Discover MaastrichtU-IDS/biothingsprovenancemodel Open Source project

🪐 JupyterLab + VisualStudio Code workspaces for data science and knowledge graphs

jupyterlab

📖 Documentation for the Data Science Research Infrastructure at Maastricht University

dsri-documentation

This repository contains educational materials for a Masters course on knowledge graphs developed by the Institute of Data Science at Maastricht University

building-and-mining-knowledge-graphs-course-materials

🧭 Resolve, visualize and browse the content of any SPARQL endpoint

into-the-graph

📖 Home for the Data2Services project documentation

d2s-docs

🔮🐍 A package to help serve predictions of biomedical concepts associations as Translator Reasoner API

translator-openpredict

This repository is a workplace for COST Action Hackathon event on Federated Query over Knowledge Graphs which will happen on 25-27 April in Izmir Turkey.

federatedQueryKG

Create perfect graph visualisations easily

perfect-graph

Resources for the KG course at IDS, Maastricht University

UM_KEN4256_KnowledgeGraphs

⚠️ DEPRECATED. See http://d2s.semanticscience.org

data2services-pipeline

☑️ A library to build and deploy FAIR metrics tests APIs that can be used by FAIR evaluation services supporting the FAIRMetrics specifications, such as FAIR enough and the FAIR evaluator.

fair-test

Helm charts for the Data Science Research Infrastructure at Maastricht University

dsri-helm-charts

Smarty

fair-enough

♻️ Service to define and run evaluations of the FAIR principles (Findable, Accessible, Interoperable, Reusable) on online resources

🧙‍♂️📝 JSON-LD web editor, with autocomplete based on the loaded ontologies concepts and properties

fair-metadata-wizard

⌨️ A Command Line Interface to help orchestrate the integration of heterogenous data sources under a common RDF Knowledge Graph using Python, RML mappings, Bash, and GitHub Actions workflows

d2s-cli

🎓 Resources for the Semantic Web course given by IDS at Maastricht University

UM_KEN3140_SemanticWeb

Using ESM2 protein embeddings and MolecularTransformer drug embeddings to train a linear classifier to predict potential drug-targets interactions

predict-drug-target

OptimAL

🌱 A qualitative and computational study using NLP on H2020 projects in the context of climate change

clean-technologies-nlp

🔬 Website to help browse and publish Nanopublications

knowledge-collaboratory

🍪🐍 A cookiecutter package to bootstrap python packages

cookiecutter-python-package

This repository is for collecting and updating existing and upcoming LLM tools and papers focusing on healthcare and medicine domain.

MedicalLLM

food-claims-kg

🧅 RDF knowledge graph for food health claims

This repo is for Machine Learning Workshop (one episode of Data Science Community Workshop Series)

machine-learning-workshop

📋 Template to build CWL workflows to convert data to a RDF Knowledge Graph and deploy services.

d2s-project-template

🤖 Guideline for designing optimal crowdsourcing experiments

crowdED

🧑‍💻 VisualStudio Code server Docker image

code-server

apache-drill

AutoR2RML

healthy-food-subs

Healthy food ingredient substitutions

🫀 Webapp to explore cohorts metadata for the iCARE4CVD project

cohort-explorer

⚡ Short workshop to start Data Science applications on the Data Science Research Infrastructure at Maastricht University

dsri-workshop-start-app

fair-enough-metrics

☑️ API to publish FAIR metrics tests written in python

🥝 Core repository with Docker, CWL, Argo scripts for the d2s tool

d2s-core

Common Workflow Language

neuro_dkg

Knowledge Graph for Neurological Disorders' Drugs

⚖️ An OWL ontology to define terms from EU company law that are relevant for cross-border mobility of EU companies.

cbcm-ontology

⚕️ Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences.

bio2rdf

Common Workflow Language

RdfUpload

📤 Simply upload RDF to a SPARQL endpoint with RDF4J

📄 A simple XML to RDF converter

xml2rdf

⚠️ DEPRECATED. Shell scripts to download datasets for the data2services project

d2s-download

Repository for SHACL Shapes at the Institute of Data Science at Maastricht University

shacl-shapes

coding-for-researchers

Resources for the Python workshop at IDS and UL, Maastricht University

Litcoin-NLP-Challenge

🛋️ Templates to publish Nanopublications in Nanobench

nanobench-templates

FaVLib

Fact Validation Library

LMKBC-2023

A short tutorial to build a RDF Knowledge Graph from 2 CSV files using YARRRML mappings

build-a-kg-example

best-practices

📚 Best practices at the Institute of Data Science at Maastricht University

Tool to evaluate how FAIR is a resource URL using the F-UJI API

fairificator

Quality Assessment of Biomedical Metadata Using Topic Modelling

metadata-unsupervised-assessment

GraphDB inspired by https://github.com/manasRK/graphdb-free

graphdb

Website for the Semanticscience Integrated Ontology (SIO)

semanticscience-website

Relevant datasets and material for a preliminary analysis of the overlap in drug indications between InContext, DrugCentral and LabeledIn

incontext-indications-analysis

This repository is for sharing PhD thesis managing and writing. Our focus group is UM (FSE/DACS/IDS) PhD students.

PhDThesis

TeX

d2s-argo-workflows

⚠️ DEPRECATED: Argo workflows to transform structured data to a target RDF using Data2Services Docker modules

crowdsourcing-workshop

Slides for the Workshop on Crowdsourcing

get-started-with-docker

🐳 A straightforward workshop to get started with Docker in an hour

⚠️ DEPRECATED. See http://d2s.semanticscience.org

data2services-ecosystem

🚉⚕️ A SOLID Station for the Personal Health Train deployed using Docker

solid-station

metadata-wizard

📊 Fairsharing metrics implementation

fairsharing-metrics

🔬 This repository is to discover COVID-19 biomarkers using Knowledge Graph technologies

covid19-biomarker-discovery

🔭 DEPRECATED - Applications for the Data Science Research Infrastructure OpenShift cluster at Maastricht University

dsri-openshift-applications

🔊 A Jupyter Notebook to edit the AudioSet ontology

audioset-owl

docker-workshop

🐳 Docker Workshop

Execute Bash scripts from URL

responsability-matrix-survey

Dart

d2s-bash-exec

Workshop about CI/CD at the Institute of Data Science at Maastricht University

workshop-ci

💊 A small dataset of off-label drug indications found in PubMed articles

off-label-drug-indications-dataset

play-fair

♟️ FAIR Data for Traditional Games

Global Repository of Injury Data API

grid-api

🪄 A LDWizard to generate RDF linked data from spreadsheets relevant to the Humanities and Social Sciences.

ldwizard-humanities

Large-scale RDF-based Data Quality Assessment Pipeline

dqa-pipeline

Data Driven Justice Challenge

data-driven-justice

🧭 10th February 2021🧭 A repo for the first FAIR essential workshop at Maastricht University

fair-workshop

d2s-scripts-repository

📜 Transformation scripts to build Data2Services knowledge graphs (SPARQL insert queries, RML mappings, Shell commands).

A project that uses prodi.gy to train a classifier to perform drug indication annotation with their medical context

FedQuery2024

prodigy-drug-indication-annotation

DoConA (Document Content and Citation Analysis Pipeline) is an open source, configurable and extensible Python tool to analyse the level of agreement between the citation network of a set of textual documents and the textual similarity of these documents.

docona

📦 A template with instructions and script to publish your scientific structured data (spreadsheets, dataframes, JSON, databases) as FAIR data

fair-data-publisher

semantic-enhancement

Template to be used in the CI/CD workshop

workshop-ci-template

brein-data-warehouse

📈 RStudio with Shiny server Docker image

rstudio

Business Analytics module part of Data Science certification

business-analytics

🎬 Showcase website for IDS projects

projects

An ontology for the description and classification of sounds

sounds

Quick demo to use the DSRI for Data Science

dsri-demo

perfect-graph-docs

PredictAD notebooks to explore ADNI data

predict-ad-notebooks

🐍 DEPRECATED - checkout the new https://github.com/MaastrichtU-IDS/cookiecutter-python-package

python-template

dqa_combine_statistics

UCMDrugClassification

case-law-analytics-app

🧊 LUCE: A Blockchain-based data sharing platform for monitoring data license accountability and compliance.

LUCE

🚰 RdfSink is a simple web service which accepts POST requests with RDF payload. It works with various RDF formats. The RDF format needs to be defined in the Content-Type Header.

RdfSink

Work materials for the Data Science Bootcamp at PGGM

data-science-bootcamp-pggm

Fact Checking via Knowledge Graph Rules and Embeddings

KGRulEm