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; this 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 forgotten account information.

Forgotten username or password

If you cannot remember your username or password for logging into PhenoTips, you can reset them by clicking the corresponding links on the Login page. Fill out a simple form to view your username or to receive, by email, instructions for resetting your password.

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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: user groups and family records

  • The ACTIVE GROUPS box lists active groups in alphabetical order and provides a link to more information about each of them, including their public contributions.
  • The MY FAMILIES box lists the family records owned by the current user. Please read below more information about data ownership.
  • The FAMILIES SHARED WITH ME box lists the family records on which the current user is a collaborator, typically because a shared patient that they own or collaborate on has been added to a family owned by another user. Please read below for more information about collaborating on families.

Right column: patient records

  • The MY PATIENTS box lists the patient records owned by the current user. Please read below more information about data ownership.
  • The PATIENTS SHARED WITH ME box lists the patient records on which the current user is a collaborator, either because they are part of the group which owns the record, or because the owner explicitly listed them as a collaborator on that record. Please read below for 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

Patient and family records owned by a user can be accessed at any time via the MY PATIENTS or MY FAMILIES boxes displayed on the homepage. At the top of each record, the owner can choose to create, modify, and delete the document at any time. Collaborators with the necessary modification privileges can also modify and delete shared records as needed.

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After editing a patient record, remember to save or discard the edits at the bottom of the page:

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PhenoTips supports by default several categories of patient information: 

  • patient information
  • family history and pedigree
  • prenatal and perinatal history
  • medical history
  • measurements
  • clinical symptoms and physical findings
  • gene panels
  • genotype information
  • diagnosis
  • case resolution

For Prenatal and perinatal history, as well as Clinical symptoms and physical findings, PhenoTips enables phenotypic data capture and storage using the standardized vocabulary defined by the Human Phenotype Ontology (HPO). Phenotypes can be selected from a predefined list of common manifestations, or from a search of the entire ontology for the relevant manifestations that have been observed in the patient. 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. 

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

Patient information

Information such as patient identifier, patient name, date of birth, gender etc. may be entered for each patient. 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.

Family history and pedigree

Besides being able to enter basic familial data such as ethnicity and consanguinity, pedigrees can be created for individual patients and their family members. The creation of a pedigree automatically creates an associated family record, a document that connects all patient record-having members of the pedigree. Such a family record could be shared between clinicians treating different members of the same family, while still hiding the sensitive medical data of individual patients. Please read below for more information about collaborating on family records.

To learn more about using the pedigree editor, read the in-depth guide here.

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Prenatal and perinatal history

Data pertaining to the conceptional, gestational, prenatal, and neonatal history of a patient can be recorded in this section. Observations entered in this section will be recorded as phenotypic data and included in the diagnostic OMIM search and gene search. To record this information but disable its contribution to the searches, click on the related terms in the search header.

Medical history

A patient's preexisting allergies and medical reports can be recorded/uploaded as their Medical history. The global age of onset of a patient's symptoms, which can be entered here, may affect gene panel results. Medical and developmental history can be entered in free-text in this section, however it is strongly recommended to enter as much information as possible in the clinical symptoms and physical findings section, in order to make use of PhenoTips' diagnostic and gene search tools.

Measurements

The Measurements section of the patient record stores standard measurements 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 using a dropdown selection menu displayed at the top-right of this section.

Clinical symptoms and physical findings

Enter the bulk of the patient's medical data in this section, by marking individual phenotypes as observed (Y), not observed and relevant (N), or not observed and/or not investigated, i.e. irrelevant (NA). Each phenotype can be annotated with information such as age of onset and pace of progression, which may help to narrow down the possible diagnoses.

As the form is being populated by the user with the patient's phenotypic description, the system suggests other phenotypes to investigate. These suggestions can be accessed by clicking on the you may want to investigate... drop-down panel at the bottom of the current phenotype selection summary. 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 strongly 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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Gene panels

Most users will not ever see this section in their PhenoTips instance, as this feature is not useful for most clinicians and is therefore disabled by default. If you want to make use of this feature, ask your PhenoTips administrator to enable it in your instance.

In the Gene panels section, potential genetic etiologies are suggested based on the clinical and phenotypic data entered on the patient. User-entered phenotypes are summarized at the top of this list, and the user may disable and reenable phenotypes by clicking on them, in order to evaluate the effect they have on the matching results. 

Genotype information

Genes for which a patient has been tested, and variants thereof, can be entered here. Genes can be manually added by clicking on + ADD GENE and entering the name of the investigated gene, ideally selected from the list of OMIM known gene suggestions. The candidacy status, test strategy, and patient-specific variants for that gene can be entered for each manually added gene. Additionally, the user may select a reference genome and then upload a VCF file containing the patient's exome sequencing data. 

Diagnosis

A diagnosis can be entered as a working clinical diagnosis linked to ORPHANET terms, and/or as a diagnosis confirmed via laboratory testing linked to OMIM terms. Typing in the text field will bring up suggestions from the associated ontology.

PhenoTips also packages a diagnostic tool in the form of an Instant OMIM Search. 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 as "Matching disorders in OMIM." Potential symptoms (ie. user-entered phenotypes) are summarized at the top of this list, and the user may disable and reenable symptoms by clicking on them, in order to evaluate the effect they have on the matching results.

Case resolution

Mark the record as a solved case if the molecular diagnosis for the patient has been confirmed. Once this is done, the PubMed ID for the case, as well any resolution notes, can be recorded in this section.

Data 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 patient record to a larger consortium if you and your patient 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 patient record, the owner is displayed at the top of the page. Ownership can be modified by the owner, i.e. transferred 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 records

To give a trusted colleague access to one of your non-public patient records. When viewing or editing a record, 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 record
  • 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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Shared families

There are two situations in which a family record might become a shared document between multiple collaborators:

  • A patient has a pedigree and is therefore automatically associated with a family record. A user with the permissions necessary to modify the record's access rights adds another user as a collaborator. The collaborator will now be able to access the family record with the same access rights that they were granted for the patient records (eg. view-only, view and modify, etc.)
  • A family record contains at least two patient records that are followed by different clinicians and therefore owned by different users. Both users, as well as any collaborators on those patient records will be able to access the family record, but not one another's patient records.

In both situations, patient records that the user does not have access rights to will remain inaccessible to the user, even if they share a family record with some of the user's patients. 

Access rights, as extended from patient records to their associated family records:

  • View-only: A user with view-only access to a single-patient family record will be able to download an SVG or PNG of the family pedigree, but will not be able to access the pedigree editor. A user with view-only access to a multi-patient family will only be able to see the names and ages of the patients included in the family, with absolutely no view of the pedigree. 
  • View and modify: A user with modification rights to a member of a family record will be able to access the pedigree editor, and will therefore be able to modify some parts of the pedigree itself. They will not be able to modify any other patient's data, but they can add and modify non-patient family members, as well as the patient(s) that they have access rights to. They will also be granted view-only access to some clinical information pertaining to all other patients in the pedigree, notably phenotypes, disorders, and cancers. If you grant a user modification rights for a patient record, you grant them the right to view modify the patient's pedigree, regardless of whether that pedigree has a single proband or is shared between multiple patients. Please be very careful when granting access rights to patient records involved in multiple-patient family records.

To learn about the pedigree editor itself, read the in-depth guide here.

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Pushing data to other servers

Data can be transferred to other PhenoTips servers (such as PhenomeCentral) with the Push functionality. Remote servers must be connected as viable destinations by an administrator before users can choose to push data to them. Once this has been done, a user can push a single record by navigating to More actions at the top right of the page. To read more about pushing records, and to read about pushing bulk data, consult the Push user guide.

Questions?

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