'''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 '''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 == == '''Morning Lecture''' == 8:30am Introduction to biomedical ontology building (Barry Smith, [http://ncor.buffalo.edu/2013/Immunology/BS.ppt Slides]) :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 :Examples ::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]) 9:15am Overview of ontologies with content relevant to immunology (Lindsay Cowell, [http://ncor.buffalo.edu/2013/Immunology/LC.pdf Slides]) :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] ::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]) ::Staph Aureus Ontology and Other IDO Extension Ontologies :The Vaccine Ontology ([http://www.violinet.org/vaccineontology/ VO]) [http://ncor.buffalo.edu/2013/Immunology/VO.ppt Slides] 9:45am Formats and tools :Brief remarks on formats: XML, RDF, OWL and OBO ::[http://www.geneontology.org/GO.format.shtml GO File Format Guide] :Brief remarks on tools ::[http://protege.stanford.edu/ Protégé Ontology Editor] ::[http://ontofox.hegroup.org/ Ontofox] [http://ncor.buffalo.edu/2013/Immunology/Ontofox.pptx 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). Participants will suggest possible target areas, expanding this list in light of their own areas of interest and expertise. :Adaptive immunity :Immune tolerance :Inflammation :Adaptive immunity :Innate immunity :Mucosal immunity :Transplantation immunology /MHC :Tumor microenvironment / Cancer :Virology (These are all areas for which a suitable single ontology does not already exist. Some of the items are taken from the DAIT list [http://www.niaid.nih.gov/about/organization/dait/Pages/default.aspx here].) 1:10 Participants will be divided into corresponding breakout groups. The task of each group will be to create a workplan for building 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 any other source Two samples: :[http://ncor.buffalo.edu/2013/Immunology/allergy-example.docx allergy and allergic disease] :[http://ncor.buffalo.edu/2013/Immunology/HIPC-Example/ soluble proteins (including cytokines and chemokines) relevant to the work of HIPC]] : 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 Each group should select a reporter, who will present the results of the group's work, and a recorder, who will take notes of the discussions and have control of the powerpoint slides documenting the results of these discussions. 2:20 Presentation of results: Each group is required to produce at least 4 slides summarizing the results of their work. :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: List of the principal ontologies selected to be used as sources / starting points for development of the needed ontology :Slide 4: List of the main terms in the ontology (if possible with some rudimentary BFO organization) [http://ncor.buffalo.edu/2013/Immunology/Slides Slides] 2.50 Summation ==Background Resources (will be reviewed in class)== '''Immunological Ontologies''' [http://ncorwiki.buffalo.edu/index.php/Immunology_Ontologies Overview] '''Portals''' 1. [http://www.obofoundry.org/ The Open Biological and Biomedical Ontologies] 2. [http://bioportal.bioontology.org/ Bioportal] 3. [http://www.ontobee.org/ Ontobee] 4. [http://www.ebi.ac.uk/ontology-lookup/ EBI Ontology Lookup Service] 5. [http://www.nlm.nih.gov/mesh/MBrowser.html MeSH] '''Literature''' Diehl AD, Augustine AD, Blake JA, Cowell LG, et al. [http://www.ncbi.nlm.nih.gov/pubmed/20123131 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. [http://www.ncbi.nlm.nih.gov/pubmed/21208450 Logical development of the cell ontology]. BMC Bioinformatics. 2011; 12. Aravind Subramanian, et al. [http://www.pnas.org/content/102/43/15545.full Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles], PNAS, 102 (43), 15545–15550.