Immunology Ontologies: Difference between revisions

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[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 text mining and NLP, document retrieval
::example: [http://www.gopubmed.org/web/gopubmed/ GOPubMed]
:to integrate heterogeneous data / heterogeneous research communities (example: the [http://www.obofoundry.org/ OBO (Open Biological and Biomedical Ontologies) Foundry])


'''1:00-3:00pm: Practical Session'''
[http://www.immuneprofiling.org/hipc/page/showPage?pg=subcommittees-bioinf HIPC]


Hands-on example of building a small ontology in the immunological domain
[http://tsb.mssm.edu/primeportal/ PRIME]


==Background Reading==
==Background Reading==

Revision as of 23:54, 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

HIPC

PRIME

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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