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-: The gene name "sym-5" does not redi... #1101

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wormbasehelp opened this issue Apr 22, 2013 · 14 comments
Closed

-: The gene name "sym-5" does not redi... #1101

wormbasehelp opened this issue Apr 22, 2013 · 14 comments

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@wormbasehelp
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@wormbasehelp wormbasehelp commented Apr 22, 2013

The gene name "sym-5" does not redirect to the let-4 page as it should.

Reported by: Anna******* (avju****************) (obscured for privacy)
Submitted From: my wormbase (/me)

Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.64 Safari/537.31

@epaule

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@epaule epaule commented Apr 22, 2013

I believe some of the other Caenorhabditis still use sym-5 as gene name instead of let-4. That should get fixed by the GNW group.

@ghost ghost assigned tuli Apr 22, 2013
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@tuli tuli commented Apr 23, 2013

Dear Anna,

Thank you for writing to WormBase.

Please can you tell me exactly what you are seeing when you query sym-5?

When I run the query myself I get 7 hits; 5 for non-elegans species and 2
for elegans. One of these is to sym-1 (due to sum-5 being mentioned in the
Description) and the other is to let-4 which is the gene you require.

I believe the ordering of the "hits" could be improved and I will raise
this with the webteam.

Best wishes,

Mary Ann

~ Mary Ann Tuli

~ WormBase Group: www.wormbase.org
~
~ EMBL-EBI
~ Wellcome Trust Genome Campus
~ Hinxton, Cambridgeshire, CB10 1SD, UK.

~ Tel: +44 (0)1223 494466

On 22 April 2013 03:28, no-reply@wormbase.org wrote:

Question:
The gene name "sym-5" does not redirect to the let-4 page as it should.

Submitted From:
my wormbase (/me)

This issue has been assigned ticket number: #1101. Follow progress on our issue
tracker #1101.

Reported by Anna Justis (avjustis@hotmail.com)
22 Apr 13 02:28

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Chrome/26.0.1410.64 Safari/537.31

This question was reported via the web interface at wormbase.org. You can
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@tuli tuli commented Apr 23, 2013

Webteam:

I think the search Anna did should have listed let-4 at the top ie an exact match of the search term in an other_name should be higher profile than the search term being cited in the Description.

Also, I think elegans hits should be higher profile than non-elegans hits.

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@epaule epaule commented Apr 23, 2013

and I think the non-elegans sym-5 should be probably renamed to let-4 (as
let-4 had it as previous name)

M

On 23 April 2013 14:12, tuli notifications@github.com wrote:

Webteam:

I think the search Anna did should have listed let-4 at the top ie an
exact match of the search term in an other_name should be higher profile
than the search term being cited in the Description.

Also, I think elegans hits should be higher profile than non-elegans hits.


Reply to this email directly or view it on GitHubhttps://github.com//issues/1101#issuecomment-16856906
.

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@tuli tuli commented Apr 23, 2013

yes yes...give me a minute! ;-)

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@acabunoc acabunoc commented Apr 23, 2013

We just started weighting C elegans hits higher than other species (~2x more) - but in this case, the gene names of the non-elegans hits match the query. A hit in the gene name is weighted ~50x more than anywhere else, which enables us to redirect gene name hits pretty well.

We can increase the weight on Other_name. But Species might be trickier to handle.

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@epaule epaule commented Apr 23, 2013

I do believe it is fair that the properly names sym-5 genes on the
non-elegans species appear quite high, as that are true positives. After we
renamed them similar to C.elegans they will only have them in the other
names and be ranked below c.elegans.

On 23 April 2013 14:41, Abigail Cabunoc notifications@github.com wrote:

We just started weighting C elegans hits higher than other species (~2x
more) - but in this case, the gene names of the non-elegans hits match the
query. A hit in the gene name is weighted ~50x more than anywhere else,
which enables us to redirect gene name hits pretty well.

We can increase the weight on Other_name. But Species might be trickier to
handle.


Reply to this email directly or view it on GitHubhttps://github.com//issues/1101#issuecomment-16858476
.

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@chris-grove chris-grove commented Apr 23, 2013

My impression was that Anna was expecting a query of "sym-5" for gene to automatically load the let-4 page, like, for example, searching for "kin-7" directly returns the let-23 gene page, as "kin-7" is an other name for let-23. Or, at least in the auto-complete suggestions of the search box, have let-4 offered when one types in sym-5. I thought that this happens for other genes. All of my points may be moot as sym-5 may be a more difficult case considering other species as Abby said.

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@tuli tuli commented Apr 24, 2013

Hmm, you may be right - I'm sure Anna will let us know! As you (and Michael) say though, it should be resolved once the updated ortholog names filter through.

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@kyook kyook commented Jun 11, 2013

As of the WS238 release, querying for sym-5 leads to the same result as Mary Ann as reported above. Should the milestone be pushed to WS239? or is there something that could be fixed for this release?

@ghost ghost assigned acabunoc Jun 13, 2013
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@acabunoc acabunoc commented Jul 31, 2013

Updated search indexer

https://github.com/WormBase/website-admin/commit/fef6da379a20f474d62b0296ef508358607b918e

Should be ready for WS239. @tharris, make sure you get fetch the latest changes before indexing Xapian for WS239.

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@kyook kyook commented Nov 6, 2013

sym-5 still does not redirect to lin-4. :-(

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@acabunoc acabunoc commented Dec 11, 2013

@kyook please test on staging

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@kyook kyook commented Dec 11, 2013

looks good. thanks!

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