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Influenza Application 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

  • A collaborative group of influenza researchers have established an influenza application ontology.
  • Working together Joanne Luciano (MITRE), Lynn Schriml (University of Maryland, School of Medicine), Burke Squires (University of Texas Southwestern Medical Center (UTSW)) and Richard Scheuermann (UTSW) have 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) with the help of Eric Bortz (Mount Sinai School of Medicine) and Torsten Staab (Los Alamos National Laboratory), and the Gemina and Influenza Virus Genome Projects. In 2009, Ryan Brinkman and Melanie Courtot joined the project.

InfluenzO Sourceforge Sites

Reference Section

Other Pages within this Site

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

External Links

Other Ontologies Referenced by InfluenzO

Ontology Name Description
Cell Ontology (CL) Cell types from prokaryotic to mammalian
Common Anatomy Reference Ontology (CARO) Anatomical structures in all organisms
Disease Ontology (DO) Types of human disease (InfluenzO is a subset of this ontology)
Dublin Core (DC) Interoperable online metadata standards
Environment Ontology (EnvO) Habitats and environments of organisms and biological samples
Foundational Model of Anatomy (FMA) Structure of the mammalian and in particular the human body
Gazetteer (GAZ) Geographic location, places and place names and their relationships
Gene Ontology (GO) Attributes of gene products in all organisms
Infectious Disease Ontology (IDO) Relevant to both biomedical and clinical aspects of infectious diseases (InfluenzO is a subset of this ontology)
Ontology for Biomedical Investigations (OBI) Design, protocol, instrumentation and analysis applied in biomedical investigations
Ontology for Clinical Investigations (OCI) Clinical trials and related clinical studies
Pathogen Transmission (TRANS) How a pathogen is transmitted from one host, reservoir, or source to another host
Phenotypic Quality Ontology (PATO) Qualities of biomedical entities
Protein Ontology (PRO) Protein types and modifications classified on the basis of evolutionary relationships
Relation Ontology (RO) Relations in biomedical ontologies
RNA Ontology (RnaO) RNA three-dimensional structures, sequence alignments, and interactions
Sequence Ontology (SO) Features and properties of nucleic acid sequences
Zebrafish Anatomical Ontology (ZAO) Anatomical structures in Danio rerio



OBO File Specifications

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