dhis2-users team mailing list archive

[Jason Pickering <jason.p.pickering@xxxxxxxxx>]

Hi Andres.

There may be some overlap here with some other scripts we have written to
syncronize category options.

Looking at this file

https://github.com/nextstrain/fauna/blob/master/source-data/flu_strain_name_fix.tsv

is seems to be a bunch of flu strains. I guess something similar exists
 for Ebola?

The approach we have taken with another system is to transform and import
these into DHIS2 through an ETL process. I think something similar might be
possible. It might be worth looking into and I would be happy to discuss
further with you about our approach.

Regards,
Jason


On Fri, Apr 7, 2017 at 2:55 PM, Andres Colubri <andres.colubri@xxxxxxxxx>
wrote:

> Hi Johan,
>
> Many thanks for your kind reply. Yes, that's correct, we would like to
> associate pathogen sequence data to clinical cases. It sounds like storing
> the link to the NCBI records in a metadata attribute would be the simplest
> solution, as long as the sequences are already deposited publicly somewhere
> else. Then the app would pull the links from the DHIS2 DB and retrieve the
> full sequences. We will look into it, and will get back with more questions.
>
> Best,
>
> Andres
>
> On Fri, Apr 7, 2017 at 4:00 AM, Johan Ivar Sæbø <johansa@xxxxxxxxxx>
> wrote:
>
>> Hi Andres,
>>
>> Welcome to the list! From what I understand, you want to associate a
>> given strain, such as MK13013 or the longer version Ebola
>> virus/H.sapiens-wt/SLE/2015/Makona-1309_C2_MK13013, with a clinical
>> case? That should be possible in several ways, either as a free text data
>> element, an option set, or as metadata attribute
>>
>> Take a look at some of the options in the manual:
>> Metadata attributes: https://docs.dhis2.org/master/
>> en/user/html/manage_attribute.html#about_attribute
>> Option sets: https://docs.dhis2.org/master/en/user/html/manage_option_set
>> .html
>>
>> If you want more of the meta-data such as the complete sequence, it
>> should in theory be possible, but a link to the ncbi would perhaps be the
>> best.
>>
>> Regards,
>> Johan Ivar Sæbø
>>
>> >-----Original Message-----
>> >From: Dhis2-users [mailto:dhis2-users-
>> >bounces+johansa=ifi.uio.no@xxxxxxxxxxxxxxxxxxx] On Behalf Of Andres
>> >Colubri
>> >Sent: Thursday, April 06, 2017 3:40 PM
>> >To: dhis2-users@xxxxxxxxxxxxxxxxxxx
>> >Subject: [Dhis2-users] storing/linking sequence metadata in DHIS2
>> >
>> >I'm new to this mailing list, and to DHIS2 in general, so would like to
>> start by
>> >saying hi to everyone!
>> >
>> >
>> >I'm looking to create an DHIS2-based app that displays viral sequencing
>> >information on top of clinical cases (something along the lines of
>> NextStrain
>> ><http://www.nextstrain.org/ebola?c=division&r=division> ). Is this
>> possible?
>> >Would I need to modify the underlying DataElement in dhis2-core to
>> support
>> >genetic metadata? Or would it be enough to add a reference to sequences
>> >stored elsewhere, for example in GenBank?
>> >
>> >Best,
>> >
>> >Andres
>>
>
>
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-- 
Jason P. Pickering
email: jason.p.pickering@xxxxxxxxx
tel:+46764147049