0.2.7

Features

n/a

Improvements

• upgrade to Jena 3.17.0
• enable usage of versioned Nomer's Corpus of Taxonomic Resource via Preston v0.3.4 integration of preston-get module (related to globalbioticinteractions/globalbioticinteractions#694 and #48). Now Nomer uses Poelen, Jorrit H. (2021). Nomer Corpus of Taxonomic Resources hash://sha256/bb6dac6461b66212c5b1826447d7765529ff5cbadeac1915f7c3be9748eda991 (0.1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5639794 to clearly define the versions of taxonomic resources as captured from specific locations. This makes the output of Nomer reproducible, at least for offline matchers like (e.g., ncbi, itis, gbif) fyi @mielliott

Bug fixes

• fix initialization bug that prevented discoverlife from getting indexed (related #61) fyi @seltmann
• re-enable NONE for offline matchers

0.2.6

Features

n/a

Improvements

• refactoring to work towards integrating TPT taxonomy in citable way (see globalbioticinteractions/globalbioticinteractions#694 )
• upgrade to globi libs v0.23.0 https://github.com/globalbioticinteractions/globalbioticinteractions/releases/tag/v0.23.0 .
• support homonyms (see #53)
• support extracting taxonomic ranks from name (e.g., variety, subspecies see #57 )

Bug fixes

• chop additional discoverlife _sic suffixes (see #51)

0.2.5

Features

n/a

Improvements

• add support for offline matching against Index Fungorum (#49 suggested by @nleguillarme and with helpful input from @dimus)
• better handling of existing discoverlife name (see #51 #52 as suggested by @seltmann)

Bug fixes

• null pointer exception thrown when using [echo -e "\Agapostemon texanus"] (e.g., #50 found by @seltmann )

0.2.4

Features

• introduce dump command to dump/export all name relations for a given matchers. Currently supported matchers: discoverlife and itis.

Example:

$ nomer dump itis | head -n2
ITIS:50	Bacteria	HAS_ACCEPTED_NAME	ITIS:50	Bacteria	kingdomBacteria	ITIS:50	kingdom	http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=50	
ITIS:51	Schizomycetes	SYNONYM_OF	ITIS:50	Bacteria	kingdom		Bacteria	ITIS:50	kingdom	http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=50	

$ nomer dump discoverlife | head -n2
https://www.discoverlife.org/mp/20q?search=Acamptopoeum+argentinum	Acamptopoeum argentinum	HAS_ACCEPTED_NAME	https://www.discoverlife.org/mp/20q?search=Acamptopoeum+argentinum	Acamptopoeum argentinum	species		Animalia | Arthropoda | Insecta | Hymenoptera | Andrenidae | Acamptopoeum argentinum	https://www.discoverlife.org/mp/20q?search=Animalia | https://www.discoverlife.org/mp/20q?search=Arthropoda | https://www.discoverlife.org/mp/20q?search=Insecta | https://www.discoverlife.org/mp/20q?search=Hymenoptera | https://www.discoverlife.org/mp/20q?search=Andrenidae | https://www.discoverlife.org/mp/20q?search=Acamptopoeum+argentinum	kingdom | phylum | class | order | family | species	https://www.discoverlife.org/mp/20q?search=Acamptopoeum+argentinum	
https://www.discoverlife.org/mp/20q?search=Acamptopoeum+calchaqui	Acamptopoeum calchaqui	HAS_ACCEPTED_NAME	https://www.discoverlife.org/mp/20q?search=Acamptopoeum+calchaqui	Acamptopoeum calchaqui	species		Animalia | Arthropoda | Insecta | Hymenoptera | Andrenidae | Acamptopoeum calchaqui	https://www.discoverlife.org/mp/20q?search=Animalia | https://www.discoverlife.org/mp/20q?search=Arthropoda | https://www.discoverlife.org/mp/20q?search=Insecta | https://www.discoverlife.org/mp/20q?search=Hymenoptera | https://www.discoverlife.org/mp/20q?search=Andrenidae | https://www.discoverlife.org/mp/20q?search=Acamptopoeum+calchaqui	kingdom | phylum | class | order | family | species	https://www.discoverlife.org/mp/20q?search=Acamptopoeum+calchaqui	

Improvements

• enhance offline ITIS matching to include match by name, synonyms, in addition to match by id (related to #46)
  Example:

$ echo -e "\tEnhydra lutris" | nomer append itis
using matcher [itis-taxon-id]
ITIS taxonomy already indexed at [/media/jorrit/data/nomer/itis/itis], no need to import.
	Enhydra lutris	HAS_ACCEPTED_NAME	ITIS:180547	Enhydra lutris	species		Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Carnivora | Caniformia | Mustelidae | Lutrinae | Enhydra | Enhydra lutris	ITIS:202423 | ITIS:914154 | ITIS:914156 | ITIS:158852 | ITIS:331030 | ITIS:914179 | ITIS:914181 | ITIS:179913 | ITIS:179916 | ITIS:179925 | ITIS:180539 | ITIS:552303 | ITIS:180545 | ITIS:552326 | ITIS:180546 | ITIS:180547	kingdom | subkingdom | infrakingdom | phylum | subphylum | infraphylum | superclass | class | subclass | infraclass | order | suborder | family | subfamily | genus | species	http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180547	

• shorten matcher names to make it easier to interact with the command-line (e.g., itis instead of itis-taxon)
• improve discoverlife name matching support (see #42)

Bug fixes

• fix flipped synonym relations (e.g., #45)

0.2.3

Features

n/a

Improvements

• introduce synonym, accepted name matching for Discover Life Apoidea taxon offline name matching (#42)

Bug fixes

n/a

0.2.2

Features

• add support for offline Discover Life Apoidea taxon name matching (#42)

Improvements

• reduce startup time by re-use previously cached GulfBase, Discover Life names

Bug fixes

n/a

0.2.1

Features

n/a

Improvements

• upgrade to globi libs v0.22.0 to incorporate various bugs and improvements. See release notes for v0.22.0 for more information.

Bug fixes

n/a

0.2.0

Features

• add support for (on-/offline) taxonomic name matching against GBIF backbone, as suggested by, an initially implemented by, @zedomel - . (see #41 #40 ). See also Poelen, Jorrit H. (2021). A Repackaged Taxonomic Backbone of Global Biodiversity Information Facility (GBIF) (0.2) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5222044 .

Improvements

• Bump commons-compress from 1.20 to 1.21 in /nomer-taxon-resolver as suggested by @dependabot
• Upgrade to Poelen, Jorrit H. (2021). Global Biotic Interactions: Taxon Graph (0.3.33) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5021869 .
• Add more taxon property name schema mappings; related to #35 as suggested by @zedomel

Bug fixes

• handle matched taxa with null ranks. fixed by @zedomel via #39 .

0.1.27

Features

n/a

Improvements

• as suggested by @zedomel - add support for path.[some rank].name (e.g., path.kingdom.name or path.kingdom.id) selectors for taxon property selection in output schema when using nomer replace (see #35). Example of output schema configuration in properties:

nomer.schema.output=[{"column":1,"type":"path.kingdom.name"}]

• introduce a way to convert "Some.name" -> "Some name" as part of nomer's globi-correct matcher ; (see #33). Example:

$ echo -e "\tHomo.sapiens" | nomer append globi-correct
	Homo.sapiens	SAME_AS		Homo sapiens	

Bug fixes

n/a

0.1.26

Features

n/a

Improvements

• upgrade to GloBI Taxon Graph v0.3.31

Bug fixes

n/aa