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globalbioticinteractions / nomer

maps identifiers and names to other identifiers and names
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include name matching offline ITIS in addition to existing offline ITIS matching by id #46

Closed jhpoelen closed 2 years ago

jhpoelen commented 2 years ago

as suggested by @seltmann .

jhpoelen commented 2 years ago

recent changes made it possible to produce the following output: 

$ echo -e "\tHomo sapiens" | nomer append itis-taxon-id
using matcher [itis-taxon-id]
ITIS taxonomy already indexed at [/media/jorrit/data/nomer/itis/itis], no need to import.
    Homo sapiens    SAME_AS ITIS:180092 Homo sapiens    species     Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Primates | Haplorrhini | Simiiformes | Hominoidea | Hominidae | Homininae | Homo | Homo sapiens   ITIS:202423 | ITIS:914154 | ITIS:914156 | ITIS:158852 | ITIS:331030 | ITIS:914179 | ITIS:914181 | ITIS:179913 | ITIS:179916 | ITIS:179925 | ITIS:180089 | ITIS:943773 | ITIS:943778 | ITIS:943782 | ITIS:180090 | ITIS:943805 | ITIS:180091 | ITIS:180092   kingdom | subkingdom | infrakingdom | phylum | subphylum | infraphylum | superclass | class | subclass | infraclass | order | suborder | infraorder | superfamily | family | subfamily | genus | species    http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180092
jhpoelen commented 2 years ago

Implemented via https://github.com/globalbioticinteractions/nomer/releases/tag/0.2.4 .

@seltmann please confirm that you are able to reproduce and close this issue: 

$ echo -e "\tHomo sapiens" | nomer append itis
using matcher [itis-taxon-id]
ITIS taxonomy already indexed at [/media/jorrit/data/nomer/itis/itis], no need to import.
    Homo sapiens    HAS_ACCEPTED_NAME   ITIS:180092 Homo sapiens    species     Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Primates | Haplorrhini | Simiiformes | Hominoidea | Hominidae | Homininae | Homo | Homo sapiens   ITIS:202423 | ITIS:914154 | ITIS:914156 | ITIS:158852 | ITIS:331030 | ITIS:914179 | ITIS:914181 | ITIS:179913 | ITIS:179916 | ITIS:179925 | ITIS:180089 | ITIS:943773 | ITIS:943778 | ITIS:943782 | ITIS:180090 | ITIS:943805 | ITIS:180091 | ITIS:180092   kingdom | subkingdom | infrakingdom | phylum | subphylum | infraphylum | superclass | class | subclass | infraclass | order | suborder | infraorder | superfamily | family | subfamily | genus | species    http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180092

and 

$ echo -e "\tArius felis" | nomer append itis
using matcher [itis-taxon-id]
ITIS taxonomy already indexed at [/media/jorrit/data/nomer/itis/itis], no need to import.
    Arius felis SYNONYM_OF  ITIS:680665 Ariopsis felis  speciesAnimalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Actinopterygii | Teleostei | Ostariophysi | Siluriformes | Ariidae | Ariopsis | Ariopsis felis    ITIS:202423 | ITIS:914154 | ITIS:914156 | ITIS:158852 | ITIS:331030 | ITIS:914179 | ITIS:161061 | ITIS:161105 | ITIS:162845 | ITIS:163992 | ITIS:164157 | ITIS:639019 | ITIS:680665 kingdom | subkingdom | infrakingdom | phylum | subphylum | infraphylum | superclass | class | superorder | order | family | genus | species http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=680665
jhpoelen commented 2 years ago

available in 0.2.6 . please re-open if issues remain.