PSB - The Pacific Symposium on Biocomputing.
Challenges
Some events in BioIE are organized around formal tasks and challenges in which groups develop their own computational solutions, given a dataset.
- BioASQ - Challenges on biomedical semantic indexing and question answering. Challenges and workshops held annually since 2013.
- BioCreAtIvE workshop - These workshops have been organized since 2004, with BioCreative VI happening February 2017 and the BioCreative/OHNLP Challenge held in 2018. See Datasets below.
- SemEval workshop - 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.
- eHealth-KD - 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.
- EHR DREAM Challenge - 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.