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organ specific terms of vascular tissue #662

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jaiswalp opened this issue Feb 13, 2017 · 11 comments
Open

organ specific terms of vascular tissue #662

jaiswalp opened this issue Feb 13, 2017 · 11 comments

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@jaiswalp
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We have terms like
Accession PO:0025612
Name stem cortex
Definition A portion of shoot axis cortex (PO:0000223) that is part of a stem (PO:0009047).

This is useful when annotating objects associated with 'cortex' region that is part_of a stem. However, we need some consistency on spatial terms like this and a guidance for users, when to have terms like this or when not to.

e.g.
we don't have similar spatial terms for use such as

  • stem metaxylem
  • root xylem
  • shoot axis (stem) xylem
  • root phloem
  • shoot axis (stem) phloem

Ideas....
Either we create spatial terms like these in an automated way or have consistency across the ontology to either have them or not have them. This would help the users. I suggest going the former route by creating them in an automated process.

Otherwise, we may have to use some annotation column in the GAF to address this relationship. Which may work for the object (gene/qtl) annotations submitted via GAF. It will not work when a person annotates a histological specimen/section of a stem or root.

@cmungall
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Yes, I suggest we write a DP for these. From there automated checking, cross-product generation etc should be easy

@phismith
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phismith commented Feb 13, 2017 via email

@cmungall
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What I propose is generation of a simple csv with the cross-product. Editors can then go through this, prune things out, and just get a general idea of the morphospace

@cmungall
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As part of this work, I suggest replacing textual definitions like this:

A portion of shoot axis cortex (PO:0000223) that is part of a stem (PO:0009047)
A portion of shoot axis cortex that is part of a stem

textual defs are for humans. Users will be able to see the equivalence axioms and the IDs (which will actually be hyperlinked) in amigo, ontobee, ols etc

@jaiswalp
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jaiswalp commented Feb 13, 2017 via email

@cmungall
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OK I started by just reverse engineering a CSV for all P and part-of some W, to give an example. We can split this into sub-modules, e.g. tissues. (curious: why the interest in vascular tissue specifically?)

https://github.com/Planteome/plant-ontology/blob/mine-design-patterns/modules/part_whole.csv

This is still on a branch, awaiting @marieALaporte review

Note you'll soon be able to edit these csvs using Taboggan (think: phenote on the web integrated with github). cc @DoctorBud

@jaiswalp
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jaiswalp commented Feb 13, 2017 via email

@jaiswalp
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jaiswalp commented Feb 13, 2017 via email

@cmungall
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@cooperl09
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So what we need is a list of the plant parts that you would like to populate with the vascular tissue part of terms- suggest we start with root, leaf and shoot axis?

@phismith
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phismith commented Feb 17, 2017 via email

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