Closed jhpoelen closed 2 years ago
An initial implementation of Catalogue of Life produces:
$ echo -e "\tArius felis" | nomer append -p my.properties col
[main] INFO org.globalbioticinteractions.nomer.match.TermMatcherRegistry - using matcher [col]
[main] INFO org.globalbioticinteractions.nomer.match.CatalogueOfLifeTaxonService - [Catalogue of Life] taxonomy already indexed at [/media/jorrit/branta/nomer/catalogue_of_life/catalogue_of_life], no need to import.
Arius felis SYNONYM_OF COL:GMX9 Ariopsis felis species Biota | Animalia | Chordata | Actinopterygii | Siluriformes | Ariidae | Ariopsis | Ariopsis felis COL:5T6MX | COL:N | COL:CH2 | COL:CT | COL:6236K | COL:6Q6 | COL:8RZ3D | COL:GMX9 unranked | kingdom | phylum | class | order | family | genus | species
and
$ echo -e "\tAriopsis felis" | nomer append -p my.properties col
[main] INFO org.globalbioticinteractions.nomer.match.TermMatcherRegistry - using matcher [col]
[main] INFO org.globalbioticinteractions.nomer.match.CatalogueOfLifeTaxonService - [Catalogue of Life] taxonomy already indexed at [/media/jorrit/branta/nomer/catalogue_of_life/catalogue_of_life], no need to import.
Ariopsis felis HAS_ACCEPTED_NAME COL:GMX9 Ariopsis felis species Biota | Animalia | Chordata | Actinopterygii | Siluriformes | Ariidae | Ariopsis | Ariopsis felis COL:5T6MX | COL:N | COL:CH2 | COL:CT | COL:6236K | COL:6Q6 | COL:8RZ3D | COL:GMX9 unranked | kingdom | phylum | class | order | family | genus | species
$ echo -e "COL:6MB3T\t" | nomer append col
[main] INFO org.globalbioticinteractions.nomer.match.TermMatcherRegistry - using matcher [col]
[main] INFO org.globalbioticinteractions.nomer.match.CatalogueOfLifeTaxonService - [Catalogue of Life] taxonomy already indexed at [/media/jorrit/branta/nomer/catalogue_of_life/catalogue_of_life], no need to import.
COL:6MB3T HAS_ACCEPTED_NAME COL:6MB3T Homo sapiens species Biota | Animalia | Chordata | Mammalia | Theria | Eutheria | Primates | Haplorrhini | Simiiformes | Hominoidea | Hominidae | Homininae | Homo | Homo sapiens COL:5T6MX | COL:N | COL:CH2 | COL:6224G | COL:6226C | COL:LG | COL:3W7 | COL:4DT | COL:4PM | COL:58L | COL:6256T | COL:JPH | COL:636X2 | COL:6MB3T unranked | kingdom | phylum | class | subclass | infraclass | order | suborder | infraorder | superfamily | family | subfamily | genus | species
and
$ nomer ls col | head
[main] INFO org.globalbioticinteractions.nomer.match.TermMatcherRegistry - using matcher [col]
[main] INFO org.globalbioticinteractions.nomer.match.CatalogueOfLifeTaxonService - [Catalogue of Life] taxonomy already indexed at [/media/jorrit/branta/nomer/catalogue_of_life/catalogue_of_life], no need to import.
COL:32 Caldiserica HAS_ACCEPTED_NAME COL:32 Caldiserica phylum Biota | Bacteria | Negibacteria | Caldiserica COL:5T6MX | COL:B | COL:622BB | COL:32 unranked | kingdom | subkingdom | phylum
COL:322 Craciformes HAS_ACCEPTED_NAME COL:322 Craciformes order Biota | Animalia | Chordata | Aves | Galliformes | Craciformes COL:5T6MX | COL:N | COL:CH2 | COL:V2 | COL:38Z | COL:322 unranked | kingdom | phylum | class | order | order
COL:32223 Cryptoripersia hypolithus HAS_ACCEPTED_NAME COL:32223 Cryptoripersia hypolithus species Biota | Animalia | Arthropoda | Insecta | Hemiptera | Coccoidea | Pseudococcidae | Cryptoripersia | Cryptoripersia trichura | Cryptoripersia hypolithus COL:5T6MX | COL:N | COL:RT | COL:H6 | COL:HP | COL:4YN | COL:F8D | COL:3WSG | COL:3222J | COL:32223 unranked | kingdom | phylum | class | order | superfamily | family | genus | species | species
COL:32224 Cryptoripersia kingii HAS_ACCEPTED_NAME COL:32224 Cryptoripersia kingii species Biota | Animalia | Arthropoda | Insecta | Hemiptera | Coccoidea | Pseudococcidae | Cryptoripersia | Cryptoripersia kingii COL:5T6MX | COL:N | COL:RT | COL:H6 | COL:HP | COL:4YN | COL:F8D | COL:3WSG | COL:32224 unranked | kingdom | phylum | class | order | superfamily | family | genus | species
COL:32225 Cryptoripersia kingii HAS_ACCEPTED_NAME COL:32225 Cryptoripersia kingii species Biota | Animalia | Arthropoda | Insecta | Hemiptera | Coccoidea | Pseudococcidae | Cryptoripersia | Cryptoripersia kingii | Cryptoripersia kingii COL:5T6MX | COL:N | COL:RT | COL:H6 | COL:HP | COL:4YN | COL:F8D | COL:3WSG | COL:32224 | COL:32225 unranked | kingdom | phylum | class | order | superfamily | family | genus | species | species
COL:32226 Cryptoripersia leucocystis HAS_ACCEPTED_NAME COL:32226 Cryptoripersia leucocystis species Biota | Animalia | Arthropoda | Insecta | Hemiptera | Coccoidea | Pseudococcidae | Cryptoripersia | Cryptoripersia leucocystis COL:5T6MX | COL:N | COL:RT | COL:H6 | COL:HP | COL:4YN | COL:F8D | COL:3WSG | COL:32226 unranked | kingdom | phylum | class | order | superfamily | family | genus | species
COL:32227 Cryptoripersia lii HAS_ACCEPTED_NAME COL:32227 Cryptoripersia lii species Biota | Animalia | Arthropoda | Insecta | Hemiptera | Coccoidea | Pseudococcidae | Cryptoripersia | Cryptoripersia lii | Cryptoripersia lii COL:5T6MX | COL:N | COL:RT | COL:H6 | COL:HP | COL:4YN | COL:F8D | COL:3WSG | COL:32228 | COL:32227 unranked | kingdom | phylum | class | order | superfamily | family | genus | species | species
COL:32228 Cryptoripersia lii HAS_ACCEPTED_NAME COL:32228 Cryptoripersia lii species Biota | Animalia | Arthropoda | Insecta | Hemiptera | Coccoidea | Pseudococcidae | Cryptoripersia | Cryptoripersia lii COL:5T6MX | COL:N | COL:RT | COL:H6 | COL:HP | COL:4YN | COL:F8D | COL:3WSG | COL:32228 unranked | kingdom | phylum | class | order | superfamily | family | genus | species
COL:32229 Cryptoripersia loweri HAS_ACCEPTED_NAME COL:32229 Cryptoripersia loweri species Biota | Animalia | Arthropoda | Insecta | Hemiptera | Coccoidea | Pseudococcidae | Cryptoripersia | Cryptoripersia loweri COL:5T6MX | COL:N | COL:RT | COL:H6 | COL:HP | COL:4YN | COL:F8D | COL:3WSG | COL:32229 unranked | kingdom | phylum | class | order | superfamily | family | genus | species
COL:3222B Cryptoripersia myrmecophylla HAS_ACCEPTED_NAME COL:3222B Cryptoripersia myrmecophylla species Biota | Animalia | Arthropoda | Insecta | Hemiptera | Coccoidea | Pseudococcidae | Cryptoripersia | Cryptoripersia myrmecophila | Cryptoripersia myrmecophylla COL:5T6MX | COL:N | COL:RT | COL:H6 | COL:HP | COL:4YN | COL:F8D | COL:3WSG | COL:3222D | COL:3222B unranked | kingdom | phylum | class | order | superfamily | family | genus | species | species
Note that is takes a little while 30-60min to initially index the Catalogue of Life for offline processing.
GloBI successfully used the Catalogue of Life (COL) offline-enable taxon resolver to add COL links to taxa. Closing issue.
@mdoering @seltmann please let me know if you have any comments/ questions / suggestions about the novel way to quickly and reliably match thousands of names without having to rely on an internet connection.
Here's a DwC-A -
https://download.catalogueoflife.org/col/annual/2021_dwca.zip .