Gramene mapping
Katica Ilic
katica at acoma.Stanford.EDU
Thu Aug 26 21:29:19 EDT 2004
Hi Anu and Pankaj,
Attached is my response to the list of Gramene terms that are unmapped to
PO. There are very few terms that need to be introduced to PO, others are
either subcellular structures, developmental stages terms, obsoleted terms
that could be mapped to the existing PO terms, or terms that already have
corresponding term in PO (though under different term name).
Bottom line here is that we do not want to loose any annotation in
Gramene, TAIR or Maize GDB. So, that's why I asked you earlier today for a
list of Gramene terms that already have annotations associated to them.
We don't have to introduce every term from Gramene and TAIR to PO. I think
we all agreed back in January in San Diego and said " We do need to go
down to granularity to allow species-specific annotation" (quoted from the
minutes). However, we also said that not all species-specific terms would
need to be introduced to the PO.
Could you send me the list of Gramene terms 'with current annotations'? We
can start from there and go up to include terms that are needed in near
future for annotation purposes.
Attached is your list of terms with my comments in red italic font.
Underlined are 'problematic terms'(in my humble opinion). I may have
omitted comments to some terms, since I commented only the most obvious.
Once you guys 'weed the list out', it will be easier to talk about terms
that need to be introduced in PO.
Greetings,
Katica
On Thu, 26 Aug 2004, Anuradha Pujar wrote:
> Hello,
>
> After mapping gramene anatomy, a list of unmapped terms has been made
> (find attached) a second list containing some terms to which synonyms can
> be assigned in POC is also attached. Please give your feedback as to
> whether these unmapped terms have to be created as new term, raised toa
> generic term or be excluded.
>
> Thanks
> anu
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Katica Ilic katica at acoma.stanford.edu
The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253
Carnegie Institution of Washington FAX: (650) 325-6857
Department of Plant Biology URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
U.S.A.
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Terms from Gramene ontology that did not map to POC
\par
\par Androgynophore :The stipe or column on which stamens and carpels are borne.
\par }{\b\f1
\par }{\b\f1\ul Aperture:}{\f1 A depressed region in the pollen wall in which thick intine is covered by thin exine; the pollen grain emerges through the aperture. }{\i\f1\cf17 (PO has mapping term)}{\f1
\par }\pard\plain \s1\ql \li0\ri0\sl360\slmult1\keepn\widctlpar\aspalpha\aspnum\faauto\outlinelevel0\adjustright\rin0\lin0\itap0 \b\f1\fs24\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {PO:0020018 : germination pore
\par }\pard\plain \ql \li0\ri0\sl360\slmult1\widctlpar\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 \fs24\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {\f1\ul Atactostele:}{\f1
A stele consisting of vascular bundles scattered throughout the ground tissue as in the Monocots}{
\par }{\f1\ul Bran:}{\f1 The pericarp, testa and usually the aleurone layer of cereal seeds which are removed in milling. }{\i\f1\cf17 (This is not a botanical term, and I doubted that any gene would need to be annotated to this term \endash KI)
\par }{\f1\ul Casparian strip: }{\f1 A band like wall formation within primary walls that contains suberin and lignin; typical of endodermal cells, in which it occurs in radial and transverse anticlinal walls. }{\i\f1\cf17 (this is a subcellular structure
\endash KI)}{\f1
\par }{\f1\ul Cotyledon primordium:}{\f1 The earliest differentiated state of a cotyledon. }{\f1\cf17 (}{\i\f1\cf17 this is really a dev stage term \endash KI)}{\i\f1
\par }{\f1 Crown: Located between the coleoptile and the mesocotyl, the crown contains the growing point where the rest of the plant will begin to form and the nodes where the nodal or permanent roots will form.
\par }{\f1\ul Cuticle:}{\f1 It is a continuous layer of cutin secreted by the epidermis, it prevents plant desiccation by being impervious to water and gas exchange and covers the aerial parts of the plant body, broken only by stomata and lenticels}{
\i\f1\cf17 . (this is perhaps GO term, though I didn\rquote t find it in GO - KI)}{\f1
\par Embryonic ground tissue: Ground tissue (parenchymatous) layers found in the embryo.
\par }{\f1\ul Fibrous root:}{\f1 Roots characterized by many similar branching roots of common length and thickness. Generally not highly adapted for food storage. \endash plant anatomy glossary.
\par }{\f1\ul Gametophytic cell:}{\f1 A haploid (1n) cell developing into a male or female gametophyte in heterosporous plants. Synonym for gametophyte.
\par }{\i\f1\cf17 (Which one, megaspore or microspore? WE have both in PO! \endash KI)}{\i\f1
\par }{\f1\ul First embryonic leaf:}{\f1 The first leaf of the plant, often found developing with the embryo (}{\i\f1\cf17 this is a dev stage term \endash KI)}{\f1
\par }{\f1\ul First leaf:}{\f1 The first mature leaf present just below the flag leaf in a cereal crop plant.}{\i\f1\cf17 (this is a dev stage term \endash KI)}{\f1
\par }{\f1\ul Floral primordium:}{\f1 Primordial tissue giving rise to the floral whorls.}{\i\f1\cf17 (this is a dev stage term \endash KI)}{\f1
\par }{\b\f1\ul Laticiferous vessel:}{\f1 An articulated laticifer in which the cell walls between cells are partially or wholly lacking. Plant anatomy glossary}{\i\f1\cf17 (PO has mapping term)}{\f1
\par }\pard\plain \s2\ql \li0\ri0\sl360\slmult1\keepn\widctlpar\aspalpha\aspnum\faauto\outlinelevel1\adjustright\rin0\lin0\itap0 \b\i\f1\fs24\cf17\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {PO:0006221 : articulated laticifer cell}{\i0
\par }\pard\plain \ql \li0\ri0\sl360\slmult1\widctlpar\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 \fs24\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {\f1\ul Leaflet midvein:}{\f1
The central conducting and supporting structure of the blade of a leaflet of a compound leaf.
\par }{\f1\ul Leaflet veinlet:}{\f1 Branched secondary veinlets conducting and supporting structure of the blade of a leaflet.
\par }{\f1\ul Medine:}{\f1 Layer between the exine and intine.
\par }{\f1\ul Nucellar cells:}{\f1 Crushed nucellar cells present in multiple layers. }{\i\f1\cf17 (Sorry, I have no idea what this is. We do have term nucellus in PO:0020020 , def: Subepidermal tissue in the ovule surrounding the megasporocyte. - KI)}{\f1
\par }{\f1\ul Organ primordium:}{\f1 An organ or a part in its most rudimentary form or stage of development.
\par }{\f1\ul Ovary inner epidermis:}{\f1 Inner epidermal layer of the ovary wall.}{\i\f1\cf17 (Obsoleted, I suppose this can be annotated to PO:0006063 : ovary epidermis, but I would need to see the original paper first\endash KI)}{\f1
\par Ovary locule : An opening or cavity within ovary. Plant anatomy glossary.
\par }{\f1\ul Ovary outer epidermis:}{\f1 Outer epidermal layer of the ovary wall.}{\i\f1\cf17 (Obsoleted, same as for inner epidermis \endash KI)}{\f1
\par Ovary parenchyma: Parenchyma layer of the ovary wall.
\par Ovary vascular system: vascular system of the ovary.
\par }{\f1\ul Perforation plate:}{\f1 That region of a cell wall which is perforated, and found in a vessel member. Plant anatomy glossary.}{\i\f1\cf17 (this is a subcellular structure \endash KI)}{\f1
\par }{\f1\ul Phloem fiber:}{\f1 Fiber found in phloem parenchyma. }{\i\f1\cf17 (Sorry, I don\rquote t know what phloem fiber is \endash KI)}{\f1
\par Phloem Parenchyma: Parenchyma found in phloem.
\par }{\f1\ul Plant organ:}{\f1 Represents the organs and its sub-types in a plant. }{\i\f1\cf17 ( ??? \endash why do you need this term for annotation? We obsoleted it)}{\f1
\par Primary endosperm nucleus: Nucleus resulting from the fusion of the male gamete and two polar nuclei in the central cell of the embryo sac.}{\i\f1\cf17
\par }{\f1 Prop root: Aerial adventitious roots which usually provide support
\par Proximal root meristem: Lies next to the quiescent centre of the root tip and participates in the formation of root epidermis, stele and cortex. -Annals of Botany, 79,375-389,1997.
\par Replum: Persistent septum after dehiscence of fruits, as in the Brassicaceae
\par }{\f1\ul Rhexigenous aerenchyma:}{\f1 Applied to an aerenchyma originating by rupture of cells (}{\i\f1\cf17 We obsoleted it)}{\f1
\par Root primordium: The primordial tissue of the root.
\par Sclerenchyma perivascular: Sclerenchyma located along the outer periphery of the vascular cylinder and not originating in the phloem.
\par }{\f1\ul Sclerenchyma sclereid cell:}{\f1 Type of sclerenchyma cell that differs from the fiber cell by not being greatly elongated
\par }{\f1\ul Sieve plate:}{\f1 Wall of a sieve element with sieve areas.}{\i\f1\cf17 (this is a subcellular structure \endash KI}{\f1
\par Septum: A partition. Plant anatomy glossary.
\par Staminal disc: A fleshy, elevated cushion formed from coalesced staminodia or nectaries.
\par Stamonodium: Sterile stamen, may be modified as a nectary or petaloid structure.
\par Stem vascular system: The vascular system of the stem.
\par }{\b\i\f1\ul Stomatal pore:}{\f1 The pore in the epidermis, surrounded by two guard cells. Meant for gaseous exchange.}{\i\f1\cf17 (PO has mapping term)}{\f1
\par }\pard\plain \s2\ql \li0\ri0\sl360\slmult1\keepn\widctlpar\aspalpha\aspnum\faauto\outlinelevel1\adjustright\rin0\lin0\itap0 \b\i\f1\fs24\cf17\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {PO:0002000 : stomatal complex
\par }\pard\plain \ql \li0\ri0\sl360\slmult1\widctlpar\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 \fs24\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {\f1\ul Third leaf:}{\f1 The thi
rd meture leaf present below the flag leaf in a cereal crop plant.}{\i\f1\cf17 (this is a dev stage term \endash KI)}{\f1
\par }{\f1\ul Vascular bundle:}{\f1 A strand of conducting tissue comprising of phloem, xylem, and cambium.}{\i\f1\cf17 (We obsoleted it)}{\f1
\par }{\f1\ul Xylem cell radial:}{\f1 The secondary xylem cell aligned, forming radial files of cells that are produced from a single cambium initial cell. http://koning.ecsu.ctstateu.edu/plant_biology/secondary.html
\par }{\b\f1\ul Xylem fiber libriform:}{\b\f1 }{\f1 A very long xylem fiber with thick walls and simple pits. Plant anatomy glossary.
\par }\pard\plain \s2\ql \li0\ri0\sl360\slmult1\keepn\widctlpar\aspalpha\aspnum\faauto\outlinelevel1\adjustright\rin0\lin0\itap0 \b\i\f1\fs24\cf17\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {PO:0000274 : xylem fiber cell
\par }\pard\plain \ql \li0\ri0\sl360\slmult1\widctlpar\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 \fs24\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {\f1\ul Xylem parenchyma axial:}{\f1
Parenchyma cells running axially, derived from elongated fusiform cambial cells.
\par }{\f1\ul Xylem parenchyma radial:}{\f1 Parenchyma cells extending radially between the secondary xylem and phloem.
\par }{\f1\ul Xylem parenchyma radial procumbent:}{\f1 The ray cell with longest diameter arranged radially.
\par }{\f1\ul Xylem parenchyma radial upright:}{\f1 The axially elongated cell in radial xylem parenchyma. Appear generally at the upper and lower margins of the ray.
\par }{\f1\ul Xylem parenchyma radial homocellular:}{\f1 Xylem ray composed of one type of cell.
\par }{\f1\ul Xylem parenchyma radial heterocellular:}{\f1 Xylem ray containing procumbent and upright cells.
\par }{\f1\ul Xylem tracheary element wall:
\par }{\f1 http://www.mhhe.com/biosci/pae/botany/crang/gloss_top.html
\par
\par }}
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