Website:Data Structure (old page)
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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
- <Version Object ID> =>
- <History Object ID> =>
Sequences
spliced()
unspliced()
translated()
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=>
- Pseudogene=>
flanking_pcr_products()
- description => "genomic features affected by this variation"
- data => scalar