SAMS - Documentation

SAMS Documentation

SAMS (Symptom Annotation Made Simple) is created for doctors and patient to digitally capture a thorough phenotype and track emerging signs and symptoms and changes thereof over time.

Homepage

On the homepage you have the option to use some SAMS functions without logging in or logging in to use the full functionality and save, edit or delete private records.

Using SAMS without an account

Phenotype a patient and create a Phenopacket

This option allows you to select symptoms, diagnoses and more and export them in a Phenopacket.

Use SAMS without login

With this option you may create SAMS records as if you were logged in. However, all information you enter is public and old records may be deleted. Please do not enter patient data here!

Show phenopacket

Show the contents of a phenopacket in a human-readable table.

Using SAMS with an account

Refer to the next section to set up your SAMS account.

In order to be able to save your records you will have to register by clicking Create a new account. For this we require a login name. We recommend that you specify a valid E-Mail address because this is the only way to recover lost passwords. Physicians may also enter their name and the name of their institution or practice.

If you forget your password, please use the Forgot password? function.
We use session cookies for authentication purposes only – these are deleted when you log off.

Physicians: Data Management

After successful registration or 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 and edit new patients, delete entries, as well as enter, read, visit or edit the results of previous visits. One click on Add visit will bring you to the entry page for signs, symptoms and diagnoses.

To add a new patient please click New patient record. Here you can select a patient ID and set the patient’s sex, and provide information of a consanguineous background.

Entry of Symptoms

On the enter phenotype page you are able to enter and track symptoms 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 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 menu in the top right allows you to select the data source (signs and symptoms from Human Phenotype Ontology and diagnoses from OMIM, Orphanet, and DIMDI¹) that you wish to search in. HPO Terms may be colored grey, if the term is imprecise. A click on the checkbox allows you to select the appropriate term, subsequent clicks allow you to set the term to “absent”. This can be particularly interesting for signs that you would expect to observe.

If you wish to select terms from a list of symptoms, instead of searching for each term manually, there are two options to do so. You can either click on Pre-defined questionnaires to access user-defined lists of symptoms 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.

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 to be able to add more signs and symptoms.

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, you can 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.

Manual adjustment of entries

Clicking on the small document icon to the right of Selection allows the user to make manual adjustments to the entry.

This can be especially useful if the user already knows the IDs of the signs, symptoms, or diseases they would like to add, or when copying over entries from a different patient or previous visit.

Editing Previous Entries

Instead of adding a new visit the physician might want to add or delete symptoms to a previous visit of the patient. This can be done by clicking Display records.

This will lead the user 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. Clicking on the pen icon allows the user 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.

In addition, we support a way for doctors to share a patient, if they are working together on the same case. This can be achieved by hitting the share symbol and sharing the link that appears. This link is only active for 24 hours.

The user who has received the link will be able to see the patient's data, but will not be able to make additional changes. In some cases a copy of a certain patients data is required so that both user may make changes to their data. This can be achieved by first exporting the patient and then importing on the other account.

Phenopackets

SAMS now additionally offers the option to export patient records as a Phenopackets. This allows the efficient collaboration with scientists and other physicians. This functionality can be accessed by clicking the down-arrow icon. There is also the option to export all patients at the same time using the Export all patients button.

Phenopackets can also be used to import data from other physicians by using Import data.

DIMDI: Deutsches Institut für Medizinische Dokumentation und Information (Alpha IDs).↩︎