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Repository for the Plant Ontology
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plant anatomical space #203

Closed planteome-user closed 8 years ago

planteome-user commented 13 years ago

At the POC meeting on 11-5-2010, we agreed to add a new root term to the PO: plant anatomical space. This would allow us to include things like stomatal pores.

Proposed definition: An anatomical space that is part of a plant. dbxref: CARO:0000005 anatomical space

Reported by: rlwalls2008

Original Ticket: obo/plant-ontology-po-term-requests/203

planteome-user commented 13 years ago

If we want to have all the independent continuants in one branch of the ontology, we should consider adding a top level term "plant anatomical entity", which would be parent to plant structure and plant anatomical space.

Original comment by: rlwalls2008

planteome-user commented 13 years ago

ok

Original comment by: dws409

planteome-user commented 13 years ago

This term was accepted at the POC meeting on 12-1-10.

Def: An anatomical space (CARO:0000005) that is part of a plant.

xref (CARO:0000005): Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.

Also, we will not use the terms pore and slit, but will make their descendants direct children of plant anatomical space.

Original comment by: rlwalls2008

planteome-user commented 13 years ago

The following terms, which had no is_a parents, were made children of plant anatomical space:

micropyle (PO:0020025): A plant anatomical space that is enclosed by and forms an opening in an integument at the apex of an ovule. part_of integument. Comment: The micropyle originates as an opening in the integuments of an ovule through which the pollen tube usually enters the embryo sac. In a mature seed the micropyle may remain visible as an occluded pore or may be obliterated.

seed micropyle (PO:0006334): A plant anatomical space that is enclosed by and forms an opening in a seed coat at the apex of a seed and is the remnant of a micropyle. relations: develops_from PO:0020025 micropyle; part_of seed coat

stomatal pore (PO:0008032): A plant anatomical space that forms an opening in an epidermis, flanked by two guard cells. [source: POC:curators] Comment: The size of the stomatal pore is variable and controlled by movement of the guard cells in response to environmental cues. synonym: "stomatal aperture" RELATED; relationship: part_of PO:0002000 stomatal complex

floral stomatal pore (PO:0008046): A stomatal pore that is part of a floral stomatal complex. [source: POC:curators] part_of floral stomatal complex

stomium (PO:0020101): A plant anatomical space that is a slit in an anther lobe formed from when a dehiscence zone dehisces. [source: POC:curators] Comment: Pollen may be released through the stomium. subset: reference, relationship: part_of PO:0005011 ! anther dehiscence zone

anther pore (PO:0025118; new term requested by TraitNet):A plant anatomical space that is a pore at the apex of an anther. [source: POC:rw] Comment: Pollen may be released through the anther pore. part_of anther

Original comment by: rlwalls2008

planteome-user commented 13 years ago

correction: anther pore was suggested by Austin Mast for legumes, not by TraitNet.

Original comment by: rlwalls2008

planteome-user commented 12 years ago

Looking through the annotations I noticed today that we have annotation on several of these terms: for example: PO:0025224: axil (1), PO:0020025 : micropyle (1), PO:0020101: stomium (2), PO:0006334 : seed micropyle (1). I believe these annotations should be on the structures surrounding the spaces, not on the spaces themselves. We should probably modify the comment to alert annotators to this.

Original comment by: cooperl09

planteome-user commented 11 years ago

The current definition of plant anatomical space references the CARO term anatomical space: Def: An anatomical space (CARO:0000005) that is part of a plant.

xref (CARO:0000005): Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.

I do not think that the plant anatomical space always "contains one or more organism substances or anatomical structures." What about a pore which only contains air?

Should we have a comment to this effect?

Original comment by: cooperl09

planteome-user commented 11 years ago

I think it won't be necessary, because in CARO2, they have dropped the last part of the definitions.

The new definition is: Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures.

Comment: Original definition: "Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures." The last clause. "contains one or more organism substances or anatomical structures" was dropped from the definition because it was an unnecessary restriction.

If you want to add a comment until CARO2 is officially released, that would be okay, but I think it will be alright as is.

Original comment by: rlwalls2008