Latest revision as of 23:16, 22 October 2010

Influenza Ontology Home Page

Project Goal

• The immediate goal of I-IDO is to apply the Influenza Infectious Disease Ontology to data collected as part of the CEIRS projects in an effort to enable influenza researchers to more easily elucidate the causes of influenza virulence and pathogenesis.

History

• This project had it's beginnings with the purpose to develop an Influenza Infectious Disease Ontology (I-IDO), as part of the IDO (Infectious Disease Ontology) family of ontologies. The IDO ontologies are a set of interoperable ontologies that together provide coverage of the infectious disease domain.
• The Influenza Application Ontology has developed and grown as part of this project into a fuller and richer ontology, extensible for any virus sequence and surveillance collection project which encompasses the core IDO biomedical and clinical aspects of infectious diseases for influenza.

Consortium Members

• Starting in the fall of 2007, a collaborative group of influenza researchers have established an influenza ontology. The influenza ontology is an application ontology.

Consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS)

• Joanne Luciano (Tetherless World Constellation, Rensselaer Polytechnic Institute)
• Lynn Schriml (University of Maryland, School of Medicine)
• Burke Squires (University of Texas Southwestern Medical Center (UTSW))
• Richard Scheuermann (UTSW)

with the help of:

• Eric Bortz (Mount Sinai School of Medicine)
• Torsten Staab (Los Alamos National Laboratory), and the
• Gemina and Influenza Virus Genome Projects.

In 2009 the project became international, with Canadian participation by:

• Ryan Brinkman
• Melanie Courtot

In 2010 the Tetherless World Constellation joined the project to complete implementation, validation and database integration of the ontology:

InfluenzO Sourceforge Sites

• InfluenzO Sourceforge Project Site
• InfluenzO Tracker

• Checking out the obo file: svn co https://influenzo.svn.sourceforge.net/svnroot/influenzo influenzo
• https://influenzo.svn.sourceforge.net/svnroot/influenzo/trunk/ontology/InfluenzO.obo InfluenzO.obo File

Reference Section

Other Pages within this Site

• Meeting Notes
• Milestones
• Development Notes
• Questions, Open and Resolved
• Creating Definitions

Documents

CEIRS documents

Minimal information for avian surveillanceInfluenza Ontology Related Documents

Tools

Chris Mungall's OBO-OWL Conversion API: http://www.berkeleybop.org/obo-conv.cgi

EBI Mapping tool (http://tab2mage.svn.sourceforge.net/viewvc/tab2mage/trunk/ontologymatching/) [ReadMe Read Me] (for the moment) ArrayExpress clean_ontology_terms

This package contains a set of perl scripts with supporting perl modules, to allow the user to map biological terms to ontology entries. The code was written by Tim Rayner at the European Bioinformatics Institute and maintained by Xiangqun Zheng Bradley.

INSTALLATION

There are a few steps required to install this package:

1. Install the following prerequisites:

  a. A version of the perl interpreter newer or equal to 5.8.1. 

  b. Perl modules: 

       Class::Std 
       GO::Parser 
       Text::Metaphone 
       Text::DoubleMetaphone 
       Lingua::EN::Inflect 

2. Run the following commands to install the core OE2magetab perl modules and scripts:

 %> perl Makefile.PL 
 %> make 
 %> make test 
 %> make install 

If you are on a windows box you should use 'nmake' rather than 'make'.

3. The ontology term matching script may now be run, as in this example:

 %> perl clean_ontology_terms.pl -i list.txt -o disease_ontology.obo -r output_file 

Run the script without any options for a full usage summary.

USAGE:

clean_ontology_terms -t <text file of terms to map> -o <the obo ontology, e.g. OBI> -r <name of file you want resutls to go to, e.g. mappings.xt> 

The text file should have a single column and the very first row should read VALUE_VALUE (this is for historic resasons but never got changed). For instance, the input test file for your flu terms might start like:

VALUE_VALUE

To start CPAN (Perl repository) perl -MCPAN -e shell Once you get to the cpan command line: cpan> install [Package name] where [Package name] is the name of the package (example, GO::Parser).

Internal Project Links

• Curation Files (all files within Google Docs/Spreadsheets - LOGIN REQUIRED)
  • Influenza Ontology Google Docs Home Page
  • I-IDO Structure Version 2
    • Burke's hierarchy of terms
  • Flu Ontology 28
  • Ontologies to Map
    • This is our overview working document, found in google docs
  • I-IDO V3 Ontology Matching
    • Spreadsheet we are now using to map terms from Burke's hierarchy, found on I-IDO V2
  • Team Members Definition Assignments
    • Joanne's definition spread sheet, with our three worksheets, splitting up the terms to define

External Project Links

• Background Reading
  • Relations in Biomedical Ontologies by Barry Smith et al. (PDF)
  • Biomedical Ontologies: How to make and use them by Nigham Shah and Barry Smith (PPT)
• Influenza Ontology External Links
• Influenza Ontology Discussion Group
  • CEIRS Pilot Project Mapping Data
  • Influenza Google Groups
  • Influenza Ontology Google Discussions
    • Influenza Ontology Discussion Group topics: join the discussion group, post questions or comments.
    • Has listservs for various topics
• EXTERNAL Ontology RESOURCES
• OBI Links
  • HTML Version of OBI
  • OBI’s Wiki
    • OBI’s Wiki: Digital Entity Terms (information entity)
  • OBI’s Google Groups page
    • obi-denrie-branch - List to discuss terms in the ontology of digital_entity/non-realizable_info_entity branch such as digital document, data set...
    • obi-role-branch - List to discuss terms in the ontology of roles such as Principle investigator, Patient, Reagent...
    • obi-instrument-branch - List to discuss terms in the ontology of instrument branch such as microarray, flow cytometer...
    • obi-relations - List to discuss terms in the ontology of relations branch such as is_manufactured_by, has_function...
  • OBI Sourceforge Issue Tracker
• OBO Foundry and EBI Links
  • OBO Foundry's wiki on naming conventions
  • EBI’s Ontology Lookup Service (list of browsable ontologies)
  • EBI’s Ontology Lookup Service Search Box
  • List of OBO Foundry Principles

Other Ontologies Referenced by InfluenzO

OBO File Specifications

• default-namespace: FLU
• namespace-id-rule: *FLU:$sequence(8,1,33333333)$