Follow up from last week's digitization meeting: specific use case

[kandakoj]

This issue stems from the previous week’s taxonworks meetings, where I asked about the best way to export specific bits of data from my taxonworks project. @mjy asked me to post what exactly I wanted to export; maybe I just need to read up more on stringing together and filtering results from API calls.

As a user, I have a set of OTUs in an observation matrix. For each of these OTUs, I want to export the following bits of data related to it for a print catalogue. The limits to the project isn't a specific taxa and all its descendants or taxa in a specific asserted distribution; I want the export limited to data related to OTUs in the observation matrix.

1. The taxon name tied to that OTU. For this, I want: -The original combination Genus species subspecies (if present) author, year: page

   • If the current combination is different from the original, the current combination and the original citation for the transfer. -If the taxon name tied to the OTU is invalid, just the specific relationship/reason why it is invalid. (e.g., Subjective synonym of XXXXX in XXX, XXXX)

2. For the taxon name tied to the OTU, there is a digitized collection object; a type specimen. For this, I want:

   • The specimen catalogue number
   • Buffered collecting event
   • Buffered other labels
   • Type of type
   • Source (if one is associated with the type)

3. Back to the observation matrix, I have some columns with data to export:

   • sex (qualitative)
   • higher grouping (qualitative)
   • Published photos (free text)
   • Remarks (free text)

[kandakoj]

Followed your advice; "sex" now included as a biocuration attribute in my project.

[mjy]

@kandakoj, almost have this, but need some clarification:

• What do you mean by "Current citation"? Is this the original citation of the currently valid name?
• Source (if one is associated with the type) Is this a Citation on a TypeMaterial record or a Citation on the Protonym?
• In section 3, can you provide the descriptor ids of the columns you are referencing? I can't, for example, find descriptors named like those columns. If the intent is to reference more than one descriptor (like your image descriptors for example) please clarify?

[kandakoj]

1. I meant the citation for the combination that is currently used; if you were running tests on my data, I don't know if I have actual examples where I included the citation for the first use of the currently accepted combination.
2. For this I meant citation on a typematerial (e.g., for subsequent lectotype, neotype designations); again haven't digitized the data for this in my dataset.
3. Sorry I hadn't created some of the columns yet. Anyways, there is some data in the following columns:

Higher groupings: 1409; Published photos: 1482; Remarks: 1453; Sex I added to as a biocuration group in my project.

[mjy]

@kandakoj script is up. I don't think it's perfect, but it should give you something to chew on. See if you can find your way through https://github.com/SpeciesFileGroup/taxonworks_api_scripts.

[mjy]

The new endpoint used here is /taxon_names/123/status. It will likely be further namespaces /taxon_names/123/inventory/status in the future.