1. OntologyEntry in MAGE Chris Stoeckert, Helen Parkinson Trish Whetzel, Joe White Gilberto Fragoso, Liju Fan, Mervi Heiskanen, Angel Pizarro Ontology Working Group MGED6 3 Sept. 2003, Aix-en-Provence, France

2. Ontology Workshop Relation of the MGED Ontology to MAGE Brief review of the MGED Ontology Policies for coding the MGED Ontology in MAGE Examples Discussion

3. OntologyEntry in MAGE BioMaterial Package

4. OntologyEntry in MAGE Description Package

5. MGED Ontology v1.1.6 “Finished” version of the MGED Ontology Available at http://mged.sourceforge.net/ontologies/MGEDontology.php Two major branches: Core and Extended Consists of classes, properties, and individuals (instances) Classes may have instances or be abstract Classes may refer to other ontologies, controlled vocabularies

6. “Finished” MGED Ontology A stable version of the MGED Ontology that can code can be based on. The next major version will be developed in concert with MAGE v2. A few minor changes to be finished up this month Additions allowed (like MAGE, as long as it won’t break code).

7. Available at http://mged.sourceforge.net/ontologies/MGEDontology.php html Daml file Rdfs file NCI DTS Browser

8. MGED Ontology is registered as GO Xref and at MOBY abbreviation: MO database: The MGED Ontology object: ontology term example: MO:Action generic_url: http://mged.sourceforge.net/ontologies/MGEDontology.php url_syntax: http://mged.sourceforge.net/ontologies/MGEDontology.php#term url_example: http://mged.sourceforge.net/ontologies/MGEDontology.php#Action

9. MO has two major branches: Core and Extended daml file in OILed

10. MO consists of classes, properties, and individuals (instances)

11. Classes may have instances or be abstract

12. Classes may refer to other ontologies, controlled vocabularies

13. Policies for coding MO in MAGE All MO terms are to be database referenced When the MAGE category in the OntologyEntry tag is a MO class with individuals. When the MAGE category in the OntologyEntry tag is a MO class without individuals because it is an abstract class. When the MAGE category in OntologyEntry tag is a MO property. The MO OntologyEntry class and its subclasses.

14. Lung Cancer (166) Lung Adenocarcinoma (127 primary + 12 metastases ) Small Cell Lung Carcinoma (6) Normal Lung (17) Squamous Cell Lung Carcinoma (21) Lung Carcinoid Tumor (20) RNA Extraction and Labeling 203 Labeled Extracts Hybridize on Affymetrix chips Hierarchical Clustering Classification of Lung Cancer, Subclassification of Lung Adenocarcinoma Bhattacharjee et al, Proc Natl Acad Sci USA. 2001 Nov 20:98(24):1390-5 Lung M. Heiskanen, G. Fragoso, L. Fan NCI

15. BioMaterialPackage Bio Material Provider Thoracic Oncology Tumor Bank Cell Type Epithelial Cell Sample ID AD145 Sex Male Organism Status Premortem Species Human Developmental Stage Elderly Somatic Cell Type (Cell Type) Epithelial Cell Age 88 Years Clinical History/ Prior Disease State Lung Adenocarcinoma ClinicalHistory/ Smoking History 20 cigarretes per day for 20 years. Disease State Recurrent Lung Adenocarcinoma Disease Stage Stage IIIA Disease Location Lung

16. BioMaterial Package

17. Ova 72 (4A) Ova 24 (2A) Ova 48 (3A) Alum 24 (5A) Alum 48 (6A) Alum 72 (7A) Ova-pre ctrl (1A) Intra-strain Hybridizations For Strain 129J High eosinophils, high airway hyperreactivity Group A Ova 72 (4B) Ova 24 (2B) Ova 48 (3B) Alum 24 (5B) Alum 48 (6B) Alum 72 (7B) Ova-pre ctrl (1B) Group B RNA Sample # is given in (parentheses) 28 Hybs COMMON POOL COMMON POOL J. White, TIGR

18. Ovalbumin induction of asthma ExperimentDesignType: time_series_design compound_treatment_design strain_or_line_design reference_design FactorValueCategory: AtomicAction Incubate: time 24 h, 48 hr, 72 hr Compound_based_treatment: Ovalbumin: alum + ovalbumin Alum: alum (adjuvent), strain_or_line: –JAX_mouse_strains: 129J, BTBR, C57BL/6, BALB/C ExperimentPackage

20. MAGE Core Interfaces

21. Discussion Questions on current policies? Need for additional policies? Plans for further MO development

22. MAGE issues Need for additional OntologyEntry associations SeqFeature basis strandType Provided in MO but can’t provide database reference in MAGE No direct association Not describable

23. BioSequence Package