Create ECTO release using axioms.owl mappings

[wdduncan]

Please create a new release of ECTO using the mappings in src/mappings/axioms.owl.
There is also a src/mappings/axioms-boomer.owl file created using boomer. I don't know if you want to incorporate it.

cc @diatomsRcool @cmungall @wdduncan

[matentzn]

Whats the timeline on this?

[matentzn]

I mean, whats the deadline?

[wdduncan]

I think they want this as soon as you can do it :(

[matentzn]

OK.

[matentzn]

Bill, what format do they want this in? OWL, OBO? Is there any document/issue that describes what exactly they want?

[matentzn]

Looks like you have been matching against an old version of ECTO... Can you re-run against the current release? None of the mappings match to anything actually in ECTO right now:

id: ECTO:0000001
is_a: NCIT:C61398
is_a: XCO:0000038
equivalent_to: NCIT:C61398
equivalent_to: XCO:0000038

There is no ECTO:0000001.

[matentzn]

Here are instructions to merge your axioms into the ECTO release:

cd src/ontology
sh run.sh make sh run.sh make ecto-incl-mappings.obo

This will generate the OWL and OBO versions for ECTO plus your mappings.

Let me know when ecto-incl-mappings.obo looks like you want it, then Anne or I will run a proper release.

[matentzn]

BTW: the corresponding ROBOT snippets are:

$(ONT)-incl-mappings.owl: ../../$(ONT).owl ../mapping/axioms.owl ../mapping/axioms-boomer.owl
	$(ROBOT) merge -i ../../$(ONT).owl -i ../mapping/axioms.owl -i ../mapping/axioms-boomer.owl \
		annotate --ontology-iri $(ONTBASE)/$@ --version-iri $(ONTBASE)/releases/$(TODAY)/$@ --output $@.tmp.owl && mv $@.tmp.owl $@

$(ONT)-incl-mappings.obo: $(ONT)-incl-mappings.owl
	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo

[matentzn]

There are also only a few mappings IMO. 35? Werent there many more before?

[wdduncan]

@matentzn Sorry a little confused.
The axioms.owl is generated using the slim-exposure.owl and probs.tsv.
slim-exposure.owl is built in part from ecto-basic.obo:
(see src/mappings/Makefile)

exposure-ecto.obo: ../../subsets/ecto-basic.obo
        cp $< $@

Does ecto-basic.obo need to be updated?

[matentzn]

Yeah that is the problem.. That file is from the neolithic area..

Change to this:

exposure-ecto.obo: ../../ecto-base.obo
        cp $< $@

[wdduncan]

@matentzn
Just created a new PR:
#100

Let me know if the new file looks good.

[matentzn]

Yeah looks better! After you merged it, can you run:

cd src/ontology
sh run.sh make ecto-incl-mappings.obo

And inspect ecto-incl-mappings.obo? Who could judge whether this is what your project needs? I think questions need to be answered:

1. Do we want the boomer axioms?
2. Does ECTO (base) have the coverage that your project needs
3. Is the mapping complete with respect to ECTO (base) (are all terms in ECTO base terms that should be mapped actually mapped).

Who can answer these questions?

[wdduncan]

@diatomsRcool can you answer @matentzn questions?

For now, I think we should exclude the boomer mappings.

When I try to run:

cd src/ontology
sh run.sh make ecto-incl-mappings.obo

I receive the error:

make: *** No rule to make target '../mapping/axioms-boomer.owl', needed by 'ecto-incl-mappings.owl'.  Stop.

[matentzn]

Well, does the file exist? ../mapping/axioms-boomer.owl ?

[wdduncan]

No. I removed it. But I don't know why run.sh would expect it.

[matentzn]

I just added it here.

You can change that in the file to:

$(ONT)-incl-mappings.owl: ../../$(ONT).owl ../mapping/axioms.owl
	$(ROBOT) merge -i ../../$(ONT).owl -i ../mapping/axioms.owl \
		annotate --ontology-iri $(ONTBASE)/$@ --version-iri $(ONTBASE)/releases/$(TODAY)/$@ --output $@.tmp.owl && mv $@.tmp.owl $@

Let me know if that works!

[wdduncan]

I fixed some problems boomer was having with the input owl files. I will make a separate ticket for those.

The command:

cd src/ontology
sh run.sh make ecto-incl-mappings.obo

runs successfully.
I will create a new PR.

[diatomsRcool]

What is the status of this?