PhenoTips » User Guide » PhenoTips: getting started

PhenoTips: getting started

PhenoTips: getting started

Your user account

Most PhenoTips instances are private and password-protected in order to ensure that patient data is kept safe. Your user account must be created and activated by an administrator of the PhenoTips instance that is running for your institution. Each user account must be associated with a valid email address which will be the destination of any messages automatically sent by PhenoTips regarding your account. Unless specifically configured otherwise, PhenoTips will only send emails at your request, when you wish to recover any forgotten account information as explained below.

Forgotten user name or password

If you cannot remember your user name or password for logging into PhenoTips, navigate from the Login page to the link corresponding to your problem. You will be presented with a very simple form and you will receive by email your user name or instructions about resetting your password to regain access to PhenoTips.

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PhenoTips patient data

Browsing the available data

The PhenoTips homepage provides quick access to all information of interest for using the system:

Left column: general information

  • The About box gives a welcome message and/or a quick description of the system.
  • The Groups lists the most active major groups and provides a link to more information about each of them, including their public contributions.

Right column: user data

  • The My data box lists the cases owned by the current user. Please read below more information about data ownership.
  • The Data shared with me box lists the cases for which the current user is a collaborator either because he or she is part of the group which owns the case, or because the owner explicitly listed them as a collaborator on that case. Please read below more information about specifying collaborators.

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The homepage is immediately accessible from any other page by clicking on the logo or on the home icon (  ) displayed at the bottom of the page header area.

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Data entry

PhenoTips supports by default several categories of patient information: 

  • demographic information
  • family history
  • medical history
  • measurements
  • phenotypes
  • diagnosis

Administrators may choose to disable any of the sections corresponding to these categories, change their order or add new custom sections relevant to a specific study. We will describe below how data should be entered in some of the most relevant sections of the patient form.

Patient information

Fields such as patient identifier, patient name, date of birth, gender etc. may be displayed in this section. The level of personal information to be entered will be configured by the PhenoTips administrator, depending on the nature of the study for which the patient data is being collected. It is crucial to enter the date of birth and the patient's gender, in order to obtain the correct interpretation of measurements (see next section).

Measurements

The Measurements section of the PhenoTips Web form permits to record standard measures taken during clinical exams: Using the patient's gender and the age at the time of measurement (which is computed based on the recorded date of birth) these parameters are automatically translated into quantiles. Growth curves are plotted instantly based on entered values. Abnormal values are automatically reported and the corresponding phenotypes are selected (e.g. microcephaly for an abnormally small head circumference) though the clinician may choose to modify these later. The administrator may enable the entry of measurement value in both metric and imperial units, in which case users can switch between the two thanks to a dropdown selection menu displayed at the top-right of this section.

Phenotypes

PhenoTips enables phenotypic data capture and storage using the standardized vocabulary defined by the Human Phenotype Ontology (HPO). Phenotypes can be selected form a predefined list of common manifestations, or to search the entire ontology for the relevant manifestations they have observed in their patients. A phenotype can be marked as observed (Y), not observed and relevant (N), or not observed and/or not investigated, i.e. irrelevant (NA).  It is not necessary to specify that a phenotype listed in the form is NOT present, unless the information about its absence is considered particularly relevant. Each phenotype can be annotated with information such as age of onset and pace of progression, which will help narrow down the possible diagnoses (see the next section).

As the form is being populated by the user with the patient's phenotypic description, the system suggests other phenotypes to investigate. The suggested features are typically phenotypes that co-occur with the ones already entered, but are specific to one disorder (or a very small number of disorders). The aim of these suggestions is to help narrow down the list of disorders that may be affecting the current patient, based on the phenotypic presentations. 

Users are encouraged to provide detailed phenotypic descriptions using ontology terms. This does not only lead to a thorough phenotypic profile for the patient, but also helps the system come up with useful suggestions of additional investigations and possible diagnoses.

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Entries owned by a contributor can be accessed at any time via the "My data" box displayed on the homepage. Users can also modify or delete the patient profiles via the patient report menu available on the right side of the page.

Diagnosis

As the form is being populated by the user with the patient's phenotypic description, PhenoTips does live searches in OMIM in order to find disorders that match the symptoms. When performing the search, the system takes into account how informative the symptoms are (a phenotype present in fewer disorders is considered more informative than a more common one) and how frequently a disorder is known to occur in the population, and scores matches accordingly. The best matches are displayed in the Diagnosis section of the form.  Symptoms are summarized at the top of this list, and the user may turn symptoms on and off by clicking on them, in order to evaluate the effect they have on the matching results.

Case ownership

By default, you are the owner of any data that you entered in the repository. Under certain circumstances, you may wish to transfer ownership of a case to a larger consortium if you and your case become part of a wider study, or to another PhenoTips user if for any reason he or she becomes responsible with following that specific patient.

When viewing or editing a case, the owner is displayed at the top of the page. Ownership can be modified by the owner, i.e. transfered to one of the owner's groups or to another user:

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Establishing visibility

PhenoTips supports by default two major levels of data visibility:

  •   hidden: hidden from everyone except the owner and their explicit collaborators; the information cannot be accessed, and the case will NOT be taken into account in statistics
  •   private: visible to the owner and their explicit collaborators; the information cannot be accessed, but the case will be taken into account in statistics
  •   public: viewable and searchable by all registered users

When viewing or editing a case, the visibility is displayed at the top of the page. Visibility can be modified by the owner:

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Adding collaborators to your cases

To give a trusted colleague access to one of your non-public cases. When viewing or editing a case, the number of collaborators is displayed at the top of the page. Collaborators can be awarded different levels of access to the case, ensuring the collaborator's ability to either:

  • view the full patient profile
  • view and modify the patient data
  • view and modify the patient data, as well as manage collaborators (invite other collaborators, terminate collaborations, change collaborators' access levels)

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Questions?

Please address your questions or report issues encountered while using PhenoTips to support@phenotips.org.