Information Representation Working Group WG Meeting September 5, 2008

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

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: Sept08 Sept08 Elaine and Li for additional comments on IRWG participant roles

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 Third Friday 2-3pm EST Charter review point after Sept 30 – October 3 meeting Draft DAM deadline for F2F no longer valid Align charter deadlines with due dates: Oct 27 and Feb 6 More items

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

Results of review of “things”/”object classes” by participants Most to least popular: Chromosome Protein Organization Person Gene Ontology Microarray Nucleotide Sequence Messenger RNA Organism Image Protocol Address Gene Protein Sequence Protocol Single Nucleotide Polymorphism Participant

Results of review of “things”/”object classes” by participants Biochemical Pathway Scientific Publication Protein Biomarker Gene Expression Microarray Reporter Exon DNA Specimen GenBank Accession Number Specimen Transcript

Results of review of “things”/”object classes” by participants Pathway UniProtKB Accession Number Data File Protein Domain Species Single Nucleotide Polymorphism Assay Online Mendelian Inheritance in Man Protein Alternative Name Scientific Publication Source UniProtKB Primary Accession Number Genomic Identifier Principal Component Analysis Anatomic Site Single Nucleotide Polymorphism Annotation Messenger RNA Genomic Identifier Orthologous Gene Peptide Molecular Genetic Abnormality Gene Alias Nucleic Acid Hybridization Variation Reporter Experiment Chromosome Location Microarray Reporter Population Group Protein Genomic Identifier Nucleic Acids Biospecimen Gene Biomarker Disease or Disorder Term Exon Microarray Reporter Molecular Specimen Homologous Gene Single Nucleotide Polymorphism Microarray Reporter Histology Database Cross-Reference Gene Genomic Identifier Procedure Study Intron

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

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.

Next Steps/Tasks