Template talk:Infobox enzyme

Semi-protected edit request on 24 September 2014

Please change BRENDA entry to BRENDA entry link is outdated Ach brenda (talk) 09:49, 24 September 2014 (UTC)

Done Stickee (talk) 01:09, 25 September 2014 (UTC)

Request to update AmiGO link

Please change AmiGO to AmiGO the link is outdated Momeara (talk) 18:04, 15 January 2015 (UTC)

Done — {{U|Technical 13}} ^{(e • t • c)} 22:41, 15 January 2015 (UTC)

Discussion of relationship to {{Infobox protein}}

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

Request to add PDBj link in PDB structures

Could you add PDBj link to the PDB structures (data12)? The description should be as following:

[https://pdbj.org/mine/sql?query=SELECT+pdbid+FROM+entity+WHERE+entity.pdbx_ec%3D%27{{{EC_number}}}%27 PDBj]

Cudo29 (talk) 07:18, 5 April 2018 (UTC)

Request to up-date EC number link

The current link doesn't work.
I'm sorry, one more thing - why is EC number required? Not all enzymes must necessarily have EC number assigned.
Another thing, not related, but maybe could you help. There is new EC class 7. That means that many enzymes have been re-assigned and thus their EC numbers shall be changed by some BOT. Could anybody help with it?
--HlTo CZ (talk) 08:42, 22 March 2019 (UTC)

I have updated the EC number link (first link in infobox) so that it works again. Is there a list of EC number that have been transferred to EC class 7? With a list, it should be straight forward to have a bot update these infoboxes. Most of the associated databases are searchable by EC number, so if you have an EC number, linking to these databases is much easier. The EC number is not strictly required, but if one is available, the rest of the infobox links are automatically activated. Without the EC number, none of these other links are displayed. Boghog (talk) 16:32, 22 March 2019 (UTC)

According to BRENDA, it appears that Category:EC 3.6.3 enzyme are being transferred to the translocases EC 7.-.-.-. Boghog (talk) 06:47, 23 March 2019 (UTC)

The first EC 7 enzyme, Ag+-exporting ATPase, has now been moved to EC 7.2.2.15. I noticed that BRENDA link for example does not work. It appears that not all of the external databases have been updated yet. Boghog (talk) 07:57, 23 March 2019 (UTC)

Fix amigo

• Change AMIGO link from http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?query={{{GO_code}}}&view=details to http://amigo.geneontology.org/amigo/term/GO:{{{GO_code}}} Artoria2e5 🌉 20:53, 4 May 2019 (UTC)

•  Fixed in this edit. Thanks for pointing out the problem. Cheers. Boghog (talk) 11:01, 5 May 2019 (UTC)

Template-protected edit request on 22 January 2020

Please change [[PRIAM enzyme specific profiles|PRIAM]] to [[PRIAM enzyme-specific profiles|PRIAM]] to eliminate an unnecessary redirect. Colonies Chris (talk) 21:58, 22 January 2020 (UTC) Colonies Chris (talk) 21:58, 22 January 2020 (UTC)

 Done - FlightTime (open channel) 22:23, 22 January 2020 (UTC)

Thanks. Colonies Chris (talk) 09:06, 23 January 2020 (UTC)

Template-protected edit request on 19 December 2020

The NiceZyme link is bad. Replace

| label8 =  [[ExPASy]]
| data8 = {{#if:{{{EC_number|}}}| [http://www.expasy.org/enzyme/{{{EC_number}}}  NiceZyme view] }}

with

| label8 =  [[ExPASy]]
| data8 = {{#if:{{{EC_number|}}}| [https://enzyme.expasy.org/EC/{{{EC_number}}}  NiceZyme view] }}

Artoria2e5 🌉 15:27, 19 December 2020 (UTC)

 Done the wub "?!" 13:24, 20 December 2020 (UTC)

@Artoria2e5 and The wub: Something that I may have done recently was going to the Template:Infobox_enzyme/testcases page and attempting to access some of the template's external links in a Web browser. I may have been considering (among other things) as to whether there were any HTTP URLs that would redirect to an HTTPS URL. Another thing I did was entering some of the template's external links, one at a time, into the httpstatus tool to see if a URL would generate one or more redirects. Of particular interest is if a URL generates one or more HTTP 301 (Moved Permanently) redirects. I recently changed the template use HTTPS when generating an ExPASy link. --Elegie (talk) 09:31, 23 December 2020 (UTC)

Template-protected edit request on 1 May 2021

To fix the RCSB PDB link, the following link line 49:

[http://www.rcsb.org/pdb/search/smartSubquery.do?smartSearchSubtype=EnzymeClassificationQuery&Enzyme_Classification={{{EC_number}}} RCSB PDB]

should be update to this URL:

[https://www.rcsb.org/search?q=rcsb_polymer_entity.rcsb_ec_lineage.id:{{{EC_number}}}}} RCSB PDB]

bonob (talk) 20:24, 1 May 2021 (UTC)

 Done * Pppery * _{it has begun...} 04:25, 2 May 2021 (UTC)

Link to ExplorEnz request 4 July 2022

As ExplorEnz is the official IUBMB-curated database (and is always more up-to-date than Expasy etc.) it seems to me that it should be linked from the enzyme template. I'm hesitant to fiddle about with the template myself, as I don't want to break the thousands of articles that call it, and in any case maybe as it's protected I can't edit it even if I want to.

The table would then have ExplorEnz in the left-hand column, and ExplorEnz entry EC 1.1.1.1 in the right-hand column (for alcohol dehydrogenase). Would that be easy to implement? Athel cb (talk) 08:59, 4 July 2022 (UTC)

Hey @Athel cb: I just saw this request of yours, there's been a related discussion on WT:MOLBIO shortly after your request, independently I guess, if you want to chime in: WT:MOLBIO#Do_we_need_two_templates_for_external_links_to_EC_number_databases?

I was thinking I'd try to tackle both topics, using ExplorEnz rather than iubmb.qmul.ac.uk in the infobox, and merging {{EnzExplorer}} and {{EC number}} (currently pointing to ExPASy) into the ExplorEnz template. bonob (talk) 18:42, 24 July 2022 (UTC)

Yes, I think it was independent, but it's a curious coincidence that both came up more or less simultaneously. Anyway, thanks for the pointer to the discussion on WT:MOLBIO, which I was unaware of until today. I'll add my comments to that. (I did so already this morning, but my browser crashed in the middle of the operation.) Athel cb (talk) 08:05, 25 July 2022 (UTC)

 Done @Athel cb: As ExplorEnz appears to be the current official IUBMB enzyme nomenclature database, I have changed the EC identifier external link in {{Infobox enzyme}} from https://iubmb.qmul.ac.uk/enzyme/ to https://www.enzyme-database.org/ in this edit. Please also note per Wikipedia:External links, External links normally should not be placed in the body of an article. Hence inserting {{EnzExplorer}} into the body of the article is against the Wikipedia manual of style. It is also redundant since the link is now provided in {{Infobox enzyme}}. Cheers. Boghog (talk) 09:53, 3 August 2022 (UTC)

Thanks for dealing with the infobox. I wasn't aware of this guideline. As there are a huge number of pages where this is violated (not only by me, with links to ExplorEnz, but others to Expasy that were there already), it'll take a while to remove them all. However, I'll do this. Athel cb (talk) 11:03, 3 August 2022 (UTC)

There is no problem with the individual enzyme pages (apart from the fact that there are an enormous number of them to deal with). The external links can go. However, I'm more worried about the index pages, such as https://en.wikipedia.org/w/index.php?title=List_of_EC_numbers_(EC_4). Here you will find a list of 810 enzymes. For each entry, such as

* EC 4.2.3.9: aristolochene synthase

clicking on the first link will take you to the relevant ExplorEnz entry; the second (if there is one) will take you to the corresponding Wikipedia page (if there is one). Removing the first link will make it much more difficult for users to find the ExplorEnz entry, and I suspect that many won't bother. However, it's important that they be encouraged to consult the up-to-date IUBMB-approved information, so it needs to be easy. For the moment, therefore, until the administrators send around a hit squad, I don't plan to remove these. Note that many of the individual pages don't seem to have been updated since 2007, and that the index pages don't have infoboxes (and it's not easy to see how they could.) Athel cb (talk) 11:33, 3 August 2022 (UTC)

CAS number

Hi all, I noticed that the template includes a CAS number for each enzyme... however, I haven't been able to find a single enzyme with a CAS link that actually works. We might need to change the template so that the a link is generated to some other database (maybe PubChem?) instead of to cas.org, since that doesn't seem to be working. Dh92 (talk) 16:19, 3 May 2023 (UTC)