Immunology Ontology: Difference between revisions

Revision as of 16:43, 11 April 2013

What: Lecture and practical session on Immunology Ontology

When: Tuesday June 11

Where: Rafik B. Hariri Institute for Computing and Computational Science and Engineering, Boston University, Boston, MA on June 10-14, 2013.

Schedule

8:00 Breakfast

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

3. How are ontologies used?

for data annotation à la GO and GMODs

in defining data standards (example: 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:

@@ Line 9: / Line 9: @@
 :00 Breakfast
-:30-10:00am Lecture
+:30-10:00am '''Lecture'''
-. Introduction to ontology
+. Introduction to biological ontology
 :what is an ontology, how is it different from a controlled vocabulary, a computerized lexicon, and a data dictionary?
@@ Line 24: / Line 24: @@
 . How are ontologies used?
 :for data annotation à la GO and GMODs
-:in defining data standards
+:in defining data standards (example: [https://immport.niaid.nih.gov/immportWeb/home/home.do?loginType=full ImmPort])
-::example: [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
 ::example: [http://www.gopubmed.org/web/gopubmed/ GOPubMed]
-:to integrate heterogeneous data types / heterogeneous research communities
+:to integrate heterogeneous data / heterogeneous research communities (example: the [http://www.obofoundry.org/ OBO (Open Biological and Biomedical Ontologies) Foundry])
-::example: the OBO [http://www.obofoundry.org/ Open Biological and Biomedical Ontologies]) Foundry
-'''1:00-3:00pm'''
+'''1:00-3:00pm: Practical Session'''
+Hands-on example of building a small ontology in the immunological domain
-Hands-on example of building a small ontology
-Practical Session
 '''Background Reading''':