Plant Ontology suggestions

[planteome-user]

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":https://sourceforge.net/p/obo/plant-ontology-po-term-requests/37

[planteome-user]

Plant Ontology terms tab delimited txt file: PO Term Suggested Parent Definition Reference PMID Contributor

Vegetative meristem PO:0009013 Meristem found in vegetative organs 10712549 Arul Prakasam

Dermatogen cell PO:0004010 Cells of the primary meristem that gives rise to epidermis 9530872 Arul Prakasam

Plerome Apical meristem The primary meristem which produces the cortical cells 9530872 Arul Prakasam

Plerome cell PO:0004010 Cells of the primary meristem which produces the cortical cells 9530872 Arul Prakasam

Periblem Apical meristem The central core of primary meristem which gives rise to all cells of the stele from the pericycle inward 9530872 Arul Prakasam

Periblem cell PO:0004010 Cells in the central core of primary meristem which gives rise to all cells of the stele from the pericycle inward 9530872 Arul Prakasam

Leaf meristem PO:0009013 Meristem found in a leaf 16730655 Arul Prakasam

Adventitious root primordia PO:0000042 An organized group of cells that will differentiate into adventitious root 16730656 Arul Prakasam

Stem-base PO:0009047 The basal part of stem 16169685 Arul Prakasam

Lodicule primordia PO:0009036 The very first appearance of a lodicule 12506001 Arul Prakasam

Shoot vascular system PO:0000034 Total of the vascular tissues in their specific arrangement in shoot 18258694 Arul Prakasam

Shoot vascular bundle Shoot vascular system "A unit strand of the vascular system containing the vascular tissues, xylem and phloem of shoot" 18258694 Arul Prakasam

Phloem sap PO:0005417 A fluid transported in phloem sieve tube elements of a plant 15032821 Arul Prakasam

Scutellar vasular system PO:0020110 Total of the vascular tissues in scutellum 17138625 Arul Prakasam

Scutellar vasular system PO:0008011 Total of the vascular tissues in scutellum 17138625 Arul Prakasam

scutellar epithelium PO:0020110 Layer of cells lining the scutellum 17138625 Arul Prakasam

Floral epidermis PO:0006035 Outer layer of the floral organs 12509525 Arul Prakasam

Floral stomatal complex Floral epidermis An opening pore on the epidermis of floral organs bordered by two guard cells and serving in gas exchange. 12509525 Arul Prakasam

Floral guard cells Floral stomatal complex One of a pair of cells flanking the stomatal pore 12509525 Arul Prakasam

Floral stomatal pore Floral stomatal complex The space of variable size controlled by stomatal guard cells in response to environmental clues 12509525 Arul Prakasam

Meristematic zone PO:0020142 "Zone of cell division, starting point of growth in stem internode" 14520573 Arul Prakasam

Elongation zone PO:0020142 Zone of pronounced cell elongation in stem internode 14520573 Arul Prakasam

Differentiation zone PO:0020142 "Region in stem internode where cells are becoming specialized to form cortex, endodermis or, vascular tissue etc " 14520573 Arul Prakasam

Original comment by: bioinarul

[planteome-user]

Hi Arul,

I have created PO id for most of terms based on your request. you should be able to find them in Revision 1.58 (http://brebiou.cshl.edu/viewcvs/Poc/ontology/OBO\_format/po\_anatomy.obo ) in POC database.

The following terms need further discussion, so I haven't create any PO id for them. Shoot vascular system Shoot vascular bundle Phloem sap

If you have any questions regarding to the entries, please let us know. Thanks,

Chih-Wei POC curator/coordinator

Original comment by: nobody

[planteome-user]

Hi Arul,

Below is the list of terms added and modified. You can find the updated reversion 1.59 in http://brebiou.cshl.edu/viewcvs/Poc/ontology/OBO\_format/po\_anatomy.obo

[Term] id: PO:0000017 name: leaf primordium namespace: plant_structure def: "An organized group of cells that will differentiate into leaf that are emerging as an outgrowth in the shoot apex (flanking the meristem). " [TAIR:ki] synonym: "leaf meristem" [] is_a: PO:0009025 ! leaf relationship: part_of PO:0000037 ! shoot apex

[Term] id: PO:0006210 name: protoderm namespace: plant_structure def: "The undifferentiated surface cell layer of the primary plant body\, which gives rise to epidermis." [GR:pj, ISBN:047124529] comment: It may or may not arise from independent initials. Some researchers also call it an epidermis in meristematic state. synonym: "Dermatogen cell" [] relationship: part_of PO:0009013 ! meristem

[Term] id: PO:0008035 name: plerome namespace: plant_structure def: "The meristem forming the core of the axis composed of the primary vascular tissues and associated ground tissue\, such as pith and interfascicular regions. " [ISBN:0471245208 "Anatomy of seed plants by K.Esau [2nd Edition]"] is_a: PO:0009013 ! meristem

[Term] id: PO:0008036 name: periblem namespace: plant_structure def: "The meristem forming the cortex" [ISBN:0471245208 "Anatomy of seed plants by K. Esau [2nd edition]"] is_a: PO:0009013 ! meristem

[Term] id: PO:0008038 name: adventitious root primordium namespace: plant_structure def: "An organized group of cells that will differentiate into adventitious root." [GR:cwt] is_a: PO:0005029 ! root primordium

[Term] id: PO:0008039 name: stem base namespace: plant_structure def: "The basal part of stem" [GR:cwt] relationship: part_of PO:0009047 ! stem

[Term] id: PO:0008040 name: lodicule primordium namespace: plant_structure def: "The primordium will differentiat into lodicule" [GR:cwt] is_a: PO:0009036 ! lodicule

[Term] id: PO:0008041 name: stem internode elongation zone namespace: plant_structure def: "Zone of pronounced cell elongation in stem internode" [GR:cwt "PMID:14520573"] relationship: part_of PO:0020142 ! stem internode

[Term] id: PO:0008042 name: stem internode differentiation zone namespace: plant_structure def: "Region in stem internode where cells are becoming specialzed to form cortex\,\, endodermis or\, vascular tissue" [GR:cwt "PMID:14520573"] relationship: part_of PO:0020142 ! stem internode

[Term] id: PO:0008043 name: floral epidermis namespace: plant_structure def: "Epidermal layer of the floral organs" [GR:cwt] is_a: PO:0006035 ! shoot epidermis relationship: part_of PO:0009046 ! flower

[Term] id: PO:0008044 name: floral stomatal complex namespace: plant_structure def: "An opening pore on the epidermis of floral organs bordered by two guard cells and serving in gas exchange" [GR:cwt] relationship: part_of PO:0008043 ! floral epidermis

[Term] id: PO:0008045 name: floral guard cell namespace: plant_structure def: "One of a pair of cells flanking the stomatal pore of floral organs" [GR:cwt] relationship: part_of PO:0008044 ! floral stomatal complex

[Term] id: PO:0008046 name: floral stomatal pore namespace: plant_structure def: "The space of variable size controlled by floral stomatal guard cells in response to environmental clues" [GR:cwt] relationship: part_of PO:0008044 ! floral stomatal complex

[Term] id: PO:0008047 name: scutellar vascular system namespace: plant_structure def: "The vascular system in scutellum" [GR:cwt] synonym: "scutellum vascular system" [] relationship: part_of PO:0008011 ! embryo vascular system relationship: part_of PO:0020110 ! scutellum

[Term] id: PO:0008048 name: scutellar epithelium namespace: plant_structure def: "A continuous layer of cylindrical cells covering the endosperm side of the scutellum. Thought to act as a secretory and absortive organ" [GR:cwt] synonym: "scutellum epithelium" [] relationship: part_of PO:0020110 ! scutellum

Thanks,

Chih-Wei

Original comment by: cwtung