#BEGIN data: gene: # a gene element/table is the collection dbxref: FBgn0000001 # of all alleles (gene model instances) name: motorhead gene_genesynonym: genesynonym: gsynonym: lemmy pub: dbxref: FBrf00000001 # pub in which synonym is used gene_genesynonym: genesynonym: gsynonym: CG11111 pub: dbxref: FBrf00050001 # pub in which synonym is used # (could be annotation paper) fset: # first we'll define the chromosome arm feature, on # which all our examples are located feature: name: 2L ftype: chromosome_arm dbxref: FBsf12 residues: ATTT.......<20megabases>......GTTGGTT featureprop: pkey: is_allele_wildtype # wildtype sequence pval: 1 # then lets define the wildtype/canonical gene model - feature: ftype: gene # gene model/instance aka allele dbxref: FBal99 # FBals for features where type=gene? name: motorhead[+] # auto assigned from gene + suffix suffix: + # we don't have this field in db currently source_feature: FBsf12 # seqfeatures have FBsfs? gene_to_feature: gene: FBgn0000001 # link to gene entity (symbol etc) featureprop: pkey: is_allele_wildtype pval: 1 feature_cvterm: # GO terms *should* be linked to protein cvterm: # but we still use gns for convenience. termname: motor # (could do both - eg in warehouse/mart?) dbxref: GO:0004773 # a gene model also includes exon structure etc; lets define these. # the composition graph (feature_relationship entries) appears # further on down feature: ftype: transcript dbxref: FBtr15 name: motorhead-RA[+] # auto assigned from gene + allele + suffix # [how do we name dicistronic trs?] suffix: A # we don't have this field in db currently source_feature: FBsf12 residues: GGTCCATGCTTAAGTCA............ATTTGAACC # *spliced* residues feature: ftype: exon dbxref: FBsf201 name: motorhead-Ex1[+] # auto assigned from gene + allele + suffix # [how do we name dicistronic exons?] suffix: 1 # we don't have this field in db currently source_feature: FBsf12 fmin: 1000 fmax: 3000 fstrand: 1 feature: ftype: exon dbxref: FBsf202 name: motorhead-Ex2[+] # auto assigned from gene + allele + suffix # [how do we name dicistronic exons?] suffix: 2 # we don't have this field in db currently source_feature: FBsf12 fmin: 4000 fmax: 9000 fstrand: 1 feature: ftype: CDS dbxref: FBsf203 source_feature: FBsf12 residues: ATG.................TCG feature: ftype: CDS_exon dbxref: FBsf204 source_feature: FBsf12 fmin: 1200 fmax: 3000 fstrand: 1 feature: ftype: CDS_exon dbxref: FBsf205 source_feature: FBsf12 fmin: 4000 fmax: 8800 fstrand: 1 feature: ftype: translation dbxref: FBpp5 name: motorhead-P1[+] # auto assigned from gene + allele + suffix # [how do we name dicistronic exons?] suffix: 1 # we don't have this field in db currently residues: MVQQQVQVQV.....PQSC* # we could have all kinds of stuff attached here: # eg, GO function, mol weight, proteomic modules # let's add a post-translationally modified protein feature: ftype: translation dbxref: FBpp6 name: motorhead-P1-mod1.1[+] # auto assigned from gene + allele + suffix suffix: 1.1 # we don't have this field in db currently featureprop: pkey: description pval: modified motorhead residues: MVQQQVQVQV.....PQSC* feature: ftype: protein_motif dbxref: FBsf30008 name: motorhead-P1[+] kinesin motor domain feature_cvterm: cvterm: termname: kinesis motor domain dbxref: IPR001752 source_feature: FBpp5 # domain located relative to pp fmin: 21 fmax: 183 fstrand: 1 # ^^^^ # ok, above is the canonical gene model on wildtype sequence # # now, we shall define any mutant alleles feature: ftype: gene # gene model/instance aka allele dbxref: FBal345 # allele identifier gene_to_feature: gene: FBgn0000001 # alleles collected by gene entity name: motorhead[12] # auto assigned from gene + suffix suffix: 12 featureprop: pkey: is_allele_wildtype pval: 0 # mutant allele feature_cvterm: cvterm: termname: X-ray # mutation method [see NOTE*] # note: we *could* instantiate mutant transcript, translation etc # but we won't bother here feature: ftype: gene # gene model/instance aka allele dbxref: FBal346 # allele identifier name: motorhead[ab] # auto assigned from gene + suffix suffix: ab gene_to_feature: gene: FBgn0000001 # alleles collected by gene entity featureprop: pkey: is_allele_wildtype pval: 0 # mutant allele # any other features here - lets have one molecularly characterised # mutation, which shall be the 'causative agent' of the # allele immediately above. lets leave the other allele as being purely # genetically/phenotypically characterised (ie no mutation feature) feature: name: motorhead{BG000001} # rules/triggers for this? suffix: BG000001 ftype: insertion # subtype of general variation type dbxref: FBti78 source_feature: FBsf12 fmin: 1582 # inserts into CDS exon fmax: 1582 fstrand: 1 featureprop: pkey: variation_type pval: CDS # lets have some more features in the region; one could be # an oligonucleotide sequence localised to the genome; this # oligo could have been used in a microarray experiment, for # example. raw data could be attached to the oligo via # a microarray module. conclusions could be transfered to # the gene or transcript object via genome coordinate # intersections with oligo feature: ftype: oligo dbxref: FBol666 # PRIMARY identifier source_feature: FBsf12 fmin: 8940 # made from 3' UTR fmax: 8964 fstrand: 1 residues: ATATTAT.........GGGG feature_dbxref: # EXTERNAL identifiers dbxref: dbname: Affy accession: 000000123 # now we'll do the graph relating features to eachother feature_relationship_set: feature_relationship: subjfeature: FBtr15 # transcript objfeature: FBal99 # gene model / allele type: Part-Of # compositional relationship feature_relationship: subjfeature: FBsf201 # exon objfeature: FBtr15 # transcript type: Part-Of feature_relationship: subjfeature: FBsf202 # exon objfeature: FBtr15 # transcript type: Part-Of feature_relationship: subjfeature: FBsf203 # CDS objfeature: FBtr15 # transcript type: Coded-By # ? use partof ? feature_relationship: subjfeature: FBpp5 # translation objfeature: FBsf203 # CDS type: Translated-From feature_relationship: subjfeature: FBpp6 # translation objfeature: FBpp5 # translation (modified) type: Produced-By feature_relationship: subjfeature: FBsf204 # CDS-exon objfeature: FBsf203 # CDS type: Part-Of feature_relationship: subjfeature: FBsf205 # CDS-exon objfeature: FBsf203 # CDS type: Part-Of feature_relationship: subjfeature: FBti78 # insertion objfeature: FBal346 # mutant allele type: Causes feature_relationship: subjfeature: FB # objfeature: FB # type: # some basic phenotypic data for our 2 alleles pset: phenotype: dbxref: FBph001 phenotype_cvterm: cvterm: termname: curly phenotype_cvterm: cvterm: termname: wings feature_phenotype: feature: FBal345 phenotype: dbxref: FBph002 phenotype_cvterm: cvterm: termname: lethal # note: dist between class and effect phenotype_cvterm: # is implicit cvterm: termname: dominant feature_phenotype: feature: FBal346 #END