Phenote+ Phenotype Curation

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Information about Phenote

Overview of the general Phenote Form (the 3 Panels)

The form is divided into three panels: Annotation Editor (data entry), Term Info Browser (output of values from .obo files) and Annotation Table. Each area is adjustable by dragging the area edges. In phenoteplus these panels can be popped out to become free-floating windows.

Annotation Editor (Tabs)

All data is entered into fields on the tabs. For specifics about the Variation-Phenotype configuration, a description of these fields can be found on the worm.cfg phenote fields page.

Term Info Browser

Reports data from .obo files and are read only. You can arrow through information already reported (or bookmarked as favorites) during the session; they are not saved when Phenote is quit. You can also select the term showing with the checkmark. The box does not update until another .obo file is browsed.

Annotation Table

  • All data being entered can be viewed here. 
  • All records that you retrieve are listed here.
  • The columns can be adjusted in width but not height.
  • The columns can be reordered manually by dragging.
  • New records can be made based on duplicating pre-existing records using the buttons along the bottom of the table.
  • To ensure a new entry is recorded, make sure to “save data”, especiallybefore hitting any “retrieve” button.
  • If you hit ‘retrieve’ without having first saved the data, you will loose any data you’ve already entered—so be careful when switching to a new record. If you press ‘save data’ without completing the entry, it will result in a warning and the option to commit anyway, allowing this save will result in the record updated with a Postgres database ID (pgdbId).
  • You can edit multiple records at once by selecting the records then changing a value in the tab panel. The new value will be viewable in the table for all records selected; remember to “save data” before hitting retrieve.
  • You can sort through and view records that contain specific info through the filter option at the bottom right. Chose the field and input a value. The records are dynamically updated in the table.
  • If you Save Data in filter mode, the function will work on all records not shown as well as on the records showing.
  • Currently there is no "clear table" function, so if you want a fresh table you will have to either close an reopen Phenote or you can do a retrieve function on a new object.  Remember to commit any data you want saved!
  • In the Date Created column, date of entry is automatically entered.

Other features

Text finishing. Dropdown lists are in the format of .obo files and populate the form each time Phenote is launched. These .obo files allow for text finishing in the corresponding field. The fields that contain dropdown lists are noted by the scroll arrows on the field. Information for the item in the dropdown list is viewable in the info panel and is not editable. Items in dropdown lists can be selected from the list or can be entered by typing with or without auto-completion. Manually entered text is not case-specific. All manually entered text has to be followed by <return> or <enter> for it to take.

Verifying objects (Variation-Phenotype feature). Object names of alleles, rearrangements and transgenes can be verified from the latest WS build by using the WS_current field to query a static file from the latest WS. These static files are manually updated from Citace after each build and scripted for readout into Phenote. The files are stored on tazendra in /home/acedb/karen/populate_gin_variation.

Save Data and Constraints. 'Save data' will assess all character lines in the table for meeting the hard-code constraints we requested. For variation-phenotype curation, these constraints require that each entry contain a curator, an object type, object name, phenotype and publication or person reference. Saving incomplete records will result in a warning box and the option to override the constraint e.g. to commit anyway. What this also means is that if you are browsing a large body of records, each one of them will be subject to the constraints and will be saved if you continue. NBP alleles are handled a bit differently and do not need a person or paper reference to be saved.