{"action":"created","issue":{"url":"https://api.github.com/repos/geneontology/go-ontology/issues/12099","labels_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12099/labels{/name}","comments_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12099/comments","events_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12099/events","html_url":"https://github.com/geneontology/go-ontology/issues/12099","id":111685237,"number":12099,"title":"NTRs: supramolecular structure/complex, protein fibril","user":{"login":"paolaroncaglia","id":4982516,"avatar_url":"https://avatars.githubusercontent.com/u/4982516?v=3","gravatar_id":"","url":"https://api.github.com/users/paolaroncaglia","html_url":"https://github.com/paolaroncaglia","followers_url":"https://api.github.com/users/paolaroncaglia/followers","following_url":"https://api.github.com/users/paolaroncaglia/following{/other_user}","gists_url":"https://api.github.com/users/paolaroncaglia/gists{/gist_id}","starred_url":"https://api.github.com/users/paolaroncaglia/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/paolaroncaglia/subscriptions","organizations_url":"https://api.github.com/users/paolaroncaglia/orgs","repos_url":"https://api.github.com/users/paolaroncaglia/repos","events_url":"https://api.github.com/users/paolaroncaglia/events{/privacy}","received_events_url":"https://api.github.com/users/paolaroncaglia/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/geneontology/go-ontology/labels/New%20term%20request","name":"New term request","color":"bfe5bf"},{"url":"https://api.github.com/repos/geneontology/go-ontology/labels/protein%20complex","name":"protein complex","color":"ededed"}],"state":"open","locked":false,"assignee":{"login":"dosumis","id":112839,"avatar_url":"https://avatars.githubusercontent.com/u/112839?v=3","gravatar_id":"","url":"https://api.github.com/users/dosumis","html_url":"https://github.com/dosumis","followers_url":"https://api.github.com/users/dosumis/followers","following_url":"https://api.github.com/users/dosumis/following{/other_user}","gists_url":"https://api.github.com/users/dosumis/gists{/gist_id}","starred_url":"https://api.github.com/users/dosumis/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dosumis/subscriptions","organizations_url":"https://api.github.com/users/dosumis/orgs","repos_url":"https://api.github.com/users/dosumis/repos","events_url":"https://api.github.com/users/dosumis/events{/privacy}","received_events_url":"https://api.github.com/users/dosumis/received_events","type":"User","site_admin":false},"milestone":null,"comments":1,"created_at":"2015-10-15T19:02:21Z","updated_at":"2015-10-16T07:15:21Z","closed_at":null,"body":"Background: Stan requested this term via TG FF:\r\n\r\nid: GO:1990870\r\nname: protein fibril\r\nnamespace: cellular_component\r\ndef: \"A polymer of proteins that form a fine fiber.\" [PMID:12764608]\r\nis_a: GO:0043234 ! protein complex\r\n\r\nAfter extensive discussion, at the editors call today we resolved the following:\r\n\r\n- David OS will implement his proposal of having a new term for ‘supramolecular structure’ (or ‘supramolecular complex’?). Where appropriate, existing terms may be housed under the new term. \r\n\r\n- ‘Protein aggregate’ - Alex Diehl has been working on this - we may wish to have a similar grouping class in GO; to be defined as David’s work progresses.\r\n\r\n- Stan’s ‘protein fibril’ will be obsoleted, because 1) it shouldn’t be a protein complex and 2) it is unclear if the structure observed in PMID:12764608 is pathological only and therefore out of scope; this may not always be the case. \r\n\r\n- Once David’s proposal is implemented, David will see if it is appropriate to host ‘protein fibril’ in GO. Possibly yes (but not under ‘protein complex’). Will keep in mind Stan’s note: “It seems that “protein fibrils” may be pathological in some cases and normal in others (zona pellucida, PMID:26043223).  It may be similar to “neurofibrillary tangle” (GO:0097418), which seems to be mostly pathological.  Maybe “protein aggregate” would be a good intermediate term to place between “macromolecular complex” (GO:0032991) and a potential protein fibril term.”\r\n\r\n- David to also consider Karen’s comment: “I was wondering whether this is intended to cover things like keratohyalin granules (storage structures for the precursor proteins which are processed to form the stratum corneum), where there is a structure composed of an indeterminate number of things, but where I think you might not be able to say it has a higher order structure. It seems we need something that can cover these sorts of less organized large scale structures.”\r\n\r\nReferences: \r\n- email thread 'protein fibril' on the ontology mailing list\r\n- minutes of today’s editors call: \r\nhttp://wiki.geneontology.org/index.php/Ontology_meeting_2015-10-15#Supramolecular_complex\r\nhttp://wiki.geneontology.org/index.php/Ontology_meeting_2015-10-15#Related_.2F_Follow-up:_protein_fibril\r\n\r\nThanks!\r\n\r\nPaola"},"comment":{"url":"https://api.github.com/repos/geneontology/go-ontology/issues/comments/148634773","html_url":"https://github.com/geneontology/go-ontology/issues/12099#issuecomment-148634773","issue_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12099","id":148634773,"user":{"login":"bmeldal","id":10517124,"avatar_url":"https://avatars.githubusercontent.com/u/10517124?v=3","gravatar_id":"","url":"https://api.github.com/users/bmeldal","html_url":"https://github.com/bmeldal","followers_url":"https://api.github.com/users/bmeldal/followers","following_url":"https://api.github.com/users/bmeldal/following{/other_user}","gists_url":"https://api.github.com/users/bmeldal/gists{/gist_id}","starred_url":"https://api.github.com/users/bmeldal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bmeldal/subscriptions","organizations_url":"https://api.github.com/users/bmeldal/orgs","repos_url":"https://api.github.com/users/bmeldal/repos","events_url":"https://api.github.com/users/bmeldal/events{/privacy}","received_events_url":"https://api.github.com/users/bmeldal/received_events","type":"User","site_admin":false},"created_at":"2015-10-16T07:15:20Z","updated_at":"2015-10-16T07:15:20Z","body":"Collagens are definitely fibrils made up of multiples of defined trimers.\r\n\r\nDavid and I worked with Sylvie from MatrixDB last year to tidy up the collagens into their morphological groups. \r\nGO:0005581 collagen trimer\r\nDef: A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures.\r\n\r\nAnd its higher order structures:\r\nGO:0098644 complex of collagen trimers\r\nDef: A complex of collagen trimers such as a fibril or collagen network. \r\n\r\n...which actually is not a complex and needs to be reworked.\r\nWe discussed this briefly last week with David in the complex ontology WG.\r\n\r\nOn the other hand, things like amyloid fibers (fibriles?) are definitely pathological. \r\n\r\nSo I think Stan & Karen were both right with their general observations but I haven't read Stan's paper to know the context of his term request.\r\n\r\nBirgit"}}