Catalog entries
Live entries,
growing with every commit
Every entry is a structured JSON-LD file in the repository. This list updates automatically on each push via CI. Contributions welcome via GitHub issues or the form below.
Total entries
53
Entry types
6/7
Dutch national health research data catalogue built on the FAIR Data Point (FDP) specification. Metadata is described using HealthDCAT-AP, t…
Swiss national health research metadata catalog operated by the SIB Swiss Institute of Bioinformatics for the Swiss Personalized Health Netw…
Multimodal medical agent benchmark that simulates end-to-end clinical workflows. Presents AI agents with patient-facing dialogue, EHR record…
Benchmark for evaluating LLM agent ability to retrieve and answer clinical questions from FHIR-structured EHR data. Contains approximately 3…
FHIR-native benchmark for evaluating AI agents on real-world clinical tasks authored by practising physicians. Contains 300 tasks across 10 …
Benchmark dataset for evaluating LLM ability to perform clinical calculator tasks — a common but under-tested dimension of medical reasoning…
MLOmics Cancer Multi-Omics Benchmark
Standardised multi-omics benchmark dataset covering all 32 TCGA cancer types across four omics modalities: mRNA expression, microRNA, DNA me…
swhNHS England Synthetic Clinical Notes
Synthetic clinical notes dataset generated by NHS England Data Science to support clinical NLP research and model development without exposi…
Exposes any FHIR R4/R5 server as an MCP server, enabling LLM agents to perform CRUD operations on FHIR resources through natural language vi…
Model Context Protocol (MCP) server for the OMOP Common Data Model. Provides a structured, secure interface for LLM agents to query and anal…
openEHR Assistant MCP (Cadasto)
MCP server bridging AI assistants with openEHR design-time workflows. Exposes CKM archetype and template search, openEHR terminology concept…
MCP server for runtime interaction with EHRbase via openEHR REST APIs. Exposes 11 MCP tools covering template operations, EHR lifecycle mana…
Experimental MCP server exposing SNOMED CT concept lookup to LLM agents via any FHIR R4 terminology server. Enables AI agents to resolve cli…
Self-verifying LLM agent for gene-set analysis that autonomously queries domain databases (Gene Ontology, KEGG, NCBI Gene, PubMed) to annota…
Self-configuring framework for 3D volumetric medical object detection, applying the same automated configuration philosophy as nnU-Net to de…
Self-configuring framework for medical image segmentation that automatically adapts its architecture, preprocessing, training, and post-proc…
Production-ready medical NLP toolkit providing state-of-the-art encoder transformers (BERT, ELECTRA, DeBERTa families) for biomedical named …
Automated segmentation of 72 white matter fibre bundles from diffusion MRI tractograms, directly from raw peaks (fibre orientation distribut…
LLM-based AI agent for therapeutic reasoning that orchestrates 211 biomedical tools spanning drug databases, genomic repositories, clinical …
Free, open-source platform for medical image informatics, image processing, and three-dimensional visualisation. Supports segmentation, regi…
Open-source access negotiation platform for biobank and research infrastructure data requests. Manages the full Data Access Request (DAR) li…
General-purpose biomedical AI agent framework from Stanford SNAP Lab. Combines LLM reasoning with retrieval-augmented planning and code exec…
FHIR R5-powered, modular open-source electronic health management information system (HMIS) developed by Open Healthcare Network Foundation …
PyTorch-based deep learning framework for accelerated MRI reconstruction from undersampled k-space data. Implements a range of state-of-the-…
Lightweight Python library for identifying drug and medication names in free text, with fuzzy matching for misspellings and integration with…
Robust and reproducible preprocessing pipeline for functional MRI (fMRI) data. Accepts BIDS-formatted input and performs brain extraction, s…
The industry-standard toolkit for variant discovery in high-throughput sequencing data, developed by the Broad Institute. Implements best-pr…
Python library for whole slide image (WSI) processing in computational pathology. Provides tissue detection, tiling, stain normalisation, an…
Kubernetes-based open-source platform toolkit for building federated medical image analysis infrastructure. Orchestrates AI workflows (nnU-N…
Clinical NLP toolkit for named entity recognition and linking in free-text clinical notes. Performs concept extraction and normalisation aga…
Open-source medical image computing toolkit combining a full-featured desktop workbench for visualization, segmentation, and registration wi…
FAIR research data platform for building and managing biobank catalogues, rare-disease registries, and cohort data portals. Provides a flexi…
Curated repository of 30+ production-ready medical imaging models in standardised MONAI Bundle format, covering segmentation, detection, cla…
Fast, interactive, multi-dimensional image viewer for Python. The standard viewer for bio-imaging and computational pathology workflows — su…
Python library for neurophysiological signal processing. Provides accessible, reproducible tools for ECG, EEG, EMG, EDA, and PPG signals — c…
Open-source platform for managing, visualising, and analysing microscopy image data. Supports 150+ imaging formats, centralised storage, web…
Enterprise electronic medical record system platform used in resource-constrained environments worldwide.
Open-source, local-first AI clinical scribe that records patient encounters and automatically generates structured clinical notes. Runs enti…
Open-source toolkit for computational pathology from Dana-Farber Cancer Institute. Covers the full digital pathology pipeline: whole slide i…
The standard Python library for reading, modifying, and writing DICOM files. Used in virtually every Python-based medical imaging pipeline —…
Open-source Python toolkit for clinical deep learning that unifies datasets, tasks, and ML models across EHR, physiological signals, and med…
Open-source cheminformatics toolkit for molecule manipulation, descriptor calculation, substructure searching, and pharmacophore analysis. T…
End-to-end open-source platform for patient-specific cardiovascular blood flow simulation. Provides a complete pipeline from medical image s…
3D Slicer extension providing a toolkit for image-guided interventions (IGT). Offers real-time instrument tracking, ultrasound and needle gu…
Leading open-source library for PET and SPECT tomographic image reconstruction. Provides iterative and analytical reconstruction algorithms,…
AI agent framework for natural-language querying of systems biology models from the BioModels database (EMBL-EBI). Enables researchers to in…
Automated segmentation of more than 100 anatomical structures in CT and MR images using nnU-Net-based models. Covers bones, muscles, organs,…
Privacy Enhancing Technology (PET) operations platform enabling federated learning and multi-party computation across distributed healthcare…
FAIR Data Point (FDP) Specification
W3C Unofficial Proposal Draft specification for a metadata service that exposes digital objects following FAIR principles (Findable, Accessi…
The dominant healthcare interoperability standard, defining a RESTful API and JSON/XML resource formats for exchanging clinical and administ…
The official EU metadata specification for describing health datasets for secondary use, extending DCAT-AP 3.0 with health-domain semantics.…
W3C recommendation for expressing policies over data assets — permissions, prohibitions, and obligations. In healthcare, used to encode data…