DEB2 is a medication indication and adverse effect knowledgebase derived from five publicly available sources: the VA’s National Drug File-Reference Terminology, MEDLINE, the US Food and Drug Administration’s drug product labels (via the SIDER2 database), the MedlinePlus consumer health information website, and DrugBank, a manually-curated drug target database. All medications, indications, and adverse effects in DEB2 are represented using the RxNorm and SNOMED-CT terminologies.
AMIA 2015 NLP Application Tutorial Below are the slides from the AMIA 2015 NLP Tutorial. Josh Denny: NLP applied to EHR phenotyping and medical education: josh amia NLP tutorial 2015.pdf Hua Xu: Introduction to pipeline NLP and Clinical Language Annotation, Modeling, and Processing Toolkit (CLAMP)
Download the mapping between ICD-9 codes and PheWAS codes, version 1.2 at https://phewascatalog.org/phecodes .
The KnowledgeMap Concept Indexer (KMCI) is the underlying natural language processing engine used in the KnowledgeMap and Learning Portfolio website, and has been used for many clinical and genomic research studies. It identifies biomedical concepts, mapped to Unified Medical Language System concepts, from natural language documents and clinical notes.
This package contains methods for performing PheWAS. Please contact PheWAS@vumc.org. if you encounter any errors or apparent bugs. The documentation is done natively in R. The command ?PheWAS once the package is loaded will direct you to the package description, including references to each function and an example. The command vignette("PheWAS-package") will display the package vignette with further "How to's".
MEDI (MEDication Indication) is an ensemble medication indication resource for primary and secondary uses of electronic medical record (EMR) data. MEDI was created based on multiple commonly used medication resources (RxNorm, MedlinePlus, SIDER 2, and Wikipedia ) and by leveraging both ontology and natural language processing (NLP) techniques.
Clinical notes are often divided into sections, or segments, such as "history of present illness" or "past medical history." These sections often have subsections as well, such as the "cardiovascular exam" section of the "physical exam." One can gain greater understanding of clinical notes by recognition of the section in which a concept lives. For instance, both a "past medical history" and the "family medical history" sections can contain a list of diseases, but the context decribes very different import to the patient about whom the note was written.