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bmaitner / RBIEN

Tools for accessing the Botanical Information and Ecology Network (BIEN) database
http://bien.nceas.ucsb.edu/bien/
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Feature Request: A trait table conversion between BIEN traits and TRY trait IDs #27

Open Rekyt opened 3 years ago

Rekyt commented 3 years ago

Hi @bmaitner 👋

For an ongoing project I'm trying to gather all traits available in both TRY and BIEN for a subset of species. One thing that I have to work on is to match the trait names in BIEN to trait IDs in TRY. I actually think that many people are trying to complement both databases (see for example this GitHub search https://github.com/search?q=BIEN+TRY+traits&type=code). It would be great to have a table that gives you directly the correspondence between BIEN trait names and TRY trait IDs.

Do you have this internally somewhere? Otherwise I'm working on it on my side and may contribute it if you're interested.

bmaitner commented 3 years ago

Hi @Rekyt this is a great idea but not something we've generated on our side, so if you're working on one we would be VERY glad to add it. Going forward we'd like to generally improve the way we store and clean trait data, and including keys to connect different databases seems like an important thing to keep on our agendas.

Rekyt commented 3 years ago

Thanks for your quick answer! (BTW, are these GitHub issues the best place to discuss features for BIEN?)

I have a quick and dirty table that makes the correspondence. However, it's not bijective between BIEN and TRY. It's rather a one to many relationships. Some traits in BIEN are simply not available in TRY because there are not defined in the same way (all maximum and minimum traits). So combining them would actually need careful examination of raw trait data in BIEN.

bmaitner commented 3 years ago

Yeah, that's about what I would have thought. Nothing is ever easy...

Regarding the best place for feature requests, this seems like a reasonable place. Although, it might be better to add feature requests directly to the github repo for the database itself (https://github.com/EnquistLab/bien), but it looks like we'd have to make that public first. @ojalaquellueva any thoughts?

ojalaquellueva commented 3 years ago

@bmaitner I don't have sufficient domain knowledge to lead the charge on this, but if you and @Rekyt are willing to build and maintain a mapping table I can map it into the DB pipeline on the next rebuild and expose this information to users.

Rekyt commented 3 years ago

Hi @bmaitner and @ojalaquellueva, I confirm that TRY doesn't provide such a table either. I've mentioned a similar issue to the maintainers of AusTraits https://github.com/traitecoevo/austraits/issues/30 and they are working on the same issue. They provided me with a draft table that does the correspondance.

Maybe it would be useful to look at it and try to do a similar work with BIEN.