Immunology Ontology: Difference between revisions
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== '''Morning | == '''Morning Lecture''' == | ||
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:How to build an ontology | :How to build an ontology | ||
::How to select appropriate starting points | ::How to select appropriate starting points | ||
::Mistakes to avoid | ::Mistakes to avoid | ||
:::Reinventing the wheel | :::Reinventing the wheel | ||
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9:15am Overview of ontologies with content relevant to immunology | 9:15am Overview of ontologies with content relevant to immunology | ||
:The Protein Ontology ([http://pir.georgetown.edu/pro/ PRO]) | :Use of ontology portals and search engines | ||
::The Cell Ontology ([http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell CL]) [http://bioportal.bioontology.org/ontologies/1006 Bioportal] | |||
::The Protein Ontology ([http://pir.georgetown.edu/pro/ PRO]) [http://bioportal.bioontology.org/ontologies/50185/?p=terms&conceptid=PR%3A000000001 Bioportal] | |||
:The Gene Ontology ([http://www.geneontology.org/ GO]) [http://www.geneontology.org/minutes/20060331_Additional-Material/posters/immunology-poster_adiehl.pdf Poster] | :The Gene Ontology ([http://www.geneontology.org/ GO]) [http://www.geneontology.org/minutes/20060331_Additional-Material/posters/immunology-poster_adiehl.pdf Poster] | ||
: | ::Relation to MeSH and similar resources | ||
: | :How are ontologies used? | ||
::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 text mining and NLP, document retrieval | |||
:::example: [http://www.gopubmed.org/web/gopubmed/ GOPubMed] | |||
:The Infectious Disease Ontology ([http://infectiousdiseaseontology.org/page/Main_Page IDO]) | :The Infectious Disease Ontology ([http://infectiousdiseaseontology.org/page/Main_Page IDO]) | ||
::Staph Aureus Ontology and Other IDO Extension Ontologies | ::Staph Aureus Ontology and Other IDO Extension Ontologies | ||
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::SPARQL | ::SPARQL | ||
== '''Afternoon Practical Session: Building Small Ontologies in the Immunological Domain''' == | |||
1:00pm Establish target areas of interest (drawing on the work initiated in the 8:30am session above) | 1:00pm Establish target areas of interest (drawing on the work initiated in the 8:30am session above) | ||
Revision as of 20:29, 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
Morning Lecture
8:30am 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
- How to select appropriate starting points
- Mistakes to avoid
- Reinventing the wheel
- Confusing words with things
- Example
- The OBO (Open Biological and Biomedical Ontologies) Foundry
- The Ontology for Biomedical Investigations (OBI)
9:15am Overview of ontologies with content relevant to immunology
- Use of ontology portals and search engines
- The Gene Ontology (GO) Poster
- Relation to MeSH and similar resources
- How are ontologies used?
- The Infectious Disease Ontology (IDO)
- Staph Aureus Ontology and Other IDO Extension Ontologies
- The Vaccine Ontology (VO) Slides
9:45am Formats and tools
- Brief remarks on formats: XML, RDF, OWL and OBO
- Brief remarks on tools
- Protégé Ontology Editor
- Ontofox Slides
- SPARQL
Afternoon Practical Session: Building Small Ontologies in the Immunological Domain
1:00pm Establish target areas of interest (drawing on the work initiated in the 8:30am session above)
First draft list of possible target areas (they should be areas for which a suitable single ontology does not already exist)
- innate immunity
- allergy and allergic disease
- autoimmune disease
- asthma
- immune tolerance
- transplantation
- medical countermeasures against radiological and nuclear threats
- tissue engineering
- wounds and injuries
(Some of the items on this list are taken from the DAIT list here.
1:10pm Participants will vote, in order to select ca. 10 topics, for each of which we have six or so people who have some relevant domain knowledge
1:20 Participants will be divided into corresponding groups. The task of each group will be to create a workplan for creating an ontology (or ontologies) for their selected area. The workplan will consist minimally of
- i. a list of main terms in their selected area -- to create this list participants can use the terminological resources they use in their own work or on any other source
- ii. a list of the main ontologies they would harvest as starting points; in identifying these ontologies participants should experiment with two or more of the ontology portals listed below
2:20 Presentation of results: Each group is required to produce at least 4 slides summarizing the results of their work in 3 minutes.
- Slide 1: Title and author list
- Slide 2: Quick comparison of the experience of using the 4 ontology
browsers listed above; optional report on experience using MeSH
- Slide 3: The list of the principal ontologies selected to be used as
sources / starting points for development of the needed ontology
- Slide 4: The list of the main terms in the ontology
2.50 Summation
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.
