planteome/plant-ontology

Repository for the Plant Ontology

plant-ontology

This is the repository for the Plant Ontology

The current release version of the PO can be accessed through its official PURLs:

• http://purl.obolibrary.org/obo/po.owl
• http://purl.obolibrary.org/obo/po.obo
• http://purl.obolibrary.org/obo/po/subsets/po-basic.obo

Or at http://planteome.org/

All releases can be found here: https://github.com/Planteome/plant-ontology/releases

Files in this repository:

• plant-ontology.obo: The editor's version of the Plant Ontology, in OBO format. Contains all relations. Relations that are inferred are not asserted

Note that this file is subject to frequent changes, and may contain terms that will later destroyed (permanently deleted from the ontology, rather than made obsolete). Users should use this file with caution.

• plant-ontology-dev.txt

A text version of the plant-ontology.obo editors' file, automatically created nightly

• plant-ontology.obo.owl

An OWL version of the plant-ontology.obo editors' file, automatically created nightly

New versions of the following two files are created only with new releases:

• po.obo

The current Release file of the Plant Ontology, in OBO format. All relations that are inferred are asserted in the release process

• po.owl

The current release file of the Plant Ontology, in OWL format. All relations that are inferred are asserted in the release process

• po-basic.obo

The current Release file of the Plant Ontology, in OBO format, with only the is_a and part_of relations.

Ontology Editors Guide

See https://github.com/Planteome/plant-ontology/blob/master/README-po-editors.md

plant-ontology's Issues

pollen tube tip PO:0000028 part_of pollentube

http://www.plantontology.org/amigo/go.cgi?view=details&search\constraint=terms&depth=0&query=[PO:0000028](http://purl.obolibrary.org/obo/PO0000028)

Can we fix the relationship.

pollen tube tip [PO:0000028](http://purl.obolibrary.org/obo/PO_0000028) part_of pollen tube [PO:0006345](http://purl.obolibrary.org/obo/PO_0006345)

Reported by: jaiswalp

Original Ticket: obo/plant-ontology-po-term-requests/30

syncytium

Do we have a PO term ‘syncytium’ (I did not find it)? If not, should it be added to PO Plant Cell Type? The Cell Type Ontology ID for syncytium is [CL:0000228](http://purl.obolibrary.org/obo/CL_0000228). Please also refer to PMID 16942607.

Thanks!

Donghui

Reported by: donghui

Original Ticket: obo/plant-ontology-po-term-requests/15

peripheral vein or tertiary vein

Term: peripheral vein → new PO or synonym to [PO:0008021](http://purl.obolibrary.org/obo/PO_0008021):tertiary vein

Definition: A vein located toward the margin of the leaf lamina

Pankaj: How different is it from tertiary vein present in the peripheral region. The said peripheral vein could be any vein second order and upwards that is present near the margins of the lamina. The only thing I can come up is these can be any vein with second and higher order with no distal ends. The suggested proximal ends merge with other veins to form a continuous vein. We will discuss this term with our experts.

See image in the attachment file.

Reported by: *anonymous

Original Ticket: obo/plant-ontology-po-term-requests/31

Leaf rolling

Leaf rolling at 5 minuts after axcision

Reported by: *anonymous

Original Ticket: obo/plant-ontology-po-term-requests/42

shoot system vascular system

Hi,

Would it be appropriate to create the term: shoot vascular system?

Author of the following paper [PMID:14973166](https://www.ncbi.nlm.nih.gov/pubmed/14973166) has used this term in his user submission.
http://www.plantcell.org/cgi/content/full/16/3/658\
We have a more specific term: stem vascular system.

Thanks, Donghui

Reported by: donghui
Original Ticket: obo/plant-ontology-po-term-requests/41

test

this is a test tracker

Reported by: jaiswalp

Original Ticket: obo/plant-ontology-po-term-requests/1

add synonym to 'valve'

How about adding a synonym ‘silique valve’ to the term ‘valve’ ([PO:0000033](http://purl.obolibrary.org/obo/PO_0000033)). Please refer to PMID: 16916932.

The term silique valve was used throughout the paper.

Donghui
TAIR

Reported by: donghui

Original Ticket: obo/plant-ontology-po-term-requests/13

leaf base vs. leaf axil?

Hello,

I’m trying to figure out whether I can use the existing term ‘leaf base’ to annotate expression of a gene in the axils of leaf primordia and leaves.

[Term]
id: [PO:0020040](http://purl.obolibrary.org/obo/PO_0020040)
name: leaf base
namespace: plant_structure
def: “The bottom part of a leaf where it attaches to the stem.” [APWeb:Glossary]
synonym: “leaf sheath base” []
relationship: part_of [PO:0009025](http://purl.obolibrary.org/obo/PO_0009025) ! leaf

From Raven, “Biology of Plants” (5th ed)
[ISBN:0](http://purl.obolibrary.org/obo/ISBN_0)-87901-532-2

axil: The upper angle of a twig or leaf and the stem from which it grows.

What do you think? New term or new synonym?

Thanks for your help,

Tanya

Reported by: tberardini

Original Ticket: obo/plant-ontology-po-term-requests/21

embryo cortex (PO:0005014)

I would like to propose the following new PO term:

name: embryo cortex (PO:new1)

synonyms: none

definition:

Tissue between the vascular system and the epidermis of hypocotyl and root in the embryo.

lineage:

cortex [PO:0005708](http://purl.obolibrary.org/obo/PO_0005708)
—[i] embryo cortex (PO:new1)

embryo [PO:0009009](http://purl.obolibrary.org/obo/PO_0009009)
—[p] embryo cortex (PO:new1)

reference: PMID 16543410

Donghui
TAIR

Reported by: donghui

Original Ticket: obo/plant-ontology-po-term-requests/9

Add tissue-type specific septum

Currently, [PO:0000030](http://purl.obolibrary.org/obo/PO_0000030): septum ( def: A thin partition or membrane that divides a cavity or mass of tissue, e.g., in anther, ovary or fruit).
To avoid having a more generic term under several different tissue types, we need three new terms

-partof-PO:carpel septum
-devfrm-Po(new): fruit septum

: anther
-partof-PO:anther septum

: fruit
-partof-PO:fruit septum

Should we make [PO:0000030](http://purl.obolibrary.org/obo/PO_0000030):septum obsolete?

chih-wei

Reported by: cwtung

Original Ticket: obo/plant-ontology-po-term-requests/16

inflorescence bifurcation stage

Definition: Stage of inflorescence development marked by the formation of two, often equal-sized, inflorescence meristems from one inflorescence meristem.

The cymose inflorescence structure is represented by Solanum lycopersicum (domesticated tomato), and species related to Solanaceae, such as tobacco and Petunia. Tomato mutants, such as falsiflora (fa – orthologue of Arabidopsis LEAFY), anantha (an – unknown), and compound inflorescence (s – unknown), are all defined by an indeterminate reiteration of “inflorescence bifurcation stages”, where two, often equal-sized, inflorescence meristems are formed from a parent inflorescence meristem. Among such mutants that generate highly compound inflorescence structures, s is the only one that bears normal fertile flowers and shows similarity to compound inflorescences in numerous wild tomato species and more distant Solanaceae. In order to develop the proper ontology needed to characterize this important developmental transition, I would like to propose the new plant ontology term of “inflorescence bifurcation stage”, which is relevant to many known mutants and wild plant species.

Zachary B. Lippman, Ph.D.
Email: [email protected]
The Hebrew University of Jerusalem
Faculty of Agriculture
Institute of Plant Sciences
Zamir Laboratory
P.O. Box 12, Rehovot 76100
Israel
Tel: [phone]
Fax: [phone]

Related References:

Allen K.D., Sussex I.M. (1996). Falsiflora and anantha control early stages of floral meristem development in tomato (Lycopersicon esculentum Mill.). Planta 200, 254–264.

Molinero-Rosales, N., Jamilena, M., Zurita, S., Gomez, P., Capel, J., and Lozano, R. (1999). FALSIFLORA, the tomato orthologue of FLORICAULA and LEAFY, controls flowering time and floral meristem identity. Plant J 20, 685-693.

Quinet, M., Dielen, V., Batoko, H., Boutry, M., Havelange, A., and Kinet, J.M. (2006a). Genetic interactions in the control of flowering time and reproductive structure development in tomato (Solanum lycopersicum). New Phytol 170, 701-710.

Quinet, M., Dubois, C., Goffin, M.C., Chao, J., Dielen, V., Batoko, H., Boutry, M., and Kinet, J.M. (2006b). Characterization of tomato (Solanum lycopersicum L.) mutants affected in their flowering time and in the morphogenesis of their reproductive structure. J Exp Bot 57, 1381-1390.

Souer, E., van der Krol, A., Kloos, D., Spelt, C., Bliek, M., Mol, J., and Koes, R. (1998). Genetic control of branching pattern and floral identity during Petunia inflorescence development. Development 125, 733-742.

Reported by: zlippman

Original Ticket: obo/plant-ontology-po-term-requests/27

add pericarp vascular bundle

I would like to propose a new term PO:new: pericarp vascular bundle (definition: the vascular bundle found in pericarp)

Pubmed ID: 11978873

Reported by: cwtung

Original Ticket: obo/plant-ontology-po-term-requests/23

Request Plant Structure Ontology terms

Request from Nicola Paterson

To the Plant Structure Ontology we’d like to add the following:-

Immature Embryo
Immature Seed
Meristematic Tissue
Seedling
Husk
Leaf Roll
Regenerated Shoots
Ear/Cob

I think that some of these may have items which exist in the ontology
but these could be synonyms of them. Again, do you think that these
would be appropriate to add and if so, how would we go about adding these?

Reported by: cwtung

Original Ticket: obo/plant-ontology-po-term-requests/39

new term: root vein

I would like to request the following plant ontology term. Please contact me if you have questions or comments.

[name] root vein (PO:new1)

[synonyms] none

[ontology] structure

[definition] A strand of vascular tissue in a root.

[lineage]

root ([PO:0009005](http://purl.obolibrary.org/obo/PO_0009005))
—[p] root vein (GO:new1)

Is there a ‘vein’ term as a second parent?

[reference] TAIR

Regards,

Donghui
TAIR Curator

Reported by: donghui

Original Ticket: obo/plant-ontology-po-term-requests/4

merge " whole plant" to "sporophyte"

Hi,

we would like to merge “whole plant” to “sporophyte” to avoid the ambiguous annotation.

The definition for both terms in PO database are:

“whole plant”- the entire plant, including roots, shoots and leaves, at any stage of its life cycle.

“sporophyte” – a plant or phase of a life cycle that bears spores formed by meiosis.

Definition from other resource:
For common flowering plants (angiosperms), the sporophyte generation comprises almost their whole life cycle (i.e. whole green plant, roots etc), except phases of small reproductive structure (pollen and ovule).

Since PO is designed to describe flowering plants at this stage, we prefer to merge “whole plant” to “sporophyte”.

Please feel free to add your comments on this.

Thanks,

Chih-Wei

Reported by: cwtung

Original Ticket: obo/plant-ontology-po-term-requests/29

8 MaizeGDB anatomy terms not yet in PO

Please see attached file with definitions which you may wish to modify.

Please inquire if you need more information. Note, most of there terms were added and defined by Leszek Vincent, as part of the Maize Mapping Project, prior to the Plant Ontology Project. I have added suggested relationsips to the PO terms currently used.

Mary Schaeffer
[email protected]

NOTE: I tried to get a Source-Forge account some days ago, but it seems to be a tad sluggish in providing said.

Reported by: *anonymous

Original Ticket: obo/plant-ontology-po-term-requests/26

test2

thsi is a test 2

Reported by: jaiswalp

Original Ticket: obo/plant-ontology-po-term-requests/2

new term: hypocotyl epidermis

I would like to propose the following new term:

name: hypocotyl epidermis (PO:new1)

synonyms: none

ontology: structure

definition: The outermost primary cell layer of the hypocotyl.

lineage:

epidermis ([PO:0005679](http://purl.obolibrary.org/obo/PO_0005679))
—[i] hypocotyl epidermis (PO:new1)

hypotocol ([PO:0020100](http://purl.obolibrary.org/obo/PO_0020100))
—[p] hypocotyl epidermis (PO:new1)

reference: PMID 15368128

Donghui
TAIR

Reported by: donghui

Original Ticket: obo/plant-ontology-po-term-requests/11

PO for Potato tuber development stages

Hi Chih-Wei,

I have a bunch of potato genes which are expressed in different tuber developmental stages (e.g. the potato pmt gene is expressed in small sprouts only http://www.ncbi.nlm.nih.gov/pubmed/16088399\).
These terms are not in PO.

how's:
-sprout development
-tuber initiation
-tuber growth
-tuber maturation

http://74.125.47.132/search?q=cache:wR\_-xdH4-ykJ:www.ag.uidaho.edu/potato/PotatoProductionSystems/Topics/Growth%26Development.pdf+potato+tuber+growth+stages&cd=7&hl=en&ct=clnk&gl=us&client=firefox-a

thanks!
-Naama

Naama Menda
Boyce Thompson Institute for Plant Research
Tower Rd
Ithaca NY 14853
USA

Reported by: cwtung

Original Ticket: obo/plant-ontology-po-term-requests/46

vascular system

The PO is_a hierarchy is:

+/ PO:0009011 ! plant structure [DEF: "Any morphological or anatomical feature of a plant."]
++is_a PO:0009007 ! tissue [DEF: "Group of cells organized into a structural and functional unit; the component cells may be alike (simple tissue) or varied (complex tissue)."]
+++is_a PO:0000034 ! vascular system *** [DEF: "Total of the vascular tissues in their specific arrangement in a plant or plant organ."]

This is different from animal anatomy ontologies which are organized by CARO in which anatomical system is a sibling to (portion of) tissue

E.g.

+is_a CARO:0000003 ! anatomical structure [DEF: "Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome."]
++is_a CARO:0000043 ! portion of tissue *** [DEF: "Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships."]
++is_a CARO:0000054 ! anatomical group [DEF: "Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue."]
+++is_a CARO:0000011 ! anatomical system *** [DEF: "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity."]

Would the CARO definition of tissue work for plants?

can we have 'anatomical system' as sibling to tissue underneath plant structure?

Also - the def of vascular system is:

PO:0000034 ! vascular system [DEF: "Total of the vascular tissues in their specific arrangement in a plant or plant organ."]

The disjunction (or) is confusing. Does an individual plant have a single vascular system, with different parts (e.g. flower vascular system)? Or does an individual plant have multiple separate vascular systems (e.g. flower vascular system)

If the former, then the relation between X vascular system and vascular system should be part_of. The definitions should read "the part of the vascular system that is in X"

If the latter, then the relation should be is_a, and the definitions should read "a vascular system that is in X"

Currentlyin PO all relations are is_a, with the exception of

PO:0000035 ! cotyledon vascular system [DEF: "Vascular system of the cotyledon."]

The definition follows the same structure as the other X vascular system terms. Any reason for the difference in ontology structure?

My preference would be to define VS as the entire system running throughout the plant. We would then have terms like "X vasculature" which would be is_a vasculature, part_of X. This would require a new term "vasculature" which would be defined as a segment of the VS in an organ.

PO also states that "flower vascular system" is_a flower. This is wrong, the relation should be part_of.

Reported by: cmungall

Original Ticket: obo/plant-ontology-po-term-requests/50

Plant Ontology suggestions

Hi Pankaj,

Please find attached the document of PO suggestion and do needful

Regards,

Arul

Reported by: bioinarul

Original Ticket: obo/plant-ontology-po-term-requests/37

Term Request from AGRON-OMICS

1. Term: rosette
Definition: A cluster of leaves in crowded circles or spirals arising basally from a crown
Ref: Merriam-Webster

2. Term: transition leaf
Definition: A leaf that is part of an heteroblastic series, and is characterized by anatomical features that are intermediate between juvenile and adult leaves.
Ref: Adapted from Telfer et al. Development, 124, 645-654 (1997).

New [PO:0008018](http://purl.obolibrary.org/obo/PO_0008018) is created.

3. Term: leaf lamina base
Definition: The region of the leaf lamina proximal to the stem and usually connected to it by means of a petiole.

New [PO:0008019](http://purl.obolibrary.org/obo/PO_0008019) is created.

4. Term: central zone of the leaf lamina
Definition: The region of the leaf lamina located between the leaf apex and the leaf lamina base.

New [PO:0008020](http://purl.obolibrary.org/obo/PO_0008020) is created.

5. Term: tertiary vein
Definition: The leaf vein arising from the secondary vein
Synonym: third order leaf vein
Ref: (Hickey, 1973)

New [PO:0008021](http://purl.obolibrary.org/obo/PO_0008021) is created

6. Term: quaternary vein
Definition: The leaf vein arising from the tertiary vein
Synonym: fourth order leaf vein
Ref: (Hickey, 1973).

New [PO:0008022](http://purl.obolibrary.org/obo/PO_0008022) is created

7. Term: higher order vein
Definition: The leaf vein arising from the quaternary or higher vein order
Synonym: fifth and higher order leaf vein

New [PO:0008023](http://purl.obolibrary.org/obo/PO_0008023) is created

9. Term: petiole base
Definition: The region of the petiole at which it attaches to the stem.
Ref: Wikipedia
Most appropriate would be ‘petiole proximal end’, with your term name as synonym. Definition: the region of the petiole proximal to its stem attachment site.

New [PO:0008024](http://purl.obolibrary.org/obo/PO_0008024) is created.

10. Term: central zone of the petiole
Definition: The region of the petiole between the part attached to the leaf and the part attached to the stem.

New [PO:0008025](http://purl.obolibrary.org/obo/PO_0008025) is created

11. Term: petiole apex
Definition: The top part of the petiole, at which it attaches to the leaf lamina.
Most appropriate would be ‘petiole distal end’, with your term name as synonym. Definition: the region of the petiole distal to its stem attachment site or proximal to the leaf lamina.

New [PO:0008026](http://purl.obolibrary.org/obo/PO_0008026) is created

12. Term: petiole adaxial epidermis
Definition: The epidermal layer of adaxial/upper surface of the petiole.

New [PO:0008027](http://purl.obolibrary.org/obo/PO_0008027) is created

13. Term: petiole abaxial epidermis
Definition: The epidermal layer of the abaxial/lower surface of the petiole.

New [PO:0008029](http://purl.obolibrary.org/obo/PO_0008029) is created

15. Term: trichome cell
Definition: Each cell which is part of a trichome.

New [PO:0008030](http://purl.obolibrary.org/obo/PO_0008030) is created

16. Term: basal cell of the trichome → [PO:0000115](http://purl.obolibrary.org/obo/PO_0000115): socket cell

17. Term: trichome branch
Definition: Each branch which is part of a trichome.
New [PO:0008031](http://purl.obolibrary.org/obo/PO_0008031) is created

18. Term: stomatal aperture
Definition: The space of variable size controlled by stomatal guard cells in response to environmental clues.

New [PO:0008032](http://purl.obolibrary.org/obo/PO_0008032) is created

Reported by: cwtung

Original Ticket: obo/plant-ontology-po-term-requests/33

Create chickpea related PO terms

Chickpea branch group

PO:0006343 (axillary soot)
-i- PO:0005001 (basal axillary shoot)
-p- PO:new (basal axillary primary branch)
-p- PO:new (basal axillary secondary branch)
-p- PO:new (basal axillary tertiary branch)

-i- PO: new (apical axillary shoot)
-p- PO:new (apical axillary primary branch)
-p- PO:new (apical axillary secondary branch)
-p- PO:new (apical axillary tertiary branch)

See picture http://books.google.com/books?id=x5285wLpJIgC&pg=PA102&lpg=PA102&dq=chickpea+apical+primary+branch&source=bl&ots=SwADIAAT0y&sig=JdKKeJfw--tSrJrxiQPV88oD8kw&hl=en&ei=VA4TSsX8KYyW8gTCtqGHBA&sa=X&oi=book\_result&ct=result&resnum=4\#PPA102,M1

Reported by: cwtung

Original Ticket: obo/plant-ontology-po-term-requests/45

Leaf trichome development

Trichome development

Definition: Stages of development of a trichome defined by characteristic morphological, structural, histological or other visible features.

Trichomes are found on the leaf, hypocotyl, and stem, so maybe there could be further terms to specify ‘Leaf trichome development’ etc. The parents of each term would be e.g. ‘Leaf development stages’

Reported by: debbiealexander

Original Ticket: obo/plant-ontology-po-term-requests/35

petal vascular system

Hi,

I would like to propose the following new term:

petal vascular system (PMID: 16525893)

This is one of the many vascular systems that need to be created.

Donghui

Reported by: donghui

Original Ticket: obo/plant-ontology-po-term-requests/20

socket cell (PO:0000115)

I would like to propose the following PO term:

name: trichome support cell (PO:new1)

synonyms: none

ontology: structure

definition:

I don’t have a good definition. Please refer to PMID 15319479. Also, according to this link: http://esa.confex.com/esa/2002/techprogram/paper\_6135.htm

‘Each (glandular) trichome was composed (from bottom to top) of a pair of support cells and four pairs of secretory cells’.

lineage:

plant cell ([PO:0009002](http://purl.obolibrary.org/obo/PO_0009002))
—[i] trichome support cell (PO:new1)

trichome ([PO:0000282](http://purl.obolibrary.org/obo/PO_0000282))
—[p]trichome support cell (PO:new1)

reference:

PMID 15319479

Donghui
TAIR

Reported by: donghui

Original Ticket: obo/plant-ontology-po-term-requests/8

new term for Hull

Hi All,

I need a new term to describe ‘hull’ in cereal plants.
I know experts say that it is nothing different than
lemma and palea, the two parts found in grass floret.
Therefore the options are to put ‘hull’ as synonyms of
both lemma and palea, which I somehow disagree because
the term ‘hull’ is never used in florets/grass flowers.
The usage is only in the grass fruits (caryopsis). It
also appears that the same term is used in other
families as well. So we need a species/organ specific
distinction as well.

1. dry outer covering of a fruit or seed or nut
2. persistent enlarged calyx at base of e.g. a
   strawberry or raspberry

-Pankaj

Reported by: jaiswalp

Original Ticket: obo/plant-ontology-po-term-requests/3

PO suggestion

Hi Pankaj,

Please find attached the document of PO and do needful

Regards,

Arul

Reported by: bioinarul

Original Ticket: obo/plant-ontology-po-term-requests/34

new term: stigma vein

I would like to request the following plant ontology term. Please contact me if you have questions or comments.

[name] stigma vein (PO:new1)

[synonyms] none

[ontology] structure

[definition] A strand of vascular tissue in the stigma.

[lineage]

stigma ([PO:0009073](http://purl.obolibrary.org/obo/PO_0009073))
—[p] stigma vein (PO:new1)

Is there a ‘vein’ term as a second parent?

[reference] TAIR

Regards,

Donghui
TAIR Curator

Reported by: donghui

Original Ticket: obo/plant-ontology-po-term-requests/5

various vascular system terms

Hi Pankaj and Chih-wei,

I would like to propose the following vascular system terms. Please comment.

1) embryo vascular system PMID 16543410

2) stigma vascular system PMID 15665497

3) filament vascular system PMID 15665497

4) anther vascular system PMID 17257168

5) hypocotyl vascular system PMID 17041031

Thanks!

Donghui

Reported by: donghui

Original Ticket: obo/plant-ontology-po-term-requests/22

new term: filament vein

I would like to request the following plant ontology term. Please contact me if you have questions or comments.

[name] filament vein (PO:new1)

[synonyms] none

[ontology] structure

[definition] A strand of vascular tissue in the stamen filament.

[lineage]

stamen ([PO:0009029](http://purl.obolibrary.org/obo/PO_0009029))
—[p] filament vein (PO:new1)

Is there a ‘vein’ term as a second parent?

[reference]

Regards,

Donghui
TAIR Curator

Reported by: donghui

Original Ticket: obo/plant-ontology-po-term-requests/6

Request Ontology term: Pollen coat

Request new PO term: Pollen coat

Reference:
http://www.plantcell.org/cgi/content/full/16/suppl\_1/S84

Chih-Wei

Reported by: *anonymous

Original Ticket: obo/plant-ontology-po-term-requests/43

new term: embryo endodermis

I would like to propose the following new PO term:

name: embryo endodermis

ontology: structure

definition: The innermost layer of the cortex in the embryos of seed plants.

lineage:

embryo ([PO:0009009](http://purl.obolibrary.org/obo/PO_0009009))
—[p] embryo endodermis (PO:new1)

endodermis ([PO:0000252](http://purl.obolibrary.org/obo/PO_0000252))
—[i] embryo endodermis (PO:new1)

reference: PMID 16543410

Donghui
TAIR

Reported by: donghui

Original Ticket: obo/plant-ontology-po-term-requests/10

Root terms: 5 new and 14 modified terms

The ISRR (International Society for Root Research has established a root nomenclature framework.
I have developed a set of terms, that are new to the po_anatomy.obo, which come from that Framework. These are ID:0000000 and ID:0000001 in the attached mini ontology. I have devised three more new terms to fill out the root nomenclature in the ontology (IDs 0000005; 0000006; 0000007).
I have modified14 terms to bring them i line with the ISRR nomenclature: PO:0000042; PO:0000043; PO:0000044; PO:0000045; PO:0000046; PO:0003005; PO:0004708; PO:0004724; PO:0009005; PO:0020031; PO:0020037; PO:0020100; PO:0020121; & PO:0020127.

Reported by: richzobel

Original Ticket: obo/plant-ontology-po-term-requests/48

dispersed meristematic cell

I would like to request the following new term:

name: dispersed meristematic cell (PO:new1)

ontology: structure

definition:

Procambial cell that is recruited in the mesophyll tissue layer and divide to form and extend the vascular tissue network of the leaf. These cells are defined here as dispersed meristematic cell (DMC).

lineage:

meristematic cell ([PO:0004010](http://purl.obolibrary.org/obo/PO_0004010))
—[i] dispersed meristematic cell (PO:new1)

reference: PMID 10545247, 16916932

Donghui
TAIR

Reported by: donghui

Original Ticket: obo/plant-ontology-po-term-requests/12

new term: pedicel vascular system

Hi,

I would like to propose the following new term. Please comment.

[name] pedicel vascular system (PO:new1)
[ontology] structure

[defintion] Vascular system of the pedicel.

[lineage]
pedicel vascular system (PO:new1)
part_of pedicel ([PO:0009052](http://purl.obolibrary.org/obo/PO_0009052))
is_a vascular system ([PO:0000034](http://purl.obolibrary.org/obo/PO_0000034))

[reference] PMID 17217456

Reported by: donghui

Original Ticket: obo/plant-ontology-po-term-requests/17

ovary septum vs carpel septum

Hi,

I need a term 'ovary septum' but not sure it should be a new term or a synonym of PO:0005009 carpel septum;

The definition of PO:0000030 listed anther septum, ovary septum and fruit septum together but not carpel septum (A thin partition or membrane that divides a cavity or a mass of tissue, e.g., in anther, ovary or fruit)

Here is the proposed new term:

PO:new1 ovary septum
A thin partition that divides the ovary, the basal portion of a carpel or group of fused carpels, that encloses the ovule(s)” [PMID:17855426]

Is_a carpel septum????
Or is_a septum?????

Related discussion. Briefly, I was going to create some development terms ‘septum development’ ‘ovary septum development’ etc. Comments welcome!

https://sourceforge.net/tracker/index.php?func=detail&aid=1843562&group\_id=36855&atid=440764

-Donghui

Reported by: donghui

Original Ticket: obo/plant-ontology-po-term-requests/44

Create new PO: Post Harvest stages

Hi,

POC would like to create a new node: post harvest stages under [PO:0007033](http://purl.obolibrary.org/obo/PO_0007033) whole plant growth stages, and several stages we will add as child of post harvest stages are still under discussion. Please submit your input about this issue, any suggestion is welcome.

Reported by: cwtung

Original Ticket: obo/plant-ontology-po-term-requests/24

Abaxial vs Adaxial

Hi,

I have a request regarding [PO:0000049](http://purl.obolibrary.org/obo/PO_0000049): leaf lamina abaxial epidermis and [PO:0000050](http://purl.obolibrary.org/obo/PO_0000050) leaf lamina adaxial epidermis.

Both of these terms have the same child terms: [PO:0006504](http://purl.obolibrary.org/obo/PO_0006504): lesf trichome, [PO:0000332](http://purl.obolibrary.org/obo/PO_0000332): pavement cell, [PO:0002000](http://purl.obolibrary.org/obo/PO_0002000) stomatal complex.

I was wondering whether these child terms can be split by adding the term abaxial or adaxial (e.g. abaxial stomatal complex, abaxial stomatal complex) to distinguish the child terms.

Your feedback is appreciated.

Thanks,
Raymond DiDonato
BIOBASE Corporation

Reported by: rdidonat

Original Ticket: obo/plant-ontology-po-term-requests/32

new term: sepal margin

I would like to request the following new PO term:

name: sepal margin (PO:new1)

synonyms: none

ontology: structure

defintion: The margin or edge of the sepal.

lineage:

sepal ([PO:0009031](http://purl.obolibrary.org/obo/PO_0009031))
—[p] sepal margin

reference: PMID 1685042

comments:

1) there is a similar term ‘leaf margin’ in PO.
2) Do we have to give each PO term a is_a parent term?

Donghui
TAIR

Reported by: donghui

Original Ticket: obo/plant-ontology-po-term-requests/7

Vegetative SAM and reproductive SAM

-Term Request from Tayna (TAIR db)
Question on a possibly missing term:
Is there something I could use to annotate expression of a gene product in the ‘vegetative meristem’ – a meristem that produces leaves as opposed to the reproductive ones (inflorescence and floral meristems)? I was going to use ‘shoot apical meristem’ but that didn’t sit quite right, especially as that term has an is_a child ‘inflorescence apical meristem’.

Reference: PMID: 15120075 (Supplemental data)

-Concern from Marty Sachs
Is there really a separate “vegetative apical meristem”? My understanding is that the shoot apical meristem gives rise to vegetative organs until it differentiates into a ‘floral meristem’. At which point, the shoot apical meristem gives rise to reproductive organs. If you’re going to have a separate “vegetative apical meristem” it would be the progenitor of the ‘reproductive meristem’.

Solution from PO group
SAM->shoot apical meristem
-is_a—VSAM—>vegetative shoot apical meristem
-—develops_from—-IAM—>inflorescence apical meristem
-—is_a—-ESAM—>embryonic shoot apical meristem
-is_a—RSAM—>reproductive shoot apical meristem
-—is_a—-IAM—>inflorescence apical meristem

Reported by: cwtung

Original Ticket: obo/plant-ontology-po-term-requests/36

epidermis lineage

GO has:

! protoderm histogenesis * [DEF: “The formation of the primary meristem or meristematic tissue that gives rise to the epidermis.”]

PO has neither a develops_from link to epidermis nor a develops_from link from protoderm

Reported by: cmungall

Original Ticket: obo/plant-ontology-po-term-requests/40

rhizome internode

rhizome internode length

Should “rhizome internode” be added to PO, under shoot internode?

There is also:

internode length internode color

But no basic “internode” term in PO. Adding this would help make PO more is_a complete

Reported by: cmungall

Original Ticket: obo/plant-ontology-po-term-requests/28

New term for root tuber

Need to define two terms clearly under 'plant structure' for 'tubers'

http://www.plantontology.org/amigo/go.cgi?xpand=[PO:0004543](http://purl.obolibrary.org/obo/PO_0004543)&search\_constraint=terms&query=[PO:0004543](http://purl.obolibrary.org/obo/PO_0004543)&view=details&show\_associations=list
they should be root tuber and stem/shoot tuber. The current term PO:0004543 : tuber is suggesting only a shoot/stem tuber only.

Pankaj

Reported by: cwtung

Original Ticket: obo/plant-ontology-po-term-requests/47

new term: anther dehiscence zone

I would like to request the following PO term:

name: anther dehiscence zone (PO:new1)

ontology: structure

synonyms: none

definition:

A narrow band of cells that extends along the entire length of the anther. This site is observed as an indentation between the locules of each theca. Upon anther maturation, cell separation within the dehiscence zone allows the anther wall to break and for pollen to be released.

lineage:

anther ([PO:0009066](http://purl.obolibrary.org/obo/PO_0009066))
—[p] anther dehiscence zone (PO:new1)

QUESTION: is a is_a parent term required? If so, please suggest one.

reference:

PMID 15319479
http://en.wikipedia.org/wiki/Dehiscent

Donghui
TAIR

Reported by: donghui

Original Ticket: obo/plant-ontology-po-term-requests/14

New term: Pulvinus

Dear Chih-Wei,

Looking to link the legacy MaizeGDB anatomy terms not yet used for annotation at MaizeGDB, to an accession in PO I need some help with ‘pulvinus’. Is it simply part of the node?

Discussion about Dec 2004 indicated this was part of ‘node’ – do you know if that is considered appropriate for now? If so, should we add pulvinus in the definition or comment part of the term?

mary

Reported by: cwtung

Original Ticket: obo/plant-ontology-po-term-requests/25

5 suggested is_a links

I suggest the following 5 is_a links be made (based on xp definitions
derived from Obol but not yet checked by a plant expert):

isa PO:0004536-fruit pedicel PO:0009052-pedicel
isa PO:0004721-paraclade cortex PO:0005708-cortex
isa PO:0005025-middle layer of ovary wall PO:0004700-middle layer
isa PO:0008004-fruit aleurone layer PO:0005360-aleurone layer
isa PO:0008005-fruit nucellus PO:0020020-nucellus

this would take the number of classes lacking is_a parents from 200 to 195

Reported by: cmungall

Original Ticket: obo/plant-ontology-po-term-requests/49

dfgdf

AT1G02730
AT1G03820
AT1G05700
AT1G08090
AT1G09090
AT1G11580
AT1G12030
AT1G17180
AT1G18250
AT1G18370
AT1G20400
AT1G21250
AT1G23020
AT1G23920
AT1G23930
AT1G24260
AT1G24280
AT1G29180
AT1G31320
AT1G32840
AT1G33130
AT1G33450
AT1G33460
AT1G34530
AT1G34610
AT1G34760
AT1G35280
AT1G35590
AT1G35600
AT1G35647
AT1G36040
AT1G36080
AT1G36090
AT1G36190
AT1G36240
AT1G36260
AT1G36460
AT1G36470
AT1G36540
AT1G37160
AT1G39110
AT1G39190
AT1G40105
AT1G40123
AT1G40125
AT1G41700
AT1G42110
AT1G42360
AT1G42370
AT1G42500
AT1G43205
AT1G43230
AT1G43800
AT1G43840
AT1G43910
AT1G44060
AT1G47400
AT1G47660
AT1G48300
AT1G49570
AT1G49860
AT1G50850
AT1G50860
AT1G51800
AT1G52700
AT1G52850
AT1G56430
AT1G59770
AT1G59930
AT1G63540
AT1G65480
AT1G65490
AT1G65680
AT1G69880
AT1G70710
AT1G71400
AT1G73600
AT1G73602
AT1G74770
AT1G77120
AT2G01840
AT2G02210
AT2G02520
AT2G04000
AT2G04210
AT2G04770
AT2G04980
AT2G06130
AT2G06330
AT2G06430
AT2G06720
AT2G07770
AT2G07780
AT2G10070
AT2G10140
AT2G10630
AT2G10640
AT2G10880
AT2G11060
AT2G12050
AT2G12210
AT2G12240
AT2G12250
AT2G12260
AT2G12300
AT2G12980
AT2G13160
AT2G13310
AT2G13870
AT2G14130
AT2G14230
AT2G14630
AT2G14950
AT2G15790
AT2G15940
AT2G16060
AT2G17850
AT2G18140
AT2G18150
AT2G19590
AT2G19850
AT2G19970
AT2G19990
AT2G20870
AT2G23480
AT2G23720
AT2G26630
AT2G27550
AT2G28780
AT2G29870
AT2G30670
AT2G31390
AT2G34130
AT2G34390
AT2G39510
AT2G39530
AT2G39700
AT2G41090
AT2G41800
AT2G43140
AT2G43620
AT2G44370
AT2G44460
AT2G45900
AT2G47550
AT3G01190
AT3G02640
AT3G02885
AT3G03270
AT3G05950
AT3G07720
AT3G09170
AT3G11340
AT3G12900
AT3G13610
AT3G13650
AT3G14210
AT3G15310
AT3G15600
AT3G15602
AT3G15650
AT3G17998
AT3G18000
AT3G21720
AT3G22840
AT3G23085
AT3G24290
AT3G24300
AT3G28500
AT3G29610
AT3G29650
AT3G29730
AT3G29787
AT3G29970
AT3G30396
AT3G30440
AT3G30670
AT3G30680
AT3G30720
AT3G30780
AT3G30830
AT3G31908
AT3G31955
AT3G32000
AT3G32230
AT3G32377
AT3G32677
AT3G32900
AT3G33066
AT3G33080
AT3G42720
AT3G42721
AT3G43190
AT3G43290
AT3G43640
AT3G44490
AT3G44500
AT3G44660
AT3G44990
AT3G45270
AT3G45820
AT3G47260
AT3G47310
AT3G47320
AT3G47330
AT3G51280
AT3G51720
AT3G54260
AT3G54730
AT3G56360
AT3G56980
AT3G58810
AT3G60270
AT3G61930
AT3G63110
AT4G02290
AT4G02314
AT4G02330
AT4G03790
AT4G03850
AT4G03900
AT4G03910
AT4G04010
AT4G04170
AT4G04430
AT4G04590
AT4G04780
AT4G05390
AT4G05640
AT4G07360
AT4G07523
AT4G08000
AT4G08010
AT4G08050
AT4G08430
AT4G08770
AT4G09370
AT4G09380
AT4G09600
AT4G11290
AT4G12480
AT4G12550
AT4G14690
AT4G15390
AT4G16370
AT4G16447
AT4G17670
AT4G18410
AT4G19690
AT4G22212
AT4G22470
AT4G22870
AT4G22880
AT4G28250
AT4G28960
AT4G28970
AT4G29200
AT4G31840
AT4G31940
AT4G33070
AT4G33560
AT4G33720
AT4G36430
AT4G36700
AT4G39675
AT5G01080
AT5G01870
AT5G02780
AT5G03090
AT5G03570
AT5G04150
AT5G04950
AT5G05250
AT5G07550
AT5G07570
AT5G10040
AT5G10210
AT5G11920
AT5G13420
AT5G14650
AT5G15120
AT5G15690
AT5G15948
AT5G15950
AT5G16250
AT5G17760
AT5G19015
AT5G19550
AT5G19890
AT5G24240
AT5G24480
AT5G27160
AT5G27180
AT5G28880
AT5G30450
AT5G33230
AT5G34900
AT5G35140
AT5G35150
AT5G35490
AT5G37385
AT5G37390
AT5G39580
AT5G39890
AT5G40590
AT5G40780
AT5G41670
AT5G43800
AT5G44415
AT5G44416
AT5G45082
AT5G45085
AT5G53450
AT5G55450
AT5G55790
AT5G56080
AT5G63600
AT5G66985

Reported by: *anonymous

Original Ticket: obo/plant-ontology-po-term-requests/38

new term: stem trichome

Hi,

I would like to propose the following new term. Please comment.

[name] stem trichome

[synonyms] none

[ontology] structure

[defintion] Trichome on/from the epidermis of the stem.

[lineage]

is_a trichome ([PO:0000282](http://purl.obolibrary.org/obo/PO_0000282))
part_of stem epidermis ([PO:0000112](http://purl.obolibrary.org/obo/PO_0000112))

[reference] PMID 17217456

Donghui
TAIR

Reported by: donghui

Original Ticket: obo/plant-ontology-po-term-requests/18

new term: xylem parenchyma

I would like to suggest a new term “xylem parenchyma cell”(def: they are relatively short cells with uniform secondary cell walls and located within the xylem)

lineage:

Primary xylem [PO:0005849](http://purl.obolibrary.org/obo/PO_0005849)
-[p] xylem parenchyma cell PO:new

Parenchyma [PO:0005421](http://purl.obolibrary.org/obo/PO_0005421)
-[p] xylem parenchyma cell PO:new

reference:
Vascular patterning. 2003 The Arabidopsis Book.

Reported by: cwtung

Original Ticket: obo/plant-ontology-po-term-requests/19