Biomedical Information Extraction
113 items from caufieldjh/awesome-bioie ★468
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BioGPT github.com
paper - A GPT-2 model pre-trained on 15 million PubMed abstracts, along with fine-tuned versions for several biomedical tasks.
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mimic-code github.com
Code associated with the MIMIC-III dataset (see below). Includes some helpful tutorials.
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ScispaCy github.com
paper - A version of the spaCy framework for scientific and biomedical documents.
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SciBERT github.com
paper - A BERT model trained on >1M papers from the Semantic Scholar database.
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OMOP Common Data Model github.com
a standard for observational healthcare data.
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Alsentzer et al Clinical BERT github.com
paper
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BioBERT github.com
paper - code - A PubMed and PubMed Central-trained version of the BERT language model.
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BlueBERT github.com
paper - A BERT model pre-trained on PubMed text and MIMIC-III notes.
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Huang et al ClinicalBERT github.com
paper
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medaCy github.com
A system for building predictive medical natural language processing models. Built on the spaCy framework.
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Anafora github.com
paper - An annotation tool with adjudication and progress tracking features.
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rentrez github.com
R utilities for accessing NCBI resources, including PubMed.
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CORD-19 github.com
A corpus of scholarly manuscripts concerning COVID-19. Articles are primarily from PubMed Central and preprint servers, though the set also includes metadata on papers without full-text availability.
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SemEHR github.com
paper - an IE infrastructure for electronic health records (EHR). Built on the CogStack project.
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CRAFT github.com
paper - 67 full-text biomedical articles annotated in a variety of ways, including for concepts and coreferences. Now on version 5, including annotations linking concepts to the MONDO disease ontology.
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II-Commons github.com
Daily-updated skill and CLI for deterministic retrieval across arXiv, PubMed/PMC, and supported US policy corpora.
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Pubrunner github.com
A framework for running text mining tools on the newest set(s) of documents from PubMed.
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TabInOut github.com
paper - a framework for IE from tables in the literature.
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DeepPhe github.com
A system for processing documents describing cancer presentations. Based on cTAKES (see above).
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Bio-SCoRes github.com
paper - A framework for biomedical coreference resolution.
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unmiri-ngs-fhir-schema github.com
Apache-2.0 JSON Schema (Draft 2020-12) API contract for cross-vendor somatic NGS interpretation output (Foundation Medicine, Tempus, Caris, Guardant), aligned with the HL7 FHIR Genomics IG. A standards-aligned target representation for biomedical information-extraction…
