Template talk:GNF Protein box

Adding ChEMBL Links

Hi, after the success of adding ChEMBL compound links to Wikipedia, we would like to extend our links to the protein pages. How would we about doing this and what would we have to provide? We are linked to UniProt, so we can give you a CSV file of the UniProt links to ChEMBLIDs? It would be great to start creating reciprocal links to our pages, such as: http://www.ebi.ac.uk/chembldb/target/inspect/CHEMBL276 thanks, Louisa (ChEMBL team) Louisajb (talk) 11:16, 22 February 2012 (UTC)

In principle this is of interest. These links would provide information about ligands that interact with proteins of pharmacological interest and would be complementary to the IUPHAR links that we already provide. In the vast majority of cases, we do not have separate Gene Wiki pages for orthologs of the same protein (e.g., we have only one article for CHRM1). In order to keep things simple, my suggestion is that the links be limited to human orthologs (e.g., link to human CHRM1 instead of rat CHRM1). Assuming there are no strong objection from others, we could add links from Gene Wiki articles back to the ChEMBL protein targets. What we would need is a mapping of human UniProt IDs to ChEMBL protein targets. Boghog (talk) 17:09, 25 February 2012 (UTC)

I have added the ChEMBL links to the sandbox and the new links can be seen here (the two right hand side infoboxes). Boghog (talk) 17:27, 25 February 2012 (UTC)

I agree this will be very useful information to add and make available from these pages. Thank you very much. A2-25 (talk) 20:45, 25 February 2012 (UTC)

This looks great. Where shall I send the mapping to? I can create this as xls, txt, csv etc. Thanks again Louisajb (talk) 15:19, 29 February 2012 (UTC)

One minor change, please could we have the full ChEMBL_ID number shown in the box. I am aware that it would look like this 'ChEMBL: CHEMBL2569' but it would keep the ChEMBL ID consistent with the compound pages and maybe prevent user confusion? Thanks again. Louisajb (talk) 16:16, 29 February 2012 (UTC)

You can send the links to me (boghog at me dot com, where "at" and "me" are replaced by "@" and "." respectively) and I can run a bot to add these links to the PBB templates. Boghog (talk) 06:24, 1 March 2012 (UTC)

Hi, have you been able to add these links? I have tried to find some but I can't seem to see them. Thanks Louisajb (talk) 12:07, 2 May 2012 (UTC)

Sorry for the delay. User:BogBot has now started to add these links. Boghog (talk) 04:42, 4 May 2012 (UTC)

Not a problem, I was just checking. The links look brilliant. Thank you! Louisajb (talk) 16:52, 8 May 2012 (UTC)

Hi, is there a list somewhere that I can get hold of that I can use create reciprocal links with from ChEMBL to these pages? I used the Uniprot ID and ChEMBL ID but not all of the Uniprot IDs will link out to their protein pages. Thanks Louisajb (talk) 10:16, 18 June 2012 (UTC)

Edit request on 11 March 2012

Sync with {{GNF Protein box/sandbox}} (diff) to include PDB query links under the "Available structures" section of the infobox as discussed here. (Also see testcases for test of requested changes.) Thanks. Boghog (talk) 19:00, 11 March 2012 (UTC)

 Done Tra (Talk) 21:46, 15 March 2012 (UTC)

More than one EC number

Hi. There are some enzyme where more than one EC numbers can be defined. But as the template is now, the EC field does not seem to accept more than two numbers. The link shows error. Can you fix this?

Please see this example: Serine_racemase.

Thank you very much.

Yasunori Hayashi. RIKEN Brain Science Institute

Correct me if I am wrong, but I believe that currently the ECnumber parameter is intended to support one and only one EC number. I do think it would be a good idea to allow the ECnumber parameter to handle more than one EC number since many proteins have more than one enzymatic activity. However I don't think there is an easy way of implementing this because of limitations in the template scripting language. Perhaps we could define another parameter called "ECnumbers" that would accept any number of {{EC number}} templates in analogy to the way the PDB parameter is currently implemented. If we change the current ECnumber parameter, then a bot would need to go through all the PBB templates to update the ECnumber to use {{EC number}} templates. Boghog (talk) 14:11, 1 April 2012 (UTC)

Some time ago, I modified the bot to handle multiple EC numbers, but I see now that it breaks the link. Boghog, if you want to make the changes to the template sandbox and get them pushed through, I'll modify PBB accordingly. Pleiotrope (talk) 19:45, 3 April 2012 (UTC)

Thanks Pleiotrope. Modifying the ECnumber parameter would be the best solution. I have edited the ECnumber parameter in the sandbox template so that it will now accept as an argument any number of {{KEGG enzyme 2}} templates instead of the current direct hard wired link. See the testcases to verify this works. If everyone is in agreement, I will request that an administrator update the template. Cheers. Boghog (talk) 05:41, 4 April 2012 (UTC)

I went back a revision to see the ECnumber change and it looks good. If this is still present in the sandbox I'm all for updating the template. Thanks for getting that working! Pleiotrope (talk) 19:21, 6 April 2012 (UTC)

The proteins in the current testcases only have one EC number. I entered three numbers in the test case just to verify that it works and it does but I went back to one number in the testcases because I did not want to create any confusion. The sandbox version will still take any number of EC templates. Boghog (talk) 21:01, 6 April 2012 (UTC)

Edit request on 4 May 2013

A request was made above to allow more than one EC number. This was never implemented as proposed above because it would require changes both to the template and to the data in the transcluded templates. The new WP:Lua based Module:String now provides a much more elegant solution that only requires changes to the template and not to the data.

The following change made in the sandbox allows linking to more than one EC number. The sandbox test cases demonstrate that multiple EC number link as implemented in the sandbox is functional. Also the change is backwards compatible (i.e., still works with a single EC number, see second row in test cases). Boghog (talk) 08:35, 4 May 2013 (UTC)

 Done — Martin (MSGJ · talk) 12:04, 9 May 2013 (UTC)

Categories

This templates add articles that use it to content categories so if it is used on user pages they then turn up in content categories. See Category:Genes on chromosome 20 for example. I thought the use of automatically adding categories using templates was discouraged. -- Alan Liefting (talk - contribs) 05:38, 12 June 2012 (UTC)

It's discouraged, but in the absence of any heads-up at all it's not productive simply to remove it unilaterally. The project should be informed if all of these categories are to be depopulated so that someone can start adding them manually. Chris Cunningham (user:thumperward) (talk) 08:33, 12 June 2012 (UTC)

In this particular case, automatic addition of gene categories make a lot of sense. These templates were created as part of the Gene Wiki project whose purpose is to create Wikipedia articles for genes coding human proteins. Each of these genes is unambiguously located on a single human chromosome and therefore each gene can unambiguously be assigned to a specific gene category. We could run a bot to explicitly add these categories to the individual articles, but what is the point? The end result (i.e., the population of the categories) would be identical. The proposed change creates a lot of unnecessary work. The only downside to the present system is that certain sandboxes have ended up in categories. These sandboxes have not been used in some time and should be deleted. Boghog (talk) 05:17, 13 June 2012 (UTC)

Deleting the sandboxes is fine by me since it achieves the aim of getting user pages out of content categories. -- Alan Liefting (talk - contribs) 05:52, 13 June 2012 (UTC)

I understand that the volume of articles involved makes categorization via template more palatable than usual in this case, but there are still something like 75 non-mainspace pages in Category:Human proteins as a result. Can we get some category suppression in place to avoid categorizing non-mainspace pages via the template? Maralia (talk) 17:03, 28 January 2013 (UTC)

I've updated this template and also {{GNF Ortholog box}} so that they don't categorize user pages anymore. -- WOSlinker (talk) 17:37, 9 May 2013 (UTC)

Brilliant, thank you! Cheers, Andrew Su (talk) 16:31, 15 May 2013 (UTC)

URL Edit request

I am a developer for the HGNC and we have changed a few of our URLs on our site. The old URLs still work thanks to redirects but we would like the URL for the HGNC gene symbol request pages in the GNF protein box changed as seen in the sandbox (diff).

The changes we have made have been noted in our New features and changes page

Many thanks,

Kristian Gray 12:08, 27 January 2014 (UTC) — Preceding unsigned comment added by KrisGray (talk • contribs)

Template-protected edit request on 7 March 2014

I am a developer for the HGNC and we have changed a few of our URLs on our site. The old URLs still work thanks to redirects but we would like the URL for the HGNC gene symbol request pages in the GNF protein box changed. These are the changes we would like to see:

| label4 = Symbol | data4 = {{{Symbol}}}{{{AltSymbols}}}

changed to

| label4 = Symbol | data4 = {{{Symbol}}}{{{AltSymbols}}}

Many thanks, Kristian Gray

As we are the official group (HUGO Gene Nomenclature Committee HGNC) that approves gene symbols how do we achieve "consensus" for the incorrect link on the Symbol label to change? Many thanks for the fix on the URL to our site.

Kris Gray

Kristian Gray 15:03, 7 March 2014 (UTC)

Partly done: Human Genome Organisation is a valid non-redirect target, so you will need a consensus to change that, but I have updated the external link for you per your request and made a few other minor formating changes to show that it is an external link and properly show AltSymbols as (AltSymbols) — {{U|Technical 13}} ^{(t • e • c)} 16:16, 7 March 2014 (UTC)