OPTIMISE MS is a system for recording data including demographics, clinical events, treatments and tests in a fashion interoperable with Clinical Data Interchange Standards Consortium (CDISC) standards for Multiple Sclerosis. OPTIMISE MS allows researchers to better monitor MS patients’ progress, record outcomes and evaluate treatments.

The user can enter demographic, medical history and family medical history, clinical event, visit, test and treatment data.

OPTIMISE MS can be used in two modes; the offline mode when networking is enabled and the online mode when networking is disabled.

This guide assumes that the OPTIMISE MS system has been successfully configured as described at Getting started. An administrator needs to be defined who can control permissions for data access and securely provide users with login details. The PC and login passwords should be kept securely.

Patient identifiers

A patient identifier is required when creating a new patient in OPTIMISE MS. The term Patient ID, used in this guide, refers to this identifier which may correspond to the patient's NHS ID. OPTIMISE MS stores an independently generated, pseudonymised ID along with the patient ID entered by the user at patient creation time- this generated identifier is referred to as OPTIMISE ID.

The generated OPTIMISE ID is included in the exported data (more about the export in the section Exporting patient data). The patient ID, which, as mentioned above, can be the NHS ID, is not included in the exported data sets. You can retrieve the patient ID using the Search tool as search by this generated ID is also possible.

Logging in

To start using the OPTIMISE MS portal, first open your favourite modern Browser.

Then, enter the hosting address in the address bar.

You should see the following screen.

login

Enter the user name and password (in the boxes as shown below) that were given to you and click the Login button. The default username is admin and the default password is admin.

credentials

If the log-in is unsuccessful, you will get a message as shown below. Re-enter user credentials and click Login.

loginFail

If the log-in is successful, you should see the following screen.

initial

Searching patients

You can search the database using the user-friendly search tool available after successful log-in.

searchTool

To search by patient ID, select Patient ID from the drop-down list labelled as 'Search by:'.

searchBy

Click on the box labelled 'Containing'- this is below the 'Search by' list- and enter the patient ID you want to search for.

searchBox

As you type in search value box ('Containing' box), the patients with ID that contain the text you entered will be shown in the area below the search box. Basic patient information for each listed ID is also shown. If no patients are listed, then there are no patients with that ID already in the database. You can begin to enter data for a new patient, by entering the ID- please see the section Creating a new patient.

searchResults

Data files generated by OPTIMISE MS using the Export option do not include the patient ID. You can retrieve the Patient ID using the Search tool. Select Anonymised ID from the drop-down 'Search by' list and enter the OPTIMISE ID (labelled as USUBJID) you see in the exported files in the 'Containing' box. This allows retrieval of the patient ID- the patient ID is shown in the search results.

Search by fields other than Patient ID and Anonymised ID (generated OPTIMISE ID) is also available. The example below refers to a search by country of origin with search value 'Canada'. The search results include two patients; patients with IDs OPTIMISE1 and OPTIMISE2.

searchCountry

Choose from the list of patient IDs below the search box by clicking on the patient box. To view and/or enter data for patient with ID OPTIMISE1, for example, click on the respective box (highlighted).

searchPatientResultsBox

The timeline and a summary of the patient's Medical History will be available in the left panel. An overview that includes the patient profile, the primary diagnosis and other sections is available in the right panel (see next screenshot). You may add, edit, or delete data for these sections as described in Entering patient data.

To exit the patient's (here, OPTIMISE1) records and return to the Patient Search page where you can search and create patients, click on examplePatientProfileClose which is located near the top centre of the page as shown below.

examplePatientProfileClose

Creating a new patient

There are two ways to create a new patient in OPTIMISE MS; by clicking directly on the button 'Add a new patient' at the top of the page or by using the search tool.

createPatientButtons

To create a new patient using the first way, click on Add a new patient. Enter the patient ID in the Patient ID input box in the new patient profile form in the right panel. The form includes the patient consent status. You need to set the consent status for patient data sharing to Yes or No at this stage.

newpatient2

Complete the form (the option Unknown may be selected where appropriate), scroll down to the end of the form and click Submit to create the patient. To cancel the patient creation, click on close at the top right corner of the screen.

newPatientProfileSubmit

A warning message will be shown if any of the fields are empty or unselected when you click Submit. All the fields in this form are required in order to add the patient to the system. If you see the following message, please ensure the new patient profile form is completed before clicking Submit.

newPatientErrorMessage

If the patient creation is successful, you should see the following page. Please note that a few fields are conditional on the patient profile (Pregnancy, for example, is conditional on sex) and may be unavailable to some patients.

newPatientAfterSubmit

At any point you can return to the patient search page by clicking on searchMagnifier in the left panel (see below).

searchMagnifier

You may also return to the patient search page by clicking on close near the top centre of the screen highlighted below.

newPatientClose

To create a new patient using the search tool, select Patient ID as the search field list and enter the patient ID in the search value box. If there are no patients with the entered ID (here, 'opt'), you may create a new patient by clicking the button

createPatientSearch

createNewPatientSearch

Once you click the Create button, you should fill the new patient profile form in the right panel as described above. The patient ID is shown at the top of the new patient profile form- this is automatically filled.

newPatientProfile

Updating patient consent

OPTIMISE MS is intended to be used after consent is given by patients to hold their data outside of a hospital or clinic IT system. The clinical user of OPTIMISE MS must indicate that appropriate consent has been given.

You may update the patient consent status at any time. Go to the main patient profile page and use the highlighted control in the right panel to update the status of patient consent.

If the current consent status is set to Yes, the text on the consent button will read as follows:

consentButton

For patient profiles currently not consenting, the consent button will look like

setConsent

setConsent

The current patient consent status is always visible on screen. Clicking the consent button in the right panel updates this label accordingly.

consentLabel

Deleting a patient

Administrator users may need to remove a patient from the database (i.e. Right to be forgotten). To delete a patient click on 'Delete this patient' in the right panel. Please note this is only available to administrator users.

deletePatientButton

deletePatient

Click on YES, I AM SURE! to confirm the deletion or click close at top right corner of the pop-up message box to cancel.

deletePatientMessage

Entering patient data

Patient overview

The Profile section in the Overview panel contains the profile data entered during patient creation. To edit the Profile section, click the button editProfileButton next to Profile. Click on pii to view the Patient Identifiable Information.

editProfileButton

Edit the Patient Demographics form as necessary and click Submit to save the changes or close to return to the Overview panel.

editProfile1

The Primary Diagnosis section in the Overview panel contains the most recent diagnosis data. To edit this or add more diagnoses, click editProfileButton next to Primary Diagnosis.

editDiagnosisButton

A list of all diagnoses is shown in the right panel. Click on delete to delete the diagnosis entry. Click on editProfileButton to edit that entry.

primaryDiagnosis

The form in the right panel below becomes available if you click editProfileButton. Complete the form as necessary and click Confirm change to save or Cancel or close to return to the Overview panel.

editDiagnosisForm

To add more primary diagnoses, click on

addDiagnosisButton

addDiagnosisButton1

Enter the diagnosis date and select the diagnosis term. Click Submit to add the entry or Cancel to return to the diagnosis panel. Click close to return to the Patient Overview.

diagnosisForm

To add or edit Pregnancy data, click on pregnancyEdit. The most recent Pregnancy record (pregnancy date) is listed in the Overview Panel.

pregnancy

Click on

pregnancy

in the right panel to record a pregnancy or click on delete or editProfileButton to edit or delete existing entries, respectively.

pregnancyForm

Fill in the form. Untick pregnancyForm to enter outcome date, outcome term and MedDRA code. Click Submit to record the pregnancy or Cancel to return to the list of Pregnancies. Click close to return to the Patient Overview.

pregnancyForm

To enter Immunisation data, click on

immunisation

immunisation

Enter data in the highlighted form shown below. Click Submit to add the new immunisation or Cancel.

immunisationForm

The immunisation records are added to the Overview panel as shown below. To remove an Immunisation entry, click del next to that particular entry.

immunisationDelete

Medical history

The filtering tool in the Medical History Summary allows you to select which medical elements are included in this section. This is especially useful for patients with considerable amount of recorded data. To include Treatments and Tests only, click on the respective buttons.

medicalHistoryFilter

Visit data

Each clinical consultation is represented as a Visit in OPTIMISE MS. A “Baseline Visit” would usually refer to the first visit to the clinical site or consultant responsible for the database.

Click on newVisit to create a new visit for the patient.

newVisit

Complete the new visit form in the right panel. Select the reason of the visit from the list of available options- this includes Routine, Drug Monitoring, Relapse Assessment and Urgent. Click Submit to create a visit.

newVisitForm

A warning message is shown if the form is incomplete when Submit is clicked.

newVisitFormError

If the visit is successfully created, it will be added to the Medical History Summary and to the Timeline. Baseline visits are labelled as such.

newVisitFormSubmit

The reason for the visit entered when the visit is created is used to label the visit entry in the Medical History Summary. A relapse assessment visit is shown below.

relapseVisit

Enter Anthropometry and Vital Signs data, if available, by clicking on the highlighed button in the Medical History Summary. Fill in the right panel form. Click Save and then click on close at the top right corner to return to the Patient Overview. To cancel the data entry and return to the Overview without saving, click on close.

vital

The data will be added to the Medical History Summary in the appropriate section e.g. Anthropometry and Vital Signs, here.

vitalAdded

Symptoms and Signs are recorded only at a high level in the OPTIMISE MS database in an attempt to maximise the efficiency of their recording in the clinic and thus encourage their completeness. Symptoms reported by the patient and Signs observed by the neurologist are recorded separately.

Click on 'Edit symptoms data for this visit' or 'Edit signs data for this visit' buttons to enter Symptoms or Signs, respectively, elicited at the visit. For baseline visits, these will be labelled as 'First symptoms/signs indicating MS'. For non-baseline clinical visits, they will be labelled simply as Symptoms/Signs.

symptomsSigns

Enter any present symptoms by clicking on the buttons or selecting a value from the drop-down lists in the right panel form. For example, the neurologist might have observed fatigue for the patient. Scroll down to the end of the form and click Save. To exit the form and return to the Patient Overview, click close at the top right corner. The form can be edited at a later time.

symptoms

Similarly, enter any signs by filling and saving the Signs form in the right panel. As an example, the patient might have shown evidence for cognitive dysfunction with impairment of memory and had reduced sensitivity to the colour red with the left eye.

signs

Click on 'Edit performance measures data for this visit' to enter Performance Measures data.

perfMeasures

The EDSS can be entered in two ways; the neurologist’s estimated EDSS or the calculated EDSS. The neurologist’s estimated EDSS score can be entered in the highlighted box in the right panel form.

estimatedEDSS

Only valid EDSS total scores (0 to 10 by 0.5 increment excluding 0.5) may be accepted in this field. Entering an invalid total EDSS, for example 100, will generate an error. Please use the dot notation for the decimal point, i.e. 4.5 is accepted while 4,5 is not.

edssError

Click Save for this estimated EDSS to be recorded. In addition, or alternatively, the functional systems can be scored separately and the total EDSS can be calculated by clicking on Open EDSS Calculator. The estimated total EDSS entered as described above is carried over to this calculator only if the score is saved (by clicking the Save button).

EDSScalculator

Select a score for each EDSS subcategory. Hover over a score button to see the respective score description highlighted on the right. The calculated total score will be shown in the score box labelled Computed total score (automatically generated). Note that an Ambulation score is required for the functional scores to be saved. The saved estimated total is carried over to the score box labelled Estimated total score (by the clinician). You may update the estimated total here as well.

Click Save to record the scores and then close to exit the calculator. To exit Performance Measures and return to the Patient Overview, click on close at the top right corner of the EDSS form.

edssCalculator

The EDSS Total and EDSS Subscores will be listed under Performance Measures in the Medical History Summary. The text of the total scores (estimated and computed) is bold and pink.

edssAdded

OPTIMISE MS supports the generation of a free-text visit report, called a Communication. This can be exported as a .txt file. You may also copy and paste the entered text directly in a document such as a clinic letter generated by other software.

Click on 'Edit or export the visit report' to edit or export a Communication for the visit.

communication

Specific field data entered for the patient from a visit can be added automatically to the Communication by selecting the appropriate buttons above the text area.

communicationReport

Click on the buttons to add the respective recorded data to the report. You may format the text using the available formatting tools. The report can be updated at a later time to include data entered after its creation.

communicationReport

For Clinical Events, Tests and Treatments, the time period to cover can be specified using the drop-down list. The default behaviour is to include observations/records of the last month. Select a different option from the list and click Add to update the report accordingly. Click the Save or Export button or close to return to the Patient Overview.

communicationTimePeriod

Treatment and clicical event information covering the entire patient medical history were added to the Communication below using the appropriate buttons and selecting the entire patient history in the time period drop-down list.

communicationTimePeriodCETreatments

A visit can be edited by clicking on edit next to the visit entry.

editVisit

To edit the visit date or the reason for the visit, click on

editVisit

and to remove a visit click on

deleteVisit

Test data

Click on newTest to create a record for a new test for the patient.

newTest

Select the date of the test, the type of test (Lumbar Puncture is selected below) and click Submit to create the new test. Click close to cancel and return to the Patient Overview.

testForm

If the test is successfully created, it will be added to the Medical History Summary in the main panel as shown below. The test is also shown on the Timeline (green symbol) above the Medical History Summary.

testFormAdded

Click on Results to enter further data for the test.

testResultsButton

Complete the form in the right panel and click Save to record the test results.

testResultsForm

Entering non-numeric input where this is invalid will generate the following error message. Correct and click Save.

testResultsFormError

At any point you can click close to cancel the test data entry and return to the Patient Overview.

Laboratory tests refer to blood or CSF tests only, e.g. total WBC, bilirubin and specific anti-body titres. After entering test results for a given reporting date, scroll down to the end of the page and click Save. Click close to return to the Patient Overview.

labForm

Entering non-numeric characters in the laboratory tests will generate the following error message as numeric input is expected.

labFormError

Currently, only data concerning the presence or absence of T1 Hypointense Lesions, number of T2 Hyperintense Lesions and gadolinium (Gd) contrast enhancing lesions and brain atrophy scan result can be entered into the OPTIMISE MS database. Some of the available fields for an MRI test type are shown below.

mriForm

The data input in the MRI form is also validated. Entering non-numeric characters in Number of enlarging lesions, for example, will generate the following error message.

mriFormError

The Evoked Potential test section allows recording of the P100 Visual Evoked Potential amplitude and latency. Sensory Evoked Potentials (SEP) with stimulation in the limbs are recorded if Abnormal. Data validation is applied here as well- only numeric input is accepted in some fields.

evokedPotentialForm

Treatment data

Click on newTreatment to enter treatment data.

newTreatment

Fill in the treatment form in the right panel. Click Submit to record the treatment or close to cancel and return to the Patient Overview. A warning message will be shown if required fields are not filled.

treatmentForm

Unticking the box treatmentEnd allows you to record a treatment discontinuation by entering the treatment end date.

treatmentEnd

Any new treatment recorded is added to the Medical History Summary and the Timeline (yellow symbol) as shown below.

treatmentAdded

To record any interruptions to a treatment, click on Interruptions and then Add interruptions in the right panel.

interruptionButton

Enter the interruption start date, uncheck 'The interruption is ongoing' to enter the interruption end date, if known, and record the Reason for the Interruption from the drop-down menu.

interruptionForm

If the interruption is related to an adverse event, the next section for Adverse Events should be clicked open. A drop-down list of adverse events defined by the Medical Dictional for Regulatory Activities (MedDRA, see https://www.meddra.org) is available. Note, however, that as MedDRA coding is subject to license, the full tree is not available on this openly downloadable version of OPTIMISE MS (lower level terms are not available). Click on the arrows interruptionFormMeddraArrow next to each grouping term in the list to follow the expanding tree of terms and identify the specific adverse event. Click on the term to store it in the MedDRA field. Any term at any level may be added as MedDRA- in the example below, clicking on 'Anaemias nonhaemolytic and marrow depression' would add this term as MedDRA while clicking on the arrows and then on 'Anaemia folate deficiency' would add the latter as the MedDRA.

interruptionFormMeddra

Complete the form and click on Submit to add the interruption details. Click the Cancel button or on close to exit the interruptions section and return to the Patient Overview.

Clinical event data

Clinical Events allow entry of data concerning relapses and other clinically relevant changes or adverse events including infections, opportunistic infections, death and other SAE likely related to treatment or malignancies.

Click on newEvent to record a new clinical event.

newEvent

Fill in the form in the right panel and click Submit to add the event or close to exit without saving and return to the Patient Overview.

eventForm

The event will be added to the Medical History Summary and to the Timeline (red symbol). You may add Symptoms and/or Signs associated with the Clinical Event using the relevant buttons in the clinical event entry in Medical History Summary, a process similar to the one for Visits described above.

eventAdded

To further describe the clinical event click on Data.

eventDataButton

Select the functional systems affected by clicking on the buttons, fill in the rest of the form as necessary, click Save and then close to exit. Click close before clicking Save to cancel the data entry.

eventData

The data fields for Infections and Opportunistic Infections are shown below- see right panel forms.

infection

oppinfection

Editing medical history

Test, medication and clinical event data can be edited at any time by clicking the highlighted buttons in the Medical History Summary and following the steps described above. Additionally, for Clinical Events, Symptoms and Signs can be edited.

editDataButtons

To edit data about concerning tests, treatments and clinical events such as dates or type or to delete these entries, click on editIcon as shown below. Click on one of the buttons in the right panel to edit or delete the entry. The informative labels in the right panel will indicate which actions and modifications are allowed.

editIcons

Using the Timeline

You may click on the coloured shapes or EDSS on the Timeline to access (view/edit) the corresponding entry in Medical History Summary. The computed total EDSS is plotted at the bottom part of the timeline. If the computed total EDSS is not available (i.e. the calculator was not used or the user chose not to save the calculated score), then the estimated EDSS is plotted.

timeline

Click on timelineIcon next to Timeline to maximise the timeline. The horizontal end point (right) of the timeline is the current date. The timeline covers the last month by default. Therefore, any data recorded during this period is shown. You may change this behaviour by reading the guide below the graph.

timelineExpand

Follow the instructions below the timeline to interact with it. Zooming in and zooming out as well as navigation to a specific time period are available. The timeline shows Treatments, Visits, Tests, Clinical Events (Relapses and Adverse Events) and EDSS using different colouring.

Zooming out allows the depiction of a larger part of the patient's Medical History. For example, the patient's medical history for the year 2017 is shown below.

timelineOneYear

Further zooming-out gives a graphical overview of the complete medical history.

timelineAll

The treatment bands (yellow colour) are overlaid with the treatment names and types.

timelineTreatment

Treatment interruptions are clearly marked with vertical lines that cover the interruption period (from the interruption start date to the interruption end date).

timelineTreatmentInterruption

Relapses can be characterised as mild, moderate or severe. The size of the circle depicts this information with larger circles representing more severe relapses. Where this information is not available, relapses are shown as relapseSymbolTimeline.

timelineRelapse

A severe relapse that started on the 7th of August 2011 and ended on the same date is shown below. The circle size represents the severity level and the dashed line the duration of the event.

timelineRelapse1

An opportunistic infection (Adverse Event) that lasted one month is shown below.

timelineAE

A line chart is used for the the recorded EDSS with the scores being represented as black labelled points (dots) on the graph.

timelineEDSS

An EDSS of 2 recorded in 2010, an EDSS of 4.5 recorded in 2013 and an EDSS of 5 recorded in 2015 are shown below. The scores are connected.

timelineEDSS

Click close at the top right corner to exit the Timeline window and return to the Patient Overview.

Exporting patient data

OPTIMISE MS currently supports the export of patient data in JSON and CSV files. This is available in the right panel on the Patient Search page.

exportAll

In order to export the database as JSON and CSV files, click on the export button (highlighted) and choose where to save the ZIP folder which you can then extract. You may want to change the name of this folder- the default is attachment.zip. Please note that any Patient Identifiable Information is excluded from the generated JSON and CSV files by default.

exportAllButton

The patient ID is not included in any of the export output files; the OPTIMISE ID (an anonymised generated ID) replaces the patient ID as described in the section Patient identifiers. The column USUBJID (Unique Subject Identifier) in the exported treatment data CSV file stores OPTIMISE ID.

You can find the respective patient ID using the search tool as described in the section Searching patients.

export

The option to export part of the database becomes available if you start using the search tool.

Click on

exportSearchButton

in the right panel to export the data stored for the patients listed in the search results area below the search tool.

You may export data based on a search by fields such as ID and treatment. Here, for example, only the data for patients diagnosed with RRMS can be exported by clicking the appropriate Export button in the right panel.

exportSearch

Admin menu

Each installation of OPTIMISE MS should have an identified administrator who manages OPTIMISE MS. The administrator can create and delete user accounts, view the action log, where all user actions are recorded, and read messages about the software (e.g. the OPTIMISE MS software version) by accessing the Admin Menu.

The administrator can click on the button located in the left panel as shown below to access the Admin Menu. Note that this is only available to users with administrator rights.

adminMenuButton

adminMenu

The administrator can manage the users (create and delete user accounts) by accessing the relevant option (Manage users) in Admin menu. In order to update or delete a user account, click on the respective entry in the list of registered user accounts in the middle panel.

manageUsersEditDelete

To update the password for a particular user, select the user from the list, fill in the User Information form as shown below and click Submit. Click Cancel to cancel the update.

editUser

To withdraw admin rights for admin users, click on the tool shown below.

editPriv

To delete a user, select from the users list and click on Delete.

deleteUser

A warning message will appear. Click close to cancel the deletion or YES, I AM SURE! to confirm the deletion.

deleteUserWarningMessage

You may create a new user account by clicking on the Create a new user button.

manageUsersNew

Fill in the highlighted form and click Submit.

newUserForm

The following error message is shown if the submitted form is incomplete. Please complete all fields and re-submit.

newUserFormError

The action log shows a detailed description of all the actions performed by users.

actionLog

System information is also available in the Admin Menu.

newUserFormError

Logging out

To log out click on the logout button.

logoutButton

This is located in the panel on the left of the page as shown below.

logout