[Feedback] Site Feedback: static content says "Josh?"

[Dan Bolser]

Hi Marcela,

References are a little tricky, but not part of a separate database.
>From this page:
http://ensemblgenomes.org/node/27171

Hover over the 'Create' menu item near top left, and select
'Publication' from the menu that appears. Once you're creating a new
reference, you can auto generate the fields by using either a PMID or
a DOI. Once you've done that, you need to link it to Zea mays using
the 'species' field towards the bottom of the form. The new reference
should then be visible in the list for Zea mays!

Yes, we store the assembly accession in the database, in the
assembly.accession field of the meta table. For Zea mays that's
currently:

+---------+------------+----------------------------------+----------------------------------------------------------------+
| meta_id | species_id | meta_key                         | meta_value
                                                    |
+---------+------------+----------------------------------+----------------------------------------------------------------+
...
|    1024 |          1 | assembly.accession               |
GCA_000005005.5                                                |
...

which creates a link automatically here:
http://plants.ensembl.org/Zea_mays (under AGPv3)

and here:
http://plants.ensembl.org/Zea_mays/Info/Annotation (at the top of the
table on the right).

Please let us know if you have any problems creating a reference,
and/or if you'd like to see those links made more prominent.

You're right, once the content is finished there, it needs to be
pushed to HTML, but this no longer happens via CVS.  Let me know when
you're done, and I'll ask the web-team to update the HTML.


Cheers,
Dan.


On 13 June 2014 20:07, Marcela K. Monaco <mmonaco at cshl.edu> wrote:
> Ok, I fixed it.  Let me know if you have a reference that you would like to
> include.  Dan (Cc:ed) mentioned that the literature references go into a
> separate DB which I do not have access but I could put it in parenthesis for
> now.
>
> Dan will also need to commit the changes to CVS.
>
> http://ensemblgenomes.org/node/27171
>
> Dan - I also wanted to include the GenBank accession ID for the assembly but
> I guess this is intrinsic to your internal DBs?
> GCA_000005005.5 [http://www.ncbi.nlm.nih.gov/assembly/GCA_000005005.5/]
>
> Marcela
>
>
> On Fri, Jun 13, 2014 at 2:31 PM, Monaco, Marcela <mmonaco at cshl.edu> wrote:
>>
>> I know.  We have asked you a couple of times if you knew the correct
>> reference for that sentence.  There is a basecamp item for this, not sure of
>> a previous mantis also, and definitely a couple of e-mails...  But kept
>> forgetting to ask you during the gramene call.  So do we just remove your
>> name, no reference?  Just so you know, anyone from us may edit the page from
>> http://ensemblgenomes.org/user
>>
>>
>> On Fri, Jun 13, 2014 at 1:55 PM,
>> feedback at gramene.org<mailto:feedback at gramene.org>
>> <feedback at gramene.org<mailto:feedback at gramene.org>> wrote:
>> URL         : http://ensembl.gramene.org/Zea_mays/Info/Annotation/
>>
>> Subject     : Site Feedback: static content says "Josh?"
>>
>> Name        : Joshua Stein
>>
>> Email       : steinj at cshl.edu<mailto:steinj at cshl.edu>
>>
>> Organization: CSHL
>>
>> Comments    :
>>
>> Can this quote be corrected:
>> "Maize is distinguished from other grasses in that its genome arose from
>> an ancient tetraploidy event unique to its lineage [Josh?]."
>>
>> It's embarrassing.
>>
>> http://www.warelab.org/bugs/view.php?id=4967
>>
>>
>> _______________________________________________
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>>
>