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jhpoelen / bigbatdb

Big Bat Database contains bat traits compiled from existing datasets and/or publications
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bat traits for indexing by Encyclopedia of Life #1

Open jhpoelen opened 1 week ago

jhpoelen commented 1 week ago

Hey @jhammock @katjaschulz -

Any suggestions for how to structure statements like those describe on the attached photo? What data format would you prefer?

Context is that Hernani and Ariadna of the Big Data DB (see https://github.com/jhpoelen/bigbatdb) are trying to figure out how to get their records on Bat dental formula's published so that they can be easily indexed by EOL. Apparently, this dental formula is a trait used a bunch by bat researchers.

The attached example was extracted from

Fenton, B., & Barclay, R. M. R. (1980). Myotis lucifugus. Mammalian Species, 142, 1–8. https://doi.org/10.5281/zenodo.13505746 https://linker.bio/hash://md5/791d7aef792ee698134b54daddb21eb4

As far as I can tell, there's a ton more trait data where that come from with highly motivated folks in the bat research community to help make this available.

Curious to hear your thoughts . . .

bigbatdb

KatjaSchulz commented 6 days ago

Off the top of my head, I would suggest to leverage the dentition vocabulary in UBERON: http://purl.obolibrary.org/obo/UBERON_0003672 in combination with "count" http://purl.obolibrary.org/obo/STATO_0000047

jhpoelen commented 5 days ago

@KatjaSchulz thanks for sharing your thoughts on how to encode "dental formula" traits. Just curious - would you recommend the data format of any particular trait dataset you've worked with? Or perhaps go with measurementOrFact as part of a darwin core occurrence archive. Just making sure to get the format that'd be the least path of resistance to include in EOL.

KatjaSchulz commented 2 days ago

Yes, we usually use the DarwinCore measurementOrFact extension to represent trait data records for import to EOL. We do not yet have any dentition data in EOL. I would recommend the following representation to get the discussion started:

measurementTypes:

measurementValues: dental formula representation for a given tooth type

statisticalMethod: http://purl.obolibrary.org/obo/STATO_0000047 - count

bibliographicCitation: The work cited for the dental formula

source: The doi link or any other link for the source of the dental formula information

measurementRemarks: For anything else you would want to add, e.g., you could provide the entire dental formula in simple notation

jhpoelen commented 21 hours ago

@KatjaSchulz thanks again for sharing your ideas on how to organize the dental formula for reuse by Encyclopedia of Life (and others).