CNAG-Biomedical-Informatics/convert-pheno

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

Language: Perl - Size: 79 MB - Last synced: about 12 hours ago - Pushed: about 15 hours ago - Stars: 9 - Forks: 1

Sage-Bionetworks/schematic

Package for biomedical data model and metadata ingress management

Language: Python - Size: 10.3 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 21 - Forks: 23

monarch-initiative/omim

Data ingest pipeline for OMIM.

Language: Python - Size: 80.6 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 6 - Forks: 2

ram-compbio/CANDO

Computational Analysis of Novel Drug Opportunities

Language: Python - Size: 11.7 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 33 - Forks: 9

nlpie/biomedicus

BioMedICUS: A biomedical and clinical NLP engine.

Language: Java - Size: 6.65 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 15 - Forks: 6

BaranziniLab/KG_RAG

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

Language: Jupyter Notebook - Size: 9.85 MB - Last synced: 7 days ago - Pushed: 29 days ago - Stars: 342 - Forks: 49

EBISPOT/DUO

Ontology for consent codes and data use requirements

Language: Makefile - Size: 6.43 MB - Last synced: 8 days ago - Pushed: over 1 year ago - Stars: 59 - Forks: 15

MUSC-TBIC/lexicon-tools

Language: Python - Size: 77.1 KB - Last synced: 9 days ago - Pushed: 11 months ago - Stars: 3 - Forks: 0

carnival-data/carnival-demo-biomedical

Demonstration Carnival Micronaut application.

Language: Groovy - Size: 10.2 MB - Last synced: 9 days ago - Pushed: 12 months ago - Stars: 2 - Forks: 0

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 Notebook - Size: 2.28 MB - Last synced: 9 days ago - Pushed: almost 2 years ago - Stars: 12 - Forks: 0

hms-dbmi/EHRtemporalVariability

R package for delineating temporal dataset shifts in Eletronic Health Records

Language: HTML - Size: 11.7 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 14 - Forks: 8

JuliaHealth/juliahealth.github.io

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

Language: Julia - Size: 2.16 MB - Last synced: 14 days ago - Pushed: about 2 months ago - Stars: 14 - Forks: 8

a-r-j/DrugTranslatoR

R package for translating between drug identifiers using the Chemical Translation Service (CTS)

Language: R - Size: 6.84 KB - Last synced: 14 days ago - Pushed: over 1 year ago - Stars: 3 - Forks: 2

mne-tools/mne-cpp

MNE-CPP: A Framework for Electrophysiology

Language: C++ - Size: 349 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 148 - Forks: 137

dipendrapant/Health_Biomedical_Informatics_Conference_Journals

List with overview of significant conferences and journals related to Biomedical & Health Informatics

Size: 26.4 KB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 1 - Forks: 0

cancervariants/disease-normalization

Services and guidelines for normalizing disease terms

Language: Python - Size: 4.17 MB - Last synced: 25 days ago - Pushed: about 1 month ago - Stars: 4 - Forks: 0

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: Python - Size: 129 KB - Last synced: 20 days ago - Pushed: 21 days ago - Stars: 5 - Forks: 1

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.

Size: 1.02 MB - Last synced: 21 days ago - Pushed: 22 days ago - Stars: 20 - Forks: 5

sejas/muia-assessment-applewatch-atrial-fibrillation-ontology

Basic ontology to represent the article: "Large-Scale Assessment of a Smartwatch to Identify Atrial Fibrillation"

Size: 2.45 MB - Last synced: 22 days ago - Pushed: over 4 years ago - Stars: 2 - Forks: 0

lmichan/PFR

Proyecto de manejo de información digital sobre pruebas de función respiratoria mediante anotación semántica con Hypothes.is

Size: 28.3 KB - Last synced: 28 days ago - Pushed: 29 days ago - Stars: 1 - Forks: 0

AnthonyMRios/pymetamap

Python wraper for MetaMap

Language: Python - Size: 45.9 KB - Last synced: 20 days ago - Pushed: almost 4 years ago - Stars: 168 - Forks: 61

tanmaybasu/Extract-Anxiety-Outcome-Measures-From-Literature

A sentence classification framework for extraction of anxiety outcome measures from relevant literature

Language: Python - Size: 18.6 MB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 1 - Forks: 0

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

A text summarization framework to identify major opinions from healthcare text

Language: Python - Size: 46.9 KB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 5 - Forks: 0

cancervariants/gene-normalization

Services and guidelines for normalizing genes

Language: Python - Size: 2.06 MB - Last synced: 25 days ago - Pushed: about 1 month ago - Stars: 1 - Forks: 2

pscedu/singularity

Just a list of Singularity definition files maintained by the Biomed Applications Group

Language: Python - Size: 178 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

ICBI/Open-Science-Projects

Open Science Projects at Georgetown-ICBI

Size: 1.36 MB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 4 - Forks: 0

deweylab/MetaSRA-pipeline

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

Language: Python - Size: 27.5 MB - Last synced: about 2 months ago - Pushed: 5 months ago - Stars: 42 - Forks: 15

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: JavaScript - Size: 3 MB - Last synced: about 2 months ago - Pushed: over 6 years ago - Stars: 6 - Forks: 1

pscedu/apptainer

Just a list of Apptainer definition files maintained by the Biomed Applications Group

Language: Python - Size: 3.91 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

suamin/MedDistant19

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

Language: Python - Size: 213 KB - Last synced: 30 days ago - Pushed: over 1 year ago - Stars: 15 - Forks: 2

mida-project/meta Fork of MIMBCD-UI/meta

:paperclip: About MIDA Project

Size: 143 MB - Last synced: 26 days ago - Pushed: over 3 years ago - Stars: 12 - Forks: 1

timsbiomed/tims-website

The overall and public TIMS repository.

Language: HTML - Size: 33.2 KB - Last synced: 8 days ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

tranSMART-Foundation/transmart-core

Core components and documentation of the tranSMART platform.

Language: JavaScript - Size: 329 MB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 6 - Forks: 2

Jeanvit/AndroidDynamometer

An Android app developed in my Master's (2014) for a biomedical electronic dynamometer with bluetooth interface.

Language: Java - Size: 14.5 MB - Last synced: 7 months ago - Pushed: almost 7 years ago - Stars: 1 - Forks: 1

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: Python - Size: 6.96 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 22 - Forks: 1

bhklab/CREAM

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

Language: R - Size: 2.47 MB - Last synced: 5 days ago - Pushed: over 3 years ago - Stars: 12 - Forks: 3

pleiadian53/tpheno

Prototypes for EHR-sequencing and temporal phenotyping. Key methods: sequence models, LSTM, attention mechanism, cluster analysis, word & document embeddings, and other NLP methods.

Language: Python - Size: 51 MB - Last synced: 9 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

mikaeldusenne/haskupcake

haskell library to send requests to the PIC-SURE api

Language: Haskell - Size: 167 KB - Last synced: 9 months ago - Pushed: about 6 years ago - Stars: 1 - Forks: 0

giffordlabcvr/HCV-NABS

Extension to HCV-GLUE project, to analyse binding sites for HCV neutralising antibodies.

Language: JavaScript - Size: 697 KB - Last synced: 9 months ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

uw-bionlp/ards

A PyTorch Wrapper of Hierarchical Attention Network with Sentence Objectives Framework for ARDS Identification

Language: Python - Size: 678 KB - Last synced: 10 months ago - Pushed: about 3 years ago - Stars: 1 - Forks: 0

SubhamoyBiswas/Simulation-of-Arrhythmia-in-a-computer-model-of-the-heart

Language: Python - Size: 951 KB - Last synced: 10 months ago - Pushed: over 2 years ago - Stars: 2 - Forks: 0

tanmaybasu/Data-Elements-Extrcation-from-Literature-Using-NLP-and-Machine-Learning

A novel sentence classification framework for information extraction from relevant literature

Language: Python - Size: 1.14 MB - Last synced: about 1 month ago - Pushed: almost 3 years ago - Stars: 2 - Forks: 1

ICBI/.github

Welcome to Georgetown University Innovation Center for Biomedical Informatics !

Size: 3.76 MB - Last synced: about 2 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

ReggieScript/ECG_arrythmia_detection

Arrythmia detection machine learning model using logistic regression ❤️

Language: Jupyter Notebook - Size: 6.63 MB - Last synced: 12 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0

tanmaybasu/Early-Prediction-of-Anorexia-and-Depression-Over-Social-Media

A text classification framework to identify anorexia and depression over social media text

Language: Python - Size: 44.9 KB - Last synced: about 1 month ago - Pushed: almost 3 years ago - Stars: 2 - Forks: 1

CompBtBs/FalseDiscoveriesAnalysis

Adjusting for false discoveries in constraint- and sampling-based differential metabolic flux analysis

Language: Jupyter Notebook - Size: 24.1 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 2 - Forks: 0

visanuwan/Nek2_singlecell

Nek2 single cell analysis

Language: R - Size: 5.86 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

visanuwan/CD24_CART_singlecell

CD24 CART single cell analysis

Language: R - Size: 8.79 KB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

carsaesi/covid19sdtool

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

Language: HTML - Size: 3.59 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 5 - Forks: 0

IVN-RIN/bio-med-BIT

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

Language: Jupyter Notebook - Size: 13.2 MB - Last synced: 3 months ago - Pushed: about 1 year ago - Stars: 4 - Forks: 0

zbmed-semtec/BioMedSem-IR-KD

A course on Biomedical Semantics, Information Retrieval and Knowledge Discovery

Language: HTML - Size: 197 MB - Last synced: 12 months ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

metadatacenter/cedar-project

Build project for all CEDAR Java repositories

Size: 145 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 12 - Forks: 1

pwatrick/DrugRepurposingToolKit

Language: R - Size: 5.51 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 5

EunBinChoi/biomedical-syntactic-analysis-master

The keywords of biomedical materials are extracted with biomedical and clinical syntactic analysis and named entity recognition models offered in Stanza.

Language: HTML - Size: 172 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

mgpopinjay/nlp-qa-outdomain

Out-domain Question Answering (QA) on SQuAD with bi-directional LSTM

Language: Python - Size: 97.5 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

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: MATLAB - Size: 3.69 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 2 - Forks: 2

AnthonyMRios/multi-label-zero-shot

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

Language: Python - Size: 598 KB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 45 - Forks: 11

aimanmuhamad/StanzaDemo

These packages offer accurate syntactic analysis and named entity recognition capabilities for biomedical and clinical text.

Language: Jupyter Notebook - Size: 320 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 1

monarch-initiative/icd10who

ICD10WHO ingest.

Language: Python - Size: 511 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

bionlproc/multi-label-zero-shot Fork of AnthonyMRios/multi-label-zero-shot

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

Language: Python - Size: 12.7 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 21 - Forks: 1

pwatrick/ddiwas

Language: R - Size: 4.63 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 1

bcbi/julia_tutorials

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

Language: Jupyter Notebook - Size: 29.5 MB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 3 - Forks: 4

carsaesi/EHRsourceVariability

Measuring and visualizing biomedical data variability/heterogeneity across data sources

Language: R - Size: 183 KB - Last synced: about 1 year ago - Pushed: almost 5 years ago - Stars: 3 - Forks: 0

hms-dbmi/connections.careers

Website for a video project that documents the training experiences of predoctoral and postdoctoral trainees from 16 National Library of Medicine-funded biomedical informatics and data science training programs.

Language: JavaScript - Size: 20.6 MB - Last synced: 29 days ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 0

sharmalab/Emory-BMI-GSoC

Emory BMI GSoC 2020 Project Ideas

Size: 268 KB - Last synced: about 1 month ago - Pushed: over 3 years ago - Stars: 8 - Forks: 2

krishnakumarsekar/Ant-Colony-Optimization-in-TensorFlow

Ant colony optimazation is a famous algorithm in image segmentation and biomedical , This project is to effectively apply ACO in tensorflow and for production purpose

Size: 0 Bytes - Last synced: about 1 year ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0

snikol03/Markov-Chain-Project

Perl implementation of Markov Chain for the course BIO331

Language: Perl - Size: 12.5 MB - Last synced: 9 months ago - Pushed: about 7 years ago - Stars: 2 - Forks: 1

cdcai/enriched-LSTMs Fork of scotthlee/enriched-LSTMs

Classifying multimodal health data with LSTMs

Language: Python - Size: 53.7 KB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 1

bionlproc/med-match-cnn Fork of AnthonyMRios/med-match-cnn

Implementation of our matching network CNN

Language: Python - Size: 19.5 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 2 - Forks: 2

AnthonyMRios/med-match-cnn

Implementation of our matching network CNN

Language: Python - Size: 22.5 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 2 - Forks: 3

xcollantes/biomed-machine-learning-CUI

Application interacts with NIH API

Language: Java - Size: 3.94 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

Glewando/Neuroinflammation-Memory

Impact of neuroinflammation of contextual memory and neuronal circuit activity

Language: R - Size: 1.48 MB - Last synced: about 1 year ago - Pushed: about 7 years ago - Stars: 0 - Forks: 1