Phenote+ Phenotype Curation

General Form Features (the 3 Panels)

The form is divided into three panels: data entry (tabs), basic info (looked up values from .obo files) and table view. Each area is adjustable by dragging the area edges. In Phenote+ these panels can be popped out of the window.

Data Entry (Tab 1,2,3) panel All data is entered in fields on the tabs. Tab 1 is for object entry and information retrieval; Tabs 2 and 3 are for entering phenotype information. The specifics of the fields are described above.

Basic Info panel 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.

Table View panel All retrieved records (either object retrieved or paper retrieved) are listed here. The columns can be adjusted in width, (can the columns be height auto-adjusted and text top justified?). The columns can also be reordered manually by dragging; these changes should be saved.

New records can be made based on copies of pre-existing records using the buttons along the bottom of the table. To ensure a new entry is recorded, make sure to “save data”, especially before 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 allele. 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.

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.

Filter. 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.

If there are too many characters in the table, you can clear the table and select only the line you want by doing a retrieve function on the object.

A Date Created column has been supplied.

Behind Phenote

Dropdown lists are supplied for many fields. The dropdown lists are in the form of .obo files that are populated each time Phenote is launched. 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 right-hand 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. For manually entering text, it is not case-specific. All entries have to be followed by <return> or <enter> for them to take.

Object names can be verified from the latest WS build. WS_latest object 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. 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. NBP alleles are handled a bit differently and do not need a person or paper reference to be saved. 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.

back --kjy 15:14, 13 March 2008 (EDT)