Items In Progress
This page is a place holder for us to put items that will be scheduled for discussion at upcoming meetings.
Please include the date when the item was added; topics will move off of here as they are dealt with.
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pericarp and seed coat
pericarp (PO:0009084):A wall of a fruit, developed from the ovary or carpel wall.
Synonyms related: fruit peel, fruit rind
endocarp ; PO:0009086, synonym inner epidermis of pericarp
exocarp ; PO:0009085 synonyms outer epidermis of pericarp,
http://en.wikipedia.org/wiki/Caryopsis
is a type of simple dry fruit — one that is monocarpelate (formed from a single carpel) and indehiscent (not opening at maturity) and resembles an achene, except that in a caryopsis the pericarp is fused with the thin seed coat.
The caryopsis is popularly called a grain and is the fruit typical of the family Poaceae (or Gramineae), such as wheat, rice, and corn.
The term grain is also used in a more general sense as synonymous with cereal (as in "cereal grains", which include some non-Gramineae). Considering that the fruit wall and the seed are intimately fused into a single unit, and the caryopsis or grain is a dry fruit, little concern is given to technically separating the terms "fruit" and "seed" in these plant structures. In many grains, the "hulls" to be separated before processing are actually flower bracts.
link to a more scientific source :http://www.jstor.org/stable/10.2307/2442251
Open items from older agendas and user requests
ovule
Moved to POC Conf. Call 5-1-12
lobe and tooth
References: AJB Hickey 1973 (http://www.jstor.org/stable/2441319), Blicher 1973 Bot Review, Harris and Harris, ISBN:0964022168, also FNA glossary.
On 1-10-12, we added the term "sinus" and agreed to add the related terms for tooth and lobe, all part_of some margin.
Margins- part_of relations: We currently have organ margin (PO:0025005), phyllome margin (PO:0025018) without part of relations. Suggest that we add organ margin is part_of lamina, phyllome margin part_of phyllome lamina. Leaf margin (PO:0020128) is already part of leaf and leaf lamina margin (PO:0025009) is part_of leaf lamina.
phyllome sinus (existing definition): A plant anatomical space that is a phyllome marginal embayment, incision or indentation between marginal projections of any sort, typically lobes, teeth, or the base of cordate phyllomes. also have term for leaf sinus
Add comment that a sinus can be angular or rounded.
Lobes can be either rounded or pointed, and are defined based on the size of the projection.
Teeth' are pointed projections that extend less than 1/4 of the way to the midline.
Crenae (sing. crena) are small rounded pointed projections that extend less than 1/4 of the way to the midline.
lobes
proposed definition, phyllome lamina lobe: A cardinal organ part (PO:0025001) that is a projection on a phyllome margin (PO:0025018) for which the corresponding phyllome sinus (PO:0025383) extends one quarter or more of the distance to the center of the long axis of the phyllome lamina (PO:0025396).
Comment: A phyllome lobe may be either rounded or angular at the tip, and may have phyllome teeth (PO:id) or phyllome crenae (PO:id) on its margin. The corresponding phyllome sinus may be rounded or angular.
part_of phyllome lamina (rather than part of lamina margin, because they lobe includes all of the tissue inside the margin).
proposed definition, leaf lamina lobe: A phyllome lobe (PO:id) that is a projection on a leaf lamina margin (PO:0025009) for which the corresponding leaf sinus (PO:0025384) extends one quarter or more of the distance to the center of the long axis of the leaf lamina (PO:0020039).
Comment: A leaf lobe may be either rounded or angular at the tip, and may have leaf teeth (PO:id) or leaf crenae (PO:id) on its margin. The corresponding leaf sinus may be rounded or angular.
part_of leaf lamina
Can add other types of lobes as needed.
ref: JSTOR:2441319
teeth
proposed definition, phyllome lamina tooth: A cardinal organ part (PO:0025001) that is an angular projection on a phyllome margin (PO:0025018) for which the corresponding phyllome sinus (PO:0025383) extends less than one quarter of the distance to the center of the long axis of the phyllome lamina (PO:0025396).
Comment: See phyllome lamina crena (PO:id) for a small rounded projection. The corresponding phyllome sinus may be rounded or angular.
part_of phyllome lamina
proposed definition, leaf lamina tooth: A phyllome lamina tooth (PO:id) that is an angular projection on a leaf margin (PO:0020128) for which the corresponding leaf sinus (PO:0025384) extends less than one quarter of the distance to the center of the long axis of the leaf lamina (PO:0020039).
Comment: See leaf lamina crena (PO:id) for a small rounded projection. The corresponding leaf sinus may be rounded or angular.
part_of leaf lamina
Can add other types of teeth as needed.
Add "teeth" as exact plural synonym to all. Other synonyms from FNA.
ref: JSTOR:2441319
crenae
proposed definition, phyllome lamina crena: A cardinal organ part (PO:0025001) that is a rounded projection on a phyllome margin (PO:0025018) for which the corresponding phyllome sinus (PO:0025383) extends less than one quarter of the distance to the center of the long axis of the phyllome lamina (PO:0025396).
Comment: See phyllome lamina tooth (PO:id) for a small angular projection. The corresponding phyllome sinus may be rounded or angular.
part_of phyllome lamina
proposed definition, leaf lamina crena: A phyllome lamina crena (PO:id) that is a rounded projection on a leaf margin (PO:0020128) for which the corresponding leaf sinus (PO:0025384) extends less than one quarter of the distance to the center of the long axis of the leaf lamina (PO:0020039).
Comment: See leaf lamina tooth (PO:id) for a small angular projection. The corresponding leaf sinus may be rounded or angular.
part_of leaf lamina
Synonyms: scallop (exact), crenule (narrow)
tuber growth and development stages
This item has been open on SF since 6/2009
From Naama Menda: 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).
Suggested stages:
-sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
-tuber initiation
-tuber growth
-tuber maturation
How we work these in will depend on restructuring of PSDS
l development in legumes (Plant Physiol, March 2003, Vol. 131, pp. 911-926
User requests open on Source Forge: Plant Anatomical Entities
Cacti terms:
spinule: word for when the spines are stipules – synonym of stipule spine
In Beentje, spinule is defined as a small spine. Could be narrow synonym for stipule spine and other kinds of spines
glochid
cladode and phylloclade
From Beentje:
cladode: single node or internode of stem or branch that is flattened and expanded to serve the functions of a leaf
phylloclade: portion of stem or branch (several nodes an dinternodes) flattened and expanded to serve the functions of a leaf.
FNA lists cladode, phylloclade, and cladophyll as exact synonyms: A stem segment that functions as a leaf; often more or less compressed.
proposed definition:
cladode: A shoot axis that is flattened and expanded.
comment: Has an increased surface area for photosynthesis and may function similar to a leaf in plants that have no or small leaves, such as cacti. Consists of one to several internodes and nodes.
synonyms: phylloclade, cladophyll
Need to open a SF tracker for these
Should also add 'rib' for cacti and other plants
root terms
Submitted by Rich Zobel (Nov 2009).
Still need to work on definitions for these terms.
PSDS term revisions
remaining terms needing name changes
Need to go through and add "stage" to the end of these terms:
(Edit the page to see them as a list - I don't want to type in all those extra carriage returns!)
PO:0007601 1 flower meristem visible PO:0007056 1 pattern formation PO:0007505 1 root primordium formation PO:0007058 2 endoreduplication PO:0007602 2 flower meristem notched PO:0007527 2 root meristem formation PO:0007061 2.00 main shoot only PO:0007087 2.01 main shoot and axillary shoots visible at one node PO:0007071 2.02 main shoot and axillary shoots visible at two nodes PO:0007080 2.03 main shoot and axillary shoots visible at three nodes PO:0007088 2.04 main shoot and axillary shoots visible at four nodes PO:0007093 2.05 main shoot and axillary shoots visible at five nodes PO:0007118 2.06 main shoot and axillary shoots visible at six nodes PO:0007122 2.07 main shoot and axillary shoots visible at seven nodes PO:0007077 2.08 main shoot and axillary shoots visible at eight nodes PO:0007110 2.09 main shoot and axillary shoots visible at nine or more nodes PO:0007059 3 branch formation PO:0007525 3 establishment of tissue systems PO:0001053 3 leaf fully expanded PO:0007616 4 anthesis PO:0007016 4 flowering PO:0007135 4 growth directionality PO:0001031 4 root elongation PO:0007042 5 fruit formation PO:0007617 5 post anthesis PO:0007519 5 root hair formation PO:0007075 5.02 20% of inflorescence emerged. PO:0007102 5.04 40% of inflorescence emerged PO:0007105 5.06 60% of inflorescence emerged PO:0007107 5.08 80% of inflorescence emerged PO:0007010 6 ripening PO:0007121 6.01 10% of flowers open PO:0007124 6.03 30% of flowers open PO:0007125 6.04 40% of flowers open PO:0007035 7-8 fruit formation and maturation PO:0007126 7.02 fruit size 20% PO:0007127 7.04 fruit size 40% PO:0007128 7.06 fruit size 60% PO:0007129 7.08 fruit size 80% PO:0001005 A archesporial cells visible PO:0007623 A megaspore mother cell enlarges PO:0007503 A2.1 root intials differntiation of primary roots PO:0007528 A2.2 root initials differentiation of lateral roots PO:0007530 A2.3 founder cell derivatives of lateral root PO:0007534 A2.4 root initials differentiation of crown roots PO:0001018 B formation of primary parietal and sporogenous cells PO:0007624 B meiosis of megaspore mother cell PO:0007524 B1 primary root meristem formation PO:0007539 B2 lateral root meristem formation PO:0007514 B3 crown root meristem formation PO:0001008 C callose wall formation in pollen mother cells PO:0001025 C four anther lobes formed PO:0007625 C tetrad of megaspores PO:0007521 C3.1 metaxylem differentiation of root. PO:0007537 C3.2 maturation of phloem elements in root. PO:0007533 C3.3 maturation of protoxylem elements in root. PO:0021002 calyx absolute size PO:0021003 calyx relationship PO:0007618 carpel primordium visible PO:0001041 chalazal and micropylar domain establishment PO:0004502 closure of carpel(s) PO:0007518 crown root emergence PO:0007504 crown root primordium formation PO:0001026 D locules established PO:0007626 D megaspore degeneration PO:0007529 E emerged root elongation PO:0001032 E tapetum degeneration initiated PO:0007627 E two nucleate megagametophyte PO:0007081 early rosette growth PO:0001028 elongation zone formation PO:0007523 establishment of initial cells PO:0007628 F four nucleate megagametophyte PO:0007531 F1 root hair initiation PO:0007526 F2 root hair elongation PO:0007026 FL.00 first flower(s) open PO:0007034 FL.01 1/4 of flowers open PO:0007053 FL.02 1/2 of flowers open PO:0007052 FL.03 3/4 of flowers open PO:0007024 FL.04 end of flowering PO:0001099 formation of aleurone and starchy layers PO:0001019 formation of leaf primordium PO:0004500 formation of leaflet primordia PO:0001021 formation of ligule primordium PO:0001098 formation of starchy endosperm PO:0001003 formation of the leaf founder cells PO:0007036 FR.00 beginning of fruit ripening PO:0007038 FR.04 fruit ripening complete PO:0001057 fully expanded lemma PO:0001079 fully expanded lodicule PO:0001071 fully expanded palea PO:0007612 fully expanded petal PO:0001045 fully expanded sepal PO:0001042 functional specialization of the endosperm PO:0001035 G anther dehiscence PO:0007629 G eight nucleate megagametophyte PO:0004501 gynoecium differentiation and expansion PO:0001036 H anther senescence PO:0001020 hood-shaped primordium PO:0007025 IE.00 inflorescence tip just visible above flag leaf sheath PO:0007048 IE.01 1/4 of inflorescence emerged from flag leaf sheath PO:0007008 IE.02 1/2 of inflorescence emerged from flag leaf sheath PO:0007002 IE.03 3/4 of inflorescence emerged from flag leaf sheath PO:0007023 IE.04 inflorescence fully emerged from flag leaf sheath PO:0007076 late rosette growth PO:0007517 lateral root emergence PO:0007511 lateral root primordium formation PO:0007133 leaf production PO:0001055 lemma primordia visible PO:0025337 life of whole plant PO:0001072 lodicule primordia visible PO:0007094 LP.01 one leaf visible PO:0007098 LP.02 two leaves visible PO:0007106 LP.03 three leaves visible PO:0007115 LP.04 four leaves visible PO:0007065 LP.05 five leaves visible PO:0007123 LP.06 six leaves visible PO:0007063 LP.07 seven leaves visible PO:0007095 LP.08 eight leaves visible PO:0007101 LP.09 nine leaves visible PO:0007103 LP.10 ten leaves visible PO:0007116 LP.11 eleven leaves visible PO:0007064 LP.12 twelve leaves visible PO:0007083 LP.13 thirteen leaves visible PO:0007085 LP.14 fourteen leaves visible PO:0007104 LP.15 fifteen leaves visible PO:0007119 LP.16 sixteen leaves visible PO:0007067 LP.17 seventeen leaves visible PO:0007072 LP.18 eighteen leaves visible PO:0007120 LP.19 nineteen leaves visible PO:0007082 LP.20 twenty or more leaves whorls visible PO:0001027 meristamtic zone formation PO:0001000 meristem eloboration PO:0007068 mid rosette growth PO:0007060 obsolete growth and development terms PO:0007532 obsolete plant growth and development terms PO:0004504 ovule differentiation and expansion PO:0007620 ovule primordium visible PO:0001058 palea primordia visible PO:0007608 petal primordium visible PO:0028001 plant life cycle phase PO:0007506 primary root primordium formation PO:0001023 rapid elongation of leaf blade PO:0001024 rapid elongation of leaf sheath PO:0007501 root cap formation PO:0007513 root cortex differentiation PO:0007510 root emergence PO:0007516 root epidermal differentiation PO:0007536 root primordium visible PO:0007509 root vascular cylinder differentiation PO:0007113 rosette growth PO:0007078 rosette growth complete PO:0007079 SE.00 stem elongation begins PO:0007091 SE.01 one node or internode visible PO:0007117 SE.02 two nodes or internodes visible PO:0007096 SE.03 three nodes or internodes visible PO:0007092 SE.04 four nodes or internodes visible PO:0007086 SE.05 five nodes or internodes visible PO:0007062 SE.06 six nodes or internodes visible PO:0007108 SE.07 seven nodes or internodes visible PO:0007070 SE.08 eight nodes or internodes visible PO:0007066 SE.09 nine nodes or internodes visible PO:0007084 SE.10 ten nodes or internodes visible PO:0007114 SE.11 eleven nodes or internodes visible PO:0007111 SE.12 twelve nodes or internodes visible PO:0007090 SE.13 thirteen nodes or internodes visible PO:0007097 SE.14 fourteen nodes or internodes visible PO:0007074 SE.15 fifteen nodes or internodes visible PO:0007100 SE.16 sixteen or more nodes or internodes visible PO:0007099 SE.97 flag leaf visible PO:0007109 SE.99 maximum stem length reached PO:0007607 sepal primordium visible PO:0007610 sepals 100% of final size PO:0007609 sepals 50% of final size PO:0001380 sepals enclosing flower bud PO:0001378 sepals enclosing meristem PO:0001030 specialization zone formation PO:0007613 stamen primordium visible PO:0007089 stem elongation PO:0004503 stigma cell differentiation PO:0001095 true leaf formation
Leaf development stages
Legume terms
All trackers are now closed. Leaving notes about bristle here for when we are ready to describe phenotypes.
bristle
(used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)
Meeting of RW, MAG and DWS on 8/29/11: we felt this would be better left as a phenotypic descriptor. Should add terms needed to PATO.
At the POC meeting on 9-27-11, it was decided that bristled stipules should best be handled as a phenotype term. Leaving these notes here for when we start to add phenotypic descriptors.
We have the term stipule spine. Could also add the term stipule bristle: A stipule that has a brush-like appearance.
A bristle is a single thing, like a stiff hair, but many things can be bristled. Better to add bristled as an adjective in PATO (like ovate or acute).
There are two meanings for bristled:
!. Stiff and sharp (e.g., a bristled trichome)
2. Bearing bristles (e.g, a bristled leaf bears many bristle-like hairs)
Suggest two new phenotype descriptors (for PO phenotype branch or for PATO):
1. bristle-like:
This is a combination of two PATO descriptors:
Something describing the shape:
PATO:0001954 (subulate, awl-shaped, needle-shaped): A shape quality inhering in a bearer by virtue of the bearer's being linear, very narrow, tapering to a very fine point from a narrow base.
or
PATO:0001873 (cylindrical): A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section.
and/or PATO:0001154 (elongated): A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width.
and something describing a quality of a substance:
PATO has:
PATO:0001544 (flexible): A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking. (bendy)
PATO:0001545 (inflexibile): A physical quality inhering in a bearer by virtue of the bearer's inability of being turned, bowed, or twisted without breaking. (stiff)
A bristle is stiff but also bendy! I think in addition to flexible/inflexible, PATO needs terms for stiff or rigid/flacid, and that stiff should be a related synonym of inflexible, rather than exact.
PATO:
quality of a substance (existing)
>flexibility (existing)
>>flexible (existing)
>>inflexible (existing)
>rigidity (new)
>>rigid (new)
>>flacid (new)
2. bristle-bearing: A pilosity quality inhering in a bearer by virtue of the bearer's having structures that are bristle-like.
is_a pilosity (PATO:0000066: A texture quality inhering in a bearer by virtue of the bearer's having hair or bristles.)
Synonym: bristly (Beentje 2010: bearing stiff strong hairs or bristles).
To describe legume stipules, we may also need a term brush-like: A shape quality inhering in a bearer by virtue of the bearer's having a shape that is a cluster of bristle-like structures.
Then if we want to, we could add terms like brush-like stipule (is_a stipule) or bristle-like stipule (is_a stipule) or bristle-bearing stipule, or users could post-compose these terms on their own.
colony/ramet/genet
(Added ~3/23/2012) On a related note, Daniel added that "IMHO plant growth/life forms should be best integrated as an extension to PO. "
Also need acrocarpous and pleurocarpous moss (these could be growth forms).
New Annotation Files
Strawberry
- Strawberry is on SVN: strawberry
Potato Annotations
LC has been in contact with the group who published the potato genome paper and they are interested in collaborating with us to assign ontology terms to the annotations.
From Dr. Richard Finker (Wageningen, The Netherlands):
"We are also interested to use trait ontologies to assist in candidate gene selection within regions of interest, I'm eager to discuss with you on the efforts of cross linking ontologies to biological relevant entities. e.g. a metabolite content trait to its e.g. chebi ontology ID, form which we could obtain info about the pathway."
This will go in the next release, do they have expression data- RNA Seq?
Annotation Guidelines
Comments from PJ from previous meeting (9-27-11): Ask MS if she can write up a small blurb on how she created the Maize annotations. Maize probe ids => gene ids methods and cut-offs, a guide for other collaborators and a page for the info. Maybe co-author it with SR
-This will also be helpful when applying for new grants
-it would be helpful to have a detailed guide on our wiki for collaborators
