Yolk - cellular component

[gocentral]

Definition: Membrane-enclosed nutrient reserve or energy source for the developing embryo; may or may not be surrounded by the yolk sac.

Reference for definition: NCBI book Developmental Biology, 6th Edition Scott F. Gilbert SWARTHMORE COLLEGE SINAUER ASSOCIATES, INC., Publishers, Sunderland, Massachusetts ISBN 0-87893-243-7 (cloth)2000 Part 1. Principles of development in biology Developmental Patterns among the Metazoa and Figure 2.22

Synonyms: Nutrient reservoir

GO hierarchy: I..Cellular Component … I..Cell ………P..Cell part ………….I..Intracellular ………………P...Intracellular part ……………………I..Cytoplasm ……………………………P..Cytoplasmic part ……………………………………..I…Yolk (new term request) …………………………………………….P….Yolk granule

Note: • Right now the existing term ‘yolk granule’ has a is_a relationship with ‘cytoplasmic part’ which should become part-of relationship with the new term ‘yolk’ once the term is assigned. • There are very less cellular component terms in development. There is a need for other cellular components terms also like egg, oocyte, yolk sac, ovarian follicle, yolk plasma and germ cell. Lot of proteins seem to be present in these developmental structures and can be annotated if the terms are available.

Reported by: lakshmipillai

Original Ticket: "geneontology/ontology-requests/5616":https://sourceforge.net/p/geneontology/ontology-requests/5616

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New Go term -yolk - cellular component

Original comment by: lakshmipillai

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The GO cellular component ontology (GO CC) is an ontology of physical entities at the cellular level, but includes mainly parts of cells, plus a few extracellular things that are biologically relevant at the level of a cell. GO CC does not include different cell types or any multicellular anatomical structures; these belong in different ontologies such as the OBO Cell Ontology and various anatomy ontologies.

Egg, oocyte, and germ cell are types of whole cells, and the ovarian follicle is a multicellular structure, so none of these would fit into GO CC. I think the yolk sac is also multicellular.

Although the yolk is present in the egg, and is therefore a subcellular component at that time (developmental stage), it is not enclosed in a membrane until later in development. I would therefore prefer to have only the existing "yolk granule" term in GO CC to avoid confusion.

What is the difference between yolk plasma and yolk?

Midori

Original comment by: mah11

[gocentral]

Hi Midori,

Yolk can be fractionated into yolk plasma and yolk granules; the plasma containing the water soluble components. So yolk plasma could be the sibling term for yolk granule and both could have a part_of relationship with yolk as cellular components. If needed, the definition I previously suggested for yolk as a cellular component could be modified to not include any multicellular structures like the yolk sac. New definition for yolk: Nutrient reserve or energy source for the developing embryo; may or may not be membrane enclosed.

Additional references: 1) PMID: 18046696 2) PMID: 17941695 3) Determination of Main Mineral Contents in Hen's Egg Yolk Fractions Toshio Wakamatu, Yasushi SatoAgric. Biol. Chem., 46 (2), 577-578, 1982 577

Thanks, Laks

Original comment by: lakshmipillai

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• assigned_to: nobody --> ukemi

Original comment by: ukemi

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Added:

GO:0060417, yolk GO:0060418, yolk plasma

Structure:

--cytoplasmic part --[i]yolk (new) ----[p]yolk plasma (new) ----[p]yolk granule --[i]yolk plasma (new) --[i]yolk granule

Original comment by: tberardini

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• status: open --> closed-fixed

Original comment by: tberardini