This template is within the scope of WikiProject Infoboxes, a collaborative effort to improve the coverage of Infoboxes on Wikipedia. If you would like to participate, please visit the project page, where you can join the discussion and see a list of open tasks.InfoboxesWikipedia:WikiProject InfoboxesTemplate:WikiProject InfoboxesInfoboxes articles
This template is within the scope of WikiProject Chemistry, a collaborative effort to improve the coverage of chemistry on Wikipedia. If you would like to participate, please visit the project page, where you can join the discussion and see a list of open tasks.ChemistryWikipedia:WikiProject ChemistryTemplate:WikiProject ChemistryChemistry articles
This template is within the scope of WikiProject Molecular Biology, a collaborative effort to improve the coverage of Molecular Biology on Wikipedia. If you would like to participate, please visit the project page, where you can join the discussion and see a list of open tasks.Molecular BiologyWikipedia:WikiProject Molecular BiologyTemplate:WikiProject Molecular BiologyMolecular Biology articles
It looks great. But it can't be used for proteins that aren't enzymes - they don't have EC number. If you can make it a little flexible, the same way you intended to do it with the EC number - to be able to display the links to the pages if the numbers (any number in the template) are provided, and when they are not, just to show the default link to that site, even when the variable is ommited intirely as it is "RefSeq" in the example bellow.
I would support that -- can you provide a sample URL? Also, does anybody object if I rebuilt the template -- perhaps to make it more like the new Template:Drugbox template? --Arcadian00:49, 29 May 2006 (UTC)[reply]
Would it make sense to add links to PDBe-KB which provides a structure-oriented view for the entire protein? The links are based on UniProt accession or pdb id code (e.g. for sonic hedgehog the link would be pdbe-kb.org/proteins/1vhh or pdbe-kb.org/proteins/Q62226). There is already a template available for PDBe-KB links. — Preceding unsigned comment added by A2-25 (talk • contribs) 13:55, 5 July 2019 (UTC)[reply]
Very nice! It's a big improvement over doing it manually, but if you get a chance to do a revision, it doesn'tseem to capture the "EntrezGene" field or the "ECnumber" field. --Arcadian19:06, 16 June 2006 (UTC)[reply]
Whoops, forgot to add the EC number -- should be fixed now. Can you give me a protein for which the tool doesn't provide an Entrez gene ID? I've tried renin, LDH, and titin and I get the Entrez info just fine. If you discover any other oddities, please let me know. Thanks, David Iberri (talk) 21:26, 16 June 2006 (UTC)[reply]
I just noticed you added splicing for the Chromosome fields -- nice job! That must have been more difficult than the other fields. And the ECnumber seems to be working now as well. But the Entrez # still seems to be intermittent -- for example, thisscramblase shows the Entrez#, but this one does not. (Unfortunately, the fields on the underlying HGNC source appear to be somewhat inconsistent.) If I could make another request -- it would be useful to populate the "Name" field with the information in "Approved Name", since in many cases it might not be identical to the default of the article name. --Arcadian15:58, 17 June 2006 (UTC)[reply]
Heh, parsing out the locus information was easier than you think, but I'll take the compliment. :-) Regarding Entrez, previously I hadn't been using the "Entrez gene ID (mapped data)" field provided by HGNC. Now I'm using it if the "Entrez gene ID" isn't provided. I'm handling the RefSeq and UniProt IDs similarly, because HGNC provides both HGNC-certified and externally provided (mapped) info for those fields as well. Cheers, David Iberri (talk) 21:54, 17 June 2006 (UTC)[reply]
The RefSeq link is still broken: it points to the UCSC genome pages and aparently their current release no longer supports this type of query ("Couldn't find [...] in hg18.knownGene"). RefSeq is an NCBI database thus links to RefSeq IDs should point to the source. Moreover RefSeqs can be for nucleotides and for proteins; suprisingly the link proposed above silently accepts both types of sequence (try NP_00939 and NM_000948). But this may be brittle and there really should be options for the two RefSeq links. I propose:
I consider it very useful for Chemist and Biochemist who are regulary accessing to CA. For the time being. I have to add every CAS number to the wiki EC pages that I have browsed. (from anon, Nov 23)
I received the following message on my talk page. "Please add Ensembl Link: It is an important and very good european resource. As in de:Vorlage:Infobox Protein -> Seite bearbeiten (edit this page) and de:Vorlage:Infobox Protein at the bottom for the link. Thank you. TraumB 00:07, 11 January 2007 (UTC)" Does anyone have any thoughts about whether we should add this field, and/or the CAS number field described above? --Arcadian14:23, 11 January 2007 (UTC)[reply]
I think we should add Ensemble at least. Wouldn't mind CAS as well. We just need to determine if adding one or two more database entries starts to make the protein template too large. Everyone will have the databases that are not included that they like to use (mine's IHOP). Can we put up a sample of what the template would look like with those sections added in on this discussion page so we can see if it is becoming more obtrusive?Jvbishop18:04, 16 February 2007 (UTC)[reply]
The following thread was from my talk page. I'm moving it here for future reference, to make it easier for others to see what changes were made to the template and why. --Arcadian01:49, 15 January 2007 (UTC)[reply]
I feel this template desperately needs an explicit statement of the organisms it is found in to try and stem the massive bias towards humans. It would make far more sense to have a general template which is not human specific with a sub-section containing human specific information... - ZephyrisTalk15:36, 25 February 2007 (UTC)[reply]
My issue really is the use of this template in general; the protbox template seems better and filled in with care gives a better NPOV... - ZephyrisTalk18:05, 11 March 2007 (UTC)[reply]
I agree that the current content is highly biased toward human, but I think we should supplement pages with cross-species links rather than trying to make the entire page species-neutral. I've tried to take a crack at an "ortholog box" at Template:GNF_Ortholog_box, example at ITK (gene). (These efforts are in the context of this discussion, and the prepending of "GNF_" to the new templates is only an effort not to muck up the existing "production" templates.) AndrewGNF19:16, 13 March 2007 (UTC)[reply]
The Zif268 page renders poorly at low browser page widths (click to enlarge).
Just noticed that the protein box in Zif268 is looking funny -- the image is five-times larger than it should be. Is that related to recent changes to this template? On the other hand, P53 looks fine, so I'm not sure if the problem is here. anyone with more experience want to comment? AndrewGNF19:21, 13 March 2007 (UTC)[reply]
Thanks... I was confused because I saw the protein template had a default width, but it didn't look like the zif268 page was respecting it. Now I understand that leaving the parameter blank (e.g., "| width=", as if one copied directly from the "Usage" section but didn't enter a value) is different from not specifying the width parameter at all. In the former case, you override the default with a blank value, so the picture defaults to its native resolution. Perhaps it's worth modifying the protein box to catch this case (don't think I'm proficient enough yet to do it myself...) AndrewGNF01:15, 14 March 2007 (UTC)[reply]
I didn't think proteins had CAS numbers assigned to them. I only know CAS numbers in the context of low molecular weight compounds. Can you point out a link to a source that links a protein to a CAS number? Anyway, if there are such links, it is pretty straightforward to add it to the protein template... AndrewGNF01:32, 22 March 2007 (UTC)[reply]
I noticed that the template doesn't display the image correctly if not width is given. That will lead to many errors from people unaware of the intricacies of the template. Expected behaviour should be that if left blank, a default width is used. Behaviour now is, no image is displayed. See here for an example: no width [1], width [2]. I first thought I type the image link badly. And I expected that the image width does not need to be specified. If there is no solution to this, it should be stated clearly on the template page, the the width needs to be written down.
This template currently displays the image caption even if there is no image, which makes no sense. Could someone fix this? (I hesitate to attempt to fix it myself, as I have no experience of editing template code.) --Zundark (talk) 14:21, 14 July 2011 (UTC)[reply]
As intended, the example to the left displays the "Name" but not the "Caption" field. Have you mistaken the name for a caption? Boghog (talk) 17:04, 14 July 2011 (UTC)[reply]
OK, sorry, now I understand what you mean. We could add code to the template to suppress the display of the caption if there is no figure, but I am not convinced that this test is really necessary. Normally one would only add a caption if a figure is present. If a figure is not present, displaying a caption might prompt someone to add a figure (similar in purpose to a WP:REDLINK). Boghog (talk) 19:58, 14 July 2011 (UTC)[reply]
A caption without an image usually results from the image having been deleted, not from someone adding a caption when there is no image. Ideally the caption would be removed when the dead image link is removed, but for various reasons this often doesn't happen. Almost all infobox templates suppress the caption when there is no image, because it would be confusing to display it (it's not like a red link, since the text of a caption often makes no sense without the image). --Zundark (talk) 20:24, 14 July 2011 (UTC)[reply]
caption with image
caption without image
chymotrypsinogen B1
Crystallographic structure of Bos taurus chymotrypsinogen.[1]
I am still not 100% convinced this test is necessary, but I see other infoboxes such as the parent {{Infobox}} contain such a test, I have therefore implemented this in the {{Infobox protein/sandbox}} and a test is displayed above. Assuming no one objects to this change, I will add the test to the production version ({{Infobox protein}}). Boghog (talk) 22:05, 14 July 2011 (UTC)[reply]
The title of this infobox from the beginning was placed within the boarders box and was recently changed without discussion so that it is now placed on top of the box. See this discussion for background. I have restored the original placement for now. I think the title should be within the boarders of the box since (1) it is less confusing when multiple boxes are stacked, (2) several protein boxes are often included in an article about a small family of proteins and the titles of these boxes are hyperlinked to the individual protein articles, so the title becomes part of the data in the infobox, and (3) for consistency with the look of {{infobox enzyme}} and {{GNF Protein box}}. Also note that the placement of the title in {{infobox protein family}} was also recently changed without discussion.
OK, but synonym for what exactly? Over at {{Infobox drug}}, there can be synonyms for: A. title; B. chemical compound; C. clinical name. -DePiep (talk) 00:45, 1 July 2016 (UTC)[reply]
Proteins are not normally given chemical names (see for example Talk:Titin/FAQ). Also proteins, with a few notable exceptions (e.g., insulin) are not drugs. Hence the only synonyms that make sense to include are for the protein name. Please note that {{Infobox protein}} contains not only information about the protein, but also the gene that encodes that protein. This template already has an |AltSymbols= parameter which is meant for alternative gene symbols. By analogy, it would make sense to add an |AltNames= parameter for protein synonyms listed in UniProt. Boghog (talk) 12:12, 1 July 2016 (UTC)[reply]
I have added |AltNames= to the sandbox and an example of how including this parameter would look can been seen in the Template:Infobox protein/testcases. My first though was to display it directly under the protein name but on second thought, it looks slightly better is placed under AltSymbols. Another advantage of this reordering of fields is that many of the alt symbols are based on alt names and placing these two fields adjacent to each other makes it easier to see the correspondence. Thoughts? Boghog (talk) 12:46, 1 July 2016 (UTC)[reply]
So the order is: name - symbol - symbol - name. I get there is logic in it, but altering the order (in the pairs) looks a bit strange. An alt is an alt for something that better be right above it. I have a slight preference for your first thought (name - name - symbol - symbol). -DePiep (talk) 13:00, 1 July 2016 (UTC)[reply]
Suggested changed for displayed names in infobox: Entrez/NCBI and HUGO/HGNC[edit]
The infobox should really be displaying the names "NCBI" or "NCBI Gene" instead of "Entrez", as NCBI no longer call this database "Entrez Gene". Also it should be displaying and linking to "HGNC" instead of "HUGO" as these are distinct entities and the ID's are assigned and maintained by HGNC, not HUGO.
Aretaon (talk) 13:47, 29 August 2019 (UTC)[reply]