Mapping file for maize terms WITH annotation in MaizeGDB

Wed Sep 15 13:37:00 EDT 2004

Mary,
Thanks for the info, we can talk more about terms in MaizeGDB and
Leszek's maize ontology in Eugene next week.

Please see my comments below:

On Tue, 14 Sep 2004, Mary Polacco wrote:

> Katica,
>
> Let me know if this format is OK. I am open to any suggestions on anything
> else here.
>
> I will send on soon the ones where we have no annotation yet in MaizeGDB.
> Where there was an (in sensu), I used the PO ID for the appropriate match in
> maize and picking the sensu ones as appropriate. The accessions listed in
> the mapping file are being placed into MaizeGDB to be used for providing
> AMIGO with the gene associations.
>
> Some notes.
>
> A.  there are a few terms where the mapping was not precise; I have checked
> with Leszek, and would like to propose that we consider adding new terms for
> these cases.
>
> MaizeGDB: 106161 tillers > PO: axillary shoot ; PO:0006343
> **preferred would be mapping to non-existent term: basal axillary shoot
>
> MaizeGDB: 15809 pollen > PO: male gametophyte ; PO:0020091
> ** pollen is a parent term for male gametophyte\

This is fine, pollen is synonym of male gametophyte in PO. However, since
there is anther sensu Zea, there should be male gametophyte sensu Zea too
(I hate to say this, but that's a reality), and this term should be mapped
to it. There might be other terms in MaizeDGB that can be mapped to
existing sensu terms, instead to generic terms.

 >
> MaizeGDB: 45980 leaf cuticle > PO: leaf epidermis ; PO:0006016
> **strictly speaking, leaf cuticle is not a 'cellular' anatomical feature,
> but is considered that way in usage.

Leaf cuticle is in fact part_of leaf epidermis, and it's one of those
terms that are borderline, since strictly speaking, it is subcellular
structure, a layeron the outer wall of (leaf) epidermal cell.
Is there anything annotated to this term for maize?

> > MaizeGDB: 58047 stalk > PO: stem ; PO:0009047
> MaizeGDB: 58047 stalk >> PO: leaf sheath ; PO:0020104
> **while stem is the major component of maize stalk, it also is composed of
> leaf sheath

I don't know about this one, I wouldn't map these two (even considering
the definitions for both), but the best is to ask Toby.

>
> MaizeGDB: 64474 mid rib > PO: mid vein ; PO:0020139
> **mid rib includes more tissue that just the mid vein, but at this time I am
> only mapping to mid vein

I think this might be OK
>
>
> B. I changed a several terms in MaizeGDB to be equivalent to those in PO:
>  culm node to node
>  sheath to leaf sheath
>  leaf blade to leaf lamina
>   etc
>
>
> C. in addition to Part A above, some terms in MaizeGDB should remain
> different, but be 'synonymized' with the PO term:
>  MaizeGDB: 11089 kernel > PO: fruit ; PO:0009001
>  MaizeGDB: 24759 cob > PO: central spike of ear ; PO:0006505
>  MaizeGDB: 24742 husk > PO: infloresence bract of ear ; PO:0006337
>
>
> -mary
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
>
> MaizeGDB: 79057 shoot apical meristem > PO: shoot apical meristem ;
> PO:0020148
>
> MaizeGDB: 64470 node > PO: node ; PO:0020141
>
> MaizeGDB: 64474 mid rib > PO: mid vein ; PO:0020139
>
> MaizeGDB: 1861 leaf > PO: leaf ; PO:0009025
>
> MaizeGDB: 24738 leaf apex > PO: leaf apex ; PO:0020137
>
> MaizeGDB: 24736 auricle > PO: auricle ; PO:0020106
>
> MaizeGDB: 45980 leaf cuticle > PO: leaf epidermis ; PO:0006016
>
> MaizeGDB: 104000 leaf epidermis > PO: leaf epidermis ; PO:0006016
>
> MaizeGDB: 131140 guard cell > PO: guard cell ; PO:0000293
>
> MaizeGDB: 64473 ligule > PO: ligule ; PO:0020105
>
> MaizeGDB: 13810 leaf sheath > PO: leaf sheath ; PO:0020104
>
> MaizeGDB: 894644 leaf base > PO: leaf base ; PO:0020040
>
> MaizeGDB: 24740 leaf lamina > PO: leaf lamina ; PO:0020039
>
> MaizeGDB: 65488 leaf margin > PO: leaf margin ; PO:0020128
>
> MaizeGDB: 11056 coleoptile > PO: coleoptile ; PO:0020033
>
> MaizeGDB: 58047 stalk > PO: stem ; PO:0009047
>
> MaizeGDB: 58047 stalk > PO: leaf sheath ; PO:0020104
>
> MaizeGDB: 60674 stem > PO: stem ; PO:0009047
>
>
>
> MaizeGDB: 106160 shoot > PO: shoot ; PO:0009006
>
> MaizeGDB: 24734 root > PO: root ; PO:0009005
>
> MaizeGDB: 106152 primary root > PO: primary root ; PO:0020127
>
> MaizeGDB: 40516 root cap > PO: root cap ; PO:0020123
>
> MaizeGDB: 894753 nodal root > PO: nodal root ; PO:0003005
>
> MaizeGDB: 100045 root hair > PO: root hair ; PO:0000256
>
>
>
> MaizeGDB: 100180 inflorescence > PO: inflorescence ; PO:0009049
>
> MaizeGDB: 64471 glume > PO: glume ; PO:0009039
>
>
>
> MaizeGDB: 24979 ear > PO: ear ; PO:0020136
>
> MaizeGDB: 11089 kernel > PO: fruit ; PO:0009001
>
> MaizeGDB: 13807 pericarp > PO: pericarp ; PO:0009084
>
> MaizeGDB: 1860 aleurone > PO: aleurone layer ; PO:000536
>
> MaizeGDB: 11053 plumule > PO: plumule ; PO:0020032
>
> MaizeGDB: 894610 cotyledon > PO: cotyledon ; PO:0020030
>
> MaizeGDB: 11087 embryo > PO: embryo ; PO:0009009
>
> MaizeGDB: 86197 embryo axis > PO: embryo axis ; PO:0019018
>
> MaizeGDB: 15814 endosperm > PO: endosperm ; PO:0009089
>
> MaizeGDB: 11042 scutellum > PO: scutellum ; PO:0020110
>
> MaizeGDB: 24759 cob > PO: central spike of ear ; PO:0006505
>
> MaizeGDB: 167982 glume of ear spikelet > PO: glume of ear spikelet ;
> PO:0006367
>
> MaizeGDB: 24742 husk > PO: infloresence bract of ear ; PO:0006337
>
> MaizeGDB: 64631 female gametophyte > PO: female gametophyte ; PO:0020092
>
> MaizeGDB: 24753 silk > PO: silk ; PO:0006488
>
>
>
> MaizeGDB: 24990 tassel > PO: tassel ; PO:0020126
>
> MaizeGDB: 64630 male gametophyte > PO: male gametophyte ; PO:0020091
>
> MaizeGDB: 15809 pollen > PO: male gametophyte ; PO:0020091
>
> MaizeGDB: 24749 anther > PO: anther ; PO:0006473
>
> MaizeGDB: 24746 glume of tassel spikelet > PO: glume of tassel spikelet ;
> PO:0006368
>
> MaizeGDB: 167379 central spike of tassel > PO: central spike of tassel ;
> PO:0006324
>
>
>
>
>
>

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Katica Ilic             		katica at acoma.stanford.edu
The Arabidopsis Information Resource 	Tel: (650) 325-1521 ext. 253
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