umls | Topic | Ecosyste.ms: Repos

Topic: "umls"

CogStack/MedCAT

Medical Concept Annotation Tool

Language: Python - Size: 14.3 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 495 - Forks: 107

Georgetown-IR-Lab/QuickUMLS

System for Medical Concept Extraction and Linking

Language: Python - Size: 89.8 KB - Last synced at: 7 days ago - Pushed at: 10 months ago - Stars: 403 - Forks: 96

razorx89/roco-dataset

Radiology Objects in COntext (ROCO): A Multimodal Image Dataset

Language: Python - Size: 12.7 MB - Last synced at: about 2 months ago - Pushed at: about 3 years ago - Stars: 204 - Forks: 22

leanderme/sytora

A sophisticated smart symptom search engine

Language: JavaScript - Size: 7.03 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 155 - Forks: 87

zjunlp/Relphormer

[Neurocomputing 2023] Relational Graph Transformer for Knowledge Graph Representation

Language: Python - Size: 28.7 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 113 - Forks: 11

CogStack/CogStack-SemEHR 📦

Surfacing Semantic Data from Clinical Notes in Electronic Health Records for Tailored Care, Trial Recruitment and Clinical Research

Language: JavaScript - Size: 4.09 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 85 - Forks: 19

CogStack/MedCATtrainer

A simple interface to inspect, improve and add concepts to biomedical NER+L -> MedCAT.

Language: Python - Size: 11.1 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 80 - Forks: 35

GanjinZero/CODER

CODER: Knowledge infused cross-lingual medical term embedding for term normalization. [JBI, ACL-BioNLP 2022]

Language: Python - Size: 5.63 MB - Last synced at: about 2 months ago - Pushed at: almost 3 years ago - Stars: 78 - Forks: 5

som-shahlab/trove

Weakly supervised medical named entity classification

Language: Python - Size: 8.06 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 68 - Forks: 21

LHNCBC/metamaplite

A near real-time named-entity recognizer

Language: Java - Size: 1010 KB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 59 - Forks: 14

cthoyt/umls_downloader

Don't worry about UMLS, RxNorm, SNOMED, or SemMedDB licensing - write code that knows how to download it automatically

Language: Python - Size: 54.7 KB - Last synced at: 30 days ago - Pushed at: about 1 year ago - Stars: 40 - Forks: 4

kbogas/medknow

Medical Relations and Entities Extraction

Language: Python - Size: 118 KB - Last synced at: 3 days ago - Pushed at: almost 3 years ago - Stars: 36 - Forks: 13

CogStack/MedCATservice

Running MedCAT as a RESTful web service

Language: Python - Size: 154 KB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 22 - Forks: 14

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 at: over 1 year ago - Pushed at: over 1 year ago - Stars: 22 - Forks: 1

Colinasda/KGdatasets

知识图谱数据集

Size: 3.31 MB - Last synced at: over 2 years ago - Pushed at: almost 4 years ago - Stars: 22 - Forks: 5

RyanDsilva/medical-ner

:hospital: Clinical NER with UMLS lookup :hospital:

Language: Jupyter Notebook - Size: 1.85 MB - Last synced at: about 1 month ago - Pushed at: about 5 years ago - Stars: 22 - Forks: 4

acadTags/Rare-disease-identification

Rare disease identification from free-text clinical notes with ontologies and weak supervision

Language: Python - Size: 4.93 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 21 - Forks: 5

dhchenx/umls-graph

Build a medical knowledge graph based on Unified Language Medical System (UMLS)

Language: Python - Size: 434 KB - Last synced at: 8 days ago - Pushed at: over 3 years ago - Stars: 20 - Forks: 2

medkit-lib/medkit

Toolkit for a learning health system

Language: Python - Size: 9.26 MB - Last synced at: about 2 months ago - Pushed at: 2 months ago - Stars: 18 - Forks: 13

dhchenx/umls-similarity

Estimate similarity of medical concepts based on Unified Medical Language System (UMLS)

Language: Perl - Size: 229 KB - Last synced at: 10 days ago - Pushed at: over 3 years ago - Stars: 16 - Forks: 1

clips/humumls

UMLS in Python with MongoDB.

Language: Python - Size: 47.9 KB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 16 - Forks: 10

suamin/MedDistant19

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

Language: Python - Size: 213 KB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 15 - Forks: 2

NCBI-Hackathons/Semantic-search-log-analysis-pipeline

Classify web visitor queries so you can chart, and respond to, trends in information seeking

Language: JavaScript - Size: 27.1 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 14 - Forks: 3

thepanacealab/OHDSIananke

OHDSI Ananke - A Tool for Mapping Between OHDSI Concept Identifiers to Unified Medical Language System (UMLS) identifiers

Language: R - Size: 6.89 MB - Last synced at: about 1 month ago - Pushed at: over 4 years ago - Stars: 14 - Forks: 2

sparrow-platform/disease-diagnostics-engine

Sparrow AI - API for disease diagnostics

Language: Python - Size: 1.54 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 13 - Forks: 11

mpancia/rUMLS

An R interface for the NLM's UMLS.

Language: R - Size: 125 KB - Last synced at: about 1 year ago - Pushed at: over 7 years ago - Stars: 13 - Forks: 4

dermatologist/umlsjs

:heartpulse: npm package for accessing UMLS REST APIs (unofficial)

Language: TypeScript - Size: 2.11 MB - Last synced at: 25 days ago - Pushed at: about 2 years ago - Stars: 11 - Forks: 4

odwyersoftware/umls-api

Python client for the UMLS REST API https://documentation.uts.nlm.nih.gov/rest/home.html

Language: Python - Size: 15.6 KB - Last synced at: 19 days ago - Pushed at: over 3 years ago - Stars: 9 - Forks: 5

umcu/dutch-medical-concepts

Instructions and code to create for a table of UMLS, SNOMED or HPO concepts containing Dutch medical names, usable in named entity recognition and linking methods such MedCAT.

Language: Jupyter Notebook - Size: 377 KB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 2

CSFelix/UML

📊 There are just some UML I made with Draw.io. To save it in GitHub, I needed create a new Public Repo and, shazam! It's here. 📊 (🔑 KeyWords: diagram.io, uml, diagram 🔑)

Size: 2.48 MB - Last synced at: about 2 months ago - Pushed at: over 3 years ago - Stars: 8 - Forks: 0

nlpie-research/umls-to-snomed-icd10-mapper

UMLS to SNOMED CT and ICD-10 mapping tool: A Python script for generating JSON files containing mappings between UMLS CUIs and SNOMED CT or ICD-10 codes using the UMLS Metathesaurus. Supports exact match, broad relations, and parent-child hierarchy mapping methods.

Language: Python - Size: 8.79 KB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 7 - Forks: 0

CSFelix/THE-LAST-APS

📊 There are just some UML I made with Draw.io. To save it in GitHub, I needed create a new Public Repo and, shazam! It's here. 📊 (🔑 KeyWords: diagram.io, uml, diagram 🔑)

Language: JavaScript - Size: 421 KB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 7 - Forks: 0

agankur21/entity_disambiguation

Neural Network models to map mention of a text to corresponding entity in the Knowledge Base

Language: Python - Size: 1.99 MB - Last synced at: about 1 year ago - Pushed at: almost 8 years ago - Stars: 7 - Forks: 3

victormurcia/PyUMLS_Similarity

This package computes a variety of similarity metrics between concepts present in the UMLS database. It also serves as a way to interface with the UMLS.

Language: Perl - Size: 475 KB - Last synced at: 15 days ago - Pushed at: 3 months ago - Stars: 6 - Forks: 1

NCBI-Codeathons/Use-UMLS-and-Python-to-classify-website-visitor-queries-into-measurable-categories

Classify your health/medical/life sciences search terms

Language: Jupyter Notebook - Size: 26.6 MB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 6 - Forks: 2

WengLab-InformaticsResearch/UMLS-EDA

A light-weighted UMLS-based data augmentation for biomedical NLP tasks including Named Entity Recognition and sentence classification.

Language: Python - Size: 60.5 KB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 5 - Forks: 1

xga0/cuiSnomed

Extract Unified Medical Language System (UMLS) Concept ID (CUI) and corresponding SNOMED CT from MedGen pages.

Language: Python - Size: 5.86 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 0

ningkko/Medical_relation

UMLS, medical relation

Language: Jupyter Notebook - Size: 98 MB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 0

vcastro/umls_mssql_load

Load UMLS Metathesaurus Files into a SQL Server Database

Language: Batchfile - Size: 7.81 KB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 5 - Forks: 4

w-is-h/umls

UMLS to PostgreSQL with PgAdmin

Language: Dockerfile - Size: 3.91 KB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 5 - Forks: 3

smujjiga/pymm

Python Wrapper for MetaMap

Language: Python - Size: 25.4 KB - Last synced at: over 2 years ago - Pushed at: almost 7 years ago - Stars: 5 - Forks: 4

joe32140/snomed-ontology-parser

Analyzing medical concept distribution of clinical text with Snomed ontology.

Language: Jupyter Notebook - Size: 617 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 4 - Forks: 2

3mcloud/umls-rat

A reasonable Python interface for the UMLS Metathesaurus REST API

Language: Python - Size: 293 KB - Last synced at: 7 days ago - Pushed at: 11 months ago - Stars: 4 - Forks: 1

LHNCBC/pymetamaplite

A minimal implementation of the MetaMapLite named entity recognizer in Python,

Language: Python - Size: 65.4 KB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 1

anaymalpani/sytora

Sytora is a multilingual symptom-disease classification app. Translation is managed through the UMLS coding standard.

Language: JavaScript - Size: 7.81 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 0

Nguyendat-bit/UMLS-KG

Build a knowledge graph from UMLS Knowledge Sources (2022) with load, visualize and query with Neo4j and Scispacy

Language: Python - Size: 868 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 2

akarazeev/BioHack2017

🔬 Biohack 3-5 of March, 2017

Language: Jupyter Notebook - Size: 33.9 MB - Last synced at: about 1 year ago - Pushed at: about 8 years ago - Stars: 4 - Forks: 1

CBIIT/UMLS-MetaMap-API-Scripts

This repository is dedicated to development of Python scripts which use API to UMLS MetaMap to map semantics of common data elemnts to UMLS and NCI concepts

Language: Python - Size: 131 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 0

E-Health/ctakes-rest-service Fork of GoTeamEpsilon/ctakes-rest-service

A JSON-based rest service to process unstructured clinical text through a smart natural language processing system.

Language: Java - Size: 181 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 3

teanalab/MRF-L

TREC'15 CDS Competition: WSU-IR at TREC 2015 Clinical Decision Support Track: Joint Weighting of Explicit and Latent Medical Query Concepts from Diverse Sources [code]

Language: C++ - Size: 15.6 MB - Last synced at: about 1 year ago - Pushed at: about 8 years ago - Stars: 3 - Forks: 1

anjani-dhrangadhariya/distant-PICO

Language: Jupyter Notebook - Size: 5.98 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 0

LHNCBC/ctb

Custom Taxonomy Builder

Language: Clojure - Size: 246 KB - Last synced at: 2 months ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 1

knowlab/ACE-NLP

Identify Adverse Childhood Experiences from free-text data using NLP

Size: 1.95 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 1

danlou/MedLinker-Social

UMLS Medical Entity Linking. Adaptation of MedLinker (ECIR 2020) for the Social Domain.

Language: Jupyter Notebook - Size: 26.9 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 0

hscells/quickumlsrest

Language: Go - Size: 8.79 KB - Last synced at: 12 days ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 0

Betterpath/EliIE Fork of Tian312/EliIE

A parser designed for free text clinical trial eligibility criteria (CTEC)

Language: Python - Size: 76.2 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 2 - Forks: 0

yoho321/SiriusWeb

A guideline of SiriusWeb for people who are new to DSML and Sirius.

Size: 1.9 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

CogStack/gate-nlp-service 📦

Running GATE NLP applications as RESTful web services

Language: Java - Size: 287 KB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 3

Catnary/py_search_umls

Language: Python - Size: 9.77 KB - Last synced at: 4 months ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

MIS-GrApH-AI/mis-graph-ai.github.io

Medical Intelligence Society Graph Applications in Health Working Group's Developer Website. Visit us at https://mis-graph-ai.github.io

Language: HTML - Size: 873 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 2

couragecowardlydog/ctakes-wrapper

A simple spring-boot wrapper for CTakes

Language: Java - Size: 151 MB - Last synced at: 3 months ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 1

erayon/Early-epidemic-detection-using-MachineLearnig

Early epidemic detection

Language: JavaScript - Size: 7.39 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 1

MorrisGlr/Automate-QuICR

QuICR is an end-to-end Python application that generates professional HTML and PDF patient documentation quality improvement reports. Automatically, QuICR produces retrospective patient chart reviews, traditionally time-consuming and labor-intensive, using generative AI, NLP, and strict formatting techniques.

Language: HTML - Size: 102 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 0 - Forks: 0

sajinjames15/unified-knowledge-system

A comprehensive unified knowledge management system integrating multiple data sources with advanced search capabilities

Size: 16.6 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

aniketnarvekar/UMLSClient

Language: Swift - Size: 189 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

lorenzobalzani/neural-subgraph-retrieval

PyTorch module that generates a subgraph originating from the UMLS Knowledge Graph (KG) when presented with a biomedical question (from MedQA). It utilizes Language Models (LMs) to solve the next relation prediction task and graph node embedding to infer the tail given a head and the predicted relation, essentially performing link prediction.

Language: Python - Size: 8.42 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

comorbidity/medgen-umls

NCBI Medical Genetics, UMLS Unified Medical Language System Concepts and PubMed linked citations

Language: Shell - Size: 5.17 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

dimfeld/umls-rs

A library and command-line utility for working with the UMLS Metathesaurus

Language: Rust - Size: 137 KB - Last synced at: 29 days ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

mahfuzmr/LoopDetector

Loop detector on triplet formatted data

Language: Python - Size: 2.25 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

albreis/staruml-gitpush

Extensão pra StarUML para fazer push automático do diretório dos seus projetos. Também é gerada a documentação HTML automaticamente.

Language: JavaScript - Size: 18.6 KB - Last synced at: 3 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

ZhenshengLee/zsUML

zsUML

Language: HTML - Size: 1.14 MB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

meerapatelmd/CallMeMaybe

R Package that calls the UMLS Rest API

Language: R - Size: 91.8 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 1

s4ndhyac/RxBot

An AI Bot that gives you information on medical drugs

Language: JavaScript - Size: 70.3 KB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

couragecowardlydog/ctakes-gui

Dictionary Creator downloaded from http://ctakes.apache.org doesn't work expected , so I made this as seperate stand-alone. Eventhough gui-res.jar contained files required by Dictionary Builder , it kept throwing missing resource required . This codebase is contains dictionary builder and resource required . I hope somebody facing the same issue can make use of this .

Language: Java - Size: 171 KB - Last synced at: 3 months ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

Betterpath/Py-UMLS Fork of chb/py-umls

Basic Python 3 tools to interact with UMLS lexica

Language: Python - Size: 193 KB - Last synced at: over 1 year ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 0