platelet formation

[gocentral]

Moved from: [ 1325781 ] term name changes - development terms https://sourceforge.net/tracker/index.php? func=detail&aid=1325781&group_id=36855&atid=440764

There is no need to read the previous item. All info has been copied here.

This term was flagged up by Chris's obol parser as being wrong:

GO:0030220 platelet formation

Suggestion: The standard def can be applied to this term. Jen

Quick question,

What would be the standardized definition of platelet formation? The current definition is quite specific and accurate for this term. Platelets are not really cells per se, but rather specialized cellular blebs lacking nuclei.

Thanks,

Alex

Reported by: jenclark

Original Ticket: "geneontology/ontology-requests/3430":https://sourceforge.net/p/geneontology/ontology-requests/3430

[gocentral]

• labels: 580925 --> Other term-related request

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=735846 Originator: YES

I sent this e-mail to Alex and David:

Hi Alex and David,

Obol has flagged up platelet formation as maybe needing the standard formation definition that goes with development terms. However from what Alex says it seems to me that maybe this is not the kind of formation that is going on here. Might this in fact be a cell organisation and biogenesis kind of a term?

https://sourceforge.net/tracker/index.php?func=detail&aid=1516350&group\_id=36855&atid=440764

Here is the standard def of formation:

x formation The process that gives rise to x. This process pertains to the initial formation of a structure from unspecified parts.

http://www.geneontology.org/GO.process.guidelines.shtml\#devDefs

Platelet formation: The process by which platelets bud from long processes extended by megakaryocytes.

Thanks,

Jen

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=865072 Originator: NO

Jen,

Platelets are of course problematic, since they are cells by many criteria (plasma membrance encloded, well organized with cytoskeleton, regulated signaling and secretion pathways, mitochondria), but they lack nuclei and are not formed via mitosis. They are also considered myeloid cells based on their lineage and origin as parts of megakaryocytes. They clearly have functions and morphology distinct from their parental megakaryocytes, so in fact they are differentiated from megakaryocytes in those respects. Also, their origin is most commonly called 'platelet formation' in the literature, so the term name is correct as far as the biologists are concerned. The definition given is also accurate as to the actual mechanism of platelet formation.

I think the best solution is to leave the term as is with its defintion intact and keep in mind that OBOL is knows nothing about actual biology. One could of course add some more specific terms, such as 'proplatelet organization and biogenesis' as a part_of child of 'platelet formation' and some sort of is_a relationship to 'cell organization and biogenesis' but at the moment I don't see the need for this child term.

Thanks,

Alex

Original comment by: addiehl

[gocentral]

Logged In: YES user_id=735846 Originator: YES

Hi Alex,

Thanks for the really clear explanation. I think that I can probably put something in the structured synonym box to warn off obol confusing this term with the standard formation terms. I'll ask Chris.

Thanks again.

Jen

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=735846 Originator: YES

Alex and I have had a chat on skype and we think the best way to solve this one is to add the structured synonym 'platelet extrusion'.

I will do that tomorrow if nobody objects.

Thanks,

Jen

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=735846 Originator: YES

Hi,

This is going to have to wait for a bug fix in obo-edit but will be done soon.

Jen

Original comment by: jenclark

[gocentral]

• status: open --> closed-out-of-date

Original comment by: jenclark

[gocentral]

• Description has changed:

Diff:

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 Moved from:
 \[ 1325781 \] term name changes - development terms
 https://sourceforge.net/tracker/index.php?

• assigned_to: Jennifer Deegan --> nobody
• Group: Plant Ontology --> None

Original comment by: cooperl09