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@ncbo National Center for Biomedical Ontology

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    48 repositories

    • bioportal_web_ui

      Public
      A Rails application for biological ontologies
      open-sourcemetadatabioinformaticsannotationrdfsemantic-webowlopen-scienceoboruby-on-rails
      Ruby
      •
      Other
      •30•21•103•5•Updated Oct 30, 2024Oct 30, 2024

    • ontologies_api_ruby_client

      Public
      A Ruby client for accessing NCBO's hypermedia api
      Ruby
      •
      Other
      •11•2•6•2•Updated Oct 28, 2024Oct 28, 2024

    • ontologies_linked_data

      Public
      Models and serializers for ontologies and related artifacts backed by 4store
      Ruby
      •
      Other
      •20•18•48•9•Updated Oct 24, 2024Oct 24, 2024

    • ncbo_cron

      Public
      Jobs that run on a regular basis in the NCBO infrastructure
      Ruby
      •
      Other
      •17•2•26•4•Updated Oct 23, 2024Oct 23, 2024

    • ontologies_api

      Public
      Hypermedia API for NCBO's ontology-related projects
      Ruby
      •
      Other
      •25•25•34•6•Updated Oct 23, 2024Oct 23, 2024

    • goo

      Public
      Graph Oriented Objects (GOO) for Ruby. A RDF/SPARQL based ORM.
      Ruby
      •
      Other
      •13•15•27•3•Updated Oct 23, 2024Oct 23, 2024

    • 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 Oct 8, 2024Oct 8, 2024

    • ncbo_annotator

      Public
      To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations.
      Ruby
      •
      Other
      •14•18•12•2•Updated Oct 8, 2024Oct 8, 2024

    • kg-bioportal

      Public
      BioPortal, as a Knowledge Graph
      knowledgegraphontologies
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•6•16•1•Updated Oct 1, 2024Oct 1, 2024

    • virtual_appliance

      Public
      Bioportal Virtual Appliance
      SCSS
      •7•5•12•0•Updated Sep 24, 2024Sep 24, 2024

    • 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
      •37•84•12•1•Updated Aug 28, 2024Aug 28, 2024

    • 4store

      Public
      4store for BioPortal
      C
      •
      GNU General Public License v3.0
      •73•3•0•0•Updated Aug 15, 2024Aug 15, 2024

    • biomixer

      Public
      BioMixer
      TypeScript
      •13•2•3•0•Updated Jun 20, 2024Jun 20, 2024

    • ncbo.github.io

      Public
      3•1•0•0•Updated May 8, 2024May 8, 2024

    • sparql-client

      Public
      SPARQL client for Ruby.
      Ruby
      •
      The Unlicense
      •58•4•1•0•Updated May 6, 2024May 6, 2024

    • ncbo_rest_sample_code

      Public
      Sample code that demonstrates the use of the NCBO REST services
      Java
      •33•40•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
      •8•0•2•0•Updated Nov 7, 2023Nov 7, 2023

    • owlapi_wrapper

      Public
      A command line utility that wraps the Java OWL-API to parse RDFS, OWL and OBO ontologies.
      Java
      •12•5•7•2•Updated Nov 4, 2023Nov 4, 2023

    • ontolobridge_api_client

      Public archive
      Ontolobridge REST API client
      Ruby
      •6•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•156•0•Updated Jul 10, 2019Jul 10, 2019

    • bioportal-sparql-proxy

      Public
      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

    • resource_access_tools

      Public archive
      Java-based code for running the Resource Access Tool population
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•2•0•0•Updated Oct 28, 2016Oct 28, 2016

    • sparql-code-examples

      Public archive
      Java, Perl, Python, Javascript, Ruby, etc. examples to query alphasparql.bioontology.org
      Java
      •
      Other
      •26•34•0•1•Updated Apr 1, 2016Apr 1, 2016