The phenotypic module facilitates the collection of structured clinical data using standard ontologies such as the Human Phenotype Ontology (HPO_), the Orphanet Rare Disease Ontology (ORDO_) and Online Mendelian Inheritance in Man (OMIM_). Below we explain how to submit a new index case, and how to add new family members to the pedigree chart. If you have any questions, please contact our helpedesk via email@example.com
Left side-bar (1) - Side-bar fixed in all phenotypic submission steps - provides direct access to different phenotype submission steps.
Bottom menus (2) - Menus containing access to different ways to introduce participants, and to browse your submitted cases.
Submission of phenotypic data¶
There are different ways to enter phenotypic information in the system:
Manual form submission (case by case approach recommended when phenotypic data is not structured using HPO/OMIM/ORDO)
Bulk import using an excel template (recommended when the data is already HPO/OMIM/ORDO encoded)
Bulk import via transfer from a PhenoTips instance
The system provides a user friendly interface and several disease templates to facilitate structured phenotypic data entry using HPO, ORDO and OMIM. New cases /families must be created by starting from the index case.
In the Phenotypic Data Submission Site enter the New Index Case section in the bottom menu. Press the Create a new case button.
Choose a template which will provide you with specific disease fields relevant to your index case, or choose the Default template for a general form.
Follow the different steps to enter the patient’s phenotypic information. Note that structured vocabulary is used to capture the data and that several fields in the Individual Information section are mandatory. Once finalised press the “submit button” to create the index case entry
To create an index case, the following fields are required:
Year of birth
Status of case (solved/unsolved)
In the case of a solved status, we ask that the final diagnosis is provided
HPO terms can be searched for in the HPO ontology using the search bar. Also, the HPO tree can be navigated in a dedicated section. When a template is selected, the HPO terms configured for that template are automatically loaded in the tree.
We strongly encourage the selection of 5+ HPO terms to describe a case’s symptoms (6-symptoms section) and to enter the suspected or confirmed clinical diagnosis (8-diagnosis), in order to facilitate downstream phenotypic and genomic analysis, as this information is fully integrated in the GPAP (cohort creation, gene filtering, variant prioritisation, patient matchmaking, etc.).
If you are in possession of this information, for each HPO term it is possible to indicate the level of severity with a slider that ranges from MILD to PROFOUND severity (HPO Classification for severity term HP:0012824).
Once submitted, a message confirming the creation of the index case will appear with different options to continue: “add a relative” (to add additional family members in the pedigree), “see my cases (to browse all your data) or “see summary (to access a downloadable summary of the submitted participant).
To perform a bulk import of phenotypic data, enter the Import Cases section in the bottom menu of the Phenotypic Data Submission Module. Currently there are two different options for bulk data upload:
1. Excel file: Download the provided template, complete all the necessary fields, and use the Upload a Local File button to upload it. Please note that several fields are mandatory. Finally press Import to complete the submission.
2. Phenotips File (.json): Upload a .json file exported from a PhenoTips instance by using the Upload a Local File button. You can see examples by hovering the mouse over example.json. Press Import to complete the submission..
Edit Index Case Pedigree¶
A pedigree is editable only after the creation of an index case with the mandatory information.
You can enter a Pedigree (and export an image of it) by accessing any record and clicking on the Pedigree button.
- The pedigree editor will enable you to:
Export the pedigree in JSON or PED format
Import a new pedigree from a PED file
Access detailed instructions to modify a pedigree
Manually modify the current pedigree
For detailed instructions, please refer to the image below. This can be also found by clicking on the detailed instructions (3).
Add a member to a pedigree¶
In the Phenotypic Data Submission Site enter the New Family member item in the sidebar (or from the homepage).
Select the Index Case ID of the family for which you want to create a new member and click on Go to participant form. In the Index Case form access the Pedigree section:
Use the Pedigree tools to add the new family member to the pedigree. Specific instructions on how to add nodes, and further information in the pedigree can be accessed by clicking on “Read the instruction” at the top right of the page. For more information, see section below: Edit Index Case Pedigree.
Assign Participant Permissions¶
By clicking the Permissions button in the Patient form page, you can share/unshare your participant’s record with other GPAP groups:
Access the participant’s record and push the “Edit” button
Access the “Permissions” button at the top-right side.
A new menu will appear showing the current owner, and a dropdown to add other groups as “Collaborators”. Add in this dropdown the groups that could have access to this record.
We rely on a set of external resources to facilitate participant data submission in a standard format.
Management of phenotypic data¶
Browse GPAP PhenoStore Cases¶
In the “Phenotypic Data Submission Site” enter the “Browse your cases” section in the bottom menu,
This section shows a summary of all your submitted data and data shared with you,
At the top you will find statistics of your submitted/shared participants.
At the bottom you have a table of your participants. You can directly access their records by clicking on their ID codes, and export all your data in .tsv format by using the “Export to TSV” button.
Export GPAP Phenostore Cases¶
From the “browse cases section”, A list of cases can be exported by clicking on the corresponding button. A .tsv file will be downloaded according to your browser settings. This file includes the list of participants currently displayed in the participant table. The fields included are the following:
GPAP Local ID
Index Case (yes or no)
Affected Status (Affected or Unaffected)
Solved Status (Solved or Unsolved)
Sex (M, F or U)
Consanguinity (Yes or No)
From the participants form, individual phenotypic information can be exported in Phenopacket and pdf formats.