So Laurel can find the new terms

Makefile

@@ -1,12 +1,14 @@
 OBO=http://purl.obolibrary.org/obo
 ONT=to
 BASE=$(OBO)/$(ONT)
-#SRC=plant-trait-ontology.obo.owl
+#SRC=plant-trait-ontology.owl
 SRC=plant-trait-ontology.obo
 RELEASEDIR=.
 ROBOT= robot
 OWLTOOLS= owltools
 DOSDP = dosdp-tools
+ROBOT_ENV = ROBOT_JAVA_ARGS=-Xmx8G
+ROBOT = $(ROBOT_ENV) robot --catalog catalog-v001.xml
 
 
 all: all_imports $(ONT).owl $(ONT).obo subsets/$(ONT)-basic.obo
@@ -17,6 +19,8 @@ $(ONT).owl: $(SRC)
 	$(ROBOT)  reason -e none -i $< -r ELK relax reduce -r ELK annotate -V $(BASE)/releases/`date +%Y-%m-%d`/$(ONT).owl -o $@
 $(ONT).obo: $(ONT).owl
 	$(ROBOT) convert -i $< -f obo --check false -o $(ONT).obo.tmp && grep -v '^owl-axioms:' $(ONT).obo.tmp > $@ && rm $(ONT).obo.tmp
+#$(ONT).json: $(ONT).owl
+#	$(ROBOT) convert --check false -f json -o $(ONT).json
 
 subsets/$(ONT)-basic.obo: $(ONT).owl
 	owltools --use-catalog $< --remove-imports-declarations --make-subset-by-properties -f BFO:0000050 --remove-dangling --remove-axioms -t EquivalentClasses --set-ontology-id $(OBO)/subsets/$(ONT)-basic.owl -o -f obo [email protected] && mv [email protected] $@

TO-README-editors.md

@@ -50,11 +50,15 @@ committed and pushed, and the travis build passes.
 
 to release, change into this directory, and type
 
-    make all
+    ./run.sh make all
 
 This generates derived files such as to.owl and to.obo. The versionIRI
 will be added.
 
+To create to.json use robot in a different terminal. Be sure you are in robot/bin directory
+
+    ./robot convert --input ~/plant-trait-ontology/to.owl --format json --output ~/plant-trait-ontology/to.json
+
 Commit and push these files to the repository
 
 IMMEDIATELY AFTERWARDS (do *not* make further modifications) go here:

imports/chebi_import.obo

@@ -593,7 +593,7 @@ is_a: CHEBI:33839 ! macromolecule
 [Term]
 id: CHEBI:15864
 name: luteolin
-def: "A tetrahydroxyflavone in which the four hydroxy groups are located at positions 3', 4' 5 and 7. It is thought to play an important role in the human body as an antioxidant, a free radical scavenger, an inflammatory agent and an immune system modulator as well as being active against several cancers." []
+def: "A tetrahydroxyflavone in which the four hydroxy groups are located at positions 3', 4', 5 and 7. It is thought to play an important role in the human body as an antioxidant, a free radical scavenger, an anti-inflammatory agent and an immune system modulator as well as being active against several cancers." []
 synonym: "2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-benzopyrone" RELATED [ChemIDplus]
 synonym: "2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-1-benzopyran-4-one" RELATED [ChemIDplus]
 synonym: "2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one" EXACT IUPAC_NAME [IUPAC]
@@ -607,9 +607,10 @@ synonym: "Salifazide" RELATED [ChemIDplus]
 is_a: CHEBI:27741 ! 3'-hydroxyflavonoid
 is_a: CHEBI:38684 ! tetrahydroxyflavone
 relationship: is_conjugate_acid_of CHEBI:57545 ! 2-(3,4-dihydroxyphenyl)-5-hydroxy-4-oxo-4H-chromen-7-olate luteolin-7-olate(1-)
-relationship: RO:0000087 CHEBI:22586 ! antioxidant
 relationship: RO:0000087 CHEBI:35610 ! antineoplastic agent
 relationship: RO:0000087 CHEBI:48422 ! angiogenesis inhibitor
+relationship: RO:0000087 CHEBI:48578 ! radical scavenger
+relationship: RO:0000087 CHEBI:50846 ! immunomodulator
 relationship: RO:0000087 CHEBI:65207 ! vascular endothelial growth factor receptor antagonist
 relationship: RO:0000087 CHEBI:67079 ! anti-inflammatory agent
 relationship: RO:0000087 CHEBI:68495 ! apoptosis inducer
@@ -922,6 +923,14 @@ synonym: "Glukose" RELATED [ChEBI]
 is_a: CHEBI:33917 ! aldohexose
 relationship: RO:0000087 CHEBI:78675 ! fundamental metabolite
 
+[Term]
+id: CHEBI:173084
+name: ferroptosis inhibitor
+def: "Any substance that inhibits the process of ferroptosis (a type of programmed cell death dependent on iron and characterized by the accumulation of lipid peroxides) in organisms." []
+synonym: "ferroptosis inhibitors" RELATED [ChEBI]
+is_a: CHEBI:35222 ! inhibitor
+is_a: CHEBI:52206 ! biochemical role
+
 [Term]
 id: CHEBI:17351
 name: linoleic acid
@@ -995,6 +1004,7 @@ synonym: "beta-Carotene" EXACT [KEGG_COMPOUND]
 synonym: "beta-Karotin" RELATED [ChEBI]
 is_a: CHEBI:139120 ! carotenoid beta-end group
 is_a: CHEBI:35163 ! cyclic carotene
+relationship: RO:0000087 CHEBI:173084 ! ferroptosis inhibitor
 relationship: RO:0000087 CHEBI:22586 ! antioxidant
 relationship: RO:0000087 CHEBI:23357 ! cofactor
 relationship: RO:0000087 CHEBI:26130 ! biological pigment
@@ -6951,6 +6961,14 @@ synonym: "angiostatic agents" RELATED [ChEBI]
 synonym: "anti-angiogenic agent" RELATED [ChEBI]
 is_a: CHEBI:23888 ! drug
 
+[Term]
+id: CHEBI:48578
+name: radical scavenger
+def: "A role played by a substance that can react readily with, and thereby eliminate, radicals." []
+synonym: "free radical scavengers" RELATED [ChEBI]
+synonym: "free-radical scavenger" RELATED [ChEBI]
+is_a: CHEBI:22586 ! antioxidant
+
 [Term]
 id: CHEBI:48705
 name: agonist
@@ -7152,6 +7170,18 @@ synonym: "Food Supplementation" RELATED [ChEBI]
 synonym: "Nutritional supplement" RELATED [ChEBI]
 is_a: CHEBI:23888 ! drug
 
+[Term]
+id: CHEBI:50846
+name: immunomodulator
+def: "Biologically active substance whose activity affects or plays a role in the functioning of the immune system." []
+synonym: "Biomodulator" RELATED [ChEBI]
+synonym: "Immune factor" RELATED [ChEBI]
+synonym: "Immunologic factor" RELATED [ChEBI]
+synonym: "Immunological factor" RELATED [ChEBI]
+synonym: "immunomodulators" RELATED [ChEBI]
+is_a: CHEBI:23888 ! drug
+is_a: CHEBI:24432 ! biological role
+
 [Term]
 id: CHEBI:50860
 name: organic molecular entity
@@ -7537,6 +7567,7 @@ id: CHEBI:59139
 name: gibberellin carboxylic acid anion
 def: "A carboxylic acid anion arising from deprotonation of one or more carboxy groups of any gibberellin." []
 synonym: "gibberellin monocarboxylic acid anions" RELATED [ChEBI]
+is_a: CHEBI:18059 ! lipid
 is_a: CHEBI:29067 ! carboxylic acid anion
 relationship: is_conjugate_base_of CHEBI:24250 ! gibberellin
 
@@ -7800,6 +7831,7 @@ name: hepatoprotective agent
 def: "Any compound that is able to prevent damage to the liver." []
 synonym: "antihepatotoxic agent" RELATED [ChEBI]
 synonym: "hepatoprotective agents" RELATED [ChEBI]
+synonym: "hepatoprotector" RELATED [ChEBI]
 is_a: CHEBI:50267 ! protective agent
 
 [Term]