Chado introduction

Ontology-oriented databases: Chado and OBD Chris Mungall Lawrence Berkeley Labs

Outline ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Chado: what is it? ,[object Object],[object Object],[object Object],[object Object],[object Object]

A brief introduction to MODs ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Must store representations of genes and genomic entities ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Must store other data types pertinent to that organism ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Must house rich annotation data using ontologies ,[object Object]

Must track provenance and evidence for data ,[object Object],[object Object],[object Object],[object Object],[object Object]

Must be an integrated source of data ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Origins of Chado ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Chado key concepts ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Chado modules ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Identifiers: dbxref s ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Ontologies and terminologies are central to Chado ,[object Object],eye ,[object Object],[object Object],ommatidium sense organ eye disc is_a part_of develops from

Ontologies: cv module ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Subset of Sequence Ontology transcript Part_of Transcript region Transcript region Is_a exon Object Type Subject

Genomics: Sequence module ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Feature table ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Feature Graphs: the feature_relationship table ,[object Object],[object Object],[object Object]

Example: alternately spliced gene ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],A (transcript) Part_of 4 (exon) B (transcript) Part_of 3 (exon) A (transcript) Part_of 3 (exon) B (transcript) Part_of 2 (exon) G (gene) Part_of B (transcript) A (transcript) Part_of 1 (exon) G (gene) Part_of A (transcript) Object Predicate Subject

Feature graph configurations are constrained by SO ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Declarative programming: SQL Functions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Tata S, Patel JM, Friedman JS, and Swaroop A Declarative querying for biological sequence databases Proc of the 22nd International Conference on Data Engineering (ICDE), April 3-7, Atlanta, GA, 2006.

Chado: ongoing work ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

NCBO: OBO and OBD ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

OBD: Storing biomedical annotations ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

The Semantic Web Datamodel ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

OBD ‘Schema’: formal ontology of annotation Within OBO Foundry Framework - uses OBO upper ontology

Implementing OBD using SemWeb technology ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Wrapping databases as SPARQL endpoints ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

GO annotations OBD Disease/pheno annotations Genome server MOD D2rq D2rq DAS Sesame Usage scenario: AJAX Gbrowse (http://genome.biowiki.org) Annotation info sparql DAS/2 sparql sparql

Conclusions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Thanks ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Feature localisation ,[object Object],[object Object],[object Object],[object Object],[object Object]

Recursive location graphs ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Nested LGs Redundant localisations can be used to ‘flatten’ LG Group>0 indicates denormalised/flattened LG - must be recalculated if group=0 coordinates change 1 0 0 group chrom1 12000..13000[+] contig1 chrom1 12100..13100[+] exon1 contig1 100..200[+] exon1 Srcfeature Loc Feature

Relational featurelocs ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

OWL entailment genomics use case ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Chado introduction

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Chado introduction