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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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general term for amyloid formation #8616

Closed gocentral closed 9 years ago

gocentral commented 13 years ago

Is there a generic term for the formation of amyloid fibrils, i.e. from all amyloid precursor proteins, not just beta-amyloid? i couldn't find one and have just finished a new pathway for this in Reactome. I imagine it would go into biological process under GO:0043206 : fibril organization.

Reported by: jupes1

Original Ticket: geneontology/ontology-requests/8404

gocentral commented 13 years ago

Original comment by: paolaroncaglia

gocentral commented 13 years ago

Original comment by: paolaroncaglia

gocentral commented 12 years ago

Need a generic term for amyloid formation for paper curation. PubMed: 21148556 discusses amyloid fibril formation of pmel17 in melanosomes.

Original comment by: cerivs

gocentral commented 12 years ago

Hi Steve and Ceri, Sorry to keep you waiting. I'll work on this during the week. Best, Paola

Original comment by: paolaroncaglia

gocentral commented 12 years ago

See also related SF request: https://sourceforge.net/tracker/?func=detail&aid=3300906&group\_id=36855&atid=440764

Original comment by: paolaroncaglia

gocentral commented 12 years ago

Hi Steve, Ceri, and Janet,

I'm having trouble finding a correct placement for the proposed new general term "amyloid fibril formation".

Steve suggested to place it under GO:0043206 : fibril organization. However, this is defined as "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of fibrils, extracellular matrix material consisting of polysaccharides and protein." and is a child of GO:0030198 extracellular matrix organization. Most amyloid fibers quoted in Ceri's suggested reference are indeed extracellular, but fibrils formed by pmel17 are intracellular aggregates. The same can be found in PMID: 18487849. So, it would be incorrect to place GO:NEW amyloid fibril formation as is_a GO:0043206 : fibril organization.

Janet suggested replacing 'beta-amyloid formation' GO:0034205 by the new general term 'amyloid fibril formation', or to alter definition of 'beta-amyloid formation' GO:0034205 to include all other known amyloid-forming proteins. My only doubt with this approach is that the current grandparent of 'beta-amyloid formation' is GO:0009100 glycoprotein metabolic process, and I'm not 100% sure that all proteins listed in the PMIDs above are indeed glycosylated, in particular the bacterial curli protein. (Pmel17 is indeed glycosylated.) Would you have any suggestions or comments on this?

Many thanks in advance for your feedback. Regards, Paola

Original comment by: paolaroncaglia

gocentral commented 11 years ago

Original comment by: paolaroncaglia

gocentral commented 11 years ago

Dear Steve and Ceri, sorry this took so long, but it's all done now.

Short answer: the term you need is GO:1990000 amyloid fibril formation.

Longer answer: For details on how I've (re)structured the fibril terms, please refer to this related SF request: https://sourceforge.net/tracker/?func=detail&aid=3557931&group\_id=36855&atid=440764

Thanks for your patience! Paola

Original comment by: paolaroncaglia