Template talk:Protein

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

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=
}}
Protein
Identifiers
Symbol  ?
Other data
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)

Contents

[edit] 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)

[edit] 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)

[edit] 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] 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)

[edit] 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. :-) Boris 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)

[edit] 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)

[edit] "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)

[edit] 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)

[edit] 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)


[edit] Image problems?

The Zif268 page renders poorly at low browser page widths (click to enlarge).
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)

[edit] 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)
Y Done. -- Boris 02:38, 24 May 2007 (UTC)

[edit] 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)