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Gene Data Model
Stuart Watt edited this page Nov 2, 2015
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2 revisions
The gene data model is fairly complex, and hierarchical, as is the nature with a document-oriented database. Glossing over some of the informal nature, and unpacking it into a pseudo-relational structure, it goes like this:
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name- readable name version-
id- the Ensembl gene ID -
transcripts- collection of GeneTranscript records -
description- a GeneDescription record
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gene- e.g., "ENSG00000186092" -
transcript- e.g., "ENST00000335137 -
position- e.g., 69345 -
genomicPositionStart- e.g., 69345 -
referenceAllele- e.g., "C" -
codonStart- e.g., 85 -
codonStop- e.g., 85 -
cdsPositionStart- e.g., 255 -
cdsPositionStop- e.g., 255 -
strand- e.g., 1 -
HGVSc- e.g., "c.255C>A" -
HGVSpr- e.g., "p.I85I", -
exon- e.g., 1 -
variantAllele- e.g., "A" -
HGVSp- e.g., "p.Ile85Ile" -
geneSymbol- e.g., "OR4F5" -
chromosome- e.g., "1"
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id- e.g., "ENST00000425967" -
versionedId- e.g., "ENST00000425967.3" -
name- e.g., "FGFR1-202" -
translationId- e.g., "ENSP00000393312" -
versionedTranslationId- e.g., "ENSP00000393312.3" lengthAminoAcid-
lengthDNA- e.g., 2562 -
numberOfExons- e.g., 18 -
seqExonStart- e.g., 150 -
seqExonStart- e.g., 33 -
length- e.g., 5375 -
seqExonEnd- e.g, 154 -
endExon- e.g., 18 -
isCanonical- e.g., true -
refSeqId- collection of strings, e.g., ["NM_001174067.1"] -
exons- collection of GeneTranscriptExon records -
domains- collection of GeneTranscriptDomain records
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gffSource- e.g., "Pfam" -
hitName- e.g., "PF07679" -
score- e.g., 47.7 -
evalue- e.g., 4.1e-16 -
perc_ident- e.g., 0 -
start- e.g., 293 -
end- e.g., 389 -
interproId- e.g., "IPR013098" -
description- e.g. "Immunoglobulin I-set"
-
start- e.g., 38315052 -
end- e.g., 38314874 -
startPhase- one of -1, 0, or 1; e.g., -1 -
endPhase- e.g., 1
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fullName- e.g., "fibroblast growth factor receptor 1" -
synonyms- collection of strings, e.g., ["FGFR1", "CD331" ...] -
summary- long text from RefSeq