Update .gitignore

.gitignore

@@ -1,12 +1,18 @@
 
+!src/ontology/tmp/README.md
 .DS_Store
+*.tmp
+*.tmp.json
+*.tmp.obo
+*.tmp.owl
 aminoacid.owl
 basic-allcycles
 basic-orphans
 basic-orphans.tmp
 basic.obo.tmp1
 bfo-check.owl
 bfo-check.txt
+bin/
 bridge-check-caro.owl
 bridge-check-caro.txt
 bridge-check-caro.txt.tmp
@@ -18,36 +24,44 @@ bridge/bridges
 bridge/uberon-bridge-to-nifstd.obo.tmp
 bridge/uberon-bridge-to-vhog.owl.ofn
 bspo.owl
+bundled-*.owl
+chebi_import.obo
 chebi.obo
 chebi.owl
-chebi_import.obo
+cl_import.obo
 cl-core.obo
 cl-with-xrefs.obo
 cl-with-xrefs.obo.tmp
-cl_import.obo
+composite-brain.obo
 composite-metazoan-basic.obo
 composite-metazoan-dv.txt
 composite-metazoan-dv.txt.tmp
 composite-metazoan.obo
 composite-metazoan.owl
 composite-stages.obo
 composite-vertebrate.obo
+composite-vertebrate.owl
+developmental-stage-ontologies/
 ext-obscheck.txt
 ext-weak.owl
 ext.owl.LOG
 ext2.owl
 extra-full-bridge-check-caro.txt
 extra-full-bridge-check-caro.txt.tmp
+fixed-*.obo
+fixed-*.owl
 full-bridge-check-caro.txt
 full-bridge-check-caro.txt.tmp
 full-bridge-check-wbbt.txt
 full-bridge-check-wbbt.txt.tmp
 full-bridge-check-wbls.txt
 full-bridge-check-wbls.txt.tmp
+go_import.obo
 go.owl
 GO.xrf_abbs
-go_import.obo
 is_ok
+local-*.obo
+local-*.owl
 m1.owl
 materialized.owl
 materialized.owl.LOG
@@ -57,31 +71,70 @@ merged-orphans.tmp
 merged-stages-xrefs.obo
 merged-stages-xrefs.obo.tmp
 metazoan-view.owl
+mirror-*.obo
+mirror-*.owl
 mirror-caro.owl
 mirror-wbbt.owl
 mirror-wbls.owl
-ncbitaxon.obo
 ncbitaxon_import.obo
-pato.owl
+ncbitaxon.obo
 pato_import.obo
+pato.owl
 phenoscape-ext-noimports.owl
 phenoscape-ext.owl
-pr.owl
 pr_import.obo
+pr.owl
 quick-bridge-check-caro.txt
 quick-bridge-check-wbbt.txt
 quick-bridge-check-wbls.txt
 reports/stages-metazoan-report.tsv
 reports/uberon_edit-object-properties.csv
-ro.owl
 ro_import.obo
 ro_import.owl.tmp.owl
-run.sh
+ro.owl
+robot_main_diff.md
+/run.sh
 seed.obo
 seed.obo.tmp
 seed.owl
+semantic.cache
+src/ontology/dosdp-tools.log
+src/ontology/ed_definitions_merged.owl
+src/ontology/imports/*_terms_combined.txt
+src/ontology/merged-uberon-edit.owl
+src/ontology/mirror
+src/ontology/mirror/*
+src/ontology/ontologyterms.txt
+src/ontology/patterns
+src/ontology/reports/*
+src/ontology/seed.txt
+src/ontology/simple_seed.txt
+src/ontology/target/
+src/ontology/tmp/*
+src/ontology/uberon-base.*
+src/ontology/uberon-basic.*
+src/ontology/uberon-full.*
+src/ontology/uberon-simple-non-classified.*
+src/ontology/uberon-simple.*
+src/ontology/uberon.json
+src/ontology/uberon.obo
+src/ontology/uberon.owl
+src/patterns/all_pattern_terms.txt
+src/patterns/data/**/*.ofn
+src/patterns/data/**/*.txt
+src/patterns/pattern_owl_seed.txt
 taxon-constraint-check.txt
+tmp/
 trunk/
+uberon_edit-cycles
+uberon_edit-obscheck.txt
+uberon_edit-plus-tax-equivs.owl
+uberon_edit-xp-check
+uberon_edit-xp-check.err
+uberon_edit.obo-gocheck
+uberon_edit.obo-iconv
+uberon_edit.owl
+uberon_edit.owl.tmp
 uberon-cycles
 uberon-discv.txt
 uberon-dv.txt
@@ -101,26 +154,15 @@ uberon-taxmod-euarchontoglires.obo
 uberon-taxmod-euarchontoglires.obo.tmp
 uberon-taxmod-euarchontoglires.owl
 uberon.obo.tmp1
-uberon_edit-cycles
-uberon_edit-obscheck.txt
-uberon_edit-plus-tax-equivs.owl
-uberon_edit-xp-check
-uberon_edit-xp-check.err
-uberon_edit.obo-gocheck
-uberon_edit.obo-iconv
-uberon_edit.owl
-uberon_edit.owl.tmp
 unreasoned.owl
 update-stages
-tmp/
-robot_main_diff.md
-developmental-stage-ontologies/
-mirror-*.owl
-mirror-*.obo
-local-*.owl
-local-*.obo
-fixed-*.owl
-fixed-*.obo
-bundled-*.owl
-composite-brain.obo
-composite-vertebrate.owl
+*.LOG
+*.tmp1
+composite-metazoan.json
+composite-vertebrate.json
+src/ontology/BUILDLOGUBERON.txt
+src/ontology/core.owl
+src/ontology/ext.owl
+src/ontology/unsat_all_explanation.md
+src/ontology/merged_collect.owl
+src/ontology/composite-metazoan-last-release.owl