AtlasOfLivingAustralia / biocache-store

Occurrence processing, indexing and batch processing
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Changes to species groups & subgroups #112

Open nickdos opened 8 years ago

nickdos commented 8 years ago

It would be good to have a few experts review our groupings and make suggestions/corrections.

Here are some known issues/improvements:

nickdos commented 8 years ago

Mosses, liverworts & hornworts info from Niels:

In the current AusMoss/APC classification, mosses is a subclass (subclass Bryidae) and you can't search on subclass in the BioCache (ALA). This query will retrieve all moss records from AVH: http://avh.ala.org.au/occurrences/search?q=*%3A*&fq=(order:%22Andreaeales%22%20OR%20order:%22Archidiales%22%20OR%20order:%22Bartramiales%22%20OR%20order:%22Bryales%22%20OR%20order:%22Buxbaumiales%22%20OR%20order:%22Dicranales%22%20OR%20order:%22Diphysciales%22%20OR%20order:%22Encalyptales%22%20OR%20order:%22Funariales%22%20OR%20order:%22Gigaspermales%22%20OR%20order:%22Grimmiales%22%20OR%20order:%22Hedwigiales%22%20OR%20order:%22Hookeriales%22%20OR%20order:%22Hypnales%22%20OR%20order:%22Hypnodendrales%22%20OR%20order:%22Orthotrichales%22%20OR%20order:%22Polytrichales%22%20OR%20order:%22Pottiales%22%20OR%20order:%22Ptychomniales%22%20OR%20order:%22Rhizogoniales%22%20OR%20order:%22Scouleriales%22%20OR%20order:%22Sphagnales%22%20OR%20order:%22Splachnales%22) (It's a beauty isn't it? That's why I haven't changed the classification yet) I expect that the search for mosses that Andi did and that returned only liverworts was in fact a search for Bryophytes: http://avh.ala.org.au/occurrences/search?q=*%3A*&fq=species_group:Bryophytes This is because the liverwort classification in APC is not in line with the rest of the APC classification (liverworts are in phylum Marchantiophyta). I am actually going to propose to CHAH that APC adopt the new Catalogue of Life classification (I think the liverwort classification already follows that). In the meantime, if it is not too much work, it would be good if the species groups could be changed as follows: Mosses: (order:%22Andreaeales%22%20OR%20order:%22Archidiales%22%20OR%20order:%22Bartramiales%22%20OR%20order:%22Bryales%22%20OR%20order:%22Buxbaumiales%22%20OR%20order:%22Dicranales%22%20OR%20order:%22Diphysciales%22%20OR%20order:%22Encalyptales%22%20OR%20order:%22Funariales%22%20OR%20order:%22Gigaspermales%22%20OR%20order:%22Grimmiales%22%20OR%20order:%22Hedwigiales%22%20OR%20order:%22Hookeriales%22%20OR%20order:%22Hypnales%22%20OR%20order:%22Hypnodendrales%22%20OR%20order:%22Orthotrichales%22%20OR%20order:%22Polytrichales%22%20OR%20order:%22Pottiales%22%20OR%20order:%22Ptychomniales%22%20OR%20order:%22Rhizogoniales%22%20OR%20order:%22Scouleriales%22%20OR%20order:%22Sphagnales%22%20OR%20order:%22Splachnales%22) Liverworts: (phylum:"Marchantiophyta") Bryophytes: (phylum:"Marchantiophyta"%20order:%22Andreaeales%22%20OR%20order:%22Archidiales%22%20OR%20order:%22Bartramiales%22%20OR%20order:%22Bryales%22%20OR%20order:%22Buxbaumiales%22%20OR%20order:%22Dicranales%22%20OR%20order:%22Diphysciales%22%20OR%20order:%22Encalyptales%22%20OR%20order:%22Funariales%22%20OR%20order:%22Gigaspermales%22%20OR%20order:%22Grimmiales%22%20OR%20order:%22Hedwigiales%22%20OR%20order:%22Hookeriales%22%20OR%20order:%22Hypnales%22%20OR%20order:%22Hypnodendrales%22%20OR%20order:%22Orthotrichales%22%20OR%20order:%22Polytrichales%22%20OR%20order:%22Pottiales%22%20OR%20order:%22Ptychomniales%22%20OR%20order:%22Rhizogoniales%22%20OR%20order:%22Scouleriales%22%20OR%20order:%22Sphagnales%22%20OR%20order:%22Splachnales%22) Bryophytes includes mosses and liverworts. It also includes hornworts, but the classification of hornworts in APC is a mess.

djtfmartin commented 6 years ago

Both species_groups and species_subgroups are configurable with external JSON configuration files in 2.x