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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)
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)
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)
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)
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)
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
This is not a List of proteins, it is a List of non-enzyme proteins. I believe the name should be changed to reflect this difference as described in the WP:LEAD of the list. Thoughts? ju66l3r 19:04, 18 January 2007 (UTC)
Am I in the wrong place for plant proteins? This is the list of ALL proteins is it not? Velella Velella Talk 20:25, 30 August 2015 (UTC)
I made a new article: List of proteins in the human body , that tries to make a framework for merging the info in this an other sub pages. let me know what you think about the idear and how it could be pulled off better? Claes Lindhardt ( talk) 12:43, 12 July 2023 (UTC)
@ Elemimele:, motivated by your comment on the lack of a readable high level articles about types of proteins, I have largely rewritten this page. This clearly needs a lot more work, but do you think it is going in the right direction? Boghog ( talk) 13:14, 25 July 2023 (UTC)
This article is rated List-class on Wikipedia's
content assessment scale. It is of interest to the following WikiProjects: | ||||||||||||||||||||||||
|
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)
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)
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)
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)
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)
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
This is not a List of proteins, it is a List of non-enzyme proteins. I believe the name should be changed to reflect this difference as described in the WP:LEAD of the list. Thoughts? ju66l3r 19:04, 18 January 2007 (UTC)
Am I in the wrong place for plant proteins? This is the list of ALL proteins is it not? Velella Velella Talk 20:25, 30 August 2015 (UTC)
I made a new article: List of proteins in the human body , that tries to make a framework for merging the info in this an other sub pages. let me know what you think about the idear and how it could be pulled off better? Claes Lindhardt ( talk) 12:43, 12 July 2023 (UTC)
@ Elemimele:, motivated by your comment on the lack of a readable high level articles about types of proteins, I have largely rewritten this page. This clearly needs a lot more work, but do you think it is going in the right direction? Boghog ( talk) 13:14, 25 July 2023 (UTC)