biomedical-informatics

There are 89 repositories under biomedical-informatics topic.

  • BaranziniLab/KG_RAG

    Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks

    Language:Jupyter Notebook8831725106

  • AnthonyMRios/pymetamap

    Python wraper for MetaMap

    Language:Python17094262

  • mne-tools/mne-cpp

    MNE-CPP: A Framework for Electrophysiology

    Language:C++16720138144
  • DUO

    EBISPOT/DUO

    Ontology for consent codes and data use requirements

    Language:Makefile671610816
  • GSoC

    uaanchorage/GSoC

    Alaska Project Ideas, mentored by the researchers and collaborators of University of Alaska and supported by open-source entities and enthusiasts in Alaska.

    538012

  • AnthonyMRios/multi-label-zero-shot

    Few- and Zero-shot Multi-Label Learning for Structured Label Spaces

    Language:Python482612

  • deweylab/MetaSRA-pipeline

    MetaSRA: normalized sample-specific metadata for the Sequence Read Archive

    Language:Python45327614
  • clinical_informatics_umls

    rcolinp/clinical_informatics_umls

    An exploratory, tutorial and analytical view of the Unified Medical Language System (UMLS) & the software/technologies provided via being a free UMLS license holder. This repo will subset 2021AB UMLS native release, introduce/build upon UMLS provided tools to load a configured subset into first a relational database --> MySQL, SQLite, PostgreSQL and MariaDB all covered within this repo. Next the UMLS subset which is stored in a relational DB will be queried, modeled and lastly loaded into a defined Neo4j label property graph. Lastly, Neo4j database containing UMLS 2021AB subset in schema promoting intuitive analysis and rich visualization will become the central datastore for analysis. The datastore contains ~5 million distinct nodes & >40 million distinct relationships (edges). Currently, Neo4j is running via Docker but deployment options are NOT limited to Docker. If choosing to deploy via Neo4j Aura, server, Neo4j Desktop, VM etc... Please note and be aware of the specific volumes and environment variables specified within this repository (docker run). The ability for the loaded Neo4j Graph to interact with RDF data (i.e. import/export RDF data to and from Neo4j) may not be possible via all Neo4j deployment avenues (i.e. Neo4j Aura currently does not support RDF integration that is demonstrated in this repository).

    Language:Python44202

  • ram-compbio/CANDO

    Computational Analysis of Novel Drug Opportunities

    Language:Python3942511

  • Sage-Bionetworks/schematic

    Package for biomedical data model and metadata ingress management

    Language:Python251161626

  • bionlproc/multi-label-zero-shot

    Few- and Zero-shot Multi-Label Learning for Structured Label Spaces

    Language:Python20202

  • nlpie/biomedicus

    BioMedICUS: A biomedical and clinical NLP engine.

    Language:Java185887

  • suamin/MedDistant19

    MedDistant19: Towards an Accurate Benchmark for Broad-Coverage Biomedical Relation Extraction (COLING 2022)

    Language:Python18422

  • hms-dbmi/EHRtemporalVariability

    R package for delineating temporal dataset shifts in Eletronic Health Records

    Language:HTML17608

  • tisimpson/pbi

    Programming for Biomedical Informatics, School of Informatics, The University of Edinburgh

    Language:Jupyter Notebook17524

  • JuliaHealth/juliahealth.github.io

    Website for the JuliaHealth organization (powered by Franklin.jl).

    Language:Julia16151810

  • CNAG-Biomedical-Informatics/convert-pheno

    A software toolkit for the interconversion of standard data models for phenotypic data

    Language:Perl15221

  • metadatacenter/cedar-project

    Build project for all CEDAR Java repositories

    14231.2k1
  • meta

    mida-project/meta

    :paperclip: About MIDA Project

    13501

  • bhklab/CREAM

    CREAM (Clustering of Functional Regions Analysis Method) is a new method for identification of clusters of functional regions (COREs) within chromosomes.

    Language:R124103

  • MUSC-TBIC/etude-engine

    ETUDE (Evaluation Tool for Unstructured Data and Extractions) is a Python-based tool that provides consistent evaluation options across a range of annotation schemata and corpus formats

    Language:Jupyter Notebook12211

  • FedericaPaoli1/Respiration-rate-and-heart-rate-detection

    Respiration-rate-and-heart-rate-detection is a project developed for the Biomedical Signal Processing exam at the University of Milan (academic year 2020-2021). It implements an algorithm to analyze accelerometric signals collected with a smartphone positioned on the thorax while supine.

    Language:MATLAB9205

  • sharmalab/Emory-BMI-GSoC

    Emory BMI GSoC 2020 Project Ideas

    81202

  • CNAG-Biomedical-Informatics/pheno-ranker

    Pheno-Ranker is a tool for comparing phenotypic data structured in JSON/YAML format, such as Beacon v2 Models or Phenopackets v2, as well as CSV.

    Language:Perl7101

  • monarch-initiative/omim

    Data ingest pipeline for OMIM.

    Language:Jupyter Notebook781313

  • biolab-unige/xtens-app

    A digital repository for biomedical data based on a flexible JSON data model ( The project has been moved to a new address https://github.com/xtens-suite/xtens-app.git )

    Language:JavaScript64401

  • cancervariants/disease-normalization

    Services and guidelines for normalizing disease terms

    Language:Python64950

  • tanmaybasu/Qualitative-Text-Analysis-of-Healthcare-Data-Using-NLP

    A text summarization framework to identify major opinions from healthcare text

    Language:Python6100

  • tranSMART-Foundation/transmart-core

    Core components and documentation of the tranSMART platform.

    Language:JavaScript6122

  • bcbi/julia_tutorials

    Materials used for introductory classes using Julia for statistics, biomedical queries and plotting

    Language:Jupyter Notebook5804
  • covid19sdtool

    carsaesi/covid19sdtool

    R code for the discovery of COVID-19 subgroups by symptoms and comorbidities.

    Language:HTML5000
  • EHRsourceVariability

    carsaesi/EHRsourceVariability

    Measuring and visualizing biomedical data variability/heterogeneity across data sources

    Language:R5000

  • DavidAI2024/DrugGeneExplorer

    This Python script is designed to provide detailed information on interactions between drugs and genes using the Sydney module for natural language processing and the Drug Gene Interaction Database (DGIdb) API. Users can input the names of three drugs separated by commas and receive information on the interactions with the corresponding genes.

    Language:Python5102

  • IVN-RIN/bio-med-BIT

    Data and source code for Localising In-Domain Adaptation of Transformer-Based Biomedical Language Models

    Language:Jupyter Notebook5100

  • ICBI/Open-Science-Projects

    Open Science Projects at Georgetown-ICBI

    4800

  • karthiksoman/biomixQA

    Repository for BiomixQA benchmark dataset

    Language:Jupyter Notebook3100