Template talk:Gene

Broken?

Clicking this: THRA regenerates: "Unable to open remote file". Whereas manual entering "THRA" into the "quick gene search box" on link title still works. I can't find any information on the HUGO website on how to link. So I am not sure if it is a problem with their web site or with this template. Any ideas? Boghog2 05:20, 2 August 2007 (UTC)[reply]

I have sent hgnc@genenames.org a bug report (http://www.genenames.org/data/get_data.php?gd_app_sym=THRA doesn't work) with a request for reply. I report here their response once I receive it. Boghog2 05:32, 2 August 2007 (UTC)[reply]
- It isn't just THRA -- the whole site seems to be down right now. --Arcadian 10:38, 2 August 2007 (UTC)[reply]
  - Working again. Sorry for the false alarm. Boghog2 20:53, 2 August 2007 (UTC)[reply]

Exact vs substring matches

I wanted to link to the "carbonic anhydrase I" HUGO gene with CA1 but as you see, it instead retrieves the record for "ABCA1 ". So the link:

http://www.genenames.org/data/hgnc_data.php?match=CA1

doesn't return what I want, however the following link:

http://www.genenames.org/data/hgnc_data.php?hgnc_id=1368

returns what I want.

Is there any way to modify the gene link to use the "HGNC ID" (as recommended here) instead of the gene name? For example:

{{gene|1368 CA1}} would link to hgnc_id=1368 but display CA1 in the wiki article. Or alternatively is there any way to force an exact string match? I experimented with several things including regular expressions, but nothing seems to work.

Cheers. Boghog2 23:38, 24 September 2007 (UTC)[reply]

OK, I created a new template:gene2 (e.g., {{gene2|CA1|1368}}) which seems to work: CA1. Boghog2 00:15, 25 September 2007 (UTC)[reply]

Dead links to HGNC need to be updated.

This addresses both gene templates, gene and gene2.

The URLs from the gene2 templates are dead, e.g. some genes linked on the page https://en.wikipedia.org/wiki/Carbonic_anhydrase .

The URLs to Gene symbol reports (when linking via HGNC ID) should all be in the format https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/{{{HGNCid}}}

However the above URL won't be suitable for the gene template because it uses a symbol search instead. This is less ideal as symbols can change, but also can bring back multiple hits in the search (eg https://www.genenames.org/tools/search/#!/genes?query=CA5B brings back two hits for the CA5B link in the above Carbonic anhydrase page). It looks like generally the intended usage is to link to a specific HGNC symbol report, so using an HGNC ID direct link will have the intended result more often than linking to a search query.

As an aside it's a bit confusing to have both templates in use and duplicates the amount of revisions that need to be made if URLs should change again in future. Any chance of merging to a single template that links via HGNC ID? I suppose the complication is that all current usage instances of the Template:gene would need to be edited as these generally link via symbol search instead of the stable HGNC ID. Thoughts?

Aretaon (talk) 13:19, 30 August 2019 (UTC)[reply]