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Chado for evolutionary biology

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Chris Mungall
Chris Mungall

Presented to NESCENT databases working group

EducaçãoTecnologia
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Chado for evolutionary science Chris Mungall HHMI (until June) National Center for Biomedical Ontologies (after June)
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],[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],[object Object]
Sequence module ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],phenotype phylogeny cv sequence
A biological ontology is: ,[object Object],eye ,[object Object],[object Object],ommatidium sense organ eye disc is_a part_of develops from
cv module ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],phenotype phylogeny cv sequence
phylogeny module ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],phenotype phylogeny cv sequence
phylogeny module status ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],phenotype phylogeny cv sequence
phenotype module ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],phenotype phylogeny cv sequence
key tables ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],phenotype phylogeny cv sequence
PATO: Attributes ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],phenotype phylogeny cv sequence
PATO: Attributes ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],phenotype phylogeny cv sequence
Combining entity terms and PATO terms ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],phenotype phylogeny cv sequence
Extensions to simple EAV? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],phenotype phylogeny cv sequence
OBD and NCBO ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],phenotype phylogeny cv sequence
Summary ,[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]
supplemental slides follow…
 
the feature_relationship table ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
 
organism module ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
 
 
phylogeny module ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
phylogeny: SQL functions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
phylogeny module ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
phylogeny module: open questions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Linking phylogeny to phenotype ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
phenotype module: status ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Software integration ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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