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new term request: axochord #574

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ANiknejad opened this Issue Sep 19, 2014 · 5 comments

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ANiknejad commented Sep 19, 2014

Hi Chris,

from very recent and exciting literature:
http://www.ncbi.nlm.nih.gov/pubmed/25214631

"We next examined whether an axochord is also present in other annelids, lophotrochozoans, or protostomes (Fig. 1C). Phalloidin stainings had revealed ventral midline muscles in almost all annelid families (table S3), yet in some cases only pairs of ventral muscles had been reported...
An ancestral state reconstruction based on our data and on a survey of bilaterian musculature (table S3) favored the presence of an axochord in protostome ancestors (fig. S14). "

Thank you

Anne

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cmungall Sep 19, 2014

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This is very cool. We should take this opportunity to unify the developmental model for notochord. Currently we have:

nt

(hmm, ectoderm doesn't seem right... I think this was from an earlier version of EHDAA2)

For the axochord, I think we need at least two classes:

  1. axochord, a muscle, which develops from:
  2. the axochord precursor, a population of mesodermal cells

but this doesn't seem to do full justice by itself, need to represent the cells and matrix somehow?

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cmungall commented Sep 19, 2014

This is very cool. We should take this opportunity to unify the developmental model for notochord. Currently we have:

nt

(hmm, ectoderm doesn't seem right... I think this was from an earlier version of EHDAA2)

For the axochord, I think we need at least two classes:

  1. axochord, a muscle, which develops from:
  2. the axochord precursor, a population of mesodermal cells

but this doesn't seem to do full justice by itself, need to represent the cells and matrix somehow?

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btw, if there is interest, we could divest annelid terms from core, and make this a separate owl module others can freely edit...

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cmungall commented Sep 19, 2014

btw, if there is interest, we could divest annelid terms from core, and make this a separate owl module others can freely edit...

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ANiknejad Mar 10, 2015

Help here for defining the classes
http://www.kalliopimonoyios.com/illustrations/EMBLAxochord.html
http://www.hhmi.ucla.edu/derobertis/EDR_MS/Evo-Devo_page/EVO-DEVO.html

Tentatives definitions for 1. and 2. above:

  1. the ventral midline of annelid embryos has a medial muscle called the axochord
  2. contractile mesodermal midline cells

I need the term 'axochord' in Uberon, thanks!

ANiknejad commented Mar 10, 2015

Help here for defining the classes
http://www.kalliopimonoyios.com/illustrations/EMBLAxochord.html
http://www.hhmi.ucla.edu/derobertis/EDR_MS/Evo-Devo_page/EVO-DEVO.html

Tentatives definitions for 1. and 2. above:

  1. the ventral midline of annelid embryos has a medial muscle called the axochord
  2. contractile mesodermal midline cells

I need the term 'axochord' in Uberon, thanks!

@cmungall cmungall closed this in c1e617b Apr 24, 2015

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ANiknejad Nov 21, 2017

Hi Chris,

'Our study of annelid development reveals a population of mesodermal cells that converge and extend along the ventral midline and express a combination of transcription factors, signaling molecules, and guidance factors that closely matches that of the vertebrate chordamesoderm.'

--> annotation done

UBERON:0004880, UBERON:0035148 | chordamesoderm, presumptive axochord | ECO:0000067 | developmental similarity evidence | CIO:0000004 | Medium confidence assertion | 6340 | Annelida

'These comparative data suggest that a similar population of mesodermal midline cells already existed in urbilaterian ancestors but leave open its ancient developmental fate.'

To report the potential homology (here said 'similarity') of the 'presumptive axochord' UBERON:0035148 with mesodermal midline cells of Bilaterian, we also need another class, the 'mesodermal bilaterian midline cell'. Thoughts?

ANiknejad commented Nov 21, 2017

Hi Chris,

'Our study of annelid development reveals a population of mesodermal cells that converge and extend along the ventral midline and express a combination of transcription factors, signaling molecules, and guidance factors that closely matches that of the vertebrate chordamesoderm.'

--> annotation done

UBERON:0004880, UBERON:0035148 | chordamesoderm, presumptive axochord | ECO:0000067 | developmental similarity evidence | CIO:0000004 | Medium confidence assertion | 6340 | Annelida

'These comparative data suggest that a similar population of mesodermal midline cells already existed in urbilaterian ancestors but leave open its ancient developmental fate.'

To report the potential homology (here said 'similarity') of the 'presumptive axochord' UBERON:0035148 with mesodermal midline cells of Bilaterian, we also need another class, the 'mesodermal bilaterian midline cell'. Thoughts?

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ANiknejad Nov 21, 2017

Also I am wondering if 'axochord' (and 'presumptive axochord') definition is too much restrictive?

relationship: only_in_taxon NCBITaxon:6340 ! Annelida

' Lauri et al. report the identification of a longitudinal muscle in an annelid worm that displays striking similarities to the notochord regarding position, developmental origin, and expression profile. Similar muscles, termed axochords, are found in various invertebrate phyla. These data suggest that the last common ancestor of bilaterians already possessed contractile midline tissue that, via stiffening, developed into a cartilaginous rod in the chordate line.'

http://science.sciencemag.org/content/345/6202/1365.full

ANiknejad commented Nov 21, 2017

Also I am wondering if 'axochord' (and 'presumptive axochord') definition is too much restrictive?

relationship: only_in_taxon NCBITaxon:6340 ! Annelida

' Lauri et al. report the identification of a longitudinal muscle in an annelid worm that displays striking similarities to the notochord regarding position, developmental origin, and expression profile. Similar muscles, termed axochords, are found in various invertebrate phyla. These data suggest that the last common ancestor of bilaterians already possessed contractile midline tissue that, via stiffening, developed into a cartilaginous rod in the chordate line.'

http://science.sciencemag.org/content/345/6202/1365.full

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