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New term request: Cotyledon colour #353

Closed KarthikaRajendran closed 8 years ago

KarthikaRajendran commented 9 years ago

Definition:A trait describing the colour of cotyledon Method:To be observed on seeds less than three months old Scale:1 to 3 colour scale Reference:Key access and utilization descriptors for lentil genetic resources (http://www.bioversityinternational.org/e-library/publications/detail/key-access-and-utilization-descriptors-for-lentil-genetic-resources/)

phismith commented 9 years ago

Traits do not describe. People describe by using words. The trait here is the color of the cotyledon BS

On Fri, Nov 13, 2015 at 3:04 PM, Karthika Rajendran < notifications@github.com> wrote:

Definition:A trait describing the colour of cotyledon Method:To be observed on seeds less than three months old Scale:1 to 3 colour scale Reference:Key access and utilization descriptors for lentil genetic resources ( http://www.bioversityinternational.org/e-library/publications/detail/key-access-and-utilization-descriptors-for-lentil-genetic-resources/ )

— Reply to this email directly or view it on GitHub https://github.com/Planteome/plant-trait-ontology/issues/353.

austinmeier commented 9 years ago

From the reference provided: "To be observed on seeds less than three months old." If lentil seeds are still considered "seedlings" before a seed is 3 months old we can use the TO term:

seedling cotyledon color (TO:0000750): A seedling cotyledon morphology trait (TO:0000774) which is the color of a seedling cotyledon (PO:0025471).

maxglycine commented 9 years ago

This is a difficult thing (what is a seedling). I found a definition that said it was a seed from germination to the development of the first true leaves. This gets around the problem of different rates of growth (germplasm X environment).

But just so I know if I am going in the correct direction, shouldn’t the definition be:

“A seedling cotyledon morphology trait (TO:0000774) which is the color (PATO:0000014) of a seedling cotyledon (PO:0025471)"

austinmeier commented 9 years ago

It is true that we should include the PATO ID of any term where we use it, but we have traditionally put the PATO ID in the comments or DBXrefs section of the OBO edit program. I am not sure how these should be handled in Protege. Maybe Chris could weigh in?

KarthikaRajendran commented 9 years ago

Dear all, cotyledon colour is the seed quality trait. Usually it is yellow, red and orange in colour. It is not the seedling trait. It is said to be observed on seeds less than three months old because when seeds get old the colour will become dull some what. Usually the phenolic compounds in the seed determines the colour retention of seed cotyledon and seed coat colour.

KarthikaRajendran commented 9 years ago

Lentil seeds have very little or no endosperm in it. Cotyledons serves the food reserve for the embryo and account for more than 80% of seed weight. Eventually they are called as cotyledon colour.

KarthikaRajendran commented 9 years ago

Definition: A trait used to classify the cotyledon color.

cooperl09 commented 9 years ago

Thank you for the clarification- in the PO this would be called "plant embryo cotyledon (PO:0025470)' since it is assessed on the seeds before germination.

austinmeier commented 9 years ago

As for Rex's terms request, I would point you to the PO definition of seedling development stage (PO:0007131): A sporophyte vegetative stage (PO:0007134) that succeeds the seed germination stage (PO:0007057) and terminates with the development of the first adult vascular leaf (PO:0006340).

If your soy trait is measured during the seedling development stage as defined by the PO, then you can use "seedling cotyledon color" (TO:0000750) as described above. If not, we can make a new term that will encompass the trait you are trying to map.

cmungall commented 9 years ago

Use TermGenie for any trait that conforms to the attribute-entity pattern

Permanent URL (up now) http://to.termgenie.org

cmungall commented 8 years ago

Follow on here: https://github.com/Planteome/plant-ontology/issues/614

austinmeier commented 8 years ago

Created new term: plant embryo cotyledon color (TO:0000980): A plant embryo cotyledon morphology trait (TO:0000775) which is the color of a plant embryo cotyledon (PO:0025470). added xref: PATO:0000014

austinmeier commented 8 years ago

added new exact synonym "plant embryo cotyledon colour"

maxglycine commented 8 years ago

Since the definition states that it is the "embryo cotyledon color” does that mean that we need a “seedling cotyledon color” also? This underscores the problem of putting a developmental state in the definition. I am of the opinion that it should not because the trait is the trait regardless of developmental state (cotyledon color). To express the developmental state, we should be able to state the following:

The trait = cotyledon color. The developmental state = embryo or seedling. The anatomical part = cotyledon (self explanatory in this instance)

Thus to fully describe a phenotype, we would need a triplet (trait, anatomical part, developmental state). This will also solve the problem of having separate terms for the same trait at different developmental time points.

What I don’t know is whether this system can be “reasoned” over.

cooperl09 commented 8 years ago

The reason we differentiate between the seedling cotyledon color and embryo cotyledon color is that these are separate plant structures in the PO.
plant embryo cotyledon (PO:0025470) and seedling cotyledon (PO:0025471).
Both these plant structures are defined in terms of the developmental stage they exist in, so the dev. stage does not need to be restated, it is inherent.

cmungall commented 8 years ago

This can indeed be reasoned over

The only decision is whether to pre-compose the term in TO, or to post-compose (use two fields at the time of annotation)

Provided the design pattern is the same, then the two representations would be inferred equivalent

 'cotyledon color' and happens_during some 'embryo stage'

On 2 Dec 2015, at 8:08, Rex Nelson wrote:

Since the definition states that it is the "embryo cotyledon color”
does that mean that we need a “seedling cotyledon color” also?
This underscores the problem of putting a developmental state in the definition. I am of the opinion that it should not because the trait is the trait regardless of developmental state (cotyledon color). To express the developmental state, we should be able to state the following:

The trait = cotyledon color. The developmental state = embryo or seedling. The anatomical part = cotyledon (self explanatory in this instance)

Thus to fully describe a phenotype, we would need a triplet (trait, anatomical part, developmental state). This will also solve the problem of having separate terms for the same trait at different developmental time points.

What I don’t know is whether this system can be “reasoned” over.

On Dec 1, 2015, at 4:56 PM, Austin Meier notifications@github.com<mailto:notifications@github.com> wrote:

added new exact def'n "plant embryo cotyledon colour"

— Reply to this email directly or view it on GitHubhttps://github.com/Planteome/plant-trait-ontology/issues/353#issuecomment-161123702.

Rex Nelson Computational Biologist G329 Agronomy Hall Iowa State University Ames, IA 50011 nelsonrt@iastate.edumailto:nelsonrt@iastate.edu 515-294-1297

"Time flies like an arrow. Fruit flies like a banana"

Reply to this email directly or view it on GitHub: https://github.com/Planteome/plant-trait-ontology/issues/353#issuecomment-161347556