the chado genetics module gmod meeting 4/26/2004 cambridge, ma david emmert flybase - harvard...
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The chado genetics module
GMOD Meeting
4/26/2004
Cambridge, MA
David EmmertFlyBase - [email protected]
general (dbxref)
cv
organism
pub
sequence
companalysis
genetic
expression
map
chado module dependencies
feature_iduniquenameetc…
feature
feature_gcontext_idfeature_idgcontext_idchromosome_idrankcgroupcvterm_id
feature_gcontext
cvterm_idnameetc…
cvterm
gcontext_iduniquenamedescriptionpub_id
gcontext
phenstatement_cvterm_idphenstatement_idcvterm_id
phenstatement_cvterm
gcontext_relationship
phenstatement_idgcontext_iddbxref_idobservable_idattr_idvaluecvalue_idassay_id
phenstatement
phenstatement_relationship
phendesc_idgcontext_iddescription
phendesc
phenstatement_cvterm_idphenstatement_idcvterm_id
phenstatement_cvterm
phenstatement_idgcontext_iddbxref_idobservable_idattr_idvaluecvalue_idassay_id
phenstatement
phenstatement_relationship
phendesc_idgcontext_iddescription
phendesc
feature_iduniquenameetc…
feature
feature_gcontext_idfeature_idgcontext_idchromosome_idrankcgroupcvterm_id
feature_gcontext
cvterm_idnameetc…
cvterm
gcontext_iduniquenamedescriptionpub_id
gcontext
gcontext_relationship
feature_iduniquenameetc…
feature
feature_gcontext_idfeature_idgcontext_idchromosome_idrankcgroupcvterm_id
feature_gcontext
cvterm_idnameetc…
cvterm
gcontext_iduniquenamedescriptionpub_id
gcontext
rank can be used for n-ploid organisms.cgroup can be used for distinguishing chromosomal groups
feature_iduniquenameetc…
feature
feature_gcontext_idfeature_idgcontext_idchromosome_idrankcgroupcvterm_id
feature_gcontext
cvterm_idnameetc…
cvterm
gcontext_iduniquenamedescriptionpub_id
gcontextPartial Genotype(aka: allele)
ab[2]
ab[2]
f_g
gcontextab[2]
rank=0cgroup=0
feature_iduniquenameetc…
feature
feature_gcontext_idfeature_idgcontext_idchromosome_idrankcgroupcvterm_id
feature_gcontext
cvterm_idnameetc…
cvterm
gcontext_iduniquenamedescriptionpub_id
gcontextSimple Stock Genotype
ab[2]/T(Y;2)E
ab[2] T(Y;2)E
f_g f_g
ab[2]/T(Y;2)E
rank=0cgroup=0
rank=1cgroup=0
feature_iduniquenameetc…
feature
feature_gcontext_idfeature_idgcontext_idchromosome_idrankcgroupcvterm_id
feature_gcontext
cvterm_idnameetc…
cvterm
gcontext_iduniquenamedescriptionpub_id
gcontextStock Genotype I:
P{hsFLP}1, w[1118]; Adv[1]/CyO
P{hsFLP}1 CyO
f_g f_g
P{hsFLP}1, w[1118]; Adv[1]/CyO
rank=0cgroup=0 rank=1
cgroup=1
f_g
w[1118]
f_g
Adv[1]
rank=0cgroup=0
rank=0cgroup=1
feature_iduniquenameetc…
feature
feature_gcontext_idfeature_idgcontext_idchromosome_idrankcgroupcvterm_id
feature_gcontext
cvterm_idnameetc…
cvterm
gcontext_iduniquenamedescriptionpub_id
gcontext
rank=0cgroup=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_grank=0cgroup=0
f_g
y[1]
f_g
C(1)DX
rank=2cgroup=0
rank=0cgroup=0
Dp(1;2;Y)w[+]
f_g
rank=1cgroup=0
feature_iduniquenameetc…
feature
feature_gcontext_idfeature_idgcontext_idchromosome_idrankcgroupcvterm_id
feature_gcontext
cvterm_idnameetc…
cvterm
gcontext_iduniquenamedescriptionpub_id
gcontext
phenstatement_cvterm_idphenstatement_idcvterm_id
phenstatement_cvterm
phenstatement_idgcontext_iddbxref_idobservable_idattr_idvaluecvalue_idassay_id
phenstatement
phenstatement_relationship
phendesc_idgcontext_iddescription
phendesc
feature_iduniquenameetc…
feature
feature_gcontext_idfeature_idgcontext_idchromosome_idrankcgroupcvterm_id
feature_gcontext
cvterm_idnameetc…
cvterm
gcontext_iduniquenamedescriptionpub_id
gcontext
phenstatement_cvterm_idphenstatement_idcvterm_id
phenstatement_cvterm
phenstatement_idgcontext_iddbxref_idobservable_idattr_idvaluecvalue_idassay_id
phenstatement
phenstatement_relationship
phendesc_idgcontext_iddescription
phendesc
cvterm_idnameetc…
cvterm
gcontext_iduniquenamedescriptionpub_id
gcontext
phenstatement_cvterm_idphenstatement_idcvterm_idrank**
phenstatement_cvterm
phenstatement_idgcontext_iddbxref_idobservable_idattr_idvaluecvalue_idassay_id
phenstatement
phenstatement_relationship
phendesc_idgcontext_iddescription
phendesc
gcontextAct-88F1
phenstatement
Allele phenotype Act-88F1
Phenotypic class: flightless | dominant
cvterm “flightless”
cvterm “dominant”
attr_id cvalue_id
cvterm_idnameetc…
cvterm
gcontext_iduniquenamedescriptionpub_id
gcontext
phenstatement_cvterm_idphenstatement_idcvterm_idrank**
phenstatement_cvterm
phenstatement_idgcontext_iddbxref_idobservable_idattr_idvaluecvalue_idassay_id
phenstatement
phenstatement_relationship
phendesc_idgcontext_iddescription
phendesc
gcontextalpha-specrg41
phenstatement
Allele phenotype alpha-specrg41
Phenotypic class: lethal | larval | recessive
cvterm “lethal”
cvterm “larval”
cvterm “recessive”
observable_id
attr_id cvalue_id
cvterm_idnameetc…
cvterm
gcontext_iduniquenamedescriptionpub_id
gcontext
phenstatement_cvterm_idphenstatement_idcvterm_idrank**
phenstatement_cvterm
phenstatement_idgcontext_iddbxref_idobservable_idattr_idvaluecvalue_idassay_id
phenstatement
phenstatement_relationship
phendesc_idgcontext_iddescription
phendesc
gcontextalphaTub67Tom-3a
phenstatement
Allele phenotype alphaTub67Tom-3a
Phenotypic class: lethal | embryonic | dominant | maternal effect | conditional cs
cvterm “lethal”
cvterm “embryonic”
cvterm “dominant”
obs_id
attr_id cvalue_id
cvterm “maternal effect”
cvterm “conditional cs”
p_c p_c
rank=2rank=1
cvterm_idnameetc…
cvterm
gcontext_iduniquenamedescriptionpub_id
gcontext
phenstatement_cvterm_idphenstatement_idcvterm_idrank**
phenstatement_cvterm
phenstatement_idgcontext_iddbxref_idobservable_idattr_idvaluecvalue_idassay_id
phenstatement
phenstatement_relationship
phendesc_idgcontext_iddescription
phendesc
gcontextalphaTub67Tom-3a
phenstatement
Allele phenotype alphaTub67Tom-3a
Phenotypic manifest in: embryonic peripheral nervous system | maternal effect
cvterm “embryonic peripheral
nervous system”
observable_id
cvterm “maternal effect”
p_c
rank=1
cvterm_idnameetc…
cvterm
gcontext_iduniquenamedescriptionpub_id
gcontext
phenstatement_cvterm_idphenstatement_idcvterm_idrank**
phenstatement_cvterm
phenstatement_idgcontext_iddbxref_idobservable_idattr_idvaluecvalue_idassay_id
phenstatement
phenstatement_relationship
phendesc_idgcontext_iddescription
phendescTransheterozygous phenotype: fafBX3/fafFO8
Phenotypic class: visible
gcontextfafBX3/fafFO8
phenstatement
cvterm “visible”
attr_id
fafBX3 fafFO8
cvterm_idnameetc…
cvterm
gcontext_iduniquenamedescriptionpub_id
gcontext
phenstatement_cvterm_idphenstatement_idcvterm_idrank**
phenstatement_cvterm
phenstatement_idgcontext_iddbxref_idobservable_idattr_idvaluecvalue_idassay_id
phenstatement
phenstatement_relationship
phendesc_idgcontext_iddescription
phendesc
gcontext_relationship
feature_iduniquenameetc…
feature
feature_gcontext_idfeature_idgcontext_idchromosome_idrankcgroupcvterm_id
feature_gcontext
Genetic Interactions
“wg1 has a wing phenotype that is enhanced by dpp1”
FlyBase Curation for wg1: visible, enhanceable { dpp[1] }
gcontextwg1
phenstatement
cvterm “visible”
objectgc_id
wg1
gcontextdpp1
dpp1
cvterm “enhances”
g_r subjectgc_id
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