Immunology Ontology: Difference between revisions
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'''8:30-10:00am Lecture''' | '''8:30-10:00am Lecture''' | ||
1. Introduction to biomedical ontology building | |||
:Identification of participant areas of interest in preparation for the afternoon practical session | :Identification of participant areas of interest in preparation for the afternoon practical session | ||
:Overview of biomedical ontology | :Overview of biomedical ontology | ||
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::How ontologies can support data-driven research | ::How ontologies can support data-driven research | ||
::Glories and miseries of the Semantic Web | ::Glories and miseries of the Semantic Web | ||
:How to build an ontology | |||
::Mistakes to avoid | ::Mistakes to avoid | ||
:Example | :Example | ||
::The [http://www.obofoundry.org/ OBO (Open Biological and Biomedical Ontologies) Foundry] | |||
::The Ontology for Biomedical Investigations ([http://obi-ontology.org/page/Main_Page OBI]) | ::The Ontology for Biomedical Investigations ([http://obi-ontology.org/page/Main_Page OBI]) | ||
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:The Vaccine Ontology ([http://www.violinet.org/vaccineontology/ VO]) [http://ncor.buffalo.edu/2013/Immunology/VO.ppt Slides] | :The Vaccine Ontology ([http://www.violinet.org/vaccineontology/ VO]) [http://ncor.buffalo.edu/2013/Immunology/VO.ppt Slides] | ||
3. Formats and | 3. Formats and tools | ||
:Brief remarks on formats: XML, RDF, OWL and OBO | :Brief remarks on formats: XML, RDF, OWL and OBO | ||
::[http://www.geneontology.org/GO.format.shtml GO File Format Guide] | ::[http://www.geneontology.org/GO.format.shtml GO File Format Guide] | ||
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4. How are ontologies used? | 4. How are ontologies used? | ||
:in defining data standards (example: [https://immport.niaid.nih.gov/immportWeb/home/home.do?loginType=full ImmPort]) | :in defining data standards (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 | :to support text mining and NLP, document retrieval | ||
::example: [http://www.gopubmed.org/web/gopubmed/ GOPubMed] | ::example: [http://www.gopubmed.org/web/gopubmed/ GOPubMed] | ||
:to integrate heterogeneous data / heterogeneous research communities | :to integrate heterogeneous data / heterogeneous research communities | ||
'''1:00-3:00pm: Practical Session''' | '''1:00-3:00pm: Practical Session: Building Small Ontologies in the Immunological Domain''' | ||
5. Establish a number of target areas of interest (drawing on the work initiated in session 1. above) | |||
==Background Resources (will be reviewed in class)== | ==Background Resources (will be reviewed in class)== | ||
Revision as of 18:41, 9 June 2013
What:
Summer School for Quantitative Systems Immunology: 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.
Who: Lindsay Cowell and Barry Smith
Schedule
8:30-10:00am Lecture
1. Introduction to biomedical ontology building
- Identification of participant areas of interest in preparation for the afternoon practical session
- Overview of biomedical ontology
- What is an ontology for?
- How ontologies can support data-driven research
- Glories and miseries of the Semantic Web
- How to build an ontology
- Mistakes to avoid
- Example
- The OBO (Open Biological and Biomedical Ontologies) Foundry
- The Ontology for Biomedical Investigations (OBI)
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)
- Staph Aureus Ontology and Other IDO Extension Ontologies
- The Vaccine Ontology (VO) Slides
3. Formats and tools
- Brief remarks on formats: XML, RDF, OWL and OBO
- Brief remarks on tools
- Protégé Ontology Editor
- Ontofox Slides
- SPARQL
4. How are ontologies used?
- 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
1:00-3:00pm: Practical Session: Building Small Ontologies in the Immunological Domain
5. Establish a number of target areas of interest (drawing on the work initiated in session 1. above)
Background Resources (will be reviewed in class)
Immunological Ontologies
Examples
[HIPC example http://ncor.buffalo.edu/2013/Immunology/HIPC-Example/]
[Allergy example http://ncor.buffalo.edu/2013/Immunology/allergy-example.docx]
Portals
1. The Open Biological and Biomedical Ontologies
2. Bioportal
3. Ontobee
4. EBI Ontology Lookup Service
5. MeSH
Literature
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.
