BiologicalRecordsCentre / Pantheon

Repository for issue tracking for the Pantheon project, and Indicia-based web portal for integration of invertebrate traits and assemblage associations
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Minor database updates/corrections for v3.7.7 #222

Open DavidRoy opened 6 years ago

DavidRoy commented 6 years ago

Make the following corrections to the database content:

  1. All drawdown species should also be under the marsh hierarchy. ACTION – any species typed only to Running water and then drawdown zone: mud/shallow litter should be reclassified as both

  2. Bembidion quadrimaculatum is wrongly listed as S41. S41 status should apply to B. quadripustulatum

johnvanbreda commented 6 years ago

@DavidRoy shall I make these changes now, or will we wait and do a version 3.7.7 with other changes at the same time? Currently there is no simple UI for making these changes - you can just about do it in the warehouse UI, but it would be quite fiddly. Changes can also be made directly in the database. We could potentially improve that UI a bit, or build a UI within Pantheon. Note that after making changes of this nature, there is a reporting table for the species index which would need updating - see https://github.com/Indicia-Team/support_files/blob/master/Pantheon/Pantheon%20data%20importer/script%2011%20-%20species_index.sql.

DavidRoy commented 6 years ago

@johnvanbreda yes please make these changes

johnvanbreda commented 6 years ago
  1. @DavidRoy Can I just clarify - if there are taxa which are typed to broad biotope=wetland, habitat=marshland, resources=drawdown zone: mud/shallow litter, then they should also be typed to broad biotope=wetland, habitat=running water, resources=drawdown zone: mud/shallow litter? What about the other way round - if they are under running water, should they also be under marshland?

I have to say I'm not sure of the biological logic - why would a marshland association always infer a running water association?

I've done point 2 in the raw data but will update the species index reporting table when 1 is done.

kitenetter commented 6 years ago

Another status update:

This is a result of the names having swapped over in the past. (I suspect there is some confusion in the habitat associations as well but that needs expert hymenopterist input to disentangle.)

Regarding the drawdown species, my understanding is that the original comment from @DavidRoy referred only to those species currently typed to "broad biotope=wetland, habitat=running water, resources=drawdown zone: mud/shallow litter". For those species, they should be retained under running water but additionally linked to habitat=marshland.

For species already linked to "broad biotope=wetland, habitat=marshland, resources=drawdown zone: mud/shallow litter", no action is required (i.e. there is no requirement to link these additionally to running water).

I don't know the background to this request, but my assumption is that any species associated with the drawdown zone is regarded as being part of the marshland fauna (because any drawdown zone qualifies as marshland), but only a subset of the drawdown zone species have a requirement for running water alongside the drawdown zone.

Davydaveth commented 6 years ago

Our original conception was that we would have the facility through a simple UI to edit the base tables, so that we could batch up reported errors and devote a bit of time correcting them. This still has much merit as an approach and could be limited to a defined editor pool drawn from the community. It would by design limit our ability to break the database, but would allow simple edits, perhaps driven by drop-down prompts for acceptable values. So, the conservation status edit could be informed by the main status classes from which the editor could choose the appropriate value and then write that to the table. It means the database would be always more up to date than the funding stream clock allows.

DavidRoy commented 6 years ago

I'll add a new issue for this editing interface. I agree it is a good thing to have