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preceded_by relations missing #520

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fbastian opened this Issue Jul 15, 2014 · 6 comments

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The following stages have no preceded_by relations:

UBERON:0007220 late embryonic stage
UBERON:0009741 tailbud stage

@fbastian fbastian added this to the bgee June 2014 release milestone Jul 15, 2014

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cmungall Jul 15, 2014

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UBERON:0007220 late embryonic stage -- should we add early/mid stage?

we can of course say preceded_by organogenesis - I think this is globally valid? Specific enough?

UBERON:0009741 - as it's currently defined it's entirely xenopus specific. I say obsolete and replaced_by XAO:1000007. If we decide to do generic amphibian stages we can do this later?

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cmungall commented Jul 15, 2014

UBERON:0007220 late embryonic stage -- should we add early/mid stage?

we can of course say preceded_by organogenesis - I think this is globally valid? Specific enough?

UBERON:0009741 - as it's currently defined it's entirely xenopus specific. I say obsolete and replaced_by XAO:1000007. If we decide to do generic amphibian stages we can do this later?

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The term with this name in FBdv has a very specific definition in terms of stages. It as added in the absence of a nice descriptive grouping term like we have for earlier stages.

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dosumis commented Jul 15, 2014

The term with this name in FBdv has a very specific definition in terms of stages. It as added in the absence of a nice descriptive grouping term like we have for earlier stages.

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fbastian Jul 15, 2014

Late embryonic is used as a grouping stage only in HsapDv and MmusDv, it seems to be enough.

No problem to obsolete UBERON:0009741, used nowhere indeed.

Late embryonic is used as a grouping stage only in HsapDv and MmusDv, it seems to be enough.

No problem to obsolete UBERON:0009741, used nowhere indeed.

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currently late-embryo stage is defined broader than mouse and human:

def: "Am embryo stage that covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching." [BGEE:ANiknejad]

It currently includes the FBdv class. So we have to make the decision whether to have a big bag that is defined loosely at the end of the embryo stage, or whether to make it something more restricted like mammalian late embryo stage

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cmungall commented Jul 15, 2014

currently late-embryo stage is defined broader than mouse and human:

def: "Am embryo stage that covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching." [BGEE:ANiknejad]

It currently includes the FBdv class. So we have to make the decision whether to have a big bag that is defined loosely at the end of the embryo stage, or whether to make it something more restricted like mammalian late embryo stage

cmungall added a commit that referenced this issue Jul 15, 2014

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fbastian Jul 16, 2014

A big bag accommodates all species for now, and the mammalian stage ontologies will rarely go into such details. Big bag is good enough in my opinion.

A big bag accommodates all species for now, and the mammalian stage ontologies will rarely go into such details. Big bag is good enough in my opinion.

@cmungall cmungall added the Stages label Sep 25, 2014

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ANiknejad Sep 25, 2014

def: "Am embryo stage that covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching." [BGEE:ANiknejad]

def: "Am = typo-error to corrige, please

def: "Am embryo stage that covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching." [BGEE:ANiknejad]

def: "Am = typo-error to corrige, please

@cmungall cmungall closed this in e01b904 Feb 16, 2015

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