1. The chado genetics module GMOD Meeting 4/26/2004 Cambridge, MA David Emmert FlyBase - Harvard emmert@morgan.harvard.edu

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

3. feature_id uniquename etc… feature feature_gcontext_id feature_id gcontext_id chromosome_id rank cgroup cvterm_id feature_gcontext cvterm_id name etc… cvterm gcontext_id uniquename description pub_id gcontext phenstatement_cvterm_id phenstatement_id cvterm_id phenstatement_cvterm gcontext_ relationship phenstatement_id gcontext_id dbxref_id observable_id attr_id value cvalue_id assay_id phenstatement phenstatement_ relationship phendesc_id gcontext_id description phendesc

4. phenstatement_cvterm_id phenstatement_id cvterm_id phenstatement_cvterm phenstatement_id gcontext_id dbxref_id observable_id attr_id value cvalue_id assay_id phenstatement phenstatement_ relationship phendesc_id gcontext_id description phendesc feature_id uniquename etc… feature feature_gcontext_id feature_id gcontext_id chromosome_id rank cgroup cvterm_id feature_gcontext cvterm_id name etc… cvterm gcontext_id uniquename description pub_id gcontext gcontext_ relationship

5. feature_id uniquename etc… feature feature_gcontext_id feature_id gcontext_id chromosome_id rank cgroup cvterm_id feature_gcontext cvterm_id name etc… cvterm gcontext_id uniquename description pub_id gcontext rank can be used for n-ploid organisms. cgroup can be used for distinguishing chromosomal groups

6. feature_id uniquename etc… feature feature_gcontext_id feature_id gcontext_id chromosome_id rank cgroup cvterm_id feature_gcontext cvterm_id name etc… cvterm gcontext_id uniquename description pub_id gcontext Partial Genotype (aka: allele) ab[2] f_g gcontext ab[2] rank=0 cgroup=0

7. feature_id uniquename etc… feature feature_gcontext_id feature_id gcontext_id chromosome_id rank cgroup cvterm_id feature_gcontext cvterm_id name etc… cvterm gcontext_id uniquename description pub_id gcontext Simple Stock Genotype ab[2]/T(Y;2)E ab[2]T(Y;2)E f_g ab[2]/T(Y;2)E rank=0 cgroup=0 rank=1 cgroup=0

8. feature_id uniquename etc… feature feature_gcontext_id feature_id gcontext_id chromosome_id rank cgroup cvterm_id feature_gcontext cvterm_id name etc… cvterm gcontext_id uniquename description pub_id gcontext Stock Genotype I: P{hsFLP}1, w[1118]; Adv[1]/CyO P{hsFLP}1CyO f_g P{hsFLP}1, w[1118]; Adv[1]/CyO rank=0 cgroup=0 rank=1 cgroup=1 f_g w[1118] f_g Adv[1] rank=0 cgroup=0 rank=0 cgroup=1

9. feature_id uniquename etc… feature feature_gcontext_id feature_id gcontext_id chromosome_id rank cgroup cvterm_id feature_gcontext cvterm_id name etc… cvterm gcontext_id uniquename description pub_id gcontext rank=0 cgroup=0 Stock Genotype II: gt[13z]/Dp(1;2;Y)w[+]/C(1)DX, y[1] f[1] f[1] f_g gt[13z]/Dp(1;2;Y)w[+]/C(1)DX,y[1] f[1] gt[13z] f_g rank=0 cgroup=0 f_g y[1] f_g C(1)DX rank=2 cgroup=0 rank=0 cgroup=0 Dp(1;2;Y)w[+] f_g rank=1 cgroup=0

10. feature_id uniquename etc… feature feature_gcontext_id feature_id gcontext_id chromosome_id rank cgroup cvterm_id feature_gcontext cvterm_id name etc… cvterm gcontext_id uniquename description pub_id gcontext phenstatement_cvterm_id phenstatement_id cvterm_id phenstatement_cvterm phenstatement_id gcontext_id dbxref_id observable_id attr_id value cvalue_id assay_id phenstatement phenstatement_ relationship phendesc_id gcontext_id description phendesc

11. feature_id uniquename etc… feature feature_gcontext_id feature_id gcontext_id chromosome_id rank cgroup cvterm_id feature_gcontext cvterm_id name etc… cvterm gcontext_id uniquename description pub_id gcontext phenstatement_cvterm_id phenstatement_id cvterm_id phenstatement_cvterm phenstatement_id gcontext_id dbxref_id observable_id attr_id value cvalue_id assay_id phenstatement phenstatement_ relationship phendesc_id gcontext_id description phendesc

12. cvterm_id name etc… cvterm gcontext_id uniquename description pub_id gcontext phenstatement_cvterm_id phenstatement_id cvterm_id phenstatement_cvterm phenstatement_id gcontext_id dbxref_id observable_id attr_id value cvalue_id assay_id phenstatement phenstatement_ relationship phendesc_id gcontext_id description phendesc observable_id: eg. larval attr_id: eg. lethal cvalue_id: eg. dominant

13. cvterm_id name etc… cvterm gcontext_id uniquename description pub_id gcontext phenstatement_cvterm_id phenstatement_id cvterm_id rank** phenstatement_cvterm phenstatement_id gcontext_id dbxref_id observable_id attr_id value cvalue_id assay_id phenstatement phenstatement_ relationship phendesc_id gcontext_id description phendesc gcontext Act-88F 1 phenstatement Allele phenotype Act-88F 1 Phenotypic class: flightless | dominant cvterm “flightless” cvterm “dominant” attr_idcvalue_id

14. cvterm_id name etc… cvterm gcontext_id uniquename description pub_id gcontext phenstatement_cvterm_id phenstatement_id cvterm_id rank** phenstatement_cvterm phenstatement_id gcontext_id dbxref_id observable_id attr_id value cvalue_id assay_id phenstatement phenstatement_ relationship phendesc_id gcontext_id description phendesc gcontext alpha-spec rg41 phenstatement Allele phenotype alpha-spec rg41 Phenotypic class: lethal | larval | recessive cvterm “lethal” cvterm “larval” cvterm “recessive” p_c rank=1rank=2rank=3

15. cvterm_id name etc… cvterm gcontext_id uniquename description pub_id gcontext phenstatement_cvterm_id phenstatement_id cvterm_id rank** phenstatement_cvterm phenstatement_id gcontext_id dbxref_id observable_id attr_id value cvalue_id assay_id phenstatement phenstatement_ relationship phendesc_id gcontext_id description phendesc gcontext alpha-spec rg41 phenstatement Allele phenotype alpha-spec rg41 Phenotypic class: lethal | larval | recessive cvterm “lethal” cvterm “larval” cvterm “recessive” observable_id attr_idcvalue_id

16. cvterm_id name etc… cvterm gcontext_id uniquename description pub_id gcontext phenstatement_cvterm_id phenstatement_id cvterm_id rank** phenstatement_cvterm phenstatement_id gcontext_id dbxref_id observable_id attr_id value cvalue_id assay_id phenstatement phenstatement_ relationship phendesc_id gcontext_id description phendesc gcontext alphaTub67 Tom-3a phenstatement Allele phenotype alphaTub67 Tom-3a Phenotypic class: lethal | embryonic | dominant | maternal effect | conditional cs cvterm “lethal” cvterm “embryonic” cvterm “dominant” obs_id attr_idcvalue_id cvterm “maternal effect” cvterm “conditional cs” p_c rank=2rank=1

17. cvterm_id name etc… cvterm gcontext_id uniquename description pub_id gcontext phenstatement_cvterm_id phenstatement_id cvterm_id rank** phenstatement_cvterm phenstatement_id gcontext_id dbxref_id observable_id attr_id value cvalue_id assay_id phenstatement phenstatement_ relationship phendesc_id gcontext_id description phendesc gcontext alphaTub67 Tom-3a phenstatement Allele phenotype alphaTub67 Tom-3a Phenotypic manifest in: embryonic peripheral nervous system | maternal effect cvterm “embryonic peripheral nervous system” observable_id cvterm “maternal effect” p_c rank=1

18. cvterm_id name etc… cvterm gcontext_id uniquename description pub_id gcontext phenstatement_cvterm_id phenstatement_id cvterm_id rank** phenstatement_cvterm phenstatement_id gcontext_id dbxref_id observable_id attr_id value cvalue_id assay_id phenstatement phenstatement_ relationship phendesc_id gcontext_id description phendesc Transheterozygous phenotype: faf BX3 /faf FO8 Phenotypic class: visible gcontext faf BX3 /faf FO8 phenstatement cvterm “visible” attr_id faf BX3 faf FO8

19. cvterm_id name etc… cvterm gcontext_id uniquename description pub_id gcontext phenstatement_cvterm_id phenstatement_id cvterm_id rank** phenstatement_cvterm phenstatement_id gcontext_id dbxref_id observable_id attr_id value cvalue_id assay_id phenstatement phenstatement_ relationship phendesc_id gcontext_id description phendesc gcontext_ relationship feature_id uniquename etc… feature feature_gcontext_id feature_id gcontext_id chromosome_id rank cgroup cvterm_id feature_gcontext

20. Genetic Interactions “wg 1 has a wing phenotype that is enhanced by dpp 1” FlyBase Curation for wg 1 :visible, enhanceable { dpp[1] } gcontext wg 1 phenstatement cvterm “visible” objectgc_id wg 1 gcontext dpp 1 cvterm “enhances” g_r subjectgc_id

21. Representing hapmap genotype data in chado (Chris Mungall and Mummi Thorisson) -Several hundred thousand human SNPs (dbSNP rs#). - 90x samples (Coriell cell lines). -genotypes for each of the 90 samples at a given SNP site. SNP sequence_variant …91 rank=0 residue_info = null featurelocchromosome_arm srcfeature_id rank=1..90 residue_info = genotype_sequence or bp

22. Representing hapmap genotype data in chado (Chris Mungall and Mummi Thorisson) -Several hundred thousand human SNPs (dbSNP rs#). - 90x samples (Coriell cell lines). -genotypes for each of the 90 samples at a given SNP site. SNP sequence_variant …91 rank=0 residue_info = null featurelocchromosome_arm srcfeature_id chromosome_arm feature for each individual …90

23. Acknowledgements genetic module design team –Chris Mungall (BDGP - Berkeley) –Pinglei Zhou (FlyBase - Harvard) –Aubrey de Grey (FlyBase - Cambridge) –Bill Gelbart (PI, FlyBase) –Stan Letovsky (FlyBase - Harvard) –FlyBase Curators at Cambridge and Harvard GMOD –Scott, Lincoln, Everybody who’s helped / commented