The chado genetics module GMOD Meeting 4/26/2004 Cambridge, MA David Emmert FlyBase - Harvard...

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



phendesc


feature


feature_gcontext

cvterm_idnameetc…

cvterm


gcontext



feature


feature_gcontext

cvterm_idnameetc…

cvterm


gcontext

rank can be used for n-ploid organisms.cgroup can be used for distinguishing chromosomal groups


feature


feature_gcontext

cvterm_idnameetc…

cvterm


gcontextPartial Genotype(aka: allele)

ab[2]

ab[2]

f_g

gcontextab[2]

rank=0cgroup=0


feature


feature_gcontext

cvterm_idnameetc…

cvterm


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


feature_gcontext

cvterm_idnameetc…

cvterm


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


feature_gcontext

cvterm_idnameetc…

cvterm


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


feature_gcontext

cvterm_idnameetc…

cvterm


gcontext




phenstatement



phendesc

cvterm_idnameetc…

cvterm


gcontext

phenstatement_cvterm_idphenstatement_idcvterm_idrank**



phenstatement



phendesc

gcontextAct-88F1

phenstatement

Allele phenotype Act-88F1

Phenotypic class: flightless | dominant

cvterm “flightless”

cvterm “dominant”

attr_id cvalue_id

cvterm_idnameetc…

cvterm


gcontext




phenstatement



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




phenstatement



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




phenstatement



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




phenstatement



phendescTransheterozygous phenotype: fafBX3/fafFO8

Phenotypic class: visible

gcontextfafBX3/fafFO8

phenstatement

cvterm “visible”

attr_id

fafBX3 fafFO8

cvterm_idnameetc…

cvterm


gcontext




phenstatement



phendesc



feature


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

The chado genetics module GMOD Meeting 4/26/2004 Cambridge, MA David Emmert FlyBase - Harvard...

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