organ specific terms of vascular tissue

[jaiswalp]

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]

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

[phismith]

I think a fully combinatorial approach would lead to regrettable overpopulation. I.e. we have a standard strategy for creating the terms, but only allow them to be created when there is some demonstrated existing use/need. BS

On Mon, Feb 13, 2017 at 3:13 PM, Pankaj Jaiswal notifications@github.com wrote:

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.

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[cmungall]

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]

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]

Great. Can you generate a csv template and we can work on it.

On 2/13/2017 1:48 PM, Chris Mungall wrote:

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

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-- Pankaj Jaiswal, PhD President, OSU Chapter Phi Kappa Phi Associate Professor Dept. of Botany and Plant Pathology 2082 Cordley Hall Oregon State University Corvallis, OR, 97331 USA

Ph.: +1-541-737-8471 Fax: +1-541-737-3573 email: jaiswalp@oregonstate.edu Web: http://jaiswallab.cgrb.oregonstate.edu http://icbo-conference.org http://phikappaphi.oregonstate.edu

[cmungall]

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]

On 2/13/2017 2:41 PM, Chris Mungall wrote:

curious: why the interest in vascular tissue specifically?

We are going to use image annotation software AISO for a class to help us annotate images with ontology terms. Idea is to build an annotated image (with labelled segments) library for teaching an d training machine learning algorithms. Baring few additional structures, the vascular system has most common structures between leaf, stem and xylem e.g. https://image.slidesharecdn.com/bio23rootstemleaf-090519192018-phpapp01/95/chapter-23-lecture-roots-stems-leaves-8-728.jpg?cb=1242761004 https://s-media-cache-ak0.pinimg.com/originals/dd/99/44/dd99440793074ec4900909f31296f1e4.jpg

-- Pankaj Jaiswal, PhD President, OSU Chapter Phi Kappa Phi Associate Professor Dept. of Botany and Plant Pathology 2082 Cordley Hall Oregon State University Corvallis, OR, 97331 USA

Ph.: +1-541-737-8471 Fax: +1-541-737-3573 email: jaiswalp@oregonstate.edu Web: http://jaiswallab.cgrb.oregonstate.edu http://icbo-conference.org http://phikappaphi.oregonstate.edu

[jaiswalp]

stems http://images.slideplayer.com/22/6381454/slides/slide_31.jpg root http://classconnection.s3.amazonaws.com/431/flashcards/2857431/jpg/root-ranunculus-5001366751256717.jpg https://classconnection.s3.amazonaws.com/263/flashcards/2443263/jpg/root-smilax-650-14112C6F5825907CC50.jpg

With common tissue types

On 2/13/2017 3:04 PM, Jaiswal, Pankaj - OSU wrote:

On 2/13/2017 2:41 PM, Chris Mungall wrote:

curious: why the interest in vascular tissue specifically?

We are going to use image annotation software AISO for a class to help us annotate images with ontology terms. Idea is to build an annotated image (with labelled segments) library for teaching an d training machine learning algorithms. Baring few additional structures, the vascular system has most common structures between leaf, stem and xylem e.g. https://image.slidesharecdn.com/bio23rootstemleaf-090519192018-phpapp01/95/chapter-23-lecture-roots-stems-leaves-8-728.jpg?cb=1242761004

https://s-media-cache-ak0.pinimg.com/originals/dd/99/44/dd99440793074ec4900909f31296f1e4.jpg

-- Pankaj Jaiswal, PhD President, OSU Chapter Phi Kappa Phi Associate Professor Dept. of Botany and Plant Pathology 2082 Cordley Hall Oregon State University Corvallis, OR, 97331 USA

Ph.: +1-541-737-8471 Fax: +1-541-737-3573 email: jaiswalp@oregonstate.edu Web: http://jaiswallab.cgrb.oregonstate.edu http://icbo-conference.org http://phikappaphi.oregonstate.edu

[cmungall]

Here is what the PO PxW XP looks like:

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

[cooperl09]

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]

sounds good to me BS

On Thu, Feb 16, 2017 at 7:44 PM, Laurel Cooper notifications@github.com wrote:

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?

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