Fix go-inferences report

[cmungall]

Migrate this from svn

[cmungall]

Here is the diff of the current ontology https://build.berkeleybop.org/job/build-go-ontology-inferences/19/artifact/target/go_inferences.diff/*view*/

[cmungall]

Some things perhaps requiring attention:

 id: GO:0002213 ! defense response to insect
-is_a: GO:0098542 {is_inferred="true"} ! defense response to other organism **CHECK ME**
+is_a: GO:0006952 {is_inferred="true"} ! defense response

 id: GO:0002215 ! defense response to nematode
-is_a: GO:0098542 {is_inferred="true"} ! defense response to other organism  **CHECK ME**
+is_a: GO:0006952 {is_inferred="true"} ! defense response

 id: GO:0009600 ! detection of nematode
-is_a: GO:0098543 {is_inferred="true"} ! detection of other organism  **CHECK ME**
+is_a: GO:0098581 {is_inferred="true"} ! detection of external biotic stimulus

 id: GO:0009601 ! detection of insect
-is_a: GO:0098543 {is_inferred="true"} ! detection of other organism  **CHECK ME**
+is_a: GO:0098581 {is_inferred="true"} ! detection of external biotic stimulus

...

 id: GO:2000068 ! regulation of defense response to insect
-is_a: GO:0002831 {is_inferred="true"} ! regulation of response to biotic stimulus
 is_a: GO:0031347 {is_inferred="true"} ! regulation of defense response
-is_a: GO:0032101 {is_inferred="true"} ! regulation of response to external stimulus
-is_a: GO:0043900 {is_inferred="true"} ! regulation of multi-organism process

[cmungall]

The technical part is done. If someone can check the differences that were introduced during the no-report interregnum (see job above) we can close this

[ValWood]

fixed my issue in todays load..

[ukemi]

Checking the diff above:

In addition to the inferred links to BFO terms (material entity and BFO:0000003), there are others that look odd.

There are many terms that have been removed from the sulfur compound hierarchy, I assume due to a change in the ChEBI structure.

There are some relationships of GO terms to external ontologies: eg. [Term] id: GO:0035618 ! root hair +is_a: CARO:0000003 {is_inferred="true"} ! anatomical structure is_a: GO:0120025 {is_inferred="true"} ! plasma membrane bounded cell projection

And then ones to just between external ontologies: +[Term] +id: UBERON:0036069 ! tracheoesophageal fold +is_a: CARO:0000003 {is_inferred="true"} ! anatomical structure

There are lots that I think are due to the equivalencies made between ChEBI and PRO protein. I think they are a bit odd because now all of these 'gene product' classes are being characterized under the chemical hierarchy. This doesn't really make sense. I suspect that @pgaudet has these in her sights: eg. +[Term] +id: GO:0042097 ! interleukin-4 biosynthetic process +is_a: GO:1901566 {is_inferred="true"} ! organonitrogen compound biosynthetic process

These are just plain weird:

[Term] -id: PR:000000001 ! protein -is_a: CHEBI:33695 {is_inferred="true"} ! information biomacromolecule +id: PO:0000002 ! anther wall +is_a: CARO:0000003 {is_inferred="true"} ! anatomical structure

[Term] -id: PR:000000008 ! TGF-beta-like cystine-knot cytokine -is_a: CHEBI:36080 {is_inferred="true"} ! protein +id: PO:0000025 ! root tip +is_a: CARO:0000003 {is_inferred="true"} ! anatomical structure

[Term] -id: PR:000000019 ! mitogen-activated protein kinase -is_a: CHEBI:36080 {is_inferred="true"} ! protein +id: PO:0000033 ! fruit valve +is_a: CARO:0000003 {is_inferred="true"} ! anatomical structure

[Term] -id: PR:000000028 ! small GTPase -is_a: CHEBI:36080 {is_inferred="true"} ! protein +id: PO:0000084 ! plant sperm cell +is_a: CARO:0000003 {is_inferred="true"} ! anatomical structure

There seem to be issues with the defense response terms now:

[Term] id: GO:1900366 ! negative regulation of defense response to insect -is_a: GO:0002832 {is_inferred="true"} ! negative regulation of response to biotic stimulus is_a: GO:0031348 {is_inferred="true"} ! negative regulation of defense response -is_a: GO:0032102 {is_inferred="true"} ! negative regulation of response to external stimulus -is_a: GO:0043901 {is_inferred="true"} ! negative regulation of multi-organism process is_a: GO:2000068 {is_inferred="true"} ! regulation of defense response to insect

[Term] id: GO:1900367 ! positive regulation of defense response to insect -is_a: GO:0002833 {is_inferred="true"} ! positive regulation of response to biotic stimulus is_a: GO:0031349 {is_inferred="true"} ! positive regulation of defense response -is_a: GO:0032103 {is_inferred="true"} ! positive regulation of response to external stimulus -is_a: GO:0043902 {is_inferred="true"} ! positive regulation of multi-organism process is_a: GO:2000068 {is_inferred="true"} ! regulation of defense response to insect

[Term] id: GO:2000068 ! regulation of defense response to insect -is_a: GO:0002831 {is_inferred="true"} ! regulation of response to biotic stimulus is_a: GO:0031347 {is_inferred="true"} ! regulation of defense response -is_a: GO:0032101 {is_inferred="true"} ! regulation of response to external stimulus -is_a: GO:0043900 {is_inferred="true"} ! regulation of multi-organism process

id: GO:0002213 ! defense response to insect -is_a: GO:0098542 {is_inferred="true"} ! defense response to other organism +is_a: GO:0006952 {is_inferred="true"} ! defense response

[Term] id: GO:0002215 ! defense response to nematode -is_a: GO:0098542 {is_inferred="true"} ! defense response to other organism +is_a: GO:0006952 {is_inferred="true"} ! defense response

This one is interesting. I think the logical def of frizzled binding in not sufficient, but we need to look at the gene family.

[Term] +id: GO:0005119 ! smoothened binding +is_a: GO:0005109 {is_inferred="true"} ! frizzled binding

Then there are these. Were they fixed in #13400 and this report is just out of date?:

[Term] id: GO:0014881 ! regulation of myofibril size -is_a: GO:0032535 {is_inferred="true"} ! regulation of cellular component size +is_a: GO:0008361 {is_inferred="true"} ! regulation of cell size

[Term] id: GO:0016243 ! regulation of autophagosome size +is_a: GO:0008361 {is_inferred="true"} ! regulation of cell size is_a: GO:1902589 {is_inferred="true"} ! single-organism organelle organization

[Term] +id: GO:0030832 ! regulation of actin filament length +is_a: GO:0008361 {is_inferred="true"} ! regulation of cell size

[Term] +id: GO:0031133 ! regulation of axon diameter +is_a: GO:0060305 {is_inferred="true"} ! regulation of cell diameter

[Term] +id: GO:0035809 ! regulation of urine volume +is_a: GO:0090066 {is_inferred="true"} ! regulation of anatomical structure size

[Term] +id: GO:0044375 ! regulation of peroxisome size +is_a: GO:0008361 {is_inferred="true"} ! regulation of cell size

[Term] +id: GO:0044656 ! regulation of post-lysosomal vacuole size +is_a: GO:0008361 {is_inferred="true"} ! regulation of cell size

[Term] +id: GO:0051036 ! regulation of endosome size +is_a: GO:0008361 {is_inferred="true"} ! regulation of cell size

[Term] +id: GO:0097298 ! regulation of nucleus size +is_a: GO:0008361 {is_inferred="true"} ! regulation of cell size

This one looks like a logical def issue:

[Term] +id: GO:0070468 ! dentin secretion +is_a: GO:0006858 {is_inferred="true"} ! extracellular transport

[dosumis]

Partial fix in #13489

But full fix requires this BFO import to be setup, as requested in #12946

This will pull the BFO hierarchy, removing redundant inferences. It should also pull disjointness axioms so that we get basic error checking. @cmungall - can this be made a priority?

[cmungall]

@ukemi - ignore the non-GO ones

@dosumis - I will do this next week.

[ukemi]

@dosumis Is this done?

[dosumis]

@dosumis Is this done?

Looks like it. Both dependent tickets fixed. Do you still see inferences to BFO?