Message-ID: <597077461.8704.1711723618129.JavaMail.confluence@ip-172-30-4-17.ec2.internal> Subject: Exported From Confluence MIME-Version: 1.0 Content-Type: multipart/related; boundary="----=_Part_8703_1434046051.1711723618126" ------=_Part_8703_1434046051.1711723618126 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Content-Location: file:///C:/exported.html Ontology Tools

Ontology Tools

Ontology Tools

The i2b2 Hive software is composed of core modules called 'cells' that c= reate a system to allow the use of patient data for research. These cells c= ommunicate through web services and use i2b2 standard XML messages to trans= fer ontology-related metadata.  To date, a subset of ICD-9 has been pr= ovided with the i2b2 demo software package.  There has been a need in = the community for access to a complete ICD-9 ontology as well as other clin= ical-based ontologies.

Extraction tool

NCBO hosts a repository of biomedical ontologies.  These ontologies= are stored in formats that are not understood by i2b2.  A command lin= e tool has been developed to not only extract these ontologies via bioporta= l REST services, but to transform them into a format that is understood by = the i2b2 ONT cell.

Mapping tools

A set of mapping tools have been created for the workbench.  These = tools were designed to assist users in assigning, editing and verifying map= pings between ontologies.  These tools consist of a set of workbench p= lugins and a new Mapper cell (MAP). In version 1.1 of the mapping tools we = add the ability to automate mappings to UMLS ontologies. 

Integration tool

A command line integration tool has been developed that integrates a sou= rce ontology into the hierarchy of a target ontology as dictated by the map= pings between the two. The feature has been absorbed into the mapping tool.=

Metadata Uploader

A Metadata Uploader tool has been created for the workbench.  This = tool was designed to assist users in loading metadata to a pre-configured i= 2b2 project resulting in new root-level categories in the Navigate Terms vi= ew.  This tool consists of a new workbench plugin.  Version 1.7.0= 8 (or later) of the ONT cell is required. 

Tutorials

i2b2 Ontology Tutoria= l - Step by step example of how metadata trees are created and= configured using both Edit View and Extraction tool

i2b2 Ontology tools = overview  -  Overview of the extraction, mapping and= integration tools and how they work together.

 

 

 

 
Navigate space
=20
=20
=20 =20 =20 =20 =20
=20
=20
=20
    =20
    =20
    =20
=20
=20 =20 =20 =20 =20 =20 =20 =20 =20 = =20 =20 =20 = =20 =20
=20 =20
=20
=20
=20
------=_Part_8703_1434046051.1711723618126--