patch fishbase/sealifebase/inaturalist/irmng taxa from globi taxon gr…

…aph for now; related to globalbioticinteractions/nomer#187 globalbioticinteractions/nomer#186 globalbioticinteractions/nomer#185

Makefile

@@ -57,6 +57,7 @@ $(TAXON_CACHE).update:
 
 	cat $(BUILD_DIR)/names_new.tsv.gz | gunzip | $(NOMER) append globi-correct | cut -f1,2,4,5 | sort | uniq | gzip > $(BUILD_DIR)/names_new_corrected.tsv.gz
 
+	cat $(BUILD_DIR)/names_new_corrected.tsv.gz | gunzip | $(NOMER) append globi | grep -P "\t(FBC:FB|FBC:SLB:|INAT_TAXON:|IRMNG:)" | gzip >> $(BUILD_DIR)/term_resolved.tsv.gz
 	cat $(BUILD_DIR)/names_new_corrected.tsv.gz | gunzip | $(NOMER) append itis | gzip >> $(BUILD_DIR)/term_resolved.tsv.gz
 	cat $(BUILD_DIR)/names_new_corrected.tsv.gz | gunzip | $(NOMER) append gbif | gzip >> $(BUILD_DIR)/term_resolved.tsv.gz
 	cat $(BUILD_DIR)/names_new_corrected.tsv.gz | gunzip | $(NOMER) append indexfungorum | gzip >> $(BUILD_DIR)/term_resolved.tsv.gz
@@ -77,6 +78,7 @@ $(TAXON_CACHE).update:
 	mv $(BUILD_DIR)/term_resolved_once.tsv.gz $(BUILD_DIR)/term_resolved.tsv.gz
 	cat $(BUILD_DIR)/term_unresolved_once.tsv | $(NOMER) append gbif-parse | cut -f1,2,4,5 | sort | uniq | gzip > $(BUILD_DIR)/term_unresolved_once_corrected.tsv.gz
 
+	cat $(BUILD_DIR)/term_unresolved_once_corrected.tsv.gz | gunzip | $(NOMER) append --properties=$(NOMER_PROPERTIES_CORRECTED) itis | grep -P "\t(FBC:FB|FBC:SLB:|INAT_TAXON:|IRMNG:)" | gzip >> $(BUILD_DIR)/term_resolved.tsv.gz
 	cat $(BUILD_DIR)/term_unresolved_once_corrected.tsv.gz | gunzip | $(NOMER) append --properties=$(NOMER_PROPERTIES_CORRECTED) itis | gzip >> $(BUILD_DIR)/term_resolved.tsv.gz
 	cat $(BUILD_DIR)/term_unresolved_once_corrected.tsv.gz | gunzip | $(NOMER) append --properties=$(NOMER_PROPERTIES_CORRECTED) discoverlife | gzip >> $(BUILD_DIR)/term_resolved.tsv.gz
 	cat $(BUILD_DIR)/term_unresolved_once_corrected.tsv.gz | gunzip | $(NOMER) append --properties=$(NOMER_PROPERTIES_CORRECTED) ncbi | gzip >> $(BUILD_DIR)/term_resolved.tsv.gz
@@ -97,6 +99,7 @@ $(TAXON_CACHE).update:
 	mv $(BUILD_DIR)/term_resolved_twice.tsv.gz $(BUILD_DIR)/term_resolved.tsv.gz
 	cat $(BUILD_DIR)/term_unresolved_twice.tsv | $(NOMER) append globi-correct | cut -f1,2,4,5 | sort | uniq | gzip > $(BUILD_DIR)/term_unresolved_twice_corrected.tsv.gz
 
+	cat $(BUILD_DIR)/term_unresolved_twice_corrected.tsv.gz | gunzip | $(NOMER) append --properties=$(NOMER_PROPERTIES_CORRECTED) globi | grep -P "\t(FBC:FB|FBC:SLB:|INAT_TAXON:|IRMNG:)" | gzip >> $(BUILD_DIR)/term_resolved.tsv.gz
 	cat $(BUILD_DIR)/term_unresolved_twice_corrected.tsv.gz | gunzip | $(NOMER) append --properties=$(NOMER_PROPERTIES_CORRECTED) itis | gzip >> $(BUILD_DIR)/term_resolved.tsv.gz
 	cat $(BUILD_DIR)/term_unresolved_twice_corrected.tsv.gz | gunzip | $(NOMER) append --properties=$(NOMER_PROPERTIES_CORRECTED) discoverlife | gzip >> $(BUILD_DIR)/term_resolved.tsv.gz
 	cat $(BUILD_DIR)/term_unresolved_twice_corrected.tsv.gz | gunzip | $(NOMER) append --properties=$(NOMER_PROPERTIES_CORRECTED) ncbi | gzip >> $(BUILD_DIR)/term_resolved.tsv.gz