1. Homology Review Human arm Lobed-fin fish fin Bat wing Bird wing Insect wing Homologous forelimbs not homologous as forelimbs or wings Definition: Structures (including genes) are homologous if they evolved from some structure in a common ancestor Wings are functionally classified, and are analagous structures not homologous as wings Which of the following structures are homologous?

2. Why do we care about homology when building an anatomy ontology? Consider an anatomy ontology of vertebrates: skeletal system cranial skeletal system parietal bone (in_organism human) parietal bone (in_organism zebrafish) frontal bone (in_organism human) frontal bone (in_organism zebrafish) Homologous : frontal bone (zebrafish) and parietal bone (human) f pa Different genes and developmental processes may underlie the development of the zebrafish frontal and the human frontal, even though they have the same name and are similarly located

3. How and where should homology information be captured? Homology between genes is already determined and recorded by the model organism community Use case: Query for phenotypes affecting the human frontal bone and its homologous structure in other species. Homologs = Synonyms

4. Gene homology Types of gene homology: Genes that diverged due to a speciation event are termed orthologs Genes that diverged due to a duplication within a species are termed paralogs Gene orthology is recorded using different types of evidence: mouse Conserved location: Kim et al., 1999 FuguA HOXB

5. Each homology assignment is associated with reference to a physical piece of evidence, a person, or literature. Homology assignments are based on specific kinds of evidence IP: Inferred from Position ID: Inferred from Development IC: Inferred from Composition Homology statements include evidence and citations, and different homology statements are used to create and refine phylogenies. Homology between anatomical structures is already determined and but not yet captured in a database the evolutionary community

6. Homologous structures are already implicit within MODs ontologies

7. 1.Do we need a relationship in OBO-REL to define homology? This is a symmetric relation between sisters and it is the relationship that requires evidence and attribution. 2.Should homology assignments be a top-down or bottom up approach?eg. Pairs of taxa vs. CARO-centric assignments? RE:domain experts are required. It might be easier to enlist help in a pairwise manner. 3.Homology needs to be captured for similarity searches. Text or synonym searches are insufficient. Does CARO take into account homology or is it a separate data set? 4.If two structures are deemed homologous, how does this information transfer down is_a chains? Need use cases. Discussion points