Immunology Ontologies: Difference between revisions

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== Events ==
[http://ncorwiki.buffalo.edu/index.php/Immunology_Ontology Lecture and practical session on Immunology Ontology] as part of
[http://www.bu.edu/computationalimmunology/summerschool/index.html Summer School for Quantitative Systems Immunology], Boston, MA, June 11, 2013


'''What''':
[http://www.bu.edu/computationalimmunology/summerschool/index.html Summer School for Quantitative Systems Immunology]: Lecture and practical session on Immunology Ontology


'''When''': Tuesday June 11
== Ontologies ==
 
'''Where''': [http://www.bu.edu/hic/directions/ Rafik B. Hariri Institute for Computing and Computational Science and Engineering, Boston University], Boston, MA on June 10-14, 2013.
 
'''Who''': [http://profiles.utsouthwestern.edu/profile/120432/lindsay-cowell.html Lindsay Cowell] and [http://ontology.buffalo.edu/smith Barry Smith]
 
== Schedule ==
 
'''8:30-10:00am Lecture'''
 
1. Introduction to biological ontology
:what is an ontology, how is it different from a controlled vocabulary, a computerized lexicon, and a data dictionary?
 
2. Overview of ontologies with content relevant to immunology


The Protein Ontology ([http://pir.georgetown.edu/pro/ PRO])
The Protein Ontology ([http://pir.georgetown.edu/pro/ PRO])
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The Infectious Disease Ontology ([http://infectiousdiseaseontology.org/page/Main_Page IDO])
The Infectious Disease Ontology ([http://infectiousdiseaseontology.org/page/Main_Page IDO])


3. How are ontologies used?
 
:for data annotation à la GO and GMODs
== Portals ==
:in defining data standards (example: [https://immport.niaid.nih.gov/immportWeb/home/home.do?loginType=full ImmPort])
 
[https://immport.niaid.nih.gov/immportWeb/home/home.do?loginType=full ImmPort]
:to support data analysis (example: GO enrichment of microarray data)
:to support data analysis (example: GO enrichment of microarray data)
:to support text mining and NLP, document retrieval  
:to support text mining and NLP, document retrieval  

Revision as of 23:52, 19 April 2013

Events

Lecture and practical session on Immunology Ontology as part of Summer School for Quantitative Systems Immunology, Boston, MA, June 11, 2013


Ontologies

The Protein Ontology (PRO) The Gene Ontology (GO) The Cell Ontology (CL) The Immune Epitope Ontology (ONTIE) The Infectious Disease Ontology (IDO)


Portals

ImmPort

to support data analysis (example: GO enrichment of microarray data)
to support text mining and NLP, document retrieval
example: GOPubMed
to integrate heterogeneous data / heterogeneous research communities (example: the OBO (Open Biological and Biomedical Ontologies) Foundry)

1:00-3:00pm: Practical Session

Hands-on example of building a small ontology in the immunological domain

Background Reading

Diehl AD, Augustine AD, Blake JA, Cowell LG, et al. Hematopoietic cell types: prototype for a revised cell ontology. J Biomed Inform. 2011; 44(1).

Meehan TF, Masci AM, Abdulla A, Cowell LG, et al. Logical development of the cell ontology. BMC Bioinformatics. 2011; 12.

Aravind Subramanian, et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles, PNAS, 102 (43), 15545–15550.

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