Question: Downloading 'suspect' NCBI data with Eutils
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gravatar for cheng#13#
2.6 years ago by
cheng#13#0
cheng#13#0 wrote:

I recently downloaded data from NCBI in XML format using EUtilities. I found records that have 'suspect' ChrStart and ChrSort fields (ChrStart = 999999999; ChrSort = ~~last) and there is no ChrStop field. See the 2 examples below.

Has someone already seen this case before?

Should I consider them as suspect or as unlocalized or maybe unreferenced genes in NCBI?

Thanks in advance

EXAMPL1: mouse spermiogenesis specific transcript

<eSummaryResult>
 <ERROR>Empty result - nothing todo</ERROR>
</eSummaryResult>

EXAMPLE2: human TRBV

<eSummaryResult>
 <DocumentSummarySet status="OK">
 <DbBuild>Build170508-2330m.1</DbBuild>

 <DocumentSummary uid="28618">
    <Name>TRBV3-2</Name>
    <Description>T cell receptor beta variable 3-2 (pseudogene)</Description>
    <Status>0</Status>
    <CurrentID>0</CurrentID>
    <Chromosome>7</Chromosome>
    <GeneticSource>genomic</GeneticSource>
    <MapLocation>7q34</MapLocation>
    <OtherAliases>TCRBV3S2, TCRBV9S2A2PT, TRBV32</OtherAliases>
    <OtherDesignations>TCR Vbeta 9.2</OtherDesignations>
    <NomenclatureSymbol>TRBV3-2</NomenclatureSymbol>
    <NomenclatureName>T cell receptor beta variable 3-2 (pseudogene)</NomenclatureName>
    <NomenclatureStatus>Official</NomenclatureStatus>
    <Mim>
    </Mim>
    <GenomicInfo>
    </GenomicInfo>
    <GeneWeight>327</GeneWeight>
    <Summary></Summary>
    <ChrSort>~~last</ChrSort>
    <ChrStart>999999999</ChrStart>
    <Organism>
        <ScientificName>Homo sapiens</ScientificName>
        <CommonName>human</CommonName>
        <TaxID>9606</TaxID>
    </Organism>
   (...)
 </DocumentSummary>
 </DocumentSummarySet>
</eSummaryResult>
genedocsum xml ncbi • 619 views
ADD COMMENTlink written 2.6 years ago by cheng#13#0
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