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open-traits-network / open-traits-network.github.io

Open Traits Network Registry and Website
https://opentraits.org
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I'd like to ... connect bee traits (e.g., intertegular span /distance) with their literature and OTN members #206

Open jhpoelen opened 2 years ago

jhpoelen commented 2 years ago

Hi!

@seltmann shared a "famous" bee trait: [intertegular_span_Apoidea] (https://www.researchgate.net/publication/256458920_Estimation_of_bee_size_using_intertegular_span_Apoidea) a proxy for dry weight or body size.

classification could be something like:

volume ~ dry weight ~ intertegular span

trait is defined in the Cane 1987 paper:

Cane, James H. "Estimation of bee size using intertegular span (Apoidea)." Journal of the Kansas Entomological Society (1987): 145-147. https://www.researchgate.net/publication/256458920_Estimation_of_bee_size_using_intertegular_span_Apoidea

@seltmann is working on a literature list for this trait at https://www.zotero.org/groups/4605590/bee_morphology_functional_and_life_history_traits/library

@Daniel-Mietchen please let me know if you need more information.

jhpoelen commented 2 years ago

There's a bunch (>400) of ITS (intertegular span) measurements for including the following 5 specimen:

Tegula length: length mm Filename institutionCode collectionCode catalogNumber
2 UCSB-IZC00000646.jpg UCSB IZC 00000646
1.8 UCSB-IZC00003496.jpg UCSB IZC 00003496
3.2 UCSB-IZC00003658.jpg UCSB IZC 00003658
0.9 UCSB-IZC00003718.jpg UCSB IZC 00003718
3.1 UCSB-IZC00004438.jpg UCSB IZC 00004438

All images are CC0 and I am working on updating the image corpus to provide reliable citations to the images.

jhpoelen commented 2 years ago

from UCSB ICZ dwca tracked via preston:

$ preston track "https://serv.biokic.asu.edu/ecdysis/content/dwca/UCSB-IZC_DwC-A.zip" $ preston ls | preston dwc-stream | grep -P "00000646|00003496|00003658|00003718|00004438" > records.json

records.json.gz

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jhpoelen commented 2 years ago

See UCSB IZC specimen with catalogNumber 00000646 has an image available at:

https://serv.biokic.asu.edu/imglib/ecdysis/UCSB_IZC/UCSB-IZC00000/UCSB-IZC00000646_had_lbs.JPG

UCSB-IZC00000646_had_lbs

https://serv.biokic.asu.edu/imglib/ecdysis/UCSB_IZC/UCSB-IZC00000/UCSB-IZC00000646.JPG

under cc0 license:

UCSB-IZC00000646

jhpoelen commented 2 years ago

Note that https://library.big-bee.net/portal/content/dwca/UCSB-IZC_DwC-A.zip will contain trait measurements as some point.

jhpoelen commented 2 years ago

Note that OTN member Katja Seltmann is a collector and determiner of some of these specimen. And, specimen can be considered a publication of sorts - a sample taken from nature with annotation added.

@Daniel-Mietchen how would you model the collected by / identified by relations to the OTN member @seltmann

Daniel-Mietchen commented 2 years ago

Thanks, @seltmann @jhpoelen . Intertegular span seems like a good choice for allometry. But by "famous", I did not exactly mean that it produces zero results in Crossref. Anyway, the Cane 1987 paper was already in Wikidata, so I tagged it, and Scholia's topic profile resulting from that one paper looks very deserted: https://scholia.toolforge.org/topic/Q113203921 .

However, I did find three other papers that used this trait in some way, and they can be explored via the /use/ profile: https://scholia.toolforge.org/use/Q113203921 . Interestingly, I know one of their authors — @gavinscode — from another open network (IGDORE), so he may want to join our party here.

Compared to these few finds, the Zotero library is much more comprehensive, and I will look into it next. Thanks to a team around @zuphilip, there is a workflow to sync metadata between Zotero and Wikidata but I haven't used that (or even Zotero) in years, so will have to undust my knowledge of that corner. In theory, we should be able to export the entire library into the Wikidata edit tool QuickStatements (which I use often and thus know well — specs here), as per this demo, and then we could work it into the above Scholia profiles.

Are there any bee traits of interest to you that actually are famous enough to occasionally make it into paper titles? For instance, here is Scholia's topic profile for proboscis length, based on 18 papers that I found so far: https://scholia.toolforge.org/topic/Q113206456 . For further example visualizations, see also the examples for plant traits discussed in the other thread: https://github.com/open-traits-network/open-traits-network.github.io/issues/197#issuecomment-1188226878 .

As for indexing individual specimens, there are no well-trodden paths, but I am eager to explore what can be done here. Wikidata has been integrated with Bionomia (cf. https://scholia.toolforge.org/P6944 ) but the focus so far was on the collectors, not on what they collected, though there are some specimen items that use discoverer or inventor (P61) statements for that purpose (example). Furthermore, we can use the Wikidata identifier on the Bionomia website to get a list of all the specimens collected, e.g. https://bionomia.net/Q14049/specimens .

I'd be happy to collaborate on working out how to properly represent natural history specimens in Wikidata and Scholia. A good starting point would be type specimens (for which Wikimedia Commons has a decent collection), especially those that were used in publications other than those describing the taxon. I have worked a bit on some of these type specimens on Commons (example), and there are even files that would lend themselves to determining intertegular span (e.g. the image 23 from here) but not much progress has been made in terms of integrating individual specimens with Wikidata, though I expect the topic to be discussed at TDWG, where we have a session dedicated to the role of the Wikimedia ecosystem in the wider biodiversity data ecosystem.