PhenoTips » News » PhenoTips 1.4 (stable) released

PhenoTips 1.4 (stable) released

Aug 24 2018

This blog post is not published yet.

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.4 release. Here are the highlights of the release:

Navigation pages

  • Now displaying homepage gadget extra actions as icons only instead of text
  • Active Groups gadget is replaced with new My Groups gadget on homepage
  • Added link to browse all owned patient records on the My patients gadget
  • Added owner column to browse all families page
  • Removed FAMILIES SHARED WITH ME widget from the home page

Patient and family records

  • 'Owner', 'Visibility' and "Collaborators" are now available for displaying in the patients table (they are not shown by default)
  • Improved look and functionality of patient and family directories
  • Advanced filters are replaced with the new FILTERS panel located on the far left side of All patient/family records pages
  • Collaborators and studies are added to the patient's FILTERS panel

AdvancedFilters.png

  • Added ability to show external identifiers in place of internal ones in the Patient and Family record forms
  • New option to remove the corresponding patient record when deleting an individual from the pedigree
  • Added Export PDF option to the More Action menu of the Family Page
  • Families now support members that are not assigned to an individual in the pedigree
  • Uniqueness check for family external ID

Pedigree editor

  • Colouring of disorders, phenotypes and genes can be turned on/off for the whole group or per individual item in the pedigree legend
  • Improved pedigree legend box
  • All abnormalities/annotations associated with person are highlighted in the legend while hovering over an individual's symbol in the pedigree
  • New and improved cancers UI in pedigree editor
  • Pedigree editor is now using standardized vocabulary for cancers
  • Same visual arrangements in PED export dialog as in pedigree legend
  • Allowed assigning "Alive and Well" status to a group of people

PedigreeColouring.png

Patient data

  • Renamed "Molecular diagnosis" to "Final diagnosis"
  • Free-text diagnoses in patient form and in pedigree editor are now supported
  • Support for Multiple external IDs per patient
  • Added option to list family members on the Patient record form
  • Removed "Global" from Global mode of inheritance and Global age of onset
  • Added alternative names, inheritance, onset, and prevalence in ORDO diagnosis info-box
  • Display human-readable symptoms and not symptoms in ORDO and OMIM diagnosis info-boxes
  • Added validation of PubMed IDs and details about the article are now shown
  • Added info button to mode of inheritance, selected phenotypes, clinical and final diagnoses
  • Added Rejected candidate gene status
  • Renamed Negative to Tested negative status
  • Gene lookup now supports free text option at the bottom as the other lookups do
  • Improved layout of the Gene suggestions section (formerly known as Gene panels section)
  • By default tested negative and rejected candidate genes are removed from Gene suggestions section

GeneSuggestions.png

  • Gene suggestions JSON is now more concise
  • Improved labeling/default for variants in Genotype section
  • Added functionality for displaying additional tabs
  • Added ability to enter groups in the owner and collaborator fields of the filtering panel, push and permission dialogs
  • The "Perinatal complications" subsection (under the "Prenatal and perinatal history" section) is now shown on the patient form
  • More robust save functionality
  • Decreased the frequency of auto save from 10 seconds to 1 minute

Text mining

  • Text mining: HPO terms are now extracted from "Indication for referral" and "Medical history" and displayed as phenotype suggestions under SUGGESTIONS FROM CLINICAL NOTES box
  • Administrators can configure the text-mining service either locally (CTAKES) or remotely through services.phenotips.org (CTAKES and NCR)

TextMining.png

Push/Export/Import

  • Improved and more user friendly export dialog
  • Uniform look for lookup fields in advanced filters and export/push dialog
  • Push dialog now displays consented fields only
  • Added ability to push, export and import medical reports, additional images and documents
  • Various fixes involving Excel export file

PushExportDialog.png

Vocabularies

  • Added support for vocabulary categories
    • instead of searching only a specific vocabulary, for example "OMIM", it is now possible to search in all vocabularies of a certain type, for example "diseases"
    • added REST API endpoints /vocabularies/categories; vocabularies/categories/{category}; vocabularies/categories/{category}?suggest)
  • More robust vocabulary reindexing operation is no longer leaving system in a bad state (e.g. after failure)
  • Suggest widgets for vocabularies are now working on the filters for groups' owned and shared cases tables, and for study cases
  • Gene suggestions are now showing the exact input provided (if found) as a first option
  • Administrators can permanently redefine the location of vocabulary sources

Permissions

  • Several improvements in case permissions module is not installed:
    • Patients and family tables are now displayed on the homepage
    • Fields 'owner' and 'visibility' are removed from advanced filters
    • All patients are now shown in the "Browse Patients" table
  • Permissions manager dialog can be extended with custom sharing options
  • Removal of one's own account as managing collaborator no longer throws exceptions
  • Implemented family permissions

REST API

  • Allowed method PATCH on patient resources
  • Allowed explicit updates, overwrites and merges when updating patient records
  • Added REST API for family permissions

Translations

  • Added support for French, German and Russian HPO translations

Administration/System

  • Enabled auditability of permissions and data sharing
  • Added support for auditing who viewed and edited records
  • Implemented indexing of OncoTree
  • Group administrators are now called Group managers
  • Added ability to consent/push/export genes and variants separately
  • Vocabulary version is now updated upon successful reindexing
  • New vocabularies can be installed as extensions
  • Upgraded XWiki to 7.4.6
  • Java 1.8 is now required

Bug fixes

  • Families shared with me are missing some families with shared patients
  • Drop-down autocomplete doesn't follow the search bar in pedigree editor
  • Layout issue in the first tab of the pedigree editor node menu
  • Gene panels should display HGNC gene symbol rather that its alias
  • Under high load, no HPO terms are extracted from clinical notes
  • Loading spinner doesn't display properly in export modal
  • Pedigree editor breaks when using non-default date input format
  • In some cases, using a decade for DOB in a pedigree breaks the editor
  • When using dd-mm-yyyy for pedigree date format (both input and display), using decades in the pedigree breaks the editor
  • Genes should be stored internally as Ensembl IDs, not HGNC IDs
  • Problems with guest users:
    - missing "owner" access on guest-owned patient records
    - wrong failure reported when deleting records
  • Corrected problem with missing person's details when exporting pedigree to PNG and SVG
  • Corrected several problems involving entering phenotype details
  • Extended negative prenatal phenotypes never stored
  • Some occasional failures to save records have been averted
  • Clicking N/A on a dropdown prenatal phenotype doesn't do the same on the duplicate
  • Excel export list EnsembleIDs in "Gene name" and "Gene symbol" columns
  • Different/inconsistent behavior when filtering in Advanced data filtering and Export
  • Obstetric History doesn't appear as an exportable/pushable information in the export preferences dialogs
  • Parental age at EDD doesn't appear to be exportable in the excel format
  • Users can remove from a family patients that they can't normally access
  • Filtering by member in the phenotips-groups macro ignores the Administrators subgroup
  • The consanguinity status of a patient isn't set when identifiable from the pedigree
  • Non-categorized custom phenotypes disappear from saved patient record
  • Filtering by gene doesn't work as expected in advanced filters, push and export
  • Guest users cannot access the families that they create
  • Unable to import pedigree using BOADICEA format
  • Family permission dialog cannot be moved around
  • Pedigree action buttons not looking good when scaling down below 90%
  • When using the PT embeddable skin, the "New Patient" button on the homepage doesn't work
  • Labels not shown on family form
  • Delete pedigree button label is white in some cases
  • 0 values for the Obstetric History fields are lost in the JSON export
  • OMIM is no longer reindexable
  • After reindexing vocabularies, spellchecked suggestions no longer work
  • Patient/Family search widget does not work for guest users
  • Records created by guest users should be accessible to everyone
  • The SVG rasterizer service caches the first requested size of the generated image
  • Variants cannot be deleted via the REST patient API
  • Problems when reindexing vocabularies:
      - an installed vocabulary from a source included inside a jar
      - a vocabulary from a source included inside a jar
      - vocabularies with special characters in their source URL
  • Gray out Cancer tab for view only users
  • View-only collaborators are presented with the option to change the study of a patient record
  • Users that are not subscribed to any studies cannot see when a patient record belongs to a study
  • When a patient is deleted the "push to remote servers" data is not removed
  • Cannot delete a family via REST
  • Group cases are not displayed in Admin/Group/Cases
  • Resolve text mining issues and turn it on by default
  • Free text option appended to the phenotype lookup, when input (phenotype) has exact match in the suggestion list
  • Free text entered as an ethnicity does not get suggested anymore
  • Nonstandard features get copied to features array in the pedigree JSON representation
  • Export as JSON is missing the Referrer (report creator) info
  • Phenotype suggestions aren't displayed if OMIM suggestions aren't enabled
  • Non-functional "Go to search page" displayed in the quick-search results
  • PED export omits cancers entered in the new cancer tab
  • Clearing Referrer and Last Author fields in families' advanced filters does not automatically refresh the results
  • Bugs in pedigree patient drop legend and unlinked patient handling
  • Typed gene name doesn't get replaced with the proper Ensembl ID after displaying gene information
  • Logging out while in edit mode can lock the object for 30 minutes
  • Unauthenticated users can edit the PatientTemplate and FamilyTemplate
  • PhenoTips won't run on Windows if username contains space character
  • PhenoTips doesn't run on Java 9
  • XSS vulnerability in patient form data