ncbo/ncbo.github.io

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ncbo/ncbo.github.io

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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

bioportal-project

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

kg-bioportal

BioPortal, as a Knowledge Graph

virtual_appliance

Bioportal Virtual Appliance

BioPortal-to-KGX

Assemble a BioPortal Knowledge Graph

ncbo_annotator_ruby_client

The NCBO Annotator Gem is a Ruby client for NCBO's Annotator Web service

ontolobridge_api_client

Ontolobridge REST API client

pubmed_xml2rdbms

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

healthdata_metadata_challenge

mc_sinatra

MC Sinatra is a skeleton Sinatra application and bootstrap/runtime environment that allows for the use of models, controllers, and helpers for creating simple, easy-to-understand web APIs.

resource_access_tools

Java-based code for running the Resource Access Tool population

ontoportal_utilities

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

hcomp_ontology_evaluation

Source code for creating and managing Mechanical Turk tasks for ontology evaluation via human computation

sparql_http

SPARQL_HTTP is a SPARQL HTTP Client for Ruby. It is developed together with the Goo library but it hash been designed as an standalone component that can be used separately.

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

resource_index_ruby_client

The NCBO Resource Index Gem is a Ruby client for NCBO's Rsource Index Web service

ncbo_api_benchmark

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.

prototype_bioportal_rest_rails

This is a prototype BioPortal web service using rails-api as the framework

resource_index_workflow

knowledge

Knowledge transfer materials

bioportal_mappings

A project to generate ontology mappings for BioPortal

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.

bfo

This is a copy of The Basic Formal Ontology (BFO). For testing and reliability NCBO/BioPortal needs to maintain its own copy of BFO.