Phenote quirks and bugs/fixes to request

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Warning for loading in data that has been saved to your desktop

  • Phenote allows you to save your current work to a file onto your computer, and reload it into phenote when you want to work with that data again. What this means is that you do not need to commit data to the postgres table until you are ready. However, if you have committed part of the data, and want to reload the file, make sure that the pgdbID (postgres database ID) of the already committed data is the same as the data in the postgres database.
  • You will duplicate a record if you load a file with a record (character line) that has no pgdbID but already exists in the database.
  • You will overwrite a record if you load in a file with a record (character line) that has the same pgdbID. 


To post on sourceforge phenote request tracker

all items have been posted (see below)


Unrepeatable weirdness<span class

(+) scroll down window for allele ontology gets stuck floating in front of everything.--kjy 17:27, 31 March 2008 (EDT)


Quirks  (require developer action if you want it different)

Various  (+) stands for items that may only effect phenote+ (these may not have been tested in phenote 1.5)

  • (+) Every ontology shows up in the "Complete Ontology Tree View"; you need to choose the ontology you want through the configure arrow.  Your configuration can be saved and will be propagated to the next time you open phenote. 
  • new data being committed is listed in the warning box as an error.


Items that have been posted on sourceforge phenote request tracker

  • fixed -> 'List field bug Phenote populates the table with the highlighted term from the dropdown list automatically. If you hit return, you will enter the value again.
  • fixed -> Clicking on undo will expand the first character line.
  • 'clear all/start over' button.  Currently if you are working on one paper/object, and want to switch to a new paper or object, the table is not cleared, all new information is appended --kjy 11:22, 1 April 2008 (EDT) Ideally it would be nice to have a "fresh slate" button, with a constraint that there is a warning button to save any unsaved data, with data review.
  • fixed -> (+)Definition/Term reference is not shown in the "Term Info" window --kjy16:34, 31 March 2008 (EDT) I would like to see all the info.
  • fixed -> clicking on duplicate seems to create a line randomly in the table, not always right under or above the line being duplicated.
  • Can the object name field or field name be bold/highlighted/outlined or anything for easy visibility. --kjy 11:49, 18 March 2008 (EDT)
  • Bulk adds, (annotating to multiple characters at once) works for anatomy terms and life stage list fields, however bulk deletes do not work. You have to correct each character one by one. --kjy 11:49, 18 March 2008 (EDT)
  • Move the retrieve buttons and multiple entry boxes to the left edge of the entry fields? --kjy 11:49, 18 March 2008 (EDT)



  • (+) cannot have an empty table, a new character line is automatically created with an updated entry date, even though this entry has no relevant information it cannot be deleted. --kjy 16:34, 31 March 2008 (EDT)
  • 'save data'  will tell you that a record being added is a commit error--kjy 14:04, 2 April 2008 (EDT)
  • Upon selecting a desired object from WS_current info, the Object Name should be autofilled (while editing the character line).--Jolene 11:45, 3 April 2008 (EDT); posted --kjy 13:14, 3 April 2008 (EDT)
  • Provide a summary of the number and names of objects associated with a particular paper reference upon hitting the Commit button. --Jolene 11:45, 3 April 2008 (EDT); posted --kjy 13:14, 3 April 2008 (EDT)


Things that Juancarlos can fix

(order of fields on the annotation editor, making .obo files for dropdown lists, connections to Postgres etc.)

  • Updates should be restricted to certain ontologies prior to loading Phenote (this will likely speed up the loading of Phenote). The ontologies that require frequent updates are:
  1. WS_current info
  2. Pub
  3. Person
  4. Phenotype
--Jolene 10:59, 4 April 2008 (EDT)
  • Change how the weekly running totals of allele objects are calculated: At present, the counts are based on the number of character lines (We like this as it summarizes allele-phenotype connections created during the week). However, we might also want the number of new objects as well as changed objects that were entered during the week. (This is identical to counts that were obtained from the CGI forms)--Jolene 12:04, 4 April 2008 (EDT)
  • Character line summary counts based on selected fields.
  1. Provide a summary of the number and names of objects associated with a particular field (such as paper reference) upon hitting the Commit button.
  2. Provide a summary of the number of references associated with an allele upon querying the allele object. --Jolene 12:06, 4 April 2008 (EDT)
  • Have a separate Tab to do queries for retrievable fields like phenotype, paper, object name, phenotype remark (already raised by Karen)--Jolene 12:04, 4 April 2008 (EDT)
  • Make new field "Published_as" as part of the evidence hash for any changes in the naming of the allele or linked gene that differs from current knowledge.--Karen
  • Add column for gene names that correspond to the allele. These should be the public_name of the gene when possible, if multiple genes are attached, maybe just a string of the names? The gene names are on the obo file. Is this possible?  --Karen


  • Added Retrieve functionality to the Phenotype Remark on 2008 April 4 (Juancarlos). This would allow us to easily track down annotations that need to be recurated. --Jolene 11:45, 3 April 2008 (EDT)
  • Added Retrieve functionality to the Phenotype on 2008 April 4 (Juancarlos). This would allow us to view all objects that have been curated to a particular phenotype as well as the total count. --Jolene 11:45, 3 April 2008 (EDT)