PhenoTips » Administration Guide » Configuration of the patient data

Configuration of the patient data

Configuration of the patient data

The patient data being collected into PhenoTips can be configured and organized to comply with the needs of your project. For instance, to keep the anonymity of the patients, you may not wish to store their names in your system and use some case identifiers instead, and you may want to obfuscate their date of birth by only collecting the month and year (this way the age is mostly correct, but the information is less identifiable). Moreover, if your study targets a specific disorder, collecting some phenotypes is more relevant than others so you may want to customize the list of phenotypes that are displayed by default in the patient form.

These customizations and others can be performed in the PhenoTips Administration section, which is accessible to any user with administrative rights via the Administration entry on the left of the topmost menu:

Administration.png

Patient form structure

The Patient form structure section of the administration screen allows administrators to organize the default patient form by dragging&dropping and enabling/disabling form sections and widgets. Administrators can also create their own custom sections for the patient form. Modifying existing widgets and creating new ones requires some development knowledge, as described in the developer guide.

Using a similar user interface, administrators can establish form structures for specific studies within the same PhenoTips installation. Studies can only use sections and widgets that have been enabled in the global administration.

PatientForm.png

Default phenotype list

Configuring a default phenotype list to be displayed in the patient form under Clinical symptoms and physical findings can be done in the Phenotypes displayed by default administration section. As administrators select one of the configurations available in the system, a preview of the phenotype list is displayed on the right.
Using a similar user interface, administrators can select a phenotype list for specific studies within the same PhenoTips installation.

DefaultPhenoTypes.png

Defining a custom phenotype list

For administrators who are also advanced users of the system, a form for creating additional phenotypes configurations is displayed in the Phenotypes displayed by default admin section. The administrator is prompted for a name for the new phenotype configuration, and upon submission will be directed to a form where the new configuration data should be entered (together with a title and optional description).

Example

Here is an example configuration and the resulting phenotype list:

[
  {
   "type"       : "section",
   "title"      : "Growth parameters",
   "categories" : ["HP:0001507"],
   "data"       : [
        {
          "type"  : "subsection",
          "id"    : "HP:0004323",
          "title" : "Weight for age",
          "data"  : [
               {"id" : "HP:0004325", "title" : "<3rd"},
               {"id" : "HP:0001513", "title" : ">97th"}
           ]
        },
        {
          "type"  : "subsection",
          "id"    : "HP:0000002",
          "title" : "Stature for age",
          "data"  : [
               {"id" : "HP:0004322", "title" : "<3rd"},
               {"id" : "HP:0000098", "title" : ">97th"}
           ]
        },
        {
          "type"  : "subsection",
          "id"    : "HP:0000240",
          "title" : "Head circumference for age",
          "data"  : [
               {"id" : "HP:0000252", "title" : "<3rd"},
               {"id" : "HP:0000256", "title" : ">97th"}
           ]
        },
        {"id" : "HP:0001528"}
    ]
  },
  {
   "type"       : "section",
   "title"      : "Neurological signs",
   "categories" : ["HP:0000707"],
   "data"       : [
        {"id" : "HP:0001290"},
        {"id" : "HP:0001250"},
        {"id" : "HP:0001251"},
        {"id" : "HP:0001332"},
        {"id" : "HP:0002072"},
        {"id" : "HP:0001257"},
        {"id" : "HP:0010301"},
        {"id" : "HP:0007319"}
    ]
  },
  {
   "type"       : "section",
   "title"      : "Other",
   "categories" : ["HP:0000118"],
   "data"       : []
  }
]

PhenotypeConfig.png

Structure explained

The configuration defines list of sections :

[
 <section>,
 <section>,
  ...
 <section>
]

Sections

A section is defined by the following information:

type
must be section and is mandatory
title
is the title of the section as it should be displayed in the form and is mandatory
categories
defines a list of (one or more) HPO terms which are the roots of the branches of the ontology that are covered by this section; for data consistency, the ids of any of the entries listed in the data field of the section should have one of these categories as an ancestor in the ontology; this field is mandatory and the values are used for restricting the domain of the suggestions provided to the users when they search for ontology terms in the section's search box (labeled Other)
data
defines a list of entries (either subsections or simple fields) that are to be displayed in this section; it is mandatory but can be empty

Subsections

A subsection can appear listed in the data field of a section and is defined by the following information:

type
must be subsection and is mandatory
id
is an HPO term which, for data consistency, should be an ancestor (or preferably direct parent) of all the entries listed in the data field of the subsection
title
is the title of the subsection as it should be displayed in the form and is mandatory
data
defines a list of fields that are to be displayed in this subsection; it is mandatory but can be empty

Fields

A field can appear listed in the data field of a section or a subsection and is defined by the following information:

type
is optional, and must be field if defined
id
is an HPO term, which is the actual value that will be stored in the database if the user "checks" this field in the patient form; if the term has descendants in the HPO structure, it will be automatically preceded by an arrow (►) symbol when displayed, which will allow users to immediately browse and select its descendants
title
is the title of the entry as it should be displayed in the form; it is optional, and if it is missing, the name of the HPO term defined by the field's id# is used by default

Patient birth date format

Section Data formats allows admins to decide how to collect and display birth dates in the patient form.

DateFormat.png

Measurement unit system

By default, all measurements collected in PhenoTips are stored using the metric system (kg/cm). The Data formats section permits to enable the use of the imperial measurement system (lb+oz/ft+in) for capturing measurements and to designate a system (metric or imperial) to be used by default for data capture. Even if entered using the imperial system, all measurements will still be stored and displayed in metric units after the data is saved.

MeasurementUnits.png

Questions?

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