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Move Viruses out of Biota #225

Open yroskov opened 3 years ago

yroskov commented 3 years ago

Viruses incorrectly got a rank of kingdom in CoL. Whereas ICTV recognize 9 kingdoms of Viruses: https://data.catalogueoflife.org/catalogue/3/assembly?datasetKey=1014

Proposal: place Viruses as unranked sister group outside another unranked group Biota with full ICTV classification (i.e. with their 9 kingdoms).

mdoering commented 3 years ago

problem with that is that we don't have a single tree root anymore. We could create yet another super group for Biota and Viruses. But is a virus not considered to belong to Life=Biota as the highest group?

mdoering commented 3 years ago

OpenTreeOfLife has cellular organisms as their highest group which could be used to group the non Virus kingdoms in COL: https://tree.opentreeoflife.org/opentree/opentree12.3@ott93302/cellular-organisms

kcopas commented 1 year ago

@mdoering we have a very interesting new dataset just added to GBIF—Philippine Bat Viruses and Pathogens—which seems to exemplify the challenge of displaying viruses, so I hope it makes sense to comment here rather than create a new issue (or, indeed, one in GBIF's GH repo).

All of the pathogen records are displayed as Incertae cedis despite having each lower-scale taxon defined, up to including the phylum (e.g. Pisuviracota).

GBIF is actively seeking to mobilize occurrence records related to human diseases. Would partnering with groups like Verena or others make it any easier to support display of Virus occurrences?

mdoering commented 1 year ago

Viruses in the current backbone are very badly treated, in fact due to an oversight when we build it: https://hosted-datasets.gbif.org/datasets/backbone/2022-11-23/README.html

This will be fixed in the next version, placing viruses again under their real classification. @kcopas maybe that solves the issue?

kcopas commented 1 year ago

Sounds like the right place to start!