1. Trevor Paterson 09 December 2015 Knowledge Capture Exercise: Representing Relationships between Mapping Data

2. Trevor Paterson 09 December 2015 1. Vertical Data Representation: how we accurately and unambiguously represent mapping data in individual datasets The framework allowing us to integrate the various different types and sources of mapping data. Important but should be solvable. Less problematic and contentious ? – A Technological problem of Architecture and Data Integration. 2. Horizontal Data Integration and Comparison: how do we establish and represent links between data – particularly across species boundaries. What are the types, meanings and reliability of the relationships between data. Crucial for the scientific rationale of ComparaGRID. A Scientific problem of data interpretation, discovery and inference. But [2] relies on [1]. Representing relationships between mapping data

3. Trevor Paterson 09 December 2015 Vertical Issues What types of Data are we interested in? What is a map? What are the types of maps? How are the types of maps related? What is the relationship between a sequence and a map? What is a Marker? What types of things can be used/represented as markers? How do we represent evidence?

4. Trevor Paterson 09 December 2015 Horizontal Issues What types of Relationships between data are we interested in? Which types of data can be related in these ways? Which types of Concepts ( Markers?) Which sources of data can be related? Which types of Maps? How do we define these relationships? How do we establish these relationships? How do we store these relationships? Permanently? With ownership and provenance? How ‘good’ are these relationships? How reliable? How accurate? How reproducible? How stable? How do we navigate/join across these relationships? What inferences can we draw from relationships? How do we represent the quality and reliability of these relationships?

5. Trevor Paterson 09 December 2015 Exercise: What are the Relationships SENARIO: Compare: My species vs Your species Or My species vsModel species

6. Trevor Paterson 09 December 2015 What types of maps do we have data for? My speciesvsYour species Meiotic linkage maps HAPPY Map Physical map of BAC fingerprints Partial Sequence Map ….…

7. Trevor Paterson 09 December 2015 What types of things are represented as markers on these maps MapMarker Meiotic linkage maps Microsatellites, Phenotypes/QTLS, Deletions, … Physical map of BAC fingerprints Restriction sites, SNPs.. ….…

8. Trevor Paterson 09 December 2015 What relationships can be drawn between (which types of) markers? - On the same map - On different maps in the same species - Across Species Some examples HomologySimilarity BiologicalGroupRelatedPhenotypes HomoeologyIdentityHomologyGroupPhenotypicAssociation Orthology SynonymyOrthologyGroupNegativeAssociation Paralogy ParalogyGroupCausalRelationship Xenology GeneFamily ProteinFamily SequenceSimilarity BestMatch ReciprocalBestMatch SyntenyWithConservedGeneOrder SyntenyWithoutConservedGeneOrder Synteny LinkageColinearityOrder

9. Trevor Paterson 09 December 2015 Do some relationships imply others or exclude others? SequenceSimilarity =>Homology, Orthology, Identity? RelatedFunction => Orthology, Homology, Paralogy ReciprocalBestMatch => Orthology PhenotypicAssociation => CausalRelationship Synonymy => Similarity Linkage+Order => SyntenyWithConservedGeneOrder Which relationships provide better evidence?