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@ncbo National Center for Biomedical Ontology

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    50 repositories

    • bioportal_web_ui

      Public
      A Rails application for biological ontologies
      open-sourcemetadatabioinformaticsannotationrdfsemantic-webowlopen-scienceoboruby-on-rails
      JavaScript
      •
      Other
      •38•23•133•6•Updated Dec 17, 2025Dec 17, 2025

    • ontologies_api

      Public
      Hypermedia API for NCBO's ontology-related projects
      Ruby
      •
      Other
      •30•26•38•5•Updated Dec 17, 2025Dec 17, 2025

    • goo

      Public
      Graph Oriented Objects (GOO) for Ruby. A RDF/SPARQL based ORM.
      Ruby
      •
      Other
      •15•15•29•3•Updated Dec 16, 2025Dec 16, 2025

    • license_server

      Public
      OntoPortal Licensing Server
      Ruby
      •0•0•6•9•Updated Dec 16, 2025Dec 16, 2025

    • bioportal-mcp

      Public
      An MCP for querying Bioportal
      Python
      •1•4•0•0•Updated Dec 1, 2025Dec 1, 2025

    • ontologies_api_ruby_client

      Public
      A Ruby client for accessing NCBO's hypermedia api
      Ruby
      •
      Other
      •13•2•8•0•Updated Nov 19, 2025Nov 19, 2025

    • ontologies_linked_data

      Public
      Models and serializers for ontologies and related artifacts backed by 4store
      Ruby
      •
      Other
      •23•19•47•6•Updated Nov 17, 2025Nov 17, 2025

    • ncbo_cron

      Public
      Jobs that run on a regular basis in the NCBO infrastructure
      Ruby
      •
      Other
      •19•3•31•3•Updated Oct 28, 2025Oct 28, 2025

    • owlapi_wrapper

      Public
      A command line utility that wraps the Java OWL-API to parse RDFS, OWL and OBO ontologies.
      Java
      •12•5•8•1•Updated Oct 21, 2025Oct 21, 2025

    • virtual_appliance

      Public
      Bioportal Virtual Appliance
      Shell
      •7•5•15•0•Updated Oct 9, 2025Oct 9, 2025

    • kg-bioportal

      Public
      BioPortal, as a Knowledge Graph
      knowledgegraphontologies
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•10•15•1•Updated Sep 2, 2025Sep 2, 2025

    • ncbo.github.io

      Public
      3•1•0•0•Updated Aug 18, 2025Aug 18, 2025

    • ncbo_annotator

      Public
      To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations.
      Ruby
      •
      Other
      •15•19•15•2•Updated Jul 17, 2025Jul 17, 2025

    • ncbo_ontology_recommender

      Public
      A ruby application that allows to obtain recommendations for the most relevant ontologies based on an excerpt from a biomedical text or a list of keywords
      Ruby
      •
      Other
      •7•5•4•2•Updated Jul 17, 2025Jul 17, 2025

    • sparql-client

      Public
      SPARQL client for Ruby.
      Ruby
      •
      The Unlicense
      •56•4•1•0•Updated Jul 9, 2025Jul 9, 2025

    • biomixer

      Public
      BioMixer
      TypeScript
      •13•2•4•0•Updated Apr 18, 2025Apr 18, 2025

    • umls2rdf

      Public
      These python scripts connect to the Unified Medical Language System (UMLS) database and translate the ontologies into RDF/OWL files. This is part of the BioPortal project.
      Python
      •
      Other
      •35•86•12•1•Updated Aug 28, 2024Aug 28, 2024

    • 4store

      Public
      4store for BioPortal
      C
      •
      GNU General Public License v3.0
      •71•3•0•0•Updated Aug 15, 2024Aug 15, 2024

    • ncbo_rest_sample_code

      Public
      Sample code that demonstrates the use of the NCBO REST services
      Java
      •33•43•6•0•Updated Jan 17, 2024Jan 17, 2024

    • reactjs_sandbox

      Public
      Experimental React code for issuing ontology change requests
      TypeScript
      •0•0•0•0•Updated Nov 13, 2023Nov 13, 2023

    • ontoportal_docker

      Public
      Scripts for running and developing ontoportal with docker
      Ruby
      •11•0•2•0•Updated Nov 7, 2023Nov 7, 2023

    • ontolobridge_api_client

      Public archive
      Ontolobridge REST API client
      Ruby
      •7•3•0•9•Updated Aug 30, 2023Aug 30, 2023

    • ontoportal_utilities

      Public
      A set of scripts for benchmarking and troubleshooting issues with NCBO software
      Ruby
      •5•2•0•2•Updated Aug 29, 2023Aug 29, 2023

    • BioPortal-to-KGX

      Public
      Assemble a BioPortal Knowledge Graph
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•4•8•0•Updated May 10, 2023May 10, 2023

    • ncbo_migration

      Public archive
      Scripts for migrating data from older NCBO systems to newer ones
      Ruby
      •4•1•0•0•Updated Feb 1, 2023Feb 1, 2023

    • documentation-dev

      Public
      A (possibly) temporary location for shared developer documentation.
      0•0•0•0•Updated Jan 7, 2023Jan 7, 2023

    • resource_index

      Public archive
      Library for working with NCBO's Resource Index backend system
      Ruby
      •
      MIT License
      •6•1•0•2•Updated Jul 21, 2022Jul 21, 2022

    • bioportal-project

      Public
      Serves to consolidate (in Zenhub) all public issues in BioPortal
      BSD 2-Clause "Simplified" License
      •5•8•186•0•Updated Jul 10, 2019Jul 10, 2019

    • bioportal-sparql-proxy

      Public archive
      This is a django app that acts as a proxy for BioPortal's public triple store. It uses a modified version of the SNORQL browser to help the navigation across graphs and codemirror for syntax highlighting.
      JavaScript
      •4•1•0•0•Updated Nov 30, 2016Nov 30, 2016

    • pubmed_xml2rdbms

      Public archive
      Loads citation records from the annual MEDLINE/PubMed XML format distribution into a MySQL table
      Java
      •5•3•0•0•Updated Nov 3, 2016Nov 3, 2016