The chado genetics module

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

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

3. gcontext_id uniquename description pub_id gcontext 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 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 gcontext_ relationship phenstatement_ relationship

4. phendesc_id gcontext_id description phendesc gcontext_id uniquename description pub_id gcontext gcontext_ relationship 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 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 phenstatement_ relationship

5. gcontext_id uniquename description pub_id gcontext rank can be used for n-ploid organisms. cgroup can be used for distinguishing chromosomal groups 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

6. gcontext_id uniquename description pub_id gcontext 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 Partial Genotype (aka: allele) ab[2] ab[2] f_g rank=0 cgroup=0 gcontext ab[2]

7. gcontext_id uniquename description pub_id gcontext 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 Simple Stock Genotype ab[2]/T(Y;2)E ab[2] T(Y;2)E f_g f_g rank=1 cgroup=0 rank=0 cgroup=0 ab[2]/T(Y;2)E

8. gcontext_id uniquename description pub_id gcontext Adv[1] 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 f_g Stock Genotype I: P{hsFLP}1, w[1118]; Adv[1]/CyO P{hsFLP}1 w[1118] CyO rank=0 cgroup=0 rank=0 cgroup=1 f_g f_g f_g rank=0 cgroup=0 rank=1 cgroup=1 P{hsFLP}1, w[1118]; Adv[1]/CyO

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

10. gcontext_id uniquename description pub_id gcontext 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 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

11. gcontext_id uniquename description pub_id gcontext 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 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

12. Allele phenotype Act-88F1 Phenotypic class: flightless | dominant gcontext_id uniquename description pub_id gcontext phendesc_id gcontext_id description phendesc phenstatement phenstatement_id gcontext_id dbxref_id observable_id attr_id value cvalue_id assay_id phenstatement_cvterm cvterm cvterm_id name etc… phenstatement_cvterm_id phenstatement_id cvterm_id rank** phenstatement_ relationship gcontext Act-88F1 phenstatement attr_id cvalue_id cvterm “flightless” cvterm “dominant”

13. Allele phenotype alpha-specrg41 Phenotypic class: lethal | larval | recessive phendesc_id gcontext_id description gcontext_id uniquename description pub_id gcontext phendesc phenstatement_id gcontext_id dbxref_id observable_id attr_id value cvalue_id assay_id phenstatement_cvterm_id phenstatement_id cvterm_id rank** cvterm cvterm_id name etc… phenstatement phenstatement_cvterm phenstatement_ relationship cvterm “lethal” cvterm “larval” cvterm “recessive” gcontext alpha-specrg41 phenstatement attr_id cvalue_id observable_id

14. Allele phenotype alphaTub67Tom-3a Phenotypic class: lethal | embryonic | dominant | maternal effect | conditional cs gcontext_id uniquename description pub_id gcontext phendesc_id gcontext_id description phendesc cvterm_id name etc… cvterm 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 p_c p_c phenstatement_ relationship gcontext alphaTub67Tom-3a phenstatement attr_id cvalue_id obs_id cvterm “lethal” cvterm “embryonic” cvterm “dominant” rank=1 rank=2 cvterm “maternal effect” cvterm “conditional cs”

15. Allele phenotype alphaTub67Tom-3a Phenotypic manifest in: embryonic peripheral nervous system | maternal effect phendesc_id gcontext_id description gcontext_id uniquename description pub_id gcontext phendesc phenstatement_id gcontext_id dbxref_id observable_id attr_id value cvalue_id assay_id phenstatement_cvterm_id phenstatement_id cvterm_id rank** cvterm cvterm_id name etc… phenstatement phenstatement_cvterm p_c phenstatement_ relationship gcontext alphaTub67Tom-3a phenstatement observable_id rank=1 cvterm “embryonic peripheral nervous system” cvterm “maternal effect”

16. Transheterozygous phenotype: fafBX3/fafFO8 Phenotypic class: visible gcontext_id uniquename description pub_id gcontext phendesc phendesc_id gcontext_id description fafBX3 fafFO8 phenstatement cvterm phenstatement_cvterm_id phenstatement_id cvterm_id rank** phenstatement_id gcontext_id dbxref_id observable_id attr_id value cvalue_id assay_id cvterm_id name etc… phenstatement_cvterm gcontext fafBX3/fafFO8 phenstatement phenstatement_ relationship attr_id cvterm “visible”

17. gcontext_id uniquename description pub_id gcontext phendesc_id gcontext_id description phendesc gcontext_ relationship cvterm_id name etc… cvterm 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 feature_id uniquename etc… feature feature_gcontext_id feature_id gcontext_id chromosome_id rank cgroup cvterm_id feature_gcontext phenstatement_ relationship

18. Genetic Interactions “wg1 has a wing phenotype that is enhanced by dpp1” FlyBase Curation for wg1: visible, enhanceable { dpp[1] } g_r dpp1 wg1 gcontext wg1 objectgc_id subjectgc_id gcontext dpp1 phenstatement cvterm “enhances” cvterm “visible”

19. 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