Template talk:Infobox protein

For context for this template, see Template talk:Protbox codes and Wikipedia:WikiProject_Molecular_and_Cellular_Biology

Creation

I've created the template User:BorisTM requested. I also cut out the amino acid row for now, since I think that's causing confusion. An example of it in use is available at Methylmalonyl Coenzyme A mutase. --Arcadian 16:53, 30 December 2005 (UTC)

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.

Code	Current result	Desired result
{{Protein |Symbol= |AltSymbols= |Chromosome= |Arm= |Band= |ECnumber= |EntrezGene= |OMIM= |UniProt= }}	Infobox protein Identifiers Symbol ?	Infobox protein Symbol(s): ? Locus: ? EC number ? EntrezGene ? OMIM ? RefSeq ? UniProt ?

What do you say chief? Can you do it? -- Boris 19:18, 30 December 2005 (UTC)

I think I've got it now -- see Titin for an example without an EC code (compared to Methylmalonyl Coenzyme A mutase, as one that has one.) --Arcadian 12:54, 31 December 2005 (UTC)

It looks better. Tnx, Arch, i'll use it now. -- Boris 14:50, 31 December 2005 (UTC)

PDB IDs?

Would it be useful to include the PDB ID of a protein in this template? --David Iberri (talk) 18:21, 28 May 2006 (UTC)

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? --Arcadian 00:49, 29 May 2006 (UTC)

Awesome. The URL would be http://www.pdb.org/pdb/cgi/explore.cgi?pdbId={{{pdb}}}. For an example, here's the entry for sonic hedgehog.

Also, the new drugbox template looks great. I'd definitely support a similar look for the protein infobox. --David Iberri (talk) 18:08, 29 May 2006 (UTC)

Done. An example of the new linked PDB field is visible at Sonic hedgehog. (It appears not to be case-sensitive.) --Arcadian 19:23, 29 May 2006 (UTC)

That was quick! :-) Thanks -- it looks great! --David Iberri (talk) 19:32, 29 May 2006 (UTC)

How about updating the URL because accesses to the current URL are redirected to https://www.rcsb.org/structure/{{{pdb}}} ? (e.g. sonic hedgehog) Moreover how about setting links to each PDB partners (RCSB PDB, PDBe and PDBj) like Template:Infobox enzyme? Cudo29 (talk) 00:41, 18 April 2018 (UTC)

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)

Template conflict

This template or one of the templates used inside it seems to have a conflict with the reference template {{ref}}
See Gonadotropin-releasing hormone --JWSchmidt 22:11, 13 June 2006 (UTC)

Converting the references with this converter fixed the problem. --JWSchmidt 13:09, 14 June 2006 (UTC)

Automated filling

Per Arcadian's suggestion, I've created this tool that fills out the protein infobox given an HGNC ID. Comments welcome. Enjoy! --David Iberri (talk) 16:54, 16 June 2006 (UTC)

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. --Arcadian 19:06, 16 June 2006 (UTC)

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)

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, this scramblase 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. --Arcadian 15:58, 17 June 2006 (UTC)

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)

edit boxes

Superoxide dismutase uses this template. How do I keep it from messing up the section edit links? --Slashme 11:54, 14 July 2006 (UTC)

RefSeq Link Broken

Please change the refseq link with this: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val={{{RefSeq}}} the current link is broken.

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:

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val={{{RefNuc}}}
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val={{{RefProt}}}

with the corresponding change in the template. :-) Steipe 18:48, 18 September 2007 (UTC)

Just tried to the use the template. The refseq link is somehow broken (also in other cases where this template was used): e.g. for titin is refers to: http://genome.cse.ucsc.edu/cgi-bin/hgGene?org=Human&hgg_gene=NM_133378&rn=1 The correct link is: http://genome.ucsc.edu/cgi-bin/hgTracks?Submit=Submit&position=NM_133378

I would fix if I knew how -- Panoramix303 11:37, 9 November 2007 (UTC)

Fixed it after some trying. When the template is added it works, with old pages it doesn't, e.g. titin. -- Panoramix303 11:51, 9 November 2007 (UTC)

Why is CAS number not included?

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)

"Ensembl Link"

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? --Arcadian 14:23, 11 January 2007 (UTC)

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?Jvbishop 18:04, 16 February 2007 (UTC)

Template:Protein

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. --Arcadian 01:49, 15 January 2007 (UTC)

Hi there Arcadian. Would it be possible for an extra field to be added to {{Protein}} that would account for more than one PDB link, like the CAS_supplemental field in {{Drugbox}}? Clostridium perfringens alpha toxin has several PDB links, and they're presently messing up the syntax. Thanks again, Fvasconcellos 22:15, 14 January 2007 (UTC)

Done. --Arcadian 01:41, 15 January 2007 (UTC)

Thanks! Fvasconcellos 01:44, 15 January 2007 (UTC)

Humans vs.

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... - Zephyris _Talk 15:36, 25 February 2007 (UTC)

A more general protein template is available, and described at Wikipedia:WikiProject Molecular and Cellular Biology/protbox usage. Alternatively, we could add some fields to this template. If you think we should add more fields, please be more specific, and propose a list. --Arcadian 16:11, 25 February 2007 (UTC)

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... - Zephyris _Talk 18:05, 11 March 2007 (UTC)

Why is there this template and the Protbox template? Is there a specific use for each? Jvbishop 18:12, 12 March 2007 (UTC)

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.) AndrewGNF 19:16, 13 March 2007 (UTC)

Image problems?

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? AndrewGNF 19:21, 13 March 2007 (UTC)

I added a value for the image width. There is still a problem on the page with the table. --JWSchmidt 20:28, 13 March 2007 (UTC)

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...) AndrewGNF 01:15, 14 March 2007 (UTC)

CAS no.

Could we get the CAS registry number in the table? Thanks — Jack · talk · 04:43, Saturday, 17 March 2007

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... AndrewGNF 01:32, 22 March 2007 (UTC)

Some are used as drugs - polypeptide hormones and cytokines, Coagulation and Fibrinolysis factors, etc. -- Boris 02:38, 24 May 2007 (UTC)

 Done. -- Boris 02:38, 24 May 2007 (UTC)

image problems when no width specified

Dear templaters,

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.

Best, Jasu 10:25, 16 May 2007 (UTC)

I hope I solved it, it looks OK in my browser (Opera, but I forgot to check what the original situation was). Have a nice day! --Dirk Beetstra ^{T C} 11:09, 16 May 2007 (UTC)

CAS No. format is not right and please correct it....

as shown in the article of Methanol--222.64.31.145 (talk) 06:46, 27 April 2009 (UTC)

Captions

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)

chymotrypsinogen B1
Identifiers
Symbol	CTRB1
NCBI gene	1504
HGNC	2521
OMIM	118890
RefSeq	NM_001906
UniProt	P17538
Other data
EC number	3.4.21.1
Locus	Chr. 16 q23.1
Search for Structures Swiss-model Domains InterPro

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)

Your example has an empty caption field. I've put something in it now, and it displays under the name. --Zundark (talk) 17:31, 14 July 2011 (UTC)

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)

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)

caption with image	caption without image
chymotrypsinogen B1 Crystallographic structure of Bos taurus chymotrypsinogen. Identifiers Symbol CTRB1 NCBI gene 1504 HGNC 2521 OMIM 118890 RefSeq NM_001906 UniProt P17538 Other data EC number 3.4.21.1 Locus Chr. 16 q23.1	chymotrypsinogen B1 Identifiers Symbol CTRB1 NCBI gene 1504 HGNC 2521 OMIM 118890 RefSeq NM_001906 UniProt P17538 Other data EC number 3.4.21.1 Locus Chr. 16 q23.1

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)

Thanks for working on this. --Zundark (talk) 08:00, 16 July 2011 (UTC)

Placement of infobox title

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.

I would be interested in hearing other editors opinions. Boghog (talk) 08:17, 4 March 2012 (UTC)

Need a synonyms parameter

Plenty of protein names have synonyms. This box lacks a parameter to handle them. Can someone tell me how to create one? I don't care if we call it "synonyms" (like Template:Infobox drug does) or "OtherNames" (like Template:Chembox does), but it needs to exist. Thanks. Quercus solaris (talk) 23:33, 30 June 2016 (UTC)

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)

For Template:Infobox protein, I think it could be any of those, depending on the instance. I would be fine with one parameter that could catch any such values. Or separate parameters, if anyone wants them, is also fine by me. The example that drove me to request it was formimidoyltransferase cyclodeaminase, which per HGNC has an (older) synonym of formiminotransferase cyclodeaminase. Quercus solaris (talk) 02:05, 1 July 2016 (UTC)

• 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)
• 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)

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)

Thanks, Boghog, for creating it. Looks great. I have no objection to either order; I think they both would be fine/no problem. Quercus solaris (talk) 21:16, 1 July 2016 (UTC)

Discussion of relationship to {{infobox enzyme}}

Wikipedia talk:WikiProject Molecular and Cell Biology#Infobox for enzyme vs protein DMacks (talk) 14:59, 3 April 2017 (UTC)

Suggested changed for displayed names in infobox: Entrez/NCBI and HUGO/HGNC

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)

 Done Thanks for the suggestions which I agree with. I have updated the template accordingly. Boghog (talk) 18:23, 29 August 2019 (UTC)