National Center for Biomedical Ontology

umls2rdf

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.

ncbo_rest_sample_code

Sample code that demonstrates the use of the NCBO REST services

sparql-code-examples

Java, Perl, Python, Javascript, Ruby, etc. examples to query alphasparql.bioontology.org

ontologies_api

Hypermedia API for NCBO's ontology-related projects

bioportal_web_ui

A Rails application for biological ontologies

ncbo_annotator

To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations.

ontologies_linked_data

Models and serializers for ontologies and related artifacts backed by 4store

goo

Graph Oriented Objects (GOO) for Ruby. A RDF/SPARQL based ORM.

bioportal-project

Serves to consolidate (in Zenhub) all public issues in BioPortal

kg-bioportal

BioPortal, as a Knowledge Graph

ncbo_ontology_recommender

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

owlapi_wrapper

A command line utility that wraps the Java OWL-API to parse RDFS, OWL and OBO ontologies.

virtual_appliance

Bioportal Virtual Appliance

BioPortal-to-KGX

Assemble a BioPortal Knowledge Graph

sparql-client

SPARQL client for Ruby.

4store

4store for BioPortal

ontolobridge_api_client

Ontolobridge REST API client

pubmed_xml2rdbms

Loads citation records from the annual MEDLINE/PubMed XML format distribution into a MySQL table

biomixer

BioMixer

ncbo_cron

Jobs that run on a regular basis in the NCBO infrastructure

ontologies_api_ruby_client

A Ruby client for accessing NCBO's hypermedia api

ontoportal_utilities

A set of scripts for benchmarking and troubleshooting issues with NCBO software

resource_access_tools

Java-based code for running the Resource Access Tool population

bioportal-sparql-proxy

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.

ncbo.github.io

ncbo_migration

Scripts for migrating data from older NCBO systems to newer ones

resource_index

Library for working with NCBO's Resource Index backend system

documentation-dev

A (possibly) temporary location for shared developer documentation.

ontoportal_docker

Scripts for running and developing ontoportal with docker

reactjs_sandbox

Experimental React code for issuing ontology change requests