Talk:List of proteins

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Perhaps we need to define our protein naming ontology here?

Generic protein classes (like billins) above more specific protein names (like phycobillin). Perhaps that is a bad example, but proteins have general names and isoforms and synonyms and alternate spellings, all of which should be described by some naming ontology to allow best use of the community effort. Currently there is no protein naming ontology in existence, where better than wiki to start one? --Dan|^(talk) 13:08, 2 August 2005 (UTC)

Possible starting place: GO slims, whole proteome analysis (wikipedia proteome root page). --JWSchmidt 02:59, 4 September 2005 (UTC)

[edit] Shouldn't even start

I don't think this list should exist. There is no use in having a list of ALL proteins - it would get so long and cumbersome that it would be of no use to anyone. We're better off starting much more specific lists, like "List of motor proteins," "List of cell cycle proteins," "List of proteins in proteolysis," etc. and then grouping those lists into a List of protein lists. Mr.Bip 20:45, 3 August 2005 (UTC)

I agree with User:Mr.Bip JOK 12:38, 7 September 2005 (UTC)

[edit] Molecular and Cellular Biology project

Organizing wikipedia coverage of proteins is a major goal of Wikipedia:WikiProject Molecular and Cellular Biology. Please help. --JWSchmidt 20:10, 28 August 2005 (UTC)

Enzymes. This page should not simply reproduce List of enzymes. This page should have categories of enzymes mainly according to biological function, not type of chemical reaction. --JWSchmidt 13:39, 2 September 2005 (UTC)

"By the reactions they catalyze" - this is how the enzymes are clasified. BorisTM 06:46, 25 October 2005 (UTC)

I recommend removing the enzymes from this page, and just having that section refer to List of enzymes. We could still include the categories of enzymes though (like Restriction enzymes, etc.), perhaps with cross references to the appropriate EC number categories. Any objections? --Arcadian 16:58, 27 November 2005 (UTC)

See also: Whole proteome analysis. --JWSchmidt 17:36, 27 November 2005 (UTC)

What's the intended future relationship between Whole proteome analysis and List of proteins? --Arcadian 20:01, 27 November 2005 (UTC)

The List of proteins was created by User:Dmb000006 on 2 August 2005 with this goal: "This list aims to organize information on the protein universe". Also on 2 August 2005, User:Dmb000006 mentioned the need for a "naming ontology" for proteins and seemed to suggest that Wikipedia could invent one (see the first entry on this page, above). On 28 August 2005 I noticed that List of proteins existed and my first concern was how to deal with enzymes. I suggested that the List of proteins could sort enzymes according to categories of biological function rather than according to reaction type (as is done at List of enzymes). By 3 September 2005 I had found that there was an existing system for categorizing proteins (at geneontology.org) and so I attempted to copy that system to the Wikipedia Whole proteome analysis page. At that time, my hope was that Wikipedia could make use of that list of protein categories to help organize information about proteins while possibly ending up with a system that would match a system used by people outside of Wikipedia. Yes, Wikipedia could develop its own unique system for categorizing proteins, but that might not be the best thing to do. However, It is not clear how influential the system from geneontology.org will be, and there has been no consensus at Wikipedia to adopt that system. The List of proteins was under development for about a month before the Whole proteome analysis page was started. My expectation is that, with time, Wikipedia will evolve an organized way to present a large amount of infomation about a large number of proteins. My best guess: the List of proteins will evolve into a set of links to the major categories of protein types. The Whole proteome analysis page will probably come to have the same list of protein categories while also including a description of each category and links to Wikipedia articles that describe the biological processes that are made possible by the various types of proteins. --JWSchmidt 21:00, 27 November 2005 (UTC)

OK. How would you feel then if Whole proteome analysis was renamed to List of types of proteins, with an opening paragraph describing the relationship to Proteomics/Proteome? Perhaps the List of proteins should have a simple taxonomy that is mutually exclusive and exhaustive, covering proteins that can't go into List of enzymes. Because so many proteins fall into multiple categories, we'll probably have to rely upon Wikipedia:Category schemes for any long-term detail work, but we could use List of types of proteins to help provide orientation. Sound okay? (It sounds like we're the only two people working on this right now.) --Arcadian 21:27, 27 November 2005 (UTC)

Since I have no talent for naming things, I just adopted a name (Whole proteome analysis) that was used at geneontology.org. I have no objection to a name change for that page.

"mutually exclusive" <-- I hope we agree that there is nothing wrong with individual proteins or even families of proteins being categorized in multiple Wikipedia protein-related categories. Many proteins are complex and have several functional domains. For such proteins there are likely to be multiple Wikipedia categories that are relevant. --JWSchmidt 23:49, 27 November 2005 (UTC)

Sounds like we're on the same page. I only meant that on List of proteins, each protein would be only listed once. Of course, when using the wikipedia category system, we can put them into as many as are appropriate. I've renamed the other page, and removed the enzyme section from this page. There are still some enzymes on this page that were in other sections, but they can be taken care of piecemeal. --Arcadian 01:51, 28 November 2005 (UTC)

If we want the molbio-science comunity to take "Wikioedia" seriously I think we should not try to create (in our own standart) something that has already been created (databases, naming systems. etc.) by hundreds of researchers from all over the world, what we can do is to add something new that will complement all this information. As of now if a researcher, a student, or just a curious reader want(s) to find a match for an amino acid or nucleotide sequence, or to find the very basic information about a gene, protein or a small molecule - such as chromosome location, gene/protein/molecule number, weight, relative position in a signaling network and so on, they can do that using many different tools wasting notime, but what if they want to learn something more about the function of that gene/protein/molecule - how this gene is activated, what proceses control its function, protein modifications and why they happen, what makes them, how they affect the function, how they(small molecules) are synthesized, what affects the speed of that synthesis and etc. - there is nothing that can provide all this in a single database source that is updated frequently, the best they can do is go to "PubMed", type the search words and get hundreds of refferences to articles, some of them old, some new - the search can be limited but still the info will be so spred out. If they are lucky to search for a better known stuff they could find a review. This is where "Wikipedia" can take over and provide all this info in a single article, kinda like this one (GLUD1) but a lot better. A for the categorization of the proteins i am totally for Whole proteome analysis. Boris 22:37, 28 November 2005 (UTC)

Sounds good. But I can't tell though from your post if you're agreeing with where we're going, or objecting to something. I agree that we should have links to the major databases on every protein or gene page. And I agree that wherever standards exist, we should use them instead of trying to come up with our own (that's one of the reasons that I wanted to remove enzymes from this page and put them on List of enzymes, since there's an established taxonomy for them.) There also seems to be some sort of standard for channel proteins (I just created a stub at TC number, but I don't know very much about it yet.) Are there any other standards you're familiar with for proteins that we could integrate? --Arcadian 23:08, 28 November 2005 (UTC)

[edit] Contradiction found

While actin is classified under fibrous proteins as a member of the cytoskeletal proteins, on its own wiki page says that it is a globular protein as seen in the first sentence. Can a protein be at the same time both fibrous and globular? by user yuanrandong on 26 Oct 2006