SourceForge meeting 2015-03-25

From GO Wiki
Jump to: navigation, search

proteolysis, protein processing, protein modification, protein maturation (Tanya)

Who belongs where? Protein processing, proteolysis, protein maturation

Is small molecule (Ub, SUMO, Ned) removal under proteolysis or not?

ChEBI mapping consult (Tanya)

https://sourceforge.net/p/geneontology/ontology-requests/11583/

What do we do with ChEBI has functional parent relationships? Reminder please.

 nucleobase-containing molecular entity (CHEBI:61120) has_functional_parent nucleobase (CHEBI:18282) 
 pyrimidine nucleobase is_a pyrimidines (CHEBI:39447) [which we are using in mapping pyrimidine-containing compound]

Result is that nucleobase BP is not inferred to be is_a nucleobase-containing compound BP.

Vesicles are always bound by a membrane

Currently, our def of ‘vesicle’ is: “Any small, fluid-filled, spherical organelle enclosed by membrane or protein.”. As such, it does not have membrane-bounded parentage. The vesicle experts disagreed with this - they claim that all bona fide vesicles are bound by a membrane. I tend to agree with this and so does wikipedia (http://en.wikipedia.org/wiki/Vesicle_(biology_and_chemistry): “In cell biology, a vesicle is a small organelle within a cell, consisting of fluid enclosed by a lipid bilayer membrane.”). Therefore, I would clean up this branch so that there is no need for membrane-bounded or non-membrane bounded vesicles. Any objections? Looking at current children of ‘vesicle’, there’s only one that is not membrane-bounded:

[Term] id: GO:0031411 name: gas vesicle namespace: cellular_component def: "A hollow structure made of protein, which usually has the form of a cylindrical tube closed by conical end caps. By regulating their relative gas vesicle content aquatic microbes are able to perform vertical migrations." [PMID:8177173] subset: gosubset_prok is_a: GO:0031410 ! cytoplasmic vesicle is_a: GO:0043232 ! intracellular non-membrane-bounded organelle [added 2005, last edited 2008]

The purely proteinaceous component is shown in figure on page 106 in the supporting ref: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC372955/ and in more detail here: http://www.jbc.org/content/early/2011/12/06/jbc.M111.313049.full.pdf (PMID:22147705) Where the ‘organelle’ status of gas vesicles is confirmed.

These are called ‘gas vacuoles’ elsewhere - note that they’re defined as membrane-bound here, but there is no evidence of membranes: http://en.wikipedia.org/wiki/Bacterial_cell_structure#Gas_vacuoles

This organelle is not spherical or fluid filled, either. I propose to - remove the ‘cytoplasmic vesicle’ parentage - polish def to say “An intracellular non-membrane-bounded organelle; a hollow structure made of protein, which usually has the form of a cylindrical tube closed by conical end caps. By regulating their relative gas vesicle content, aquatic microbes are able to perform vertical migrations.” - add PMID:22147705 - add definition comment: Note that although this organelle is commonly referred to as a ‘vesicle’ or ‘vacuole’ in the literature, it is not surrounded by a membrane. - add related synonym: gas vacuole

Note for self: ‘gas vesicle organization’ would need to be edited accordingly.

A minor note: this other child of ‘vesicle’ might need a small tweak to better fit under this branch:

[Term] id: GO:1990257 name: piccolo-bassoon transport vesicle namespace: cellular_component def: "A cytoplasmic dense-core vesicle, or aggregate of vesicles and proteins, that range in size from approximately 80 nm in diameter for dense core vesicles to 130 nm by 220 nm in area for aggregates. Proteins transported by piccolo-bassoon transport vesicle (PTVs) include piccolo, bassoon, N-cadherin and syntaxin. PTVs are packaged via the trans-Golgi network before being transported through the axon." [GOC:dr, PMID:21569270] synonym: "PTV" EXACT [] is_a: GO:0031410 ! cytoplasmic vesicle

These are vesicles - the ‘aggregate’ is the vesicle carrying some of the proteins by its outside membrane, rather than enclosed within the vesicle. (If you do a Google search for images for ‘piccolo-bassoon transport vesicle’ you’ll see what I mean.) I think we’d still represent this as a vesicle, rather than a different type of organelle. Agree? If yes, I’d leave the term as is but modify its def slightly to

“A cytoplasmic dense-core vesicle that transports a range of proteins including piccolo, bassoon, N-cadherin and syntaxin. The transported proteins may be associated with the external side of the vesicle, rather than being contained within the vesicle, therefore forming an aggregate of vesicle and proteins. Piccolo-bassoon transport vesicles (or PTVs) range in size from approximately 80 nm in diameter for dense core vesicles to 130 nm by 220 nm in area for aggregates. They are packaged via the trans-Golgi network before being transported through the axon.”

And I’d make the PTV synonym related instead of exact (BTW, David H, did you have a chance to ask Judy about synonyms perhaps?).

Wrong TG template?

In today's TG review queue:

name: negative regulation of transcription from RNA polymerase II promoter involved in negative regulation of neuron apoptotic process

name: positive regulation of transcription from RNA polymerase II promoter involved in neuron fate specification

name: positive regulation of transcription from RNA polymerase II promoter involved in neuron differentiation

Supporting papers show transcription upstream of apoptosis/specification/differentiation. Use results_in template and then change en masse?