search

Planteome / plant-ontology

Repository for the Plant Ontology
Creative Commons Attribution 4.0 International
57 stars 17 forks source link

plant gall #641

Open jaiswalp opened 7 years ago

jaiswalp commented 7 years ago

Sirarat Sarntivijai ‏from twitter @SSirarat 6h6 hours ago

What would be your recommended term for plant's 'gall tissue' (MAT_00003541) if I were to map to PO?

cooperl09 commented 7 years ago

There are many different types of plant galls that can arise as a result of insects or pathogens, including, of course, Agrobacterium tumefaciens (causal agent of crown gall)

The term 'gall tissue' in the MAT is not defined: (http://www.ontobee.org/ontology/MAT?iri=http://purl.obolibrary.org/obo/MAT_0000351), so it's a bit difficult to know exactly what the term is referring to but the closest term in the PO would be:

plant callus: A portion of plant tissue (PO:0009007) that consists of mass of undifferentiated plant cells (PO:0009002). Comment: Consists primarily of parenchyma cells but may contain other cell types as the callus begins to differentiate. May be formed as a result of wounding or may develop in culture.

jaiswalp commented 7 years ago

We may need a generic term Plant Gall...A ground tissue generated in response to an external factor. And then have multiple subclass for -bacteria induced plant gall -insect induced plant gall -etc.

phismith commented 7 years ago

I think that '[portion of] gall tissue' should be added to the Plant Anatomy Ontology -- perhaps as a sibling of 'plant callus' BS

On Thu, Oct 27, 2016 at 8:54 PM, Laurel Cooper notifications@github.com wrote:

There are many different types of plant galls that can arise as a result of insects or pathogens, including, of course, Agrobacterium tumefaciens (causal agent of crown gall)

The term gall tissue in the MAT is not defined: (http://www.ontobee.org/ ontology/MAT?iri=http://purl.obolibrary.org/obo/MAT_0000351), so it's a bit difficult to know exactly what the term is referring to but the closest term in the PO would be:

plant callus: A portion of plant tissue (PO:0009007) that consists of mass of undifferentiated plant cells (PO:0009002). Comment: Consists primarily of parenchyma cells but may contain other cell types as the callus begins to differentiate. May be formed as a result of wounding or may develop in culture.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Planteome/plant-ontology/issues/641#issuecomment-256736060, or mute the thread https://github.com/notifications/unsubscribe-auth/AH6qN2OKeR5Il-FBbxND2_B_5wBo_xtgks5q4PNZgaJpZM4KijH5 .

cmungall commented 6 months ago

@adeans has a proposed gall ontology https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2522 he will be attending the planteome workshop. I suggest this ticket is updated and closed after that workshop. I am curious to see the plan - what will the mutual dependencies be? Will PO import GALLONT or vice versa...?

cooperl09 commented 5 months ago

Revising the definition after further discussions with @adeans plant gall (PO:0025626): A multi-tissue plant structure (PO:0025496) that develops in response to a plant animal damage (PSO:0000004).

cooperl09 commented 5 months ago

Further revision: plant gall (PO:0025626): A multi-tissue plant structure (PO:0025496) that develops in response to a biotic stress (PSO:0000011).