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
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: Home - DHIS2 Documentation
Option sets: Home - DHIS2 Documentation
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@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 DHIS2I'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
<auspice; ). 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
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@ifi.uio.no wrote:
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
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@lists.launchpad.net] On Behalf Of Andres
Colubri
Sent: Thursday, April 06, 2017 3:40 PM
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?
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@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
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
–
On Fri, Apr 7, 2017 at 4:00 AM, Johan Ivar Sæbø johansa@ifi.uio.no wrote:
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
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@lists.launchpad.net] On Behalf Of Andres
Colubri
Sent: Thursday, April 06, 2017 3:40 PM
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?
Jason P. Pickering
email: jason.p.pickering@gmail.com
tel:+46764147049
Hi Jason,
Yes, in principle we would like to link a number of clinical cases with Ebola sequences such as these.
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.pickering@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.colubri@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
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.pickering@gmail.com
tel:+46764147049
–
On Fri, Apr 7, 2017 at 4:00 AM, Johan Ivar Sæbø johansa@ifi.uio.no wrote:
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
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@lists.launchpad.net] On Behalf Of Andres
Colubri
Sent: Thursday, April 06, 2017 3:40 PM
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?
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.colubri@gmail.com wrote:
Hi Jason,
Yes, in principle we would like to link a number of clinical cases with Ebola sequences such as these.
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.pickering@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.colubri@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
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.pickering@gmail.com
tel:+46764147049
–
On Fri, Apr 7, 2017 at 4:00 AM, Johan Ivar Sæbø johansa@ifi.uio.no wrote:
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
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@lists.launchpad.net] On Behalf Of Andres
Colubri
Sent: Thursday, April 06, 2017 3:40 PM
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?
Jason P. Pickering
email: jason.p.pickering@gmail.com
tel:+46764147049