The chado genetics module

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The chado genetics module
new and improved
V

• GMOD Meeting
• 4/26/2004
• Cambridge, MA

David Emmert FlyBase - Harvard emmert_at_morgan.harva
rd.edu
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chado module dependencies
general (dbxref)
organism
map
pub
sequence
genetic
expression
cv
companalysis
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gcontext_ relationship
phenstatement_ relationship
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Partial Genotype (aka allele) ab2
ab2
f_g
rank0 cgroup0
gcontext ab2
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Simple Stock Genotype ab2/T(Y2)E
ab2
T(Y2)E
f_g
f_g
rank1 cgroup0
rank0 cgroup0
ab2/T(Y2)E
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Stock Genotype I PhsFLP1, w1118 Adv1/CyO
PhsFLP1
CyO
w1118
rank0 cgroup0
rank0 cgroup1
f_g
f_g
f_g
rank0 cgroup0
rank1 cgroup1
PhsFLP1, w1118 Adv1/CyO
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Allele phenotype Act-88F1 Phenotypic class
flightless dominant
gcontext Act-88F1
phenstatement
attr_id
cvalue_id
cvterm flightless
cvterm dominant
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Allele phenotype alpha-specrg41 Phenotypic
class lethal larval recessive
gcontext alpha-specrg41
phenstatement
rank1
rank2
rank3
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Allele phenotype alpha-specrg41 Phenotypic
class lethal larval recessive
gcontext alpha-specrg41
phenstatement
attr_id
cvalue_id
observable_id
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Allele phenotype alphaTub67Tom-3a Phenotypic
class lethal embryonic dominant
maternal effect conditional cs
gcontext alphaTub67Tom-3a
phenstatement
attr_id
cvalue_id
obs_id
cvterm lethal
cvterm embryonic
cvterm dominant
rank2
rank1
cvterm maternal effect
cvterm conditional cs
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Allele phenotype alphaTub67Tom-3a Phenotypic
manifest in embryonic peripheral nervous
system maternal effect
gcontext alphaTub67Tom-3a
phenstatement
observable_id
rank1
cvterm embryonic peripheral nervous system
cvterm maternal effect
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Transheterozygous phenotype fafBX3/fafFO8 Phenot
ypic class visible
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Genetic Interactions wg1 has a wing phenotype
that is enhanced by dpp1 FlyBase Curation for
wg1 visible, enhanceable dpp1
dpp1
wg1
gcontext wg1
objectgc_id
gcontext dpp1
subjectgc_id
phenstatement
cvterm enhances
cvterm visible
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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.
sequence_variant
featureloc
chromosome_arm
rank0 residue_info null
srcfeature_id
91
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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.
sequence_variant
featureloc
chromosome_arm
rank0 residue_info null
srcfeature_id
91
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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 whos helped / commented