LinEpig: Developing a taxonomic reference using collections-management systems
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Presentation to the 2015 meeting of the American Arachnological Society on migrating LinEpig, from a public photo-sharing site to a museum-orientated relational database. LinEpig provides a reference to the only North American spiders with no key to genus.
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LinEpig: Developing a taxonomic reference using collections-management systems
- 1. LinEpig: Developing a taxonomic reference using collections-management systems
- 3. Erigoninae Linyphiidae is the 2nd-most speciose spider family in the world, and it has the most genera. The erigonines account for 90% of linyphiid diversity. North America has more than 120 erigonine genera – 42% of them monotypic – and over 650 species.
- 4. Stylish male Erigone atra representing the subfamily at Wikipedia Spiders of North America: An Identification Manual, 2005
- 6. Intended use: Subverted use: But spider ID reference was not really what Picasa was meant for…
- 7. And now Picasa was going away. The images in Google+ were better – but they were no longer presented in a useful way.
- 8. But there were also other things we couldn’t do even on the old Picasa Erigonines in Cooliris display, David Shorthouse ispiders.blogspot.com December 2008
- 10. And palps … but now we had the Leica with automontage and that created new possibilities Ceratinopsis nigriceps by N. Dupérré, 2003
- 11. And by this point, the Field Museum had acquired a collection-management system This created the possibility of re-creating LinEpig as a custom-built, taxonomically rich resource in its proper home at the museum.
- 12. Authors Moving in… First name Last name Year born Year died ID Taxa Genus Species Parent taxon Author(s) Year ID Images Species Sex Anatomy View Creator Institution ID Specimen Date Location Habitat Collection method Collected by Det as Det by Institution ID
- 13. Authors 291 =>
- 14. Some of them required a bit of disambiguation
- 15. Taxa 4,474 =>
- 16. The result 4474 linyphiid taxa => 291 linyphiid authors => 241 LinEpig images => <= specimen info will go here, with a field for the institution
- 20. Which is great for collections, when you know you’re looking for, and want to see if we have it. It’s not so helpful for the mystery specimen in your dish… What you want is one of those mug books like the police have, so you can identify your suspect
- 21. The New LinEpig DEMO: http://bit.ly/LinEpigdemo YOUR COMMENTS: http://bit.ly/LinEpigfeedback This is a shared Google doc in which you can all make comments right now, simultaneously, as we look at the demo, or later, on your own.
- 26. One thing I haven’t added yet is the locality info. We have better data than what was in Picasa It will be up to GBIF standards EOL map based on GBIF Linyphiidae occurrence records eol.org/pages/8781/maps
- 27. <= Go to MCZ collection record
- 28. The specimen record in MCZbase
- 29. What do we want to build? <=Equipment <=Code Spiders =>
- 30. • Internal links/filters • External links • Info enrichment Ways to make LinEpig more useful
- 31. Internal links/filters • Show larger/research view of image • Show all species of this genus • Show all species by this author • Select states or regions • Select certain genera Example:
- 32. External links • Lending institution’s specimen record • Link to species page in World Spider Catalog • Link to species page in BOLD, GBIF, etc. http://www.wsc.nmbe.ch/species/14755/Ceraticelus_bulbosus http://www.boldsystems.org/index.php/TaxBrowser_TaxonPage? taxon=Ceraticelus+bulbosus Examples:
- 33. Information enrichment • Literature references • More info on authors • Descriptive narrative, possibly for genus • Character coding (eg, has epigynal atrium) Grammonota tends to have an abdominal chevron Li Shuqiang is at the Chinese Academy of Sciences’ Institute of Zoology in Beijing Examples:
- 34. Things to consider • How effort much would it take? • Is it something someone else is already doing, or should be doing, or could do better? (the classic cybertaxonomy dilemma) • Should the effort go into imaging more of the Erigoninae?
- 35. Data issues • Data rights issues • Contributed images • Accuracy issues • Updates and maintenance Gnathonarium famelicum palp & epigynum by D. Buckle, 2011 Example:
- 36. What are your thoughts? DEMO: http://bit.ly/LinEpigdemo YOUR COMMENTS: http://bit.ly/LinEpigfeedback This is a shared Google doc in which you can make comments at any time.
- 37. Thank you Field Museum colleagues • Petra Sierwald, arachnids & myriapods • Corrie Moreau, Stephanie Ware, Robin Delapena, Alexandra Westrich, and everybody at our Collaborative Invertebrate Lab and Moreau Ant Lab • Sharon Grant, technology liaison to science • Pete Herbst, web & database specialist
- 38. Thank you friends and supporters • Norman Platnick, World Spider Catalog 2000-14 • David Shorthouse, Nearctic Spider Database • My linyphiid elders and mentors Rod Crawford, Mike Draney, Robert Edwards, Don Buckle • LinEpig contributors Paula Cushing, Rich Bradley, Rick Vetter, Tom Prentice, GB Edwards, Marc Milne, Derek Sikes & Brandi Fleshman, Jim Steffen, Claudia Copley & Derek Copley, Gonzalo Giribet & Laura Leibensperger • Lee Sandlin
- 39. Nina Sandlin Spiders - Zoology The Field Museum 1400 South Lake Shore Drive Chicago, IL 60605-2496 USA nsandlin@fieldmuseum.org llinepig.fieldmuseum.org
Editor's Notes
- Hi. My name is Nina Sandlin, and I’m an associate at the Field Museum in Chicago.
- Some of you are familiar with the LinEpig gallery where I have been posting microscope images of linyphiid epigyna, particularly the Erigoninae. I started putting this stuff up on a photo-sharing site called Picasa back in 2007.
- Now, the Erigoninae, as we know, are a very big group of very small spiders – and they are in special need of help, taxonomically speaking.
- Because female erigonines are the only North American spiders with no key to genus.
- The Scientific American blog had a guest post on the project in 2011. And that helped give LinEpig a boost.
- But Picasa was never really intended to be a scholarly platform. I had to put taxonomic info in the Comments section, and there was no way of showing relationships – such as what belonged to the same genus.
- And in 2013, Google started sunsetting the platform (not because it didn’t work well for LinEpig!) and redirecting visitors to its new product, GooglePlus.
- One thing there had never been a good way to do on Picasa was to include habitus. Originally, we were sending those to the Nearctic Spider Database…
- But we hadn’t had that for a while either. And really, a lot of what I’m doing now is just trying to recapture – or re-create – at least for this one subgroup – some of the functionality the Nearctic Spider Database had once offered.
- Another thing I couldn’t do is palps – because they are just too 3-dimensional for the imaging equipment I was using. But the Leica Application Suite will take like 60 slices from the top to the bottom of your palp, and composite them as you watch.
- And now, the museum had a new Drupal-based website, and a new database system. And that was much more like the kind of infrastructure that LinEpig needed.
- A database kind of wants you to add objects in a one-to-many sequence – so one author described many species, and one species can have multiple specimens and images. Now, I focus on Nearctic erigonines. But you know, a species found in Alaska might be described from Siberia. And there is some fuzziness about what even constitutes an erigonine… So it basically only made sense to do the whole family.
- At that time, there were 291 authors for linyphiid taxa, from Ourida Abrous to Helen Zorsch.
- Those early citations were clearly marked as Octavius Pickard-Cambridge or Frederick Octavius. But not so much for Jeremy Miller and František Miller (1902-1983). To say nothing of the 3 Chens, 3 Wangs and 4 Li’s occurring just among the linyphiid authors.
- Once the authors were in, we could import the nearly 4,500 linyphiid taxa, pre-linked to their author – for example, 5357 aka Ralph Chamberlin, who described all those Zygottuses and Wubanas, some of them with Ivie (6785). And lastly, in kind of an anticlimax, the 241 epigyna.
- And the result is a data set that we can do all kinds of neat things with. What most places are doing with their collections-management software is working in that catalog module, filling in details on the specimens or artifacts in their collection.
- And they’re using that to provide online access to the material in their collection, like in this specimen search at MCZ.
- Or this arthropod search at the Field Museum.
- Your search for a particular thing, and you get the results in a list.
- But when you have a specimen and you don’t know what it is, what you need is something to visually compare it with.
- So this is the part where I do the LinEpig preview – and you get to help design how it’s going to work. Multiple people can write in this file at the same time. Type your name if you want to have a discussion about it later, or I won’t know whose comment it is.
- This is the new LinEpig. It has the full set of images from Picasa, and they are all clickable. If you’re looking at the live demo on your device – CERATICELUS BULBOSUS is the demo species. It’s the ONLY ONE where there’s anything besides the epigynum to click ON.
- Clicking gives you the close-up, just like in Picasa but without the “friends and family” stuff. Instead, we now have some relevant links – both navigationally for LinEpig, and anatomically for things you might want to see besides the epigynum
- For example, Does this species look anything like the actual spider you are looking at under the scope?
- And if you click on one of those, you get that close-up. This being a relational database, you could go on like this forever.
- The collection data still needs to be imported into the database. David Shorthouse, back in 2008, told me to use Darwin Core – and I have been – so we have decent data. But since this belongs to the specimen, rather than the taxon, it will go into a different module, and I haven’t done that yet.
- But some places have their material databased, and in those cases we are building in links to those records.
- Which will take you right to everything that they know or don’t know about that particular specimen.
- So those are the basic elements. And now we have everything we need in place – the equipment, the code, and the spiders. And now we come to the limitless possibilities…
- So what do we want to do with it – apart from growing the resources by adding more species, that is? Most of the things that might make LinEpig more useful fall into one of these three categories, which I will briefly talk about.
- So first, there is the stuff that is already in the database, and it’s a matter of writing the code to present it in the most useful way. You might want to compare some genera that are related taxonomically but not so close alphabetically. Or only show the species that are known from the geographic area where your specimen was found. Or maybe see all the species by a particular author.
- Then there’s linking to the relevant information located elsewhere. For example, it would be great to link to the taxonomic history in the World Spider Catalog. But it has a database reference number – which is not the URN, by the way – in the URL, so it can’t be automated in an effortless way. By contrast, BOLD Systems has a machine-predictable URL for the species page – so actually, I’ve already automated the link for every species that is in BOLD.
- And finally, there is adding things into the database, such as citations for the species descriptions, or new field values. For example, one could add an author’s nationality. Or there could be additional narrative text providing more background. One might wish we had a few words about the each genus. Or it might be nice to know what characters an author tended to stress in his or her descriptions. One problem with these kinds of things is that they tend to not only take time, but also judgment.
- So basically, we are looking to do the most useful enhancements for the least effort, as much as possible.
- There are also data issues. Time keeps moving forward, and there are new species and authors – and the need to obtain new permissions from the new maintainers of the spider catalog There are sometimes misidentifications that need to be corrected and noted. And I’ve had some inquiries about the possibility of including contributed images. We definitely want to set up a process for that, because there are some excellent images out there, like this set of Gnathonarium famelicum from Don Buckle. And now that I’m having to shoot palps from multiple views and write code, it is hard not to fall further and further behind.
- Now, I’m presenting this not only to share what I’ve been up to, but to get byour input on what would best serve the principal users of this kind of taxonomy reference. So please do write notes in the Google doc or corner me between sessions.
- I have many people to thank, both at the Field Museum…
- … and elsewhere. And thanks to all of you.
- Here is how to find me.