A rails application for biological ontologies, see http://bioportal.bioontology.org/
Jobs that run on a regular basis in the NCBO infrastructure
SPARQL client for Ruby.
Models and serializers for ontologies and related artifacts backed by 4store
Hypermedia API for NCBO's ontology-related projects
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
To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations.
Graph Oriented Objects (GOO) for Ruby. A RDF/SPARQL based ORM.
Serves to consolidate (in Waffle) all public issues in BioPortal
A command line utility that wraps the Java OWL-API to parse RDFS, OWL and OBO ontologies.
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.
Sample code that demonstrates the use of the NCBO REST services
Loads citation records from the annual MEDLINE/PubMed XML format distribution into a MySQL table
Java-based code for running the Resource Access Tool population
Library for working with NCBO's Resource Index backend system
A Ruby client for accessing NCBO's hypermedia api
Scripts for migrating data from older NCBO systems to newer ones
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.
NIH NLM Value Set as a SKOS ontology
Knowledge transfer materials
A Flash-based visualization tool for ontologies using NCBO's retired REST API
This is a copy of The Basic Formal Ontology (BFO). For testing and reliability NCBO/BioPortal needs to maintain its own copy of BFO.
Cube: A system for time series visualization.
4store for BioPortal
A set scripts to create logs of calls that can be run in Jmeter. Only compatible with the new infrastructure to be released in 2013.
Git hooks that are useful in the NCBO development context
A project to generate ontology mappings for BioPortal