PhenoTips » News » PhenoTips 1.4 Milestone 4 Released

PhenoTips 1.4 Milestone 4 Released

Jun 15 2018

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.4 Milestone 4 release. The highlights of the release are:


Patients data

  • Families now support members that are not assigned to an individual in the pedigree
  • Added owner, collaborators and visibility to family directory filters
  • Renamed "Report date" to "Creation date" on the landing page
  • Permissions: Clicking on the new owner field automatically select "Transfer ownership to another user or group"
  • Added info button to Mode of inheritance
  • 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 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 labeling/default for variants in Genotype section
  • Gene panels section:
      - renamed section title to Suggested Genes
      - now more user friendly
      - shows the number of genes associated with each phenotype,
      - sorts phenotypes by number of associated genes in descending order,
      - nonstandard terms are marked with an icon
      - rejected genes are now displayed with a strike-through
      - Rejected Candidate is added to existing Exclude Negative Genes filter
  • Same visual arrangements in PED export dialog as in pedigree legend
  • More robust save functionality
  • Uniform look for lookup fields in advanced filters and export/push dialog


  • 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
  • New support for auditing who viewed and edited records
  • Added ability to show external identifiers in place of internal ones in the Patient and Family record forms
  • Upgraded XWiki to 7.4.6


  • 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

See the full list of changes in JIRA.