PhenoTips » News » Blog categories » Announcements

Announcements

Category: Announcements (58 posts) [RSS]

Subcategories

Nov 17 2017

PhenoTips 1.3.6 (stable) Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3.6 release.
In this is release, the following items have been addressed:

Improvements

PT-3490 - Upgrade to Solr 5.5.5

Defects

PT-2986 - The "Perinatal complications" subsection (under the "Prenatal and perinatal history" section) is no longer shown on the patient form
PT-3442 - Users can remove from a family patients that they can't normally access
PT-3499 - "Browse groups" button is missing from the "My Groups" gadget

Oct 24 2017

PhenoTips 1.3.5 (stable) Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3.5 release.
In this is release, the following items have been addressed:

New Feature

PT-3451 - Add a "My groups" gadget on the homepage

Bug fixes and improvements

PT-3104 - Different/inconsistent behavior when filtering in Advanced data filtering and Export
PT-3450 - Filtering by member in the phenotips-groups macro ignores the Administrators subgroup
PT-3452 - Enable support for free-text diagnoses in the patient record form and in the pedigree editor
PT-3460 - Non-categorized custom phenotypes disappear from saved patient record

Sep 22 2017

PhenoTips 1.3.3 (stable) Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3.3 release. In this is release, the following issues have been resolved:

Pedigree editor:

  • PT-3272 - Upon deletion of a pedigree node, its carrier genes are still present in the legend
  • PT-3320 - Pedigree node hover boxes do not fade out when they should in some cases
  • PT-3321 - Drop-down autocomplete doesn't follow the search bar in pedigree editor
  • PT-3355 - Some functionality is broken in IE9 (most notably pedigree editor can not be opened)
  • PT-3385 - Unauthenticated users can't save new pedigree
  • PT-3438 - Pedigree editor breaks when using non-default date input format
  • PT-3248 - Rename "disorders" to "final diagnosis" in pedigree editor
  • PT-3275 - Improve info text in pedigree legend box
  • PT-3357 - In pedigree editor do not show A&W options on hoverboxes for patients which are read-only for current user

Family charts:

  • PT-2804 - All families should only list current user's families
  • PT-2815 - Family updates and patient JSON updates should be performed under the correct user
  • PT-2824 - "Families shared with me" are missing some families with shared patients

Patient records:

  • PT-3315 - Phenotypes from the predefined list disappear from phenotype selection after JSON import from edit mode
  • PT-3319 - Long custom entries in the genes table cause layout issues
  • PT-3338 - In the excel export, paternal ethnicity should be left, maternal ethnicity should be right
  • PT-3345 - When importing a new patient, a new owner object is created even if the owner already exists
  • PT-3353 - Terms added from the ontology browser are always added in the main clinical symptoms section, regardless of where the browser was triggered from
  • PT-3408 - Wrong failure reported when guest users delete their records
  • PT-3416 - Loading spinner doesn't display properly in export modal
  • PT-3377 - Remove negative phenotypes from Gene panel section

See the full list of changes on JIRA.

Aug 23 2017

PhenoTips 1.4 Milestone 1 Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.4 Milestone 1 release. The highlights of the release are:

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
  • Allowed assigning "Alive and Well" status to a group of people
  • Corrected problem with missing person's details when exporting to PNG and SVG

PedigreeColouring.png

Patient and family records

Data tables

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

AdvancedFilters.png

Patient form

  • 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
  • Renamed "Molecular diagnosis" to "Final diagnosis"
  • Added info button to selected phenotypes, clinical and final diagnoses
  • Improved layout of the Gene panels section
  • Added new option to filter out genes that have been ruled out in gene panels (turned on by default)
  • Corrected several problems involving entering phenotype details

TextMining.png

GenePanels.png

Push/Export/Import

  • Added ability to push, export and import medical reports, additional images and documents
  • Improved and more user friendly export dialog
  • Various fixes involving Excel export file

ExportDialog.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

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

Other

  • Java 1.8 is now required
  • Removed FAMILIES SHARED WITH ME widget from the home page
  • Gene Panels JSON is now more concise

See the full list of changes in JIRA.

Jul 24 2017

PhenoTips 1.3.2 (stable) Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3.2 release. In this is release, the following 19 issues have been resolved:

  • PT-3221 - Gene Comments panel is too short, Strategy panel too long
  • PT-3265 - getTerm in HGNC vocabulary should match on exact input provided
  • PT-3273 - Gene strategies and variant evidence have an extra semicolon when exported to Excel
  • PT-3278 - Export doesn't take into account the filters for genes and for clinical diagnosis
  • PT-3279 - "Delete all x" option does not work in the Advanced Search and in the Export dialog
  • PT-3284 - Suggestions do not work on the filters for groups' owned and shared cases tables, and for study cases
  • PT-3287 - In the advanced data filters, when filtering by more than one owner no results are returned
  • PT-3294 - A phenotype can appear as both positive and negative in the "Current selection" in certain conditions
  • PT-3295 - Selecting from the quick search suggestions a phenotype that is already selected and had details attached appears to cause the loss of the details
  • PT-3297 - Phenotype details re-appear in view mode, with no pre-notice in edit mode about the extra data
  • PT-3304 - "New patient" button in the browse patient page should be underlined on mouse hover
  • PT-3305 - Empty family tables displayed on the homepage when the permissions module is not installed
  • PT-3306 - No patients table displayed on the homepage when the permissions module is not installed
  • PT-3307 - A&W box does not clear in some situations, causing problems with export to png
  • PT-3308 - Export to PNG SVG initiated in pedigree editor is missing person's details other than internalID
  • PT-3309 - Remove quotation marks from Export to PNG/SVG buttons
  • PT-3311 - TermsForGene.toJSON should create a summary for each term instead of calling term.toJSON
  • PT-3313 - Not all patients are shown in the "All Patients" table when the permissions module is not installed
  • PT-3314 - When the permissions module is not installed, do not show the 'owner' and 'visibility' advanced filters

Jun 19 2017

PhenoTips 1.3.1 (stable) Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3.1 release. This is a bugfix release, with minor changes in functionality. The following fixes are in this release:

  • PT-3261 - Unable to import some patients through import JSON option
  • PT-3199 - 'Present' column in exported excel is blank for some cases
  • PT-3223 - Variant Interpretation column lacks human-readable UI strings
  • PT-3229 - LifeStatusController does not handle life status changes well on import
  • PT-3208 - In pedigree editor export JSON the very first patient is marked as proband
  • PT-3235 - Pedigree editor may be broken after a node is deleted
  • PT-3260 - The permissions REST API always returns the 'owner' access level for collaborators with administrative rights on a patient record, regardless of the recorded collaborator level
  • PT-3236 - Reindexing HGNC through REST fails if url isn't provided
  • PT-3220 - Cannot administer users on virtual instances
  • PT-3239 - Unclickable labels for several administrative section elements
  • PT-3245 - Cannot install PhenoTips on systems with java < 1.8.101
  • PT-3212, PT-3230, PT-3253 - Cleanup diagnoses titles in All Patient Data view

May 01 2017

PhenoTips 1.3 (stable) released

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

NEW: Family records

Extensive improvements in the pedigree editor now enable physicians to create, follow and update multiple patients within one family in one place. All family members share a single pedigree, accessible either from the patient record or from the newly added Family record.

Almost all of the patient data changes in the pedigree editor will now be reflected on the corresponding patient record and vice versa. An entire family can be constructed within the pedigree editor: existing PhenoTips patient records can be linked to (and unlinked from) individuals in the pedigree, and new patient records can be created as well.

The existing access rights functionality enables different physicians to share access to their patients, so one family can contain a collection of patients that are cared for by different clinicians or scientists. The access level for each individual patient is defined in the patient record by their caring physician.

All families that a user can access are now available for browsing on the homepage, as well as on the newly added Families Directory page.

HomePage.png
FamiliesDirectory.png

The old way of entering family studies through explicitly linking patient records is now disabled. The data that was previously entered is preserved and can be viewed in read only mode once an administrator enables the visibility of it. Existing families will be automatically migrated. The automated migration may not be possible for families with ambiguous relationships or for patients cared for by different physicians (the latter is to preserve patient privacy). Those families will require manual adjustments in the pedigree editor.

For more information please refer to Family Records section of our User guide.

Patient record improvements

  • Added an "Unknown" option for the patient sex, selected by default
  • Added "Life status" field in the patient form to allow more logical workflow when entering patient data
  • Added support for recording twin number (A/B/Other) for patients from a multiple gestation
  • Embryonal and Fetal onsets are now options under the newly added "Antenatal onset" category in Global age of onset and the phenotype modifiers
  • The list of subcategories (if they exist) is automatically expanded upon selecting YES for a phenotype
  • Pressing Enter now selects the first phenotype suggestion from the drop-down
  • OMIM diagnosis suggestions are now shown in view mode too
  • Improved support for recording genes and variants
  • PhenoTips is now storing genes by using Ensembl IDs internally instead of using gene symbols
  • The new Gene panels section, that can be enabled in the Administration, displays suggested genes based on the phenotypes describing the patient. Similarly to the OMIM suggestions, this section offers an interactive interface allowing to select which phenotypes to ignore when looking for matching genes. The phenotype-to-gene annotations that enable these gene suggestions are provided by the HPO team and are available for download on their website
  • Working clinical diagnosis was added to the Diagnosis section 
  • Global mode of inheritance and global age of onset are taken into account when determining suggestions for diagnosis and other phenotypes to investigate
  • When navigating away from a record, a warning is shown if there are unsaved changes
  • It is now possible to filter patient records by candidate gene and working clinical diagnosis 

GenePanels.png
GenotypeInformation.png
Diagnosis.png

NEW: Patient consents

Support for configuring and recording consents obtained from the patient has been added. Consents can be either passive, allowing the simple recording of the consents the patient has granted, or they can be active, affecting what information can be entered. Consents marked as mandatory prevent any data from being recorded until they are checked. Alternatively, a consent can restrict only certain fields from the patient record.

AdministrationConsents.png
PatientRecordWithConsents.png

Pedigree editor improvements

  • Improved pedigree load time
  • The pedigree image service now supports downloading the file instead of just displaying it
  • Pedigrees can be exported as PNG/SVG directly from the patient record and from the pedigree export dialog
  • Improved pedigree JSON export and import
  • Pedigree editor now allows any node to have any gender
  • The order of the proband parents is enforced to be father-left mother-right
  • Moved "create sibling" handle to the right of the parent link
  • Upper bound for number of children is eliminated
  • Ages are now easier to read in the cancers tab
  • Cancer dx is summarized under pedigree symbol
  • Added "thyroid cancer"
  • Added ability to select confirmed causal and carrier genes and to display rejected genes
  • Add ability to enter only year in pedigree date fields
  • Enabled reassignment of the proband  P 
  • Added marking to the current patient  C 
  • If identifiable from the pedigree, the consanguinity status of a patient is set in their patient record
  • Newly added menu option in the Pedigree Editor allows physicians to quickly mark pedigree node as "Alive & Well" or "Deceased"
  • Adopted individuals can now have their children and partners represented in the pedigree
  • Users are now able to select what traits (disorders, genes, cancers and phenotypes) are reflected in the "affected" column when exporting the PED file of a pedigree
  • Added ability to import PED files with comment lines
  • Better scaling of Pedigree legend containing large number of annotations
  • ...and many more small improvements

For more information please refer to Pedigree editor section of our User guide.

PedigreeEditor.png

Export, import and push functionality improvements

  • Almost all patient data can now be exported and re-imported via JSON, as well as pushed to other PhenoTips instances
    • Information that is not currently supported: Pedigree, Medical reports, Copy number variants, and Additional files
  • Push receiver component is now included by default, although no remote instances are allowed to push by default
  • Full support for Consents from the remote server, they are queried and displayed before pushing a patient record
  • Added verification if the source and target PhenoTips instances support the same push protocol version
  • Previously entered/pushed data on the remote server can be cleared, by deleting it on the source server and pushing it to the remote server again

For more information please see Push functionality in our User guide.

PushConsents.png

New RESTful APIs

  • New REST APIs for accessing:
  • Enabled creation/update of multiple patients at once via REST by POSTing a JSONArray with all patients to the /patients endpoint
  • JSON import (symmetric with the Export JSON functionality) is now available on the Patient Record page for individual patient import, and as bulk on the All Patient Records page
  • Sending a JSON to a non-existing patient using the /patients/eid/ REST endpoint creates a new patient record
  • The XML output has been removed, only JSON is now returned by the REST services
  • Related resources are now more consistently linked, to support better discoverability
  • Allowed methods (GET, PATCH, POST, PUT, DELETE...) are now listed for all resource links, reflecting both the methods supported by each resource, as well as the rights of the authenticated user

For more information please refer to the API section in our Developer Guide.

NEW: Multiple language support

PhenoTips now supports multiple languages and can be configured to work either in single or multi-language mode, by setting multilingual option in the administration's localization page. Single language mode operates in the language chosen as the default in the administration's localization page.

The Human Phenotype Ontology is actively being translated into multiple languages!

Spanish translation

We would like to express our gratitude to Manuel Posada De La Paz and Estrella Lopez Martin for their time and effort devoted translating the entire PhenoTips user interface into Spanish language.

With an almost complete translation into Spanish of all the term names, PhenoTips can now also search and display symptoms in Spanish.

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

spanish-hpo.png

French translation (Beta)

Many thanks to Sophie Nambot and Julien Thevenon for their work on French translation of PhenoTips user interface, allowing our team to release our French beta version as well.
If you wish to see PhenoTips and the HPO translated in another language, please contribute to PhenoTips translations and HPO translations on CrowdIn.

Packaging

  • The Mac OS X .dmg package should now start when only the JRE is installed (previously it sometimes failed when JDK 1.6 was installed, but only the JRE for 1.7 or 1.8).
  • When installed on Windows, PhenoTips data is now stored under the current user's home directory by default, allowing installation under Program Files and easier upgrades.
  • User self-registration is disabled by default, an administrator must either re-enable self-registration or create user accounts.

Other changes

  • URLs are shorter, as bin/ has been removed by default.
  • Starting with this version, each PhenoTips installation sends anonymous general installation and usage metadata to a central server located at https://stats.phenotips.org/. The information consists of:

    • Technical data, such as OS, java version and vendor, servlet container, database used, PhenoTips version, enabled extensions, which help us 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 metadata: 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.

The full list of changes on Jira per milestone/release candidate:

Release Issues in release Release date
Milestone 1 107 issuesApr 27, 2016
Milestone 2 136 issuesAug 29, 2016
Milestone 3 132 issuesOct 17, 2016
Milestone 4  58 issuesNov 21, 2016
Milestone 5  41 issueJan 16, 2017
Milestone 6  24 issuesFeb 9, 2017
Release Candidate 1     50 issues                    Mar 20, 2017                  
Release Candidate 2  13 issuesMar 21, 2017
Release Candidate 3   7 issuesMar 22, 2017
Release Candidate 4  22 issuesMar 31, 2017
Stable   6 issuesApril 26, 2017
Full list596 issues

Mar 22 2017

PhenoTips 1.3 Release Candidate 3 Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3 Release Candidate 3. The following fixes and  improvements are in this release:

Defects

PT-1688 - Check box and delete icon are both visible in OMIM diagnosis field.
PT-3151 - Upgrading the RPM installation does not add the ORPHANET index
PT-3154 - Incorrect text in OMIM disorder field description - "i" button
PT-3158 - "phenotips.IndexOntology.version" displayed in place of the actual version in vocabulary term descriptions

Improvements

PT-3152 - Add "Clinical Diagnosis (ORDO)" and "Molecular Diagnosis (OMIM)" label to clinical diagnosis and molecular diagnosis sections
PT-3153 - Change "Orphanet" and "ORPHA" to "ORDO"
PT-3155 - Add field description for Clinical Diagnosis - "i" button

Mar 21 2017

PhenoTips 1.3 Release Candidate 2 Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3 Release Candidate 2. The following fixes and improvements are in this release:

Defects

  • PT-3133 - Download of Safari-created pedigree PNG image fails
  • PT-3137 - Existing entries in the push configuration tables in the administration can no longer be modified
  • PT-3139 - Excel export fails when there are patients without a clinical diagnosis
  • PT-3140 - Unparsed code displayed when displaying PhenomeCentral's consents in the Push dialog
  • PT-3141 - Suggested gene panels in UI differ from curl REST call
  • PT-3142 - Date of death and cause of death display is not always updated in pedigree editor
  • PT-3143 - Non-admin users shouldn't be allowed to Export patient and family records as XARs
  • PT-3145 - Pedigree fails to apply automatic layout in some cases
  • PT-3147 - Pedigree node removal and redraw algorithm is sometimes terminated by a (silently hidden) exception

Improvements

  • PT-2965 - Minor correction in language used in pedigree editor
  • PT-3144 - Change labeling of "Instant OMIM Search" to "Matching Disorders in OMIM"
  • PT-3146 - Change labeling of "Instant Gene Search" to "Matching Genes"
  • PT-2703 - Make it more obvious that disabled form sections / fields can be re-activated

Mar 20 2017

PhenoTips 1.3 Release Candidate 1 Released

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

New features

  • Working Clinical Diagnosis linked to ORPHANET is added in addition to the existing Molecularly confirmed diagnosis.

Improvements

  • Added support for searching for families in the header search box
  • When PhenoTips is used in a language other than English, the vocabulary terms are now also displayed in that language, if a translation is available
    • Added support for French and Italian HPO
  • Numerous ui improvements in Push dialog, Export dialog and Pedigree editor
  • On the patient record form paternal and maternal ethnicities are swapped, so paternal is now on the left side and maternal ethnicity on the right
  • In the pedigree, the order of the proband's parents is enforced to father-left mother-right
  • Added fourth gene status option "carrier" in Genotypes section of the Patient record form
  • Added support for carrier genes in the Pedigree editor
  • Upper bound for number of children is now eliminated in the Pedigree editor
  • Improved the look of Administration: Vocabulary Index page
  • OMIM can again be re-indexed from the administration, although you have to request a valid download URL for your institution

See the full list of changes on Jira.