UBERON:0008979 name: carcass and FlyBase annotation

[ANiknejad]

Hi Chris,

http://flyatlas.org/about_atlas.html

annotation of drosophila 'carcass' dataset is a bit tricky

http://flybase.org/reports/FBlc0000183.html

Actually FlyAtlas does not used the term 'carcass' in the same way Uberon does, please see

http://flyatlas.org/about_atlas.html

Adult carcass	What’s left of the thorax and abdomen after the gut and sexual tracts have been removed.

while

[Term] id: UBERON:0008979 name: carcass namespace: uberon def: "A body of a multi-cellular organism that is no longer living." [UBERON:cjm] synonym: "cadaver" RELATED [BTO:0001965] synonym: "dead body" RELATED [BTO:0001965] xref: BTO:0001965 xref: C113674 xref: http://www.snomedbrowser.com/Codes/Details/127853004 is_a: UBERON:0000468 ! multi-cellular organism relationship: has_quality PATO:0001422 ! dead

Something to harmonize here?

thank you for your help

Anne

[marcrr]

To make things more complicated, some annotations from carcass in Flybase follow different definitions:

http://flybase.org/reports/FBlc0000220.html

[cmungall]

it's not even clear that dead bodies should be in uberon.

The flybase terms seems to be getting more into experimental preparation rather than anatomy.

what's the use case here for bgee purposes? aren't you only doing wild-type / evolved gene expression?

[tfhayamizu]

In our experience with mouse embryo expression data, "carcass" is used inconsistently, most often for blot-type data (ie. northern, western, RT-PCR), to describe what remains after they have removed the organs or other specific structures of interest (shown in other lanes in the blot) for a particular experiment. As our coding policy, we annotate positive expression data to a higher level term (e.g. "embryo") with a specimen note. In cases where expression is shown to be absent, this is somewhat more problematic, so we annotate to whatever term or terms best describe what we determine to be represented in the sample.

[marcrr]

@cmungall carcass is relevant to wild-type: if a wild-type insect is dissected, and part of the dissection is the carcass = what's left, then it's part of the wild-type expression. It's difficult to classify, but is relevant to some usage, for example calculating tissue-specificity or presence of expression at a certain developmental stage.

[gouttegd]

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