WIP: Using CARO

[cmungall]

#13898

[cmungall]

This is what the reasoner diff looks like:

commit 4bbd7a784234526cf631366604ad989a0d6b0458
Merge: a4d2933 77a0f28
Author: Chris Mungall <[email protected]>
Date:   2017-07-14 15:36:18 -0700

    Merge branch 'master' of github.com:geneontology/go-ontology into issue-13898

changes in entailments

--- go_inferences.obo-previous	2017-07-14 06:26:39.000000000 -0700
+++ go_inferences.obo	2017-07-14 15:37:50.000000000 -0700
@@ -1384,6 +1384,7 @@
 [Term]
 id: GO:0001556 ! oocyte maturation
 is_a: GO:0022412 {is_inferred="true"} ! cellular process involved in reproduction in multicellular organism
+is_a: GO:0071695 {is_inferred="true"} ! anatomical structure maturation
 
 [Term]
 id: GO:0001559 ! regulation of cell growth by detection of nuclear:cytoplasmic ratio
@@ -1999,6 +2000,10 @@
 is_a: GO:0002054 {is_inferred="true"} ! nucleobase binding
 
 [Term]
+id: GO:0002070 ! epithelial cell maturation
+is_a: GO:0071695 {is_inferred="true"} ! anatomical structure maturation
+
+[Term]
 id: GO:0002074 ! extraocular skeletal muscle development
 is_a: GO:0060538 {is_inferred="true"} ! skeletal muscle organ development
 
@@ -11744,7 +11749,7 @@
 [Term]
 id: GO:0010431 ! seed maturation
 is_a: GO:0003006 {is_inferred="true"} ! developmental process involved in reproduction
-is_a: GO:0021700 {is_inferred="true"} ! developmental maturation
+is_a: GO:0071695 {is_inferred="true"} ! anatomical structure maturation
 
 [Term]
 id: GO:0010433 ! bract morphogenesis
@@ -30300,6 +30305,10 @@
 is_a: GO:1901681 {is_inferred="true"} ! sulfur compound binding
 
 [Term]
+id: GO:0036179 ! osteoclast maturation
+is_a: GO:0071695 {is_inferred="true"} ! anatomical structure maturation
+
+[Term]
 id: GO:0036181 ! protein localization to linear element
 is_a: GO:1903084 {is_inferred="true"} ! protein localization to condensed nuclear chromosome
 
@@ -30504,6 +30513,10 @@
 is_a: GO:1901701 {is_inferred="true"} ! cellular response to oxygen-containing compound
 
 [Term]
+id: GO:0036345 ! platelet maturation
+is_a: GO:0071695 {is_inferred="true"} ! anatomical structure maturation
+
+[Term]
 id: GO:0036346 ! cellular response to L-cysteine
 is_a: GO:0071230 {is_inferred="true"} ! cellular response to amino acid stimulus
 is_a: GO:1901367 {is_inferred="true"} ! response to L-cysteine
@@ -32049,6 +32062,10 @@
 is_a: GO:0043467 {is_inferred="true"} ! regulation of generation of precursor metabolites and energy
 
 [Term]
+id: GO:0042551 ! neuron maturation
+is_a: GO:0071695 {is_inferred="true"} ! anatomical structure maturation
+
+[Term]
 id: GO:0042558 ! pteridine-containing compound metabolic process
 is_a: GO:0006725 {is_inferred="true"} ! cellular aromatic compound metabolic process
 is_a: GO:0046483 {is_inferred="true"} ! heterocycle metabolic process
@@ -33406,6 +33423,10 @@
 is_a: GO:0051128 {is_inferred="true"} ! regulation of cellular component organization
 
 [Term]
+id: GO:0043249 ! erythrocyte maturation
+is_a: GO:0071695 {is_inferred="true"} ! anatomical structure maturation
+
+[Term]
 id: GO:0043253 ! chloroplast ribosome
 is_a: GO:0009547 {is_inferred="true"} ! plastid ribosome
 is_a: GO:0044434 {is_inferred="true"} ! chloroplast part
@@ -42064,6 +42085,10 @@
 is_a: GO:0044703 {is_inferred="true"} ! multi-organism reproductive process
 
 [Term]
+id: GO:0048628 ! myoblast maturation
+is_a: GO:0071695 {is_inferred="true"} ! anatomical structure maturation
+
+[Term]
 id: GO:0048631 ! regulation of skeletal muscle tissue growth
 is_a: GO:0048638 {is_inferred="true"} ! regulation of developmental growth
 is_a: GO:0048641 {is_inferred="true"} ! regulation of skeletal muscle tissue development
@@ -42337,6 +42362,10 @@
 is_a: GO:0030154 {is_inferred="true"} ! cell differentiation
 
 [Term]
+id: GO:0048764 ! trichoblast maturation
+is_a: GO:0071695 {is_inferred="true"} ! anatomical structure maturation
+
+[Term]
 id: GO:0048765 ! root hair cell differentiation
 is_a: GO:0010053 {is_inferred="true"} ! root epidermal cell differentiation
 
@@ -57907,6 +57936,10 @@
 is_a: GO:0022414 {is_inferred="true"} ! reproductive process
 
 [Term]
+id: GO:0090380 ! seed trichome maturation
+is_a: GO:0071695 {is_inferred="true"} ! anatomical structure maturation
+
+[Term]
 id: GO:0090381 ! regulation of heart induction
 is_a: GO:0003156 {is_inferred="true"} ! regulation of animal organ formation
 is_a: GO:2000826 {is_inferred="true"} ! regulation of heart morphogenesis

[ukemi]

These all look reasonable to me. @tberardini @vanaukenk ?

[tberardini]

Looks reasonable.

id: GO:0048856
name: anatomical structure development
intersection_of: GO:0032502 ! developmental process
intersection_of: results_in_development_of CARO:0000003 ! connected anatomical structure

Still need to fix:

[Term]
id: GO:0010070
name: zygote asymmetric cell division
namespace: biological_process
def: "The division of the zygote into two daughter cells that will adopt developmentally distinct potentials." [GOC:tb]
synonym: "zygote asymmetric cytokinesis" RELATED []
is_a: GO:0008356 ! asymmetric cell division
intersection_of: GO:0008356 ! asymmetric cell division
intersection_of: occurs_in CL:0000365 ! zygote

Is there a CARO term for zygote? I couldn't find one, looking here: http://www.ebi.ac.uk/ols/ontologies/caro/