Integrate SAMS as an iframe
The SAMS search interface can be readily integrated into hospital information systems as an HTML5 iframe and will return a Phenopacket. No data is stored on our server. Simply include the following code:
<iframe src="https://www.genecascade.org/sams-cgi/enter_phenotype.cgi"
style="position: fixed; top: 0px; bottom: 0px; right: 0px; width: 100%; border: none;
margin: 0; padding: 0; overflow: hidden; z-index: 999999; height: 100%;">
</iframe>
See an example implementation on this page. The style parametes can be adjusted to fit your needs.
Programmatic access to SAMS
Linking to SAMS from external systems
Please note that you have to be logged into SAMS in your browser to access your patient data.
In the examples below, replace
myPatID
, the patient ID (parameter: external_id), with the pseudonomised ID
you have given to your patient.
Record and edit a visit
Link to the interface for recording a visit for a specific patient. You may also provide the visit date and details
about the patient.
If a patient with the given external ID does not yet exist, it will be created.
If a visit for the given date already exists, you may edit this visit.
Call
entry.cgi
with
mode=visit
and your chosen parameters for
external_id
,
sex
,
consanguinity
and
visit_date
.
Parameters:
-
external_id
is the only obligatory parameter.
-
sex
can take the values m
for male or f
for female. If no parameter is
given the sex is recorded as other/unknown. If a new patient is created, this value will be used. Note that this
does not change the sex of an exisiting patient with this external id.
-
consanguinity
can be true
, if the patient has consanguineous patients or
false
if the patient has non-consanguineous parents. If no parameter is given the consanguinity is
recorded as unknown. Note that this does not change the consanguinity of an exisiting patient with this external id.
-
visit_date
is the date of the visit that you want to create or edit. Provide the date in the
following format: yyyy-mm-dd
(e.g. 2023-01-05 for fifth of January 2022). Note that if you do not
provide the date here, it is possible that you will overwrite an existing visit.
Example link:
https://www.genecascade.org/sams-cgi/entry.cgi?external_id=myPatID&sex=m&consanguinity=true&visit_date=2023-07-12&mode=visit
Show patient overview
Link to the overview of all previous visits of a specific patient.
Call
entry.cgi
with
mode=show
and your
external_id
.
Example link:
https://www.genecascade.org/sams-cgi/entry.cgi?external_id=myPatID&mode=show
Export patient record as Phenopacket
Export all recorded visits of a specific patient as a
GA4GH
Phenopacket in JSON format.
Call
export_phenopacket.cgi
with your
external_id
.
Example link:
https://www.genecascade.org/sams-cgi/export_phenopacket.cgi?external_id=myPatID
Integrating SAMS into your sytems
If you are interested in syncing the SAMS patient management functionality with a local patient management system, please
contact us at dominik.seelow (at) bih-charite.de, janina.schoenberger (at) bih-charite.de or robin.steinhaus (at)
bih-charite.de.