[PhenoTips Announcement] PhenoTips 1.3 (stable) released

PhenoTips Announcements announcements at phenotips.org
Mon May 1 16:26:11 EDT 2017

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.

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

== 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
* 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
* 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

=== 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.

== 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
* 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
* Added marking to the current patient
* 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

== 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.

== New RESTful APIs ==

* New REST APIs for accessing:
** vocabularies
** patient record permissions, enabling users to access/manage patient
record's owner(s), visibility, and collaborator(s)
** multiple patients can now be retrieved at once via REST given a list
of (internal or external) IDs.
** gene panels
* 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
* Related resources are now more consistently linked, to support better
* 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

== 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

=== 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:

* log in with an administrative account
* open the administration by clicking the Administration link in the
upper left corner
* open the Configuration -> Localization section
* 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
* don't forget to Save the configuration

=== 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 anonymous
general installation and usage data 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 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.

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