Website:Data Structure (old page)

I'm keeping this around so I don't always have to look in the code!

This page will document the contents of the data structure of the new site. Each section describes the returning data structure for a method.

Gene

Overview

ids()

description => "Data for gene WBGeneID"

data =>

common_name => scalar

locus_name => scalar

version => scalar

aceview_id => scalar

refseq_id => scalar

other_names => array

sequence_names => array

public_name()

description => ""

data => scalar

common_name()

description => ""

data => scalar

concise_description()

description => "A manually curated description of the gene's function"

data =>

<WBGeneID> => scalar

gene_models()

description => "gene model summary for the gene"

data =>

... no data pack?

history()

description => ""

data =>

<History Object ID> =>

<Version Object ID> =>

type => scalar

date => scalar

action => scalar

remark => scalar

curator => scalar

Variation

Overview

name()

description => "The object name of the variation"

data => scalar

common_name()

description => "The public name of the variation"

data => scalar

cgc_name()

description => "The Caenorhabditis Genetics Center (CGC) name for the gene"

data => scalar

other_names()

description => "other possible names for the variation"

data => array

variation_type()

description => "the general type of the variation"

data => scalar

remarks()

description => "curator remarks for the variation"

data => array

Molecular Details

type_of_mutation()

description => "the type of mutation and its molecular change"

data => scalar

nucleotide_change()

description => "raw nucleotide changes for this variation"

data => scalar

flanking_sequences()

description => "probes used for CGH of deletion alleles"

data =>

left_flank => scalar

right_flank => scalar

cgh_deleted_probes()

description => "probes used for CGH of deletion alleles"

data =>

left_flank => scalar

right_flank => scalar

context()

description => "wildtype and mutant sequences in an expanded genomic context"

data =>

wildtype_fragment => scalar

wildtype_full => scalar

mutant_fragment => scalar

mutant_full => scalar

wildtype_header => "> Wild type N2, with 250 bp flanks<br>wildtype_full",

mutant_header => "> $object with 250 bp flanks<br>mutant_full"

deletion_verification()

description => "the type of mutation and its molecular change"

data => scalar

features_affected()

description => "the method used to verify deletion alleles"

data =>

Pseudogene=>

<entry>=>

Transcript=>

Predicted_CDS=>

Gene=>

Clone=>

Chromosome=>

flanking_pcr_products()

description => "genomic features affected by this variation"

data => scalar