OBO-Edit Graph Viewer and ancestor views

[Nomi Harris]

I was looking at this Phenote bug report: https://sourceforge.net/tracker/?func=detail&aid=2970560&group_id=76834&atid=887913
which complains that when you show terms in the Graph Viewer in
Phenote, it shows only the immediate parent of the term, not complete
paths to root. David included a screenshot of what he used to see in
the Graph Viewer:

[Nicole Washington]

my only addition is that if the reasoner is turned on in phenote, at this time, it will probably run out of memory!

On May 14, 2010, at 1:35 PM, Nomi Harris wrote:

> I was looking at this Phenote bug report: https://sourceforge.net/tracker/?func=detail&aid=2970560&group_id=76834&atid=887913
> which complains that when you show terms in the Graph Viewer in Phenote, it shows only the immediate parent of the term, not complete paths to root. David included a screenshot of what he used to see in the Graph Viewer:
>
>
>

> I started looking at OBO-Edit, since the Graph Viewer is an OBO-Edit component used by Phenote, to try to figure out what's going on, and it seems to me that, contrary to what the OBO-Edit userguide claims, the Graph Viewer in OBO-Edit now shows only the immediate parent(s) of the term, unless you turn on the reasoner. I tried showing the term "negative regulation of cell proliferation involved in contact inhibition", which is shown in the userguide with a full path to biological_process. The current OBO-Edit just shows the immediate parents:
> <1.6b7-2.jpg><Picture 1.png>
>
> with my Graph Viewer configured as follows:
> <Picture 2.png>
>
>
> If I turn on the reasoner, I can see the whole graph up to biological_process, which the userguide shows as the NON-reasoner display. So has the Graph Viewer behavior changed? If so, maybe the userguide should be updated?
>
> Speaking of which, I looked at the online userguide, and it seems to be a much older version. See, for example, http://oboedit.org/docs/html/The_Graph_Viewer_Plugin.htm
> The whole table of contents is different in the online userguide vs. the one you get inside OBO-Edit.
>
> Anyway, my conclusion is that, based on the current behavior of OBO-Edit, there is no way for me to fix the Graph Viewer display in Phenote. I certainly don't think we should turn on the OBO-Edit reasoner from Phenote. Any thoughts?
>
> Nomi--
> You received this message because you are subscribed to the Google Groups "OBO-Edit Developers Group" group.
> To post to this group, send email to obo-ed...@googlegroups.com.
> To unsubscribe from this group, send email to obo-edit-dev...@googlegroups.com.
> For more options, visit this group at http://groups.google.com/group/obo-edit-dev?hl=en.
>

--
You received this message because you are subscribed to the Google Groups "OBO-Edit Developers Group" group.
To post to this group, send email to obo-ed...@googlegroups.com.
To unsubscribe from this group, send email to obo-edit-dev...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/obo-edit-dev?hl=en.

[Nomi Harris]

Good news: Amina has fixed this Graph Viewer bug in OBO-Edit, so Phenote will now be able to show complete trees when you open the Graph Viewer in it. If you're not working from the Phenote source, you will see this in the next Phenote release (which I can do soon if this is a high priority for you, David).
Nomi

On May 14, 2010, at 1:35 PM, Nomi Harris wrote:

> I was looking at this Phenote bug report: https://sourceforge.net/tracker/?func=detail&aid=2970560&group_id=76834&atid=887913
> which complains that when you show terms in the Graph Viewer in Phenote, it shows only the immediate parent of the term, not complete paths to root. David included a screenshot of what he used to see in the Graph Viewer:

> <1.6b7-2.jpg>

>
>
> I started looking at OBO-Edit, since the Graph Viewer is an OBO-Edit component used by Phenote, to try to figure out what's going on, and it seems to me that, contrary to what the OBO-Edit userguide claims, the Graph Viewer in OBO-Edit now shows only the immediate parent(s) of the term, unless you turn on the reasoner. I tried showing the term "negative regulation of cell proliferation involved in contact inhibition", which is shown in the userguide with a full path to biological_process. The current OBO-Edit just shows the immediate parents: