#95 genomic-variation-events example

[Philip Ogren]

The genomic-variation-events example is in serious disrepair and needs to be revisited. The following are some notes Helen jotted down when she slogged through this example.

Step 3 in the README: a general gripe i have about knowtator is that until i was familiar
w/ the knowtator icons, i didn't know to distinguish them from the protege icons.
Since this is a tutorial, i suggest pointing out that in the middle of the toolbar
there is a string "text source collection", and after that reside the Knowtator specific icons.
Let me add here that once i figured out the difference,
the icons themselves, their placement, and their roll-over text is very clear.

Step 5: FYI - this step was superfluous. The "textsources" file loaded itself when i opened the
genomic-variation-events project.

Step "some things to observe":
Text source 1: gene_db_id:
-- is there supposed to be a value filled in for the gene_db_id? (there is not).
-- picky little thing: you talk about "protein class" in the readme, but the class is labeled "gene in the project.

Text source 2:
-- "select the annotation" in the README ...
There should be a note to advance to the next annotation.
As a neophite, i would've liked to see directions on how to do it too.
(This is the same gripe as above: once i figured out the icons they made sense,
but figuring them out at the onset was not obvious to me.)

-- "select the annotation presented as ..."
There's no directions on how to find that annotation in particular.
i suggest you include explicit directions that explain how to click on a class and find all annotation of that class.

-- "the display of the annotation ..." & "The annotation that fill ..."
It took me a long time to understand this bullet.
i changed some things in the form, and i saw that different items showed up
in my "variation event" list when i left-clicked it, but i wasn't quite sure what it meant.

Also, the nice dark-bars that light up on top & bottom of an annotation do not appear
for the annotations in this "variation event" class.
They do appear for the other classes

-- "Clicking the 'Add instance' button ..."
Are we still on the Forms tab here? (that's not clear to me)
If we are, maybe i found an "Add instance" button in the main body of the screen?
There is a big problem here: the title of the field is cut off by the view/create/add/remove instance icon-buttons,
so i can't tell it says "Variation-location". This is not a problem w/ screensize: i have the screen maximized.
Further, the title text and buttons look to be grayed out, and clicking the "add instance" button
only draws a green highlight line around the whole field, but doesn't do anything else.

Text source 3:
-- "Right click on the list of annotations ... "
What/where is the list of annotations? I never found it.
Instead, i left-clicked the filter icon in the menu bar and played around w/ the different filter views.