dhis2-users team mailing list archive

[Andres Colubri <andres.colubri@xxxxxxxxx>]

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
>