PhenoTips » News » PhenoTips 1.3 Milestone 1 released

PhenoTips 1.3 Milestone 1 released

Apr 27 2016

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3 Milestone 1 release. The highlights of the release are:

  • Improved support for recording genes and variants
  • Added support for configuring and recording consents obtained from the patient
  • Almost all patient data can now be exported and re-imported via JSON
  • A new REST API for accessing vocabularies
  • Added an "Unknown" option for the patient sex, selected by default
  • Added support for recording twin number (A/B/Other) for patients from a multiple gestation
  • Each PhenoTips instance sends anonymous general installation and usage data back to for statistics (see below for details)
  • Push functionality improvements:
    • Push receiver component is now included by default, although no remote instances are allowed to push by default
    • Consents from the remote server are queried and displayed before pushing a patient record
    • Added verification if the source and target PhenoTips instances support the same push protocol version
    • Added ability to push almost all patient data such as genes, variant data, phenotypes, diagnoses, age of onset and mode of inheritance
  • Pedigree improvements:
    • Improved the pedigree load time
    • The pedigree image service now supports downloading the file instead of just displaying it
    • Moved "create sibling" handle to the right of the parent link
    • Ages are now easier to read in the cancers tab
    • Cancer dx is summarized under pedigree symbol
    • Added "thyroid cancer"
    • Added ability to import PED files with comment lines
  • Other improvements:
    • Automatically expand the list of subcategories (if it exists) when selecting YES for a phenotype
    • Pressing Enter now select the first phenotype suggestion from the drop-down
    • Made shorter URLs by removing the /bin/ part of the URL
    • Upgraded to Solr 5.3.1
    • Upgraded to XWiki 7.1.4
  •  Bug fixes:
    • Failure when reindexing HPO from the default URL
    • The monarch patient scorer didn't work at all anymore
    • The monarch patient scorer didn't work for patients with many phenotypes selected
    • Can't back up and restore PhenoTips instances with 1000 pages
    • Import functionality broken in pedigree editor
    • PDF export fails due to OutOfMemory exception
    • Automatically selected phenotypes, for example by abnormal measurements, do not appear in differential
    • Inconsistent appearance of negative phenotypes on patient form
    • Detailed physical phenotype configuration lists Polydactyly twice in the upper extremities section

As mentioned above, starting with this version, each PhenoTips instance sends regular "pings" with general information about itself to a central server located at The information consists of:

  • Technical data, such as OS, java version and vendor, servlet container, database used, PhenoTips version, enabled extensions, which enable us to focus our efforts on the most popular configurations and know when it's a good time to switch to a new version or drop compatibilities without affecting our users
  • Generic usage data: number of users, number of patient records, which will be used, in an aggregated form, in grant applications to receive funding that allows us to continue developing PhenoTips as free software.

PhenoTips installations running in closed networks without access to the internet will not be able to send any data to our stats server. This does not affect in any way the functioning of the software.

See the full list of changes on Jira.