SAMS Documentation
SAMS (Symptom Annotation Made Simple) is created for medical professionals to digitally capture a patient's diagnosis, clinical signs, and symptoms, and to keep track of their changes over time.
SAMS with all of its functions is and always will be completely free of charge. However, you must credit us; for details refer to the licence.
You may use some of the functions that SAMS offers without logging in, such as creating and/or viewing a GA4GH Phenopacket. However, please note that saving data in our database requires registration.
Landing page
On the start page, you can either create a new SAMS account for yourself, log in, or create and/or view a Phenopacket.
Using SAMS without an account
Phenotype a patient and create a Phenopacket
This option allows you to select clinical signs, symptoms, diagnoses, and more and export them as a Phenopacket.
Use SAMS without login
With this option you may use SAMS as if you were logged in. However, all information you enter is public and records may be deleted or modified by anyone. SAMS displays a red warning message to remind you.
Show phenopacket
Show the contents of a phenopacket in a human-readable fashion.
Using SAMS with an account
Registration and Login
In order to be able to save your records, you will have to register by
clicking Create a new account. For this you will need a
login name. We recommend that you specify a valid email address
because this is the only way to recover lost passwords, but an email address is not mandatory. Physicians
may optionally enter their name and the name of their institution or
practice.
Patients are encouraged to phenotype themselves (or their sick children) in collaboration with their doctors. SAMS is not a diagnostic tool - any diagnosis
or decicions about therapies must be made by medical professionals.
Whenever you log in to SAMS, a session cookie is set – these are deleted automatically after 4 hours or when you log off.
If you forget your password, please use the Forgot password? link.
Physicians: Data Management
After successful login, you are able to manage the records of all of your patients. Your patients will be displayed as a list (see screenshot) You will be able to create new patients (New patient record) and enter their phenotypes on a certain date (Add visit). You may of course also view, edit, or delete patients and their phenotypes.
To add a new patient, please click New patient record. Here you can enter a patient ID and set the patient's sex and provide information of a consanguineous background.
Add phenotypic data
On the enter phenotype page, you are able to enter and track clinical signs
that were observed during the current examination. Physicians will
arrive on this page when clicking the Add visit button, patients are
redirected here directly after login. First set the date of the visit
and start by searching for a term (this might be a symptom, a clinical finding, or even a diagnosis) using the search bar at the top. A
drop-down menu will appear (see screenshot), where you can select the
appropriate term from a list of possible matches. It is also possible
to search for terms by their ID (i.e. HP:0100758). The coloured items
in the top right allow you to select the data sources that you wish to include (e.g. signs and
symptoms from Human Phenotype Ontology and diagnoses from
Orphanet) .
Clicking on the checkbox left of the text allows you to select the appropriate term,
subsequent clicks set the term to “absent”. This can be
particularly interesting for findings that you would actually expect to be present.
Please note that 'unspecific' HPO Terms are greyed out.
If you want to record a patient's clinical signs in a standardised fashion
with a checklist,
you can either click on Pre-defined questionnaires
to access user-defined lists or select an Orphanet
disease and click Choose signs.
Both options will refer you to a list of HPO terms, which will be
transferred to your selection, when clicking
Send to SAMS.
Should you want to add a customised questionnaire, please email us!
It is possible to assign clinical modifiers to HPO terms. To select modifiers, click the Add modifiers button next to the term that you want to assign modifiers to. You can then search for a specific modifier or navigate in the tree structure. When you are satisfied with the selected modifiers, click Save modifiers.
You can have a look at the current selection of entries under the banner Selection on the right side. If you wish to reset your selection, you can do so by hitting the Reset button. When you are happy with your selection, finish phenotyping by clicking the Save visit button. The current date will be used, if you have not entered one yourself.
This will create a report and save your input when you click Save records to DB. You can also Export Phenopacket if you do not want to store the data in our database but only save them locally.
Manual adjustment of entries / copy and paste
Click on the icon to the right of the Selection / to copy the phenotype as text or to add a list of terms (as IDs, e.g. ORPHA:287) from text.
This can be especially useful, if you already know the IDs of the different phenotype terms or when copying entries from a different patient or previous visit.
Editing Previous Entries
Instead of adding a new visit, you might also want to see and/or modify a previous visit of the patient. This can be done by clicking Display records.
This will lead to a list of all previously entered visits. The entries that were made during each visit can be made visible by clicking on the double arrow symbol. Click on the pen to make changes to this particular visit. Copy to clipboard will copy the recorded terms of the respective visit to the clipboard in the same format as in the Selection.
Here you also have the option to display the changes of signs, symptoms and diagnoses of a patient over time. You can access this view by clicking Time course.
Share Patients
You can easily share data of one of your patients (or yourself) with others by hitting the share symbol and share the link that appears. This link is only active for 24 hours and the recipient must be logged in to accept it.
The recipient can see the patient's data, but will not be able to make additional changes. If you want to add or modify data of a patient shared with you, you can export the patient as a Phenopacket and re-import it.
Phenopackets
SAMS offers the option to export patient records as GA4GH Phenopackets (by clicking the down-arrow icon ). To export all patient records, click the Export all patients button.
Phenopackets can also be used to import data (by clicking on Import data).
Read more about Phenopackets in the documentation or in the scientific publication.
Download SAMS
SAMS is open source and licensed under CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0/), which includes giving "appropriate credit". When crediting us, please cite our publication.
The source files are available at https://git-ext.charite.de/genecascade/sams. Please note that we cannot provide support for locally installed versions.
Contact
If you have suggestions or ideas regarding SAMS, please get in touch.
Drop us an email at dominik.seelow (at) bih-charite.de, janina.schoenberger (at) bih-charite.de or robin.steinhaus (at) bih-charite.de.
DIMDI: Deutsches Institut für Medizinische Dokumentation und Information (Alpha IDs).↩︎