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phenoscape / Phenex

Phenex is an application for annotating character matrix files with ontology terms using the Entity-Quality syntax for describing phenotypes.
http://phenex.phenoscape.org/
MIT License
10 stars 3 forks source link

Error Loading Ontologies #102

Open JCGiron opened 2 years ago

JCGiron commented 2 years ago

I recently downloaded Phenex to start annotating beetle matrices with ontology terms. When trying to use it, it starts loading until I get this message: "An error occurred while loading ontologies: Load Error, line 39521"

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When I press OK, the program finishes loading and opens the expected window. The problem is that certain functions are not working. For example, View> Config> Ontology Sources doesn't do anything. I was able to open a NexML matrix. When trying to annotate a phenotype for a character state it doesn't even load UBERON terms.

Am I doing something wrong?

balhoff commented 2 years ago

The cause is Phenex's brittle old OBO parser, and this problem in Uberon: https://github.com/obophenotype/uberon/issues/2373

I will try to find a workaround. Usually you can open Ontology Sources and set different ontology locations, even when a loading error occurs.

balhoff commented 2 years ago

If you are able to open Ontology Sources, you can set the Uberon location to http://purl.obolibrary.org/obo/uberon/releases/2021-11-28/ext.obo to avoid this error for now.

wdahdul commented 2 years ago

@JCGiron, feel free to get in touch with me if you would like a quick demo of Phenex, or need further help getting Phenex started! my email is wdahdul @gmail.com

wdahdul commented 2 years ago

You may also need to set the OBO relations source to: http://purl.obolibrary.org/obo/ro/releases/2021-10-27/ro.obo

JCGiron commented 2 years ago

If you are able to open Ontology Sources, you can set the Uberon location to http://purl.obolibrary.org/obo/uberon/releases/2021-11-28/ext.obo to avoid this error for now.

That is the issue, Ontology Sources does not open any options. Actually, none of the options under View are working for me.

JCGiron commented 2 years ago

The problem was that I had only downloaded the Source code, but not the app. I just downloaded the app file, unzipped it and double cklicked the file. Now the options under View seem to be working properly, even though the ontology loading error is still showing up. Perhaps it would be helpful for others to make the installation instructions more clear?