Biopragmatics Stack

bioregistry

📮 An integrative registry of biological databases, ontologies, and nomenclatures.

pyobo

📛 A Python package for using ontologies, terminologies, and biomedical nomenclatures

biomappings

🗺️ Community curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources.

bioversions

🪝 What's the latest version for each database?

curies

🐸 Idiomatic conversion between URIs and compact URIs (CURIEs) in Python

bioontologies

🏷️ Unified access to biomedical ontologies

obo-db-ingest

🗄️ Conversion of biomedical nomenclatures like HGNC to OBO

oquat

🎬 Ontology Quality Assesment Toolkit

semra

🛣️ Semantic Mapping Reasoning Assembler (SeMRA): tooling for semantic mappings

curies.rs

🦀 Idiomatic conversion between URIs and compact URIs (CURIEs) in Rust

biolookup

🔍 The Biolookup Service retrieves metadata and ontological information about biomedical entities.

biolexica

📘 Generate and apply coherent biomedical lexical indices for NER and NEN

biolookup-docker

🐋 A dockerfile for the frontend to the Biolookup Service

biopragmatics.github.io

GitHub site for the Biopragmatics Stack

bioregistry-docker

🐋 A dockerfile for the Bioregistry web app

biosynonyms

☎️ A decentralized database of synonyms for biomedical concepts

debio

🥮 Decentralized Biomedical Ontology

.github

providers

🌐 Providers for prefixes that don't have one, but are available in PyOBO