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ALA matched taxon terms lack namespace . #6

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jhpoelen opened this issue May 10, 2018 · 1 comment
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ALA matched taxon terms lack namespace . #6

jhpoelen opened this issue May 10, 2018 · 1 comment

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@jhpoelen
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Currently, when running: $ echo -e "\tCoelomomyces iliensis" | java -jar nomer/target/nomer-0.0.1-SNAPSHOT-jar-with-dependencies.jar append globi-enrich

The following match is produced:

	Coelomomyces iliensis	SAME_AS	3022afe8-3ca1-49a0-b4be-48a7ed53c6bb	Coelomomyces iliensis	species		Fungi | Chytridiomycota | Blastocladiomycetes | Blastocladiales | Coelomomycetaceae | Coelomomyces | Coelomomyces iliensis	urn:lsid:indexfungorum.org:names:90156 | urn:lsid:indexfungorum.org:names:90736 | urn:lsid:indexfungorum.org:names:90742 | urn:lsid:indexfungorum.org:names:90414 | urn:lsid:indexfungorum.org:names:80619 | urn:lsid:indexfungorum.org:names:20136 | 3022afe8-3ca1-49a0-b4be-48a7ed53c6bb	kingdom | phylum | class | order | family | genus | species	

Expected behavior is to append ids (e.g., 3022afe8-3ca1-49a0-b4be-48a7ed53c6bb) to be prefixed with a namespace that helps to figure out origin and way to resolve the identifier.

jhpoelen pushed a commit to globalbioticinteractions/globalbioticinteractions that referenced this issue May 10, 2018
@jhpoelen
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Now, nomer returns:

	Coelomomyces iliensis	SAME_AS	ALATaxon:3022afe8-3ca1-49a0-b4be-48a7ed53c6bb	Coelomomyces iliensis	species		Fungi | Chytridiomycota | Blastocladiomycetes | Blastocladiales | Coelomomycetaceae | Coelomomyces | Coelomomyces iliensis	ALATaxon:urn:lsid:indexfungorum.org:names:90156 | ALATaxon:urn:lsid:indexfungorum.org:names:90736 | ALATaxon:urn:lsid:indexfungorum.org:names:90742 | ALATaxon:urn:lsid:indexfungorum.org:names:90414 | ALATaxon:urn:lsid:indexfungorum.org:names:80619 | ALATaxon:urn:lsid:indexfungorum.org:names:20136 | ALATaxon:3022afe8-3ca1-49a0-b4be-48a7ed53c6bb	kingdom | phylum | class | order | family | genus | species	

With this, it is a little more straight forward to link to associated resources, like https://bie.ala.org.au/species/3022afe8-3ca1-49a0-b4be-48a7ed53c6bb or https://bie.ala.org.au/species/urn:lsid:indexfungorum.org:names:20136 .

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