Building a Foundation to Enable Semantic Technologies for Phylogenetically-Based Comparative Analyses

2. Phyloinformatics 06/24/11 Motivation “ Nothing in biology makes sense except in the light of evolution ” (Theodosius Dobzhansky, 1973)…. and Nothing in evolution makes sense except in the light of phylogeny

3. 06/24/11 For example - Prediction of gene and protein function Jonathan A. Eisen, 1998,Genome Research, 8:163-167 Phyloinformatics 1. Choose gene of interest 2. Identify homolog 3.Align sequences 4.Calculate gene tree 5.Overaly known functions onto tree 6. Hypothesize function for all genes 7. Reconcile gene and species trees After Eisen 1998,Genome Research

4. 06/24/11 Example 2 – Testing congruence among phylogeographic analyses Knowles 2009 after Avis 1992 Phyloinformatics 1. Compile results of phylogeographic analyses for multiple species from the same geographic region 2. Apply demographic models to account for variation in generation times and substitution rates After Knowles 2009, Annu. Rev. Ecol. Evol. Syst.

5. Applying Semantics to Bioinformatics Integrative bioinformatics experimentation cycle 06/24/11 1.Problem Definition 2. Experimental Design 3. Data Integration 4. Data Analysis 15. Interpretation Biological hypothesis Protocol Raw integration result Analysis result knowledge 1. Imported or create data and knowledge models 2.Use data models to transform raw data to RDF data 3. Link data models to knowledge models 4. Select common domain 5. Construct and run semantic query Raw integration result Lennart J.G. Post, Marco Roos, M. Scott Marshall, Roel van Driel and Timo M. Breit. A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data, Vol. 23 no. 22 2007, pages 3080–3087 doi:10.1093/bioinformatics/btm461

7. Bioinformatics and phylogeny 06/24/11 Proposed components of a minimum reporting standard for phylogenetic analyses: Leebens-Mack et al. 2006 OMICS

11. Phyloinformatics 06/24/11 Tree estimation program ontology

12. Phyloinformatics 06/24/11 Data analysis ontology diagram

13. Phyloinformatics 06/24/11 Models for character state transitions (e.g. nucleotide substitution model)