Releases

Category: Releases (48 posts) [RSS]

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.

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.

Nov 21 2016

PhenoTips 1.3 Milestone 4 Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3 Milestone 4 release. The highlights of the release are:

Spanish translation of PhenoTips

PhenoTips now supports English and Spanish 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.

Phenotips_Administration_Localization_Language.gif

In this version the Spanish version of HPO hasn't been included yet, that will happen in the next milestone. Other translations are under development. If you would like to make PhenoTips available in your language, you can contribute translations at https://crowdin.com/project/phenotips

Pedigree editor

  • Pedigree editor now allows any node to have any gender
  • 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
  • Many small improvements such as better scaling of Pedigree legend containing large number of annotations

Other improvements

  • JSON import (symmetric with the Export JSON functionality) is now available on the Patient page for individual patient import and as bulk on the All Patient records page
  • Added chromosome, start position, end position and reference genome as fields for variants
  • Bug fixes in EXCEL export, user interface, etc...

See the full list of changes on Jira.

Oct 17 2016

PhenoTips 1.3 Milestone 3 released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3 Milestone 3 release. The highlights of the release are:

Family charts

Extensive improvements in the pedigree editor now enable physicians to follow/create/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 page.

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 the caring physician.

Other improvements

  • Enabled creation/update of multiple patients at once via REST by POSTing a JSONArray with all patients to the /patients endpoint
  • Collaborator names are now visible in the Patient record
  • Embryonal and Fetal onsets are now subterms of a newly added "Antenatal onset" (Global age of onset and the phenotype modifiers)
  • Users are now able to select what traits are reflected in the "affected" column when exporting the pedigree as a PED file
  • Pedigrees can be exported as PNG/SVG directly from the patient record and from the pedigree export dialog
  • Enabled reassignment of the proband in the pedigree editor (P arrow)
  • Added marking to the current patient in the pedigree editor (C arrow)
  • If identifiable from the pedigree, the consanguinity status of a patient is set in their patient record
  • Credits are displayed for the vocabularies in use

Bug fixes

  • When pushing patient data PhenomeCentral rejects logins from clients using newer PhenoTips versions (pushing from 1.3M2 to 1.3M1 fails)
  • Export database as Excel file fails in some cases
  • Patient creation through REST API fails in some cases
  • Corrected the order of phenotypes saved in the "Prenatal and perinatal history" section
  • Phenotypes from systems not found in the mapping, such as "Endocrine" or "Voice", are placed under the heading of "Other"
  • Guest users cannot create patients (on instances that are supposed to allow that)
  • The pedigree editor UI doesn't display fully with the embedded skin
  • Many minor UI fixes in various parts of the application

See the full list of changes on Jira.