Latest MO build

[kbeckenrode]

@wdduncan @lwaldron I'm sharing my latest MO build in this repo. It is messy, so let me share what I'm going for:

1. I subsetted the taxon list of microbes we are including into the ontology. I chose taxa that are known to be human-associated microbes. The subset included taxon at different hierarchies (phylum to species). We can decide to add other microbes later, but for now, I'd like to work with this set.
2. I added the full PATO ontology. In my ontology foundation readings, I read that if you think you'll use over 50% of an ontology, but go ahead and add the entire ontology into yours. So, that was my motivation.
3. I also add a "human microbiome" branch from OHMI.
4. Here are my problems:

• I can't seem to create a hierarchy. I want PATO terms to be separated (Bill, like how you had the 'striated example' file set up) from the taxa list.

• Similar as the PATO hierarchy, I want all the taxon to be a child of the human microbiome branch. But again, I can't seem to make the correct hierarchy structure.

I look forward to learning what I'm doing wrong :)

[kbeckenrode]

The build is named "MO_20200830.owl" in the main repo

[kbeckenrode]

Hi @wdduncan, tagging you just in case you missed this :)

[wdduncan]

Hi @kbeckenrode ... thanks for tagging me :) Sorry, I haven't had a chance to look at it yet :(

[wdduncan]

@kbeckenrode

I can't seem to create a hierarchy. I want PATO terms to be separated (Bill, like how you had the 'striated example' file set up) from the taxa list.

Are you referring to my use of the reasoner to create defined class? If so, you have to use the correct axioms to get classes to classify correctly. This can be tricky. Do you know what PATO qualities you are wanting to use for this?

You can also assert that something is subclass of something else.

As a side note, should rename the import file URIs into something recognizable. For example, see the names of the URIs your ontology imports:

I would like to resolve these, but now I have to go and open up each import to see which one file is referenced by the URI ... which creates more work :(