A Summary Classification can be saved at any time during the curation process. To be able to save, first select the "View Classification Summary" button in the top panel of the gene-disease curation record.
The summary classification panel appears below the Classification Matrix and allows you to save the current clinical validity classification. In the panel, you can also select whether the evidence for a strong classification has been replicated over time (required for a "Definitive" classification). A free-text evidence summary must be provided before saving.
By default, the Clinical Validity Classification value calculated from the scored evidence will be saved. This value can be manually modified; to do so, select the chosen clinical validity term from the drop-down menu. If a modification is made, an explanation in the "Explain Reason(s) for Change" field is required.
A free-text summary of the gene curation evidence must be entered in the “Evidence Summary” box; this summary will be displayed on the website when the final clinical validity classification is published. Specific guidance and a sample Evidence Summary text is provided here. The Evidence Summary text can be entered and formatted using the edit tool on the left hand side, and the right hand side panel will automatically show how the formatted text will be displayed on the website when it is published.
Clicking the “Save” button at the bottom of the Calculated Classification Matrix box will save the Classification.
Saving a Classification at this step is not marking it as Provisional or Approved, but will bring up the option to save it as Provisional.
Upon saving, the contents of the panel will be updated to reflect the saved options, including a time stamp for the saving operation. Buttons that link back to the Record Curation page (Curation Central), to re-edit the Summary Classification, or to view the current Evidence Summary (which opens in a new tab or window) are provided.
With every visit to the "View Classification Summary" page, the three editable fields in the panel are available to be edited and saved again (i.e. you may update the modification based on any new Calculated Classification, update the "Reason(s) for Change" text, and/or update the evidence summary text).
If the final classification of a GDM is "No Known Disease Relationship", the calculated classification was not modified, and only animal models were counted towards the experimental evidence, an "Animal Model Only" tag is displayed.
If the new calculated Total Points now suggest a Calculated Classification that is the same as a modified classification saved on the last visit, the modified classification will be reset to “No Modification”, and a red warning message will be displayed to explain this. If the Summary Classification has been saved previously, the tag will appear in the "My classification" section of the GDM dashboard.
Gene-disease curation records move between different states that are indicated by colored labels.
While you are entering evidence, the gene-disease record is shown with an label. When evidence collection is complete and the record is ready for GCEP review, you can save it with a classification label. The Provisional classification will facilitate review of the record by the GCEP by providing summaries of the curated evidence and the associated scores. After the GCEP has discussed the evidence and any requested modifications have been made and saved, the classification can be approved and will then be shown with the classification label.
By saving a Summary or Provisional Classification or approving a classification, you are creating a snapshot of the gene-disease record. You can continue to curate and modify all aspects of the record. However, the snapshot is permanently saved, and its Evidence Summary will be viewable using links in the "Saved Provisional and Approved Classification(s)" section at the bottom of the page when you view the Classification Summary.
When curation of a record is complete and ready for review by the expert panel, it can be moved to Provisional status.
Below the saved Summary Classification panel (see previous step), a new option enables you to save the curation and Summary Classification as a Provisional record. You can enter the date the curation was reviewed by you prior to saving, and add any additional comments in a free-text field.
If you move away from the Summary Classification page before previewing and saving the classification as a Provisional record, you have to re-save the Summary Classification (no changes are needed) to get the option to save as a Provisional record.
When you are ready to save the gene-disease curation as Provisional, select the "Preview Provisional" button.
The preview will show the timestamp of the submission, which is equivalent to the time at which the Provisional Classification is saved. Select the "Submit Provisional" button when you are ready.
After submitting/saving a Provisional classification, a panel providing the option to approve the gene-disease record will appear (see following section). The panel below that summarizes the saved classifications for the gene-disease record. Selecting the "Provisional Summary" link will open a new page or tab that shows the current Evidence Summary for the saved classification.
The top panel of the Evidence Summary shows top-level information about the gene-disease record and is followed by a panel containing the free-text curation summary (also labeled "Evidence Summary").
This is followed by the Calculated Classification Matrix and Scored Evidence tables. As in the preview version (see the description here), the tables summarize the saved evidence, sorting it according to evidence types (Case Level, Case Level for segregation evidence when there is no associated proband, Case-Control, and Experimental). Evidence with a score status of “Score,” “Review,” or “Contradicts” is shown. Only those rows of evidence where the score status was set as “Score” are included in the calculation for the total points shown at the bottom of each evidence table.and a series of tables
Below the Curation Central header panel, the central panel will now show the Provisional classification. It also now gives you the option to "View/Approve Current Provisional".
Once a Provisional Classification is submitted, it can not be edited. It will remain viewable and can be saved as Approved if no further changes are needed. However, the curation interface will remain active -- new evidence can be added and existing evidence can be edited. Updated Summary Classifications can be saved and submitted as a new Provisional Classification. The prior Provisional Classification will then be archived.
After the expert panel has met and voted to approve the gene-disease record, the provisional record can be approved in the GCI.
When your saved Provisional record is ready to be approved, either select the "View/Approve Current Provisional" button in the "My classification" section of the Curation Central page:
or select the "Approve" button at the bottom of the Classification Summary page:
Both options will bring up a new panel. If you need to acknowledge other contributors (e.g. other GCEPs), select the button, which will expand the section of the panel and enables you to enter additional contributors. Guidance on acknowledging other contributors can be found in Appendix D of the SOP.
To approve a classification, you must enter the final approval date. This should be the date on which the GCEP has voted to approve the gene-disease classification and can predate the date the approval is saved in the GCI. If curation was performed using criteria from an older version of the SOP, you can select it from the drop-down menu. The current version is shown by default.
Once you select "Preview Approval," you will be able to see the information (date, approver, additional comments etc.) for the Approval. Selecting "Submit Approval" will save the record as "Approved".
After submitting/saving the approval, a panel providing the option to publish the gene-disease record will appear (see following section). The "Saved Provisional and Approved Classification(s)" panel below shows all saved classifications for the gene-disease record; the newly approved classification will be marked with a green flag indicating that it is the most current approved record. Selecting the "Approved Summary" link will open a new page or tab that shows the current Evidence Summary for the saved classification.
Below the Curation Central header panel, the central panel will now show the Approved classification; the "View Current Approved" button opens a new window or tab with the approved Evidence Summary.
Once an Approved Classification is submitted, it can not be edited. It will remain viewable and can be published if no further changes are needed. However, the curation interface will remain active -- new evidence can be added and existing evidence can be edited. Updated Summary Classifications can be saved and submitted as a new Provisional and Approved classifications. The prior Provisional and Approved classifications will then be archived.
