0.4.8

Features

• include Debian package to help facilitate installation of Nomer and their java dependencies using apt related to globalbioticinteractions/globalbioticinteractions#853 (comment) @jrhillae

Improvements

• re-use taxonomic inferences made by GBIF parser (#137)

Bug fixes

n/a

0.4.7

Features

n/a

Improvements

• index Catalogue of Life names without the subgenus jhpoelen/Mormoopidae#1

Bug fixes

n/a

0.4.6

Features

n/a

Improvements

• upgrade to globi-libs 0.24.7
• upgrade to Nomer Corpus of Taxonomic Resource v0.9 hash://sha256/dac5… Also see Poelen, Jorrit H. (2022). Nomer Corpus of Taxonomic Resources hash://sha256/dac5911a81fb605fab012e90c98b37e990a076d77f9264fdb38ec7f379d82108 hash://md5/46fab6751bafd4de4f49aaa8c511e39d (0.9) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7405576 .
• include authorship for ITIS/GBIF taxonomy indexes #130

Bug fixes

• prevent gn-parse a null name

0.4.5

Features

n/a

Improvements

• upgrade to OTT v0.3.4 via Poelen, Jorrit H. (2022). Nomer Corpus of Taxonomic Resources hash://sha256/a0b5570204881a594cf0cca0d4b50c0ddca6f91c2086541516138a400620fb5b hash://md5/d05224a5c2933cd16f092ad28549f3e2 (0.8) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7343032

Bug fixes

• re-enable Open Tree of Life name alignment method #127 . Name alignment by id, name, and synonyms are supported.
  echo "NCBI:9606" | nomer append ott (lookup OTT name relations by NCBI taxon id), echo -e "\tArius felis" | nomer append ott (lookup OTT synonym relations by name, echo -e "\tAriopsis felis" | nomer append ott lookup accepted relations by name.

• make globi-taxon-rank suitable for versioning by Preston #129

0.4.4

Features

n/a

Improvements

n/a

Bug fixes

• resolve commons-codec:commons-codec dependency conflict that caused premature stopping of Plazi treatment indexer #126

0.4.3

Features

n/a

Improvements

n/a

Bug fixes

• avoid cache conflict by letting batnames matcher use their own independent cachdir, not the same cachedir as discoverlife 24c29e1

0.4.2

Features

n/a

Improvements

n/a

Bug fixes

• allow use of versioned copy of GloBIs taxon graph as retrieved by Nomers Corpus of Taxonomic Resources #125

0.4.1

Features

n/a

Improvements

• upgrade to preston lib v0.5.0 . See related bio-guoda/preston#201 and #124 for context.

Bug fixes

n/a

0.4.0

Features

n/a

Improvements

• upgrade to globi lib v0.24.4 related to #121 @zedomel
• reduce log levels for indexed matches
• include authorship in default schema @jtmiller28 related to #112 #104
  ⚠️ note that including authorship changes the default input/output schema and inserts a columns. So, if you are using Nomer input/output based on column numbers, you may have to update your scripts. fyi @nleguillarme

echo -e "\tHomo sapiens Linnaeus, 1758"\
 | java -jar nomer.jar append gn-parse --include-header\
 | mlr --itsvlite --omd cat

now produces:

providedExternalId	providedName	relationName	resolvedExternalId	resolvedName	resolvedAuthorship	resolvedRank	resolvedCommonNames	resolvedPath	resolvedPathIds	resolvedPathNames	resolvedPathAuthorships	resolvedExternalUrl
	Homo sapiens Linnaeus, 1758	SAME_AS		Homo sapiens	Linnaeus 1758

Bug fixes

n/a

0.3.2

Features

• add support for Foundational Taxonomic Resources For The Terrestrial Parasite Tracker (TPT) Project @njdowdy @EMTuckerLab @Jegelewicz @vijaybarve globalbioticinteractions/globalbioticinteractions#694 njdowdy/tpt-taxonomy#17 . To use:

# list all indexed TPT name relations
nomer ls tpt

# align some name to TPT using tsv input/output
echo -e '\tIxodes ricinus' | nomer append tpt --include-header
providedExternalId	providedName	relationName	resolvedExternalId	resolvedName	resolvedRank	resolvedCommonNames	resolvedPath	resolvedPathIds	resolvedPathNames	resolvedExternalUrl	resolvedThumbnailUrl
	Ixodes ricinus	HAS_ACCEPTED_NAME		Ixodes ricinus	species		Animalia | Arthropoda | Arachnida | Acari | Parasitiformes | Ixodida | Ixodoidea | Ixodidae | Ixodes | Ixodes | ricinus		kingdom | phylum | class | subclass | superorder | order | superfamily | family | genus | infragenericEpithet | specificEpithet		
	Ixodes ricinus	HAS_ACCEPTED_NAME		Ixodes ricinus	species		Animalia | Arthropoda | Arachnida | Acari | Parasitiformes | Ixodida | Ixodoidea | Ixodidae | Ixodes | Ixodes | ricinus | gibbosus		kingdom | phylum | class | subclass | superorder | order | superfamily | family | genus | infragenericEpithet | specificEpithet | infraspecificEpithet		
	Ixodes ricinus	HAS_ACCEPTED_NAME		Ixodes ricinus	species		Animalia | Arthropoda | Arachnida | Acari | Parasitiformes | Ixodida | Ixodoidea | Ixodidae | Ixodes | ricinus | pacificus		kingdom | phylum | class | subclass | superorder | order | superfamily | family | genus | specificEpithet | infraspecificEpithet		

Improvements

n/a

Bug fixes

n/a