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Feb 16 2017

PhenoTips 1.2.6 (stable) Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.2.6 release. This is a bugfix release, with minor changes in functionality. The following fixes are in this release:

  • PT-2069 - Two dashed lines in OMIM list creates strikethrough
  • PT-2604 - Unable to update patient's DOB and DOD through REST
  • PT-2642 - Pedigree editor save behavior gives incorrect feedback and is not error-tolerant
  • PT-2713 - Cannot transfer ownership to groups containing " or ~ in their name
  • PT-2714 - Owner group containing < or ~ in their name aren't displayed correctly
  • PT-2715 - Cannot attach/display custom images for workgroups containing special characters in their name
  • PT-2717 - Cannot select a study with special characters in it
  • PT-2718 - Studies with special characters in their name break the patient record UI
  • PT-2719 - Bad links generated for studies with special characters in their names in the administration and in the groups using them
  • PT-2720 - Studies with special characters in their name fail to display the list of workgroups using them
  • PT-2721 - Bad links generated for workgroup with special characters in their names on the homepage dashboard, administration, and in the studies using them
  • PT-2722 - Workgroups with special characters in their name fail to display the list of subscribed Studies
  • PT-2735 - Cannot filter by more than one type of file for the attachment picker
  • PT-2759 - The pedigree editor UI doesn't display fully with the embeddable skin
  • PT-2764 - Embryonal and Fetal onsets are no longer displayed
  • PT-2810 - Fixed-width icons aren't really fixed width
  • PT-2908 - APGAR header only covers one of the two APGAR columns in Excel export
  • PT-2909 - Assisted Reproduction header is always included in the Excel export, even when no relevant fields are selected
  • PT-2910 - Donor Egg and Donor Sperm values are swapped in the Excel export
  • PT-2953 - Broken images displayed on the dashboard for groups without a specific image attached to them
  • PT-2967 - Entering ethnicities or allergies with a pipe | in them will actually split the value in two
  • PT-2968 - Adding phenotype details for non-standard phenotypes may fail when the term contains characters not valid in an URL
  • PT-3003 - Users shouldn't be allowed to add comments on code pages
  • PT-3004 - JSON returned by /bin/get/PhenoTips/ExportPatient API doesn't include rejectedGenes if Phenotips Gene field is blank, even when Comments field is non-empty
  • PT-3057 - Reindexing HPO version 2017-01-23 results in many terms showing {has_synonym_type=layperson} in their name
  • PT-3071 - Images and documents entered as phenotype details are not displayed correctly in view mode

Feb 09 2017

PhenoTips 1.3 Milestone 6 Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3 Milestone 6 release. The highlights of the release are:

Suggested gene panels

PhenoTips now suggests which genes should be investigated, based on the phenotypes describing the patient. This uses the phenotype-to-gene annotations provided by the HPO team, and similar to the OMIM suggestions, offers an interactive interface allowing to select which phenotypes to ignore when looking for matching genes.

genepanels.png

Additionally, suggested gene panels can be accessed via a RESTful API that is documented in our developer guide.

Spanish translation of the Human Phenotype Ontology

The Human Phenotype Ontology is actively being translated into multiple languages! With an almost complete translation into Spanish of all the term names, PhenoTips can now also search and display symptoms in Spanish.

spanishhpo.png

The Spanish language can be enabled from the PhenoTips administration:

  1. log in with an administrative account
  2. open the administration by clicking the Administration link in the upper left corner
  3. open the Configuration -> Localization section
  4. either switch the default language to es, to use only Spanish, or switch Multilingual to Yes, and make sure es appears in the list of Supported languages
  5. don't forget to Save the configuration

enablespanish.png

If you wish to see PhenoTips and the HPO translated in another language, please contribute to PhenoTips translations and HPO translations on CrowdIn.

See the full list of changes on Jira.

Jan 16 2017

PhenoTips 1.3 Milestone 5 Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3 Milestone 5 release. The highlights of the release are:

Patient record form

  • When navigating away from a record, a warning is shown if there are unsaved changes
  • Added "Life status" field in the patient form to allow more logical workflow when entering patient data.
  • OMIM diagnosis suggestions are now shown in view mode too.
  • PhenoTips is now storing genes by using Ensembl IDs internally, instead of using gene symbols. 
  • Special wiki markup in several fields used to be interpreted; this has been disabled

Family charts

  • Newly added menu option in the Pedigree Editor allows physicians to quickly mark pedigree node as "Alive & Well" or "Deceased".

Rest api

Bug fixes

  • Cannot specify variant coordinates for variants entered prior to version 1.3M4
  • The Families REST API endpoint does not check permissions properly
  • Global mode of inheritance and Global age of onset cannot be pushed or imported
  • "Chromosome: NA" displayed in the variant summary in edit mode
  • Broken images displayed on the dashboard for groups without a specific image attached to them
  • 'New patient' button often adds multiple patients from one click
  • Legend is broken in pedigree editor
  • An empty family with no pedigree has rights that are too permissive
  • Users shouldn't be allowed to add comments on code pages

See the full list of changes on Jira.