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fruit #76

Closed planteome-user closed 9 years ago

planteome-user commented 14 years ago

Currently has no is_a parent. Is part_of infructescence.

Suggest making fruit an is_a child of plant organ.

Reported by: rlwalls2008

Original Ticket: obo/plant-ontology-po-term-requests/76

planteome-user commented 14 years ago

compound organ I guess.

Original comment by: jaiswalp

planteome-user commented 14 years ago

While I agree, I would point out that in may well be a complex organ when multiple carpels are involved in syncarpous fruits.

Original comment by: dws409

planteome-user commented 14 years ago

Perhaps: fruit is_a 'collective plant structure' and part_of infructescence.

CPS: a proper part of a plant and is composed of two or more organs and any associated portions of plant tissue.

Original comment by: cooperl09

planteome-user commented 14 years ago

Fruit is traditionally defined as a mature ovary or, perhaps better, a mature gynoecium. Since we define gynoecium as a collective plant structure (child of whorled structure), fruit should be a collective plant structure.

In cases where the gynoecium contains a single carpel, then both gynoecium and fruit will be plant organs. We should deal with this the same way we talked about dealing with reduced whorls.

I suggest adding terms like simple gynoecium, simple androecium, and simple fruit as children of plant organ.

Original comment by: rlwalls2008

planteome-user commented 14 years ago

Its a derived/develops_from relationship between ovary/gynoecium and the fruit. For is_a relationship collective plant structure would work.

Also remember we are trying to avoid 'simple/compound' attributes in the term names (we did that e.g. in the case of leaf). Everything is by default is a simple structure. The compound/complexity/modified forms structure e.g. of uni/multi-carpellary are phenotype terms.

Original comment by: jaiswalp

planteome-user commented 14 years ago

This is what Spjut (1994, A Systematic Treatment of Fruit Types) says: "A fruit is a propagative unit developing from one or more fertilized egg cells (or rarely by parthenocarpy) enclosed by integuments and attached to megasporophylls or a megasporophyll-scale complex in a strobilus, cone, gynoecium, concrescent gynoecia or gynoecia that disseminate together at the time it or its seed(s) are dispersed from the plant, or just prior to germination on the plant, and it may also include any other attached scales, bracts, modified branches, perianth, or inflorescence parts."

This definition may be too broad for us, because it includes gymnosperms, but the part about the fruit being the unit that disperses together (thus a compound fruit is a single fruit) is noteworthy. Also important is the concept that fruits often contain more than just mature ovary tissue,

Original comment by: rlwalls2008

planteome-user commented 14 years ago

New proposed definition (modified slightly from Gleason and Cronquist 2nd edition, via Dennis): A collective plant structure that contains a ripened ovary, together with any other structures that ripen with it and form a unit with it.

Original comment by: rlwalls2008

planteome-user commented 14 years ago

are there any instances where we have other parts of the carpel as well in addition to just the ovary. I presume yes.

Suggestion on similar lines. I have avoided the use of word 'ripe'. To my understanding its the post fertilization development and growth of the carpel and some remnant floral whorls.

: A collective plant structure that develops in majority from post fertilization stage of the carpel and may contain, remnants of other flower whorls, developed seed, embryo and the parts that either develop newly and/or acquire new form post fertilization.

Original comment by: jaiswalp

planteome-user commented 14 years ago

Proposed def'n: A collective plant structure that contains a mature gynoecium, together with any other structures that ripen with it and form a unit with it. POC curators

Original comment by: cooperl09

planteome-user commented 14 years ago

looks fine. Avoid the word 'ripen'. That's the final state of the fruit development. Also mature gynoecium is somewhat discreet. It is mature before fertilization (likely). In fruit we are looking at strictly post-fertilization stage.

A collective plant structure that contains a post-fertlization stage gynoecium together with any other remnant structures of the flower that form a unit with it.

Original comment by: jaiswalp

planteome-user commented 14 years ago

I agree that having a discrete event like fertilization is preferable to the vague term mature, but there are many fruits that mature without fertilization. Is there another event that we can use to define when a fruit is mature? I see that 'fruit development stages' (PO:0001002) is still without children, so this is something we need to think about. It would be great if we could put in a cross product between fruit and the appropriate developmental stage.

Original comment by: rlwalls2008

planteome-user commented 14 years ago

As we refer to the fruit by post fertilization stage (in normal conditions, exception parthenocarpy or other hormone induced), We are always looking at normal majority behavior. Normally it is also a seed bearing structure (with some exceptions, there is no seed). I think use of 'mature' is a relative ambiguity. This plant part part is likely to be used in combination with a varying degree of maturity (growth stage) in the annotations.

Original comment by: jaiswalp

planteome-user commented 14 years ago

POC conf call: Proposed new def'n: A collective plant structure that contains a post-fertilization stage gynoecium and any other structures of the flower that mature with it. (Comment: exception parthenocarpy or other-hormone induced condition)

Original comment by: nobody

planteome-user commented 14 years ago

POC Conf call: A collective plant structure that contains a post-fertilization stage gynoecium. Comment: may contain other remanant structures of the flower need to work further on this

Original comment by: cooperl09

planteome-user commented 14 years ago

I agree with yesterday post :A collective plant structure that contains a post-fertilization stage gynoecium but we need to add in the Pankaj's comment on parhtenocarpic fruits.

Original comment by: magandolfo

planteome-user commented 14 years ago

I agree with Pankaj and Alejandra. I am not sure how to do it to include parthenocarpy. Something about a ripening gynoecium? Perhaps add "or a ripening gynoecium."

Original comment by: dws409

planteome-user commented 14 years ago

Fruit would always be there as an organ. In a normal case it will have seeds. You can have another child 'parthenocarpic fruit' and since that's mostly abnormal behavior, I believe its a cross product with PO and GO with the terms 'parthenocarpy' existing in the GO biological process.

Original comment by: jaiswalp

planteome-user commented 14 years ago

That works well. One the impending problems is going to fruits from epigynous flowers.

Original comment by: dws409

planteome-user commented 14 years ago

At the POC meeting on 7-14-10, we came up with a new definition.

Proposed def.: A collective plant structure that develops from a gynoecium containing one or more embryos. Comments: A fruit may contain additional plant structures that were part of the flower that mature along with the gynoecium, such as a receptacle. A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions.

The advantage of using embryo in the definition, rather than post-fertilization stage gynoecium, is that it encompasses fruits that develop without fertilization.

Original comment by: rlwalls2008

planteome-user commented 14 years ago

is there an equivalent in non-angiosperms like fruiting body.

Original comment by: jaiswalp

planteome-user commented 14 years ago

The gynoecium is made of carpels, and carpels are megasporophylls. In gynomsperms (at least some, not sure if all), the megasporophyll is known as the ovuliferous scale, and it remains attached to the seed, so it is similar to a fruit. In my comment below from 2010-04-13, this is what Spjut refers to when he talks about fruits in the very broad sense.

There are sporophylls in pteridophytes, but I think in all cases the spores are dispersed, so the sporophyll does not mature with the embryo and there is no structure comparable to fruit..

Original comment by: rlwalls2008

planteome-user commented 14 years ago

Definition accepted at POC meeting on 7-21-10: A collective plant structure containing one or more embryos, which as a whole, develops from a gynoecium.

Comments: AA fruit may contain additional plant structures that were part of the flower that mature along with the gynoecium, such as a receptacle. A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions. Fruits only occur in angiosperms.

develops_from gynoecium

Dbxref to parthenogenesis: MP:0009443

Did not add dbxref to NCBI taxon Angiosperm. Waiting to see if we decide to make this a general practice.

Original comment by: rlwalls2008

planteome-user commented 14 years ago

I am closing this item.

Did not include dbxref to parthenogenesis (to broad).

Original comment by: rlwalls2008

planteome-user commented 12 years ago

Based on discussion at POC meeting on 6-12-12, we decided to make fruit a subclass of the new term multi-tissue plant structure (PO:0025496).

Fruit develops from gynoecium, which is a collective plant structure, but it can actually develop from one or more carpels (depending on type of gynoecium) and it includes other structures as well.

New proposed definition, based on existing definition, but with new is_a parent: A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062) and has or more plant embryos (PO:0009009) located within it.

comment: A fruit may contain additional plant structures that were part of the flower that mature along with the gynoecium, such as a receptacle. A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions. Fruits only occur in angiosperms.

Original comment by: rlwalls2008

planteome-user commented 12 years ago

The embryos, are actually located in the seeds, which are part of a fruit. Why not say a fruit has as parts one or more seeds, instead of saying it has one or more embryos located in it. Seems like we are adding an extra layer.

Original comment by: rlwalls2008

planteome-user commented 12 years ago

I think the new parent works well, but not all fruits contain seeds with embryos , as we mention in the comment.

New proposed definition: A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062) and usually has as parts one or more seeds located in it

Original comment by: cooperl09

planteome-user commented 12 years ago

At the POC meeting on 6-19-12, we agreed to make fruit a subtype of multi-tissue plant structure, and to modify the comment to say it has seeds as parts, rather than embryos.

revised def.: A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062) and may have as parts one or more seeds (PO:0009010).

comment: A fruit may contain additional plant structures (PO:0009011) that were part of a flower (PO:0009046) and mature along with the gynoecium, such as a receptacle (PO:0009064). A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions and may not always contain seeds. Fruits only occur in angiosperms.

Original comment by: rlwalls2008

planteome-user commented 12 years ago

Comment from DWS: in the manuscript: Parthenocarpy is a type of apomixes so that is redundant here.

Original comment by: cooperl09

cooperl09 commented 8 years ago

Proposed revisions to fruit (PO:0009001): New child terms for fruit types

At the Oct. 11, 2016 conference call, we decided to add the various the fruit types to the PO as separate terms. This will improve the coordination between Plant Ontology and the Trait Ontology. http://wiki.planteome.org/index.php/Oct_11th,_2016_Ontology_Working_Group_Meeting

The fruit types that are currently listed as synonyms will be added as stand alone terms in the PO. The main categories of fruits will be (see the associated trackers for each):

Thanks so much to @btsinn and @DarioJCavaliere for all the hard work on this!

cooperl09 commented 8 years ago

Also proposing a slight modification of the definition and comment to accommodate this change:

Current Def’n: A multi-tissue plant structure (PO:0025496) which develops from a gynoecium (PO:0009062) and may have as parts one or more seeds (PO:0009010).

Current Comment: A fruit may contain additional plant structures (PO:0009011) that were part of a flower (PO:0009046) and mature along with the gynoecium, such as a receptacle (PO:0009064). A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions and may not always contain seeds. Fruits only occur in angiosperms.

Proposed Def’n Revision: A multi-tissue plant structure (PO:0025496) which develops from a gynoecium (PO:0009062), or a single carpel (PO:0009030), and may have as parts one or more seeds (PO:0009010).

Proposed Comment Revision: A fruit may contain additional plant structures (PO:0009011) that were part of a flower (PO:0009046) and mature along with the gynoecium, such as a receptacle (PO:0009064). A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions and may not always contain seeds. When annotating to fruit (PO:0009001) that are referred to as ‘aggregate’, ‘multiple’, or ‘compound’, please annotate directly to the appropriate plant structure, such as receptacle, hypanthium (PO:0009065) or infructescence (PO:0006342). Fruits only occur in angiosperms.