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@jhpoelen jhpoelen released this 20 Oct 21:15
· 547 commits to main since this release
0.2.4
48b94b1

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)
Assets 3
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