pcastellanoescuder / foodbiomarkerontology Goto Github PK

Hello FOBI development team, as I'd mentioned to @ddooley I was looking over FOBI the other day and I noticed that there are some examples of FOBI terms which might be duplicative of existing CHEBI terms.

For example FOBI:Fatty acid esters seems like it might be a duplication of CHEBI:fatty acid ester. Just for reference it's encouraged practice within OBO ontologies, (obo principal 5) to reuse existing terms when possible. If so perhaps you could import such chebi terms and then insert them into your existing hierarchy? I can see the need to have a slightly different top level hierarchy than CHEBI, but if there are correspondences with CHEBI then perhaps you could be reusing CHEBI terms themselves?

Just thought I'd point it out, hope it's helpful and perhaps something to consider moving forward.

Cheers,
Kai

Is that intentional? That is, is the chirality of the glucuronide compounds in FBOnto_Annotation_File.csv not important in food, and are all stereoisomers equivalent?

The OBO Foundry has recently created a topics page at https://github.com/topics/obofoundry. It would be great if you could add the obofoundry topic to your repository, since it's currently listed as active in the OBO Foundry. If you're not sure how to do that, follow the instructions here. The main issue for this task is at OBOFoundry/OBOFoundry.github.io#1538 in case you want some more context or to join the larger discussion.

It seems we have an error when parsing FOBI in AgroPortal using the OWL API

ERROR o.s.ncbo.oapiwrapper.OntologyParser - http://purl.obolibrary.org/obo/fobi.owl#FOBI:050339

It seems this Annoation Property is not defined as the other in the OWL file.
Still the ontology opens in Protégé on my side (same parser...)

Could you check.

I never noticed this before, but see http://dashboard.obofoundry.org/dashboard/fobi/dashboard.html

Trying to run ROBOT (any command):

robot -vvv remove -i fobi.owl --term BFO:0000050 -o test.owl

will cause:

For details see: http://robot.obolibrary.org/errors#invalid-element-error
java.io.IOException: errors#INVALID ELEMENT ERROR "http://purl.obolibrary.org/obo/fobi.owl#FOBI:050339" contains invalid characters
	at org.obolibrary.robot.IOHelper.saveOntologyFile(IOHelper.java:1745)
	at org.obolibrary.robot.IOHelper.saveOntology(IOHelper.java:846)
	at org.obolibrary.robot.CommandLineHelper.maybeSaveOutput(CommandLineHelper.java:667)
	at org.obolibrary.robot.RemoveCommand.execute(RemoveCommand.java:156)
	at org.obolibrary.robot.CommandManager.executeCommand(CommandManager.java:244)
	at org.obolibrary.robot.CommandManager.execute(CommandManager.java:188)
	at org.obolibrary.robot.CommandManager.main(CommandManager.java:135)
	at org.obolibrary.robot.CommandLineInterface.main(CommandLineInterface.java:60)

Looking in more depth, something about these terms has to be gone wrong:

In the obo file there is a mix of words starting with upper and lower case letters. We need to make everything consistent. A good idea would be to only used lowercase letters