1. Information Representation Working Group WG Meeting September 5, 2008

2. Agenda ICR F2F Announcements Review point after September 30 Results of review of “things”/”object classes” by participants Next Steps/Tasks

3. ICR F2F September 23-24,2008 Day 1: Tuesday, July 23rd, 2008, 8:00 AM - 6:00 PM Day 2: Wednesday, June 24th, 2008, 8:00 AM - 3:00 PM The Broad Institute of MIT and Harvard in Cambridge, MA More info: https://cabig.nci.nih.gov/workspaces/ICR/Meetings/index_html/ICR_F2F_ Sept08 https://cabig.nci.nih.gov/workspaces/ICR/Meetings/index_html/ICR_F2F_ Sept08 Elaine and Li for additional comments on IRWG participant roles

4. Announcements Time change First Friday 3-4pm EST (Telecon info?) Third Friday 2-3pm EST Charter review point after Sept 30 – October 3 meeting Draft DAM deadline for F2F no longer valid Align charter deadlines with due dates: Oct 27 and Feb 6 More items

5. Proposals for Methods CDE-centric approach (Bottom-up) Use caDSR Identify heavily used CDEs using caDSR => Identify “characteristics” first Include standard CDEs Build model based on CDE-related Object Classes and their associations Preserve CDE mappings Object Class-centric approach (Top-down) Use caDSR Identify heavily used object classes using caDSR => Identify “things” first Build model in order of Object Classes, associations and attributes Use standard CDEs as applicable Preserve CDE mappings Model-centric approach Use information models Use classes and manually curate Use standard CDEs as applicable 1 2

6. Results of review of “things”/”object classes” by participants Most to least popular: 2223314Chromosome 2223335Protein 2407006Organization 2236731Person 2514026Gene Ontology 2223346Microarray 2223318Nucleotide Sequence 2322230Messenger RNA 2223316Organism 2423453Image 2223331Protocol 2341906Address 2223326Gene 2223336Protein Sequence 2236759Protocol 2514028Single Nucleotide Polymorphism 2407061Participant

7. Results of review of “things”/”object classes” by participants 2223321Biochemical Pathway 2224105Scientific Publication 2528727Protein Biomarker 2716124Gene Expression Microarray Reporter 2629688Exon 2528719DNA Specimen 2433356GenBank Accession Number 2241613Specimen 2629695Transcript

8. Results of review of “things”/”object classes” by participants 2528725Pathway 2342268UniProtKB Accession Number 2422748Data File 2451992Protein Domain 2519311Species 2528730Single Nucleotide Polymorphism Assay 2433353Online Mendelian Inheritance in Man 2223337Protein Alternative Name 2228374Scientific Publication Source 2544909UniProtKB Primary Accession Number Genomic Identifier 2528763Principal Component Analysis 2429762Anatomic Site 2528732Single Nucleotide Polymorphism Annotation 2544902Messenger RNA Genomic Identifier 2514027Orthologous Gene 2612311Peptide 2223332Molecular Genetic Abnormality 2223313Gene Alias 2236728Nucleic Acid Hybridization 2528729Variation Reporter 2619601Experiment 2529489Chromosome Location 2716127Microarray Reporter 2528721Population Group 2544901Protein Genomic Identifier 2726731Nucleic Acids Biospecimen 2528724Gene Biomarker 2734873Disease or Disorder Term 2716122Exon Microarray Reporter 2513348Molecular Specimen 2223338Homologous Gene 2716121Single Nucleotide Polymorphism Microarray Reporter 2404668Histology 2228343Database Cross-Reference 2544899Gene Genomic Identifier 2233215Procedure 2430995Study 2629693Intron

9. Results of review of “things”/”object classes” by participants “Things” of interest based on results received so far (from Elaine): Protocol/study/procedure/treatment/experiment Data/finding/evidence Protein, Gene, RNA Pharmacologic substance/compound Chromosome/Gene Location SNP Disease/disorder/phenotype Biomarker Pathway/Biochemical Pathway Publication/Reference GO Term/Gene Ontology/ Anatomic site/tissue Microarray Assay Reporter/probe Measurements/Quantitation Investigator/research personnel/site investigator Organization/Institution/Clinical trial site

10. Results of review of “things”/”object classes” by participants Comments from Sue: It is much easier to make the decision if we discuss the use cases from the sub-domains that got selected and how the different use-cases from the different sub-domains interact with each other, and perhaps decide one set of core use cases for the DAM from which we could select the core sets of domain objects Apart from the core domain objects, for the LIMS related objects (Storage, Container, Laboratory, etc.), I think we should reference what caLIMS2 provides. Even though it's at version 0.5 and has not submitted for silver-level review. It already has extensive study on objects used within a lab setting Remove the object classes that somewhat implementation specific, e.g. Identifiable Class, Extendable Class, Describable Class, Parameterizable Application. For object classes that are similar in nature, can we integrate? e.g. Measurement, Unit, Data, Data Set, Biology Data Cube, Derived Bioassay Class Data, Measured Bioassay Data, Value, etc. From a drug-discovery pipeline perspective, the DAM heavily focuses on target discovery and validation (gene, protein, pathway, disease, animal models, microarray, etc) aspect and is missing subdomains that discuss hit identification and assay developments. Is this on the list of future directions? I know caNanoLab discuss about in-vitro and in vivo assays from a nanoparticle perspective, but not sure if there are other models that we could already make use of.

11. Next Steps/Tasks