include 0.4.0 notes; workaround for globalbioticinteractions/nomer#155

globalbioticinteractions · Mar 21, 2023 · db9fa6a · db9fa6a
1 parent 6a19354
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diff --git a/Makefile b/Makefile
@@ -119,7 +119,7 @@ $(TAXON_CACHE).update:
 	cat $(BUILD_DIR)/term_resolved.tsv.gz | gunzip | grep "SIMILAR_TO" | sort | uniq | gzip > $(BUILD_DIR)/term_fuzzy.tsv.gz
 
 	# validate newly resolved terms and their links
-	cat $(BUILD_DIR)/term_match.tsv.gz | gunzip | $(NOMER) validate-terms | grep "all validations pass" | gzip > $(BUILD_DIR)/term_match_validated.tsv.gz
+	cat $(BUILD_DIR)/term_match.tsv.gz | gunzip | cut -f4,5,7- | $(NOMER) validate-terms | grep "all validations pass" | gzip > $(BUILD_DIR)/term_match_validated.tsv.gz
 	cat $(BUILD_DIR)/term_link_match.tsv.gz | gunzip | $(NOMER) validate-term-link | grep "all validations pass" | gzip > $(BUILD_DIR)/term_link_match_validated.tsv.gz
 
 	cat $(BUILD_DIR)/term_link_match_validated.tsv.gz | gunzip | grep -v "FAIL" | cut -f3- | gzip > $(TAXON_MAP).update

diff --git a/static/README b/static/README
@@ -275,3 +275,8 @@ org.globalbioticinteractions.taxon v0.3.36, 2022-03-29
 
 1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.6394931
 
+org.globalbioticinteractions.taxon v0.4.0, 2023-03-21
+
+1. update elton, nomer, and globi taxon graph versions
+2. attempt to align all names, including those aligned previously. Replaced incremental name alignment. Incremental name alignment was a optimization needed because of web api performance. Now, no web apis are used, so the optimization is no longer needed.
+take names from https://globalbioticinteractions.org/data verbatim-interactions.tsv.gz instead of parsing verbatim names from their sources