phenex-users — Mailing list for all discussion of Phenex and its development.

Re: [Phenex-users] getting Phenex to recognize the PO

[Walls, R. <rw...@ny...>]

Jim,

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
up. 

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.

Ramona



On 9/7/12 2:08 PM, "Jim Balhoff" <ba...@ne...> 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
>are helpful:
>
>http://phenoscape.org/wiki/Phenex#Entry_field_filters
>
>Thanks,
>Jim
>
>____________________________________________
>James P. Balhoff, Ph.D.
>National Evolutionary Synthesis Center
>2024 West Main St., Suite A200
>Durham, NC 27705
>USA
>
>
>

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?

Thanks,
Ramona


>

Re: [Phenex-users] getting Phenex to recognize the PO

[Jim B. <ba...@ne...>]

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 are helpful:

http://phenoscape.org/wiki/Phenex#Entry_field_filters

Thanks,
Jim

____________________________________________
James P. Balhoff, Ph.D.
National Evolutionary Synthesis Center
2024 West Main St., Suite A200
Durham, NC 27705
USA

[Phenex-users] getting Phenex to recognize the PO

[Walls, R. <rw...@ny...>]

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?

Thanks,
Ramona