SRI International
         Why Create a PGDB?                      Bioinformatics
         Perform pathway analyses as part of a genome 
           project
         Analyze omics data
         Create a central information resource for the 
           organism 
         Create an FBA model
         Perform comparative analyses
                                                      SRI International
                                                       Bioinformatics
          Model Organism Databases
          DBs that describe the genome and other information about 
            an organism
          Curated by experts for that organism
              No one group can curate all the world’s genomes
              Distribute workload across a community of experts to create a community 
               resource
          Every sequenced organism with an active experimental 
            community requires a MOD
              Integrate genome data with information about the biochemical and 
               genetic network of the organism
              Integrate literature-based information with computational predictions
                                                 SRI International
         Rationale for MODs                      Bioinformatics
         Each “complete” genome is incomplete in several 
           respects:
            40%-60% of genes have no assigned function
            Roughly 7% of those assigned functions are incorrect
            Many assigned functions are non-specific
         MODs are platforms for global analyses of an 
           organism
            Interpret omics data in a pathway context
            In silico prediction of essential genes
            Characterize systems properties of metabolic and genetic 
              networks
                                               SRI International
         What is Curation?                      Bioinformatics
         Ongoing updating and refinement of a PGDB
         Correct false-positive and false-negative 
          predictions
         Incorporate information from experimental 
          literature
            Update genome sequence
            Update gene functions, gene positions, gene names
            Author comments and citations
            Add new pathways, modify existing pathways
            Enter information about regulatory networks
                                                 SRI International
                                                 Bioinformatics
         Issues in Creating Public MODs
         Obtaining funding
         Scoping the project
         Identify user community
         Obtain buy-in and help from scientific community
         IT: Set up database server, Web server
         Hire and train curators