Difference between revisions of "Main Page"

From Influenza Ontology Wiki
Jump to: navigation, search
(External Links)
(Consortium Members)
 
(44 intermediate revisions by 4 users not shown)
Line 1: Line 1:
<big>'''Influenza Application Ontology Home Page'''</big>
+
<big>'''Influenza Ontology Home Page'''</big>
  
 +
==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 ==
 
== History ==
Line 7: Line 9:
  
 
==Consortium Members==
 
==Consortium Members==
*A collaborative group of influenza researchers have established an influenza application ontology.
+
*Starting in the fall of 2007, a collaborative group of influenza researchers have established an influenza ontology. The influenza ontology is an 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.
+
  
==Project Goal==
+
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)
*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.
+
* [http://tw.rpi.edu/wiki/Joanne_S._Luciano Joanne Luciano] (Tetherless World Constellation, Rensselaer Polytechnic Institute)
 +
* [http://medschool.umaryland.edu/facultyresearchprofile/viewprofile.aspx?id=20337 Lynn Schriml] (University of Maryland, School of Medicine)
 +
* Burke Squires (University of Texas Southwestern Medical Center  (UTSW))
 +
* [http://www8.utsouthwestern.edu/findfac/personal/0,2358,16416,00.html 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==
 +
*[https://sourceforge.net/projects/influenzo/ InfluenzO Sourceforge Project Site]
 +
*[https://sourceforge.net/tracker/?group_id=233412&atid=1089708 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===
 +
*[http://influenzaontologywiki.igs.umaryland.edu/wiki/index.php/Meeting_Notes Meeting Notes]
 +
*[http://influenzaontologywiki.igs.umaryland.edu/wiki/index.php/Milestones Milestones]
 +
*[http://influenzaontologywiki.igs.umaryland.edu/wiki/index.php/Development_Notes Development Notes]
 +
*[http://influenzaontologywiki.igs.umaryland.edu/wiki/index.php/Questions Questions, Open and Resolved]
 +
*[http://influenzaontologywiki.igs.umaryland.edu/wiki/index.php/Definitions Creating Definitions]
 +
 
 +
===Documents===
 +
 
 +
=CEIRS documents=
 +
 
 +
Minimal information for avian surveillance[[Influenza 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
  
==Links==
+
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===
 
===Internal Project Links===
*Curation Files
+
*Curation Files (all files within Google Docs/Spreadsheets - LOGIN REQUIRED)
**Burke's hierarchy of terms: [http://docs.google.com/Doc?id=dgp2p9fd_0dfrnshd4&pli=1 I-IDO Structure Version 2]
+
**[http://spreadsheets.google.com/ccc?key=pvfRkQJl1OsnJh58Nmzf1Tg&inv=lynn.schriml@gmail.com Ontologies to Map]
+
 
**[http://docs.google.com/#people/burkesquires%40gmail.com Influenza Ontology Google Docs Home Page]
 
**[http://docs.google.com/#people/burkesquires%40gmail.com Influenza Ontology Google Docs Home Page]
**This is our overview working document, found in google docs: [http://spreadsheets.google.com/ccc?key=pcKtQNrJvmRiyx-T29fA_TQ&hl=en flu ontology 28]:  
+
**[http://docs.google.com/Doc?id=dgp2p9fd_0dfrnshd4&pli=1 I-IDO Structure Version 2]
 +
***Burke's hierarchy of terms
 +
**[http://spreadsheets.google.com/ccc?key=pcKtQNrJvmRiyx-T29fA_TQ&hl=en Flu Ontology 28]
 +
**[http://spreadsheets.google.com/ccc?key=pvfRkQJl1OsnJh58Nmzf1Tg&inv=lynn.schriml@gmail.com Ontologies to Map]
 +
***This is our overview working document, found in google docs
 
**[http://spreadsheets.google.com/ccc?key=pcKtQNrJvmRg5PSubPUqOdg&inv=lynn.schriml%40gmail.com&t=525179600742449631 I-IDO V3 Ontology Matching]
 
**[http://spreadsheets.google.com/ccc?key=pcKtQNrJvmRg5PSubPUqOdg&inv=lynn.schriml%40gmail.com&t=525179600742449631 I-IDO V3 Ontology Matching]
*** Spreadsheet we are now using to map terms from Burke's hierarchy, found on (1 : I-IDO V2)
+
*** Spreadsheet we are now using to map terms from Burke's hierarchy, found on I-IDO V2
**[http://spreadsheets.google.com/ccc?key=pvfRkQJl1OskeHzFmmUaiQA&inv=lynn.schriml%40gmail.com&t=3725831644864612901  Team Members Definition Assignments]: Joanne's definition spread sheet, with our three worksheets, splitting up the terms to define
+
**[http://spreadsheets.google.com/ccc?key=pvfRkQJl1OskeHzFmmUaiQA&inv=lynn.schriml%40gmail.com&t=3725831644864612901  Team Members Definition Assignments]
 +
***Joanne's definition spread sheet, with our three worksheets, splitting up the terms to define
  
===External Links===  
+
===External Project Links===
 +
*Background Reading
 +
**[http://genomebiology.com/content/pdf/gb-2005-6-5-r46.pdf Relations in Biomedical Ontologies] by Barry Smith et al. (PDF)
 +
**[http://www.bioontology.org/wiki/images/0/00/ISMB_2007_Final.ppt Biomedical Ontologies: How to make and use them] by Nigham Shah and Barry Smith (PPT)
 +
*'''Influenza Ontology External Links'''
 +
*Influenza Ontology Discussion Group
 
**[http://influenza-ontology.googlegroups.com/web/MSSM%20Pilot%20project%20data%20mapping.xls?gda=hx1Gq1QAAADCAyaeQDRoTcvhEI7zWNXvm0Lg6am5weqzdWIHVTC5fmG1qiJ7UbTIup-M2XPURDT6lhHJIpl9SO2iiV6hQZagW-CkPC9xMtCyRv0uZTHkrKmGjL_aT2pnt3gzCHCrqco CEIRS Pilot Project Mapping Data]
 
**[http://influenza-ontology.googlegroups.com/web/MSSM%20Pilot%20project%20data%20mapping.xls?gda=hx1Gq1QAAADCAyaeQDRoTcvhEI7zWNXvm0Lg6am5weqzdWIHVTC5fmG1qiJ7UbTIup-M2XPURDT6lhHJIpl9SO2iiV6hQZagW-CkPC9xMtCyRv0uZTHkrKmGjL_aT2pnt3gzCHCrqco CEIRS Pilot Project Mapping Data]
 
**[http://groups.google.com/group/influenza-ontology Influenza Google Groups]
 
**[http://groups.google.com/group/influenza-ontology Influenza Google Groups]
 +
**[http://groups.google.com/group/influenza-ontology/topics?hl=en&start= 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
 
**[http://obi.svn.sourceforge.net/viewvc/*checkout*/obi/trunk/docs/user/obi-lsw-report.html?revision=535 HTML Version of OBI]
 
**[http://obi.svn.sourceforge.net/viewvc/*checkout*/obi/trunk/docs/user/obi-lsw-report.html?revision=535 HTML Version of OBI]
**[http://www.ebi.ac.uk/ontology-lookup/ontologyList.do] EBI’s Ontology Lookup Service (list of browsable ontologies)]
 
**[http://www.ebi.ac.uk/ontology-lookup/ EBI’s Ontology Lookup Service Search Box]
 
 
**[https://wiki.cbil.upenn.edu/obiwiki/index.php/HomePage OBI’s Wiki]
 
**[https://wiki.cbil.upenn.edu/obiwiki/index.php/HomePage OBI’s Wiki]
 
***[https://wiki.cbil.upenn.edu/obiwiki/index.php/DigitalEntityTerms OBI’s Wiki: Digital Entity Terms (information entity)]
 
***[https://wiki.cbil.upenn.edu/obiwiki/index.php/DigitalEntityTerms OBI’s Wiki: Digital Entity Terms (information entity)]
 
**[http://groups.google.com/group/obi-biomaterial OBI’s Google Groups page]
 
**[http://groups.google.com/group/obi-biomaterial OBI’s Google Groups page]
***Has listservs for various topics like
+
***[http://groups.google.com/group/obi-denrie-branch obi-denrie-branch] - List to discuss terms in the ontology of digital_entity/non-realizable_info_entity branch such as digital document, data set...
****[http://groups.google.com/group/obi-denrie-branch obi-denrie-branch] - List to discuss terms in the ontology of digital_entity/non-realizable_info_entity branch such as digital document, data set...
+
***[https://lists.sourceforge.net/lists/listinfo/obi-role-branch obi-role-branch] - List to discuss terms in the ontology of roles such as Principle investigator, Patient, Reagent...
****[https://lists.sourceforge.net/lists/listinfo/obi-role-branch obi-role-branch] - List to discuss terms in the ontology of roles such as Principle investigator, Patient, Reagent...
+
***[https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch obi-instrument-branch] - List to discuss terms in the ontology of instrument branch such as microarray, flow cytometer...
****[https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch obi-instrument-branch] - List to discuss terms in the ontology of instrument branch such as microarray, flow cytometer...
+
***[https://lists.sourceforge.net/lists/listinfo/obi-relations obi-relations] - List to discuss terms in the ontology of relations branch such as is_manufactured_by, has_function...  
****[https://lists.sourceforge.net/lists/listinfo/obi-relations obi-relations] - List to discuss terms in the ontology of relations branch such as is_manufactured_by, has_function...  
+
 
**[http://sourceforge.net/tracker/?group_id=177891&atid=886178 OBI Sourceforge Issue Tracker]
 
**[http://sourceforge.net/tracker/?group_id=177891&atid=886178 OBI Sourceforge Issue Tracker]
 +
*OBO Foundry and EBI Links
 
**[http://obofoundry.org/wiki/index.php/Naming OBO Foundry's wiki on naming conventions]
 
**[http://obofoundry.org/wiki/index.php/Naming OBO Foundry's wiki on naming conventions]
 +
**[http://www.ebi.ac.uk/ontology-lookup/ontologyList.do EBI’s Ontology Lookup Service (list of browsable ontologies)]
 +
**[http://www.ebi.ac.uk/ontology-lookup/ EBI’s Ontology Lookup Service Search Box]
 +
**[http://www.obofoundry.org/wiki/index.php/OBO_Foundry_Principles List of OBO Foundry Principles]
 +
 +
===Other Ontologies Referenced by InfluenzO===
 +
{| border="1"
 +
|+
 +
! 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)
 +
|-
 +
| [http://dublincore.org/ 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
 +
|-
 +
| [http://www.infectiousdiseaseontology.org/Home.html 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
 +
|-
 +
| [http://www.obofoundry.org/cgi-bin/detail.cgi?id=transmission 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:$sequence(8,1,33333333)$

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

Reference Section

Other Pages within this Site

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

External Project 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:$sequence(8,1,33333333)$