Re: [Dhis2-users] storing/linking sequence metadata in DHIS2

[Jason Pickering]

Hi Andres,

As Johan mentioned, the best way to do this probably would be with an
option set.  Looking at NextStrains process, they import some metadata on
Ebola strains (
https://github.com/nextstrain/augur/blob/master/ebola/ebola.py#L117) and
process this into the format they need for the website. I think it should
be possible to do the same for DHIS2, and process this into an option set (
https://docs.dhis2.org/master/en/developer/html/webapi_csv_metadata_import.html#webapi_csv_option_sets)
which could then be imported into your DHIS2 database. Once you have the
metadata in the correct format, it would just be a matter of importing it
as an option set into DHIS2. Once you do that, you could then use the
events module to link an event (like a case detection) .

The link you provided looks much more unstructured, so it might be more
difficult to parse and scrape this data.


Regards,
Jason




On Mon, Apr 10, 2017 at 4:48 AM, Andres Colubri <andres.colu...@gmail.com>
wrote:

> Hi Jason,
>
> Yes, in principle we would like to link a number of clinical cases with
> Ebola sequences such as these
> <https://www.ncbi.nlm.nih.gov/nuccore?term=257197[BioProject]>.
>
> But more generally, l we are interested in a number of viral pathogens in
> addition to Ebola (Lassa fever, Zika, etc).
>
> By using ETL process you mean that we should be able to integrate the
> sequence information directly into the DHIS2 DB?
>
> Andres
>
> On Fri, Apr 7, 2017 at 11:14 AM, Jason Pickering <
> jason.p.picker...@gmail.com> wrote:
>
>> 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.colu...@gmail.com>
>> 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 <joha...@ifi.uio.no>
>>> 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...@lists.launchpad.net] On Behalf Of Andres
>>>> >Colubri
>>>> >Sent: Thursday, April 06, 2017 3:40 PM
>>>> >To: dhis2-users@lists.launchpad.net
>>>> >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!
>>>> >
>>>

Re: [Dhis2-users] storing/linking sequence metadata in DHIS2

[Andres Colubri]

Hi Jason,

Yes, in principle we would like to link a number of clinical cases with
Ebola sequences such as these
<https://www.ncbi.nlm.nih.gov/nuccore?term=257197[BioProject]>.

But more generally, l we are interested in a number of viral pathogens in
addition to Ebola (Lassa fever, Zika, etc).

By using ETL process you mean that we should be able to integrate the
sequence information directly into the DHIS2 DB?

Andres

On Fri, Apr 7, 2017 at 11:14 AM, Jason Pickering <
jason.p.picker...@gmail.com> wrote:

> 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.colu...@gmail.com>
> 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 <joha...@ifi.uio.no>
>> 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...@lists.launchpad.net] On Behalf Of Andres
>>> >Colubri
>>> >Sent: Thursday, April 06, 2017 3:40 PM
>>> >To: dhis2-users@lists.launchpad.net
>>> >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=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
>>>
>>
>>
>> ___
>> Mailing list: https://launchpad.net/~dhis2-users
>> Post to : dhis2-users@lists.launchpad.net
>> Unsubscribe : https://launchpad.net/~dhis2-users
>> More help   : https://help.launchpad.net/ListHelp
>>
>>
>
>
> --
> Jason P. Pickering
> email: jason.p.picker...@gmail.com
> tel:+46764147049 <+46%2076%20414%2070%2049>
>
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Re: [Dhis2-users] storing/linking sequence metadata in DHIS2

[Jason Pickering]

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.colu...@gmail.com>
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 <joha...@ifi.uio.no>
> 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...@lists.launchpad.net] On Behalf Of Andres
>> >Colubri
>> >Sent: Thursday, April 06, 2017 3:40 PM
>> >To: dhis2-users@lists.launchpad.net
>> >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=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
>>
>
>
> ___
> Mailing list: https://launchpad.net/~dhis2-users
> Post to : dhis2-users@lists.launchpad.net
> Unsubscribe : https://launchpad.net/~dhis2-users
> More help   : https://help.launchpad.net/ListHelp
>
>


-- 
Jason P. Pickering
email: jason.p.picker...@gmail.com
tel:+46764147049
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Re: [Dhis2-users] storing/linking sequence metadata in DHIS2

[Andres Colubri]

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 <joha...@ifi.uio.no> 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...@lists.launchpad.net] On Behalf Of Andres
> >Colubri
> >Sent: Thursday, April 06, 2017 3:40 PM
> >To: dhis2-users@lists.launchpad.net
> >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=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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Re: [Dhis2-users] storing/linking sequence metadata in DHIS2

[Johan Ivar Sæbø]

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...@lists.launchpad.net] On Behalf Of Andres
>Colubri
>Sent: Thursday, April 06, 2017 3:40 PM
>To: dhis2-users@lists.launchpad.net
>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=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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[Dhis2-users] storing/linking sequence metadata in DHIS2

[Andres Colubri]

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 ). 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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