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chado

chado. Generic model organism database schema. Presented at the NESCent GMOD Meeting 20 January, 2005 David Emmert emmert@morgan.harvard.edu. Chado modules. Genetics Module. Genetic/phenotypic interactions in genotypic/environmental context. Sequence Module.

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chado

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  1. chado Generic model organism database schema Presented at the NESCent GMOD Meeting 20 January, 2005 David Emmert emmert@morgan.harvard.edu

  2. Chado modules Genetics Module Genetic/phenotypic interactions in genotypic/environmental context Sequence Module Biological sequences and objects which can be localized on them Map Module Adjunct to sequence module for non-sequence localization Expression Module Transcript and protein expression events Companalysis Module Adjunct to sequence module for in-silico analysis CV Module Controlled vocabularies and ontologies Organism Module Taxonomy / species information Pub Module Publication / Biblio / Reference information General Module General information / database cross-references

  3. chado module dependencies organism general (dbxref) map pub sequence genetic expression cv companalysis

  4. cvterm dbxref feature_relationship feature_dbxref feature_cvterm feature featureloc featureprop feature_synonym organism featureprop_pub pub synonym

  5. flexible property types cv property type • push as many attributes as possible into property tables • control property types with controlled vocabs • link properties to publications type_id table tableprop record_id property_id pub

  6. flexible relationship types cv relationshp type • using controlled vocabularies for relationship types makes customization and extension possible without altering the schema. type_id table_relationship subject_id object_id table

  7. Bill Gelbart, FlyBase PI chado schema design Chris Mungall (HHMI/BDGP/FlyBase) Colin Wiel (FlyBase) Pinglei Zhou (FlyBase) Aubrey de Gray (FlyBase) Bill Gelbart (FlyBase) Stan Letovsky (FlyBase) chado I/O chadoXML & chado loader Pinglei Zhou and Stan Letovsky Bioperl chadoxml.pm Peili Zhang and Chris Mungall GAME -> chadoXML converter Frank Smutniak GFF3 -> chado loader Scott Cain GMOD Lincoln Stein (PI) Scott Cain Comments and Feedback Mark Yandell (BDGP) Sam Angiuoli (TIGR) Jennifer Wortman (TIGR) Owen White (TIGR) Many others… Acknowledgements

  8. chado

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