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trias-project / uredinales-belgium-checklist

🍃 Catalogue of the Rust Fungi of Belgium
https://trias-project.github.io/uredinales-belgium-checklist
MIT License
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Some decisions needed #7

Closed LienReyserhove closed 6 years ago

LienReyserhove commented 6 years ago

I'm currently mapping the data to DwC Archive, but some questions arise. @qgroom can you help me with this?

  1. Which data will we use eventually? Now, the checklist is a mixture of alien and native species (in the field Column). In case of alien, I suppose this means "an alien rust fungus on a native plant", in case of native, this is "a native rust fungus on an alien plant". Or am I wrong? Anyway, I would only include alien rust fungi.

  2. What exactly do you mean with catalogueNumber? Is this the same as taxonID, specifically generated for this checklist? Now, it's the same as the row number of the species.

  3. nomenclaturalCode = ICBN?

  4. What does the information in part and number describe exactly? e.g.: part = 3 (Vanderweyen, A., & Fraiture, A. (2012). Catalogue des Uredinales de Belgique, 3ème partie, Pucciniaceae (genre Puccinia). Lejeunia, Revue de Botanique), Page: 16. Is this the full description of the species? Or rather just a small paragraph discussing its distribution? or...

peterdesmet commented 6 years ago

On 1. we indeed to know how the species are alien, but I would publish both alien and non alien species in this checklist. It’s the scope of the dataset and we can easily differentiate between the two.

Also, are the host plants included in the data?

qgroom commented 6 years ago

  1. The publication does specify when some species are alien, but there are others not mentioned as alien, but are found on alien plants, so presumably alien. It depends on if you consider crops like wheat alien.

  2. The catalogueNumber is the number give to that taxon in the publication. It is described in the Darwin Core documentation as "An identifier (preferably unique) for the record within the data set or collection". This sounds about right.

  3. Yes, stick with ICBN, though this should be looked at by someone. The latest code should be called the ICNAFP or just ICN. It really needs a controlled vocabulary, which includes the dates. Having said that I have no idea why we need nomenclaturalCode in observation data!

  4. The Catalogue was published in three seperate parts, several species treatments were on each page and each treatment was numbered. There is little description of the species, most of the information is about taxonomy, observations and the hosts.

peterdesmet commented 6 years ago
  1. We'll have to make a decision then on which ones we consider alien.
  2. That fits the definition, but it is really used for specimens... which might be confusing here. In any case, it's not available for taxa. It's a taxonID. Since we'll create our own taxonID, we'll have to decide if and where we want to keep this original ID.
qgroom commented 6 years ago
  1. just use the alien status that is in the far right of the table for now. I will try to review then soon, but there will be few new aliens.
  2. I'm fine dropping catalogueNumber or putting it somewhere else.

You did find the associateTaxa column in the data for the host species?

LienReyserhove commented 6 years ago

So,

  1. I'm keeping all species (alien and native) in the checklist. I will specify their status in establishmentMeans, as I did before for the other checklists:
raw_data establishmentMeans
native native
alien introduced
NA NA

Later, we can still decided which species to integrate in the unified checklist...

  1. In my opinion, I would drop catalogueNumber. You could perhaps integrate it in the Types and Specimens Extension, but that extension would not add a lot of information to the checklist (bibliographicCitation is already in the Taxon Core).

  2. I stick with ICBN

  3. I will integrate part and number under bibliographicCitation in the Taxon Core, as this appears to be the most appropriate to me.

  4. and yes, associatedTaxa is in the raw data. @peterdesmet : perhaps something for the Resource Relationship Extension?

peterdesmet commented 6 years ago
peterdesmet commented 6 years ago

Creating separate issue for associated taxa #8

qgroom commented 6 years ago

I agree with 1-4 and creating a new issue on associatedTaxa. I am keen to capture the host information. Among other reasons it is highly relevant to species impacts.