Thank you for the quick response. I had tried to use the search panel to
search for PO terms, and they don't show up (therefore, I couldn't set up
filters allowing PO terms). However, I just tried View > Ontology >
Complete Ontology Tree View, and the PO terms are there, so the file is
loading. Afterwards, I quit the program and restarted (for about the 30th
time today) and lo and behold, the PO terms showed up in the search panel.
It seems I finally managed to get rid of whatever cache was messing things
Next to the field type filters. Even though I had no filter files left, it
was still using the old filters, so when I created a new filters folder
and saved my new filter there, it worked the way I want it to. The
software now seems to be working the way I want it to.
Thanks for the help. Without your response, I wasn't sure if I was doing
it right. I thought I was following the directions, and in fact I was, but
it seems it was just a question of restarting the program enough times to
clear out any old cache. I think the directions on the wiki page are
sufficient for someone who has used OboEdit a lot (which I have), but it
may be tough for a newby.
On 9/7/12 2:08 PM, "Jim Balhoff" <balhoff@...> wrote:
>Hi Ramona (sending again via list),
>I saw your email to the phenex-users list. I think you are the first
>person to ever post to the list. I think the issue might be that you need
>to configure filters for your field types. The list of ontologies
>specifies which files Phenex will download and add to the OBO session.
>But then separately you specify a query which controls the list of terms
>available for autocomplete in each type of field. You can check to see if
>PO is being loaded by opening View > Ontology > Complete Ontology Tree
>View. Do you see PO terms in the tree view?
>The built in field filters are set up for Phenoscape. You can override
>them by creating your own filter files. Let me know if these instructions
>James P. Balhoff, Ph.D.
>National Evolutionary Synthesis Center
>2024 West Main St., Suite A200
>Durham, NC 27705
I don't know if anyone actually uses this list, because it says there is
no archive, but I will give it a try. I am trying to use Phenex to score
some plant phenotypes. I have edited the ontology source list to contain
PATO, GO, PO, and a few others. It seems to recognize the other
ontologies, but not PO. I have checked the PO url and actually tried
several different urls, any of which should work. I tried removing the
ontology cache, which allowed it to recognize GO instead of TAO, but it
didn't help with PO. I also removed the entire <user's
home>/Library/Application Support/Phenex folder, but it didn't seem to
change anything. Any suggestions?