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

Recommended

Recommended

More Related Content

What's hot

What's hot (20)

Viewers also liked

Viewers also liked (6)

Similar to Chado introduction

Similar to Chado introduction (20)

More from Chris Mungall

More from Chris Mungall (20)

Recently uploaded

Recently uploaded (20)

Chado introduction