BioCaching with iNaturalist Trips

BioCaching: Rediscover Nature
BioCaching puts the power to conduct a biodiversity resurvey in your hands. Search for and revisit places where plants and animals have been observed in your community, or anywhere in the world. By using this app you will update our knowledge of current biodiversity distributions.

Our app works together with iNaturalist (an online platform for recording and sharing biodiversity observations). Learn more about the iNaturalist community and sign-up to the platform at (you can also sign-up through the BioCaching app if you're not already a member).

With one click, you will see all of the plants and animals that have been observed around you. Next, choose previously observed species that you can recognize and would like to try and resurvey. You are now ready to conduct a ‘trip’, attempting to re-document those species. Start looking and record whether or not you are able to relocate each frog, toad, tree, bee, spider, shrub or whatever comes up on your list. If you find what you are looking for, record new field observations. Your entire trip and your finds will be recorded on and all verified reports will become new records available to scientists. The BioCaching app is a concrete way for you to connect with nature and bear witness to habitat loss and biodiversity change.

The BioCaching app, was developed and designed by Andy Jeffrey in partnership with the California Academy of Sciences Library, Academy Citizen Science and iNaturalist and was funded by the Institute of Museum and Library Studies National Leadership Grant, Connecting Content: A Collaboration to Link Field Notes to Specimens and Published Literature, LG- 05-010-0048.

Posted by ahospers ahospers, August 09, 2019 17:35



The basic back end of trips was added to iNat back in 2014 to support this app 5 was built by a third party developer on the iNat back end with a very small grant from BHL. The basic idea was for the app to show you nearby historic GBIF points, for you to try to relocate them and record presence with a new iNat obs, and to store absences in this trips structure. The app never really worked either because it didn’t have the funding to properly build/support it and/or it was just poorly conceived. The app is not maintained and no longer works but I think all of the older trips cmcheatle mentioned aside from a few us on the team made for testing are from this app. The website also had the basic web UI for trips stubbed out since 2014 but because the tool was only there to support the biocaching app, we didn’t put too much thought into it being user facing.

This year, our Citizen Science colleagues at the California Academy of Sciences has a ‘UBIF’ collaboration with land managers that are interested in developing this work a bit further. Their interest is in the presence/absence of surrogate species to better understand how their managing habitat - e.g. whether this habitat in the San Francisco Presidio has California Man-root which could be a surrogate for the ecosystem they’re trying to manage for 1

Internally, we’re also interested in better understanding/modeling species distributions on the site to improve iNaturalist as both a species identification tool and conservation tool (understanding species distributions is important for both of this). I don’t think we know exactly where we’re going with this yet but we’ve been doing a little bit of work modeling distributions from iNat data and validating it with eBird presence/absence data and its possible that having access to presence/absence data for non-bird data may help validate and improve these models. Here’s a paper I like from a colleague at Berkeley 1
and some of the cool work folks are doing at eBird
if you want to get a sense for the general distribution modeling arena we’re exploring

Back to the trips feature - ( a ) the UBIF collaboration, ( b ) our interest in understanding/modeling/validating distributions, and ( c ) vague but persistent interest in this area fro the iNat community were behind the recent updates to the trips feature - which mainly entailed revamping what was there in 2014, creating the infrastructure for rendering out a presence/absence table from trips and accompanying observations]=36204 1, better documentation, and some rounds of user testing with the UBIF collaborators. We didn’t publicize the updates because (a) its been a busy time of year with Spring, CNC, Seek updates, and other things we’ve been involved in and (b) we’re still trying to get a handle on use-cases for this kind tool and how it does or does not fit into the iNat universe.

An important thing to note about trips which is relevant to some of the forum threads, is that we’re generating presence absence data from plain ol’ observations and the context that trips provide around them rather than collecting a whole new parallel type of presence/absence data. This is appealing because it means we can explore the utility of this kind of data and data use without building and having to maintain a parallel system more or less unrelated to the core of iNat (obs and identifications) - think Guides which is a good example of what we don’t want to repeat. Its also cool because from a presence absence standpoint you can exactly mimic eBird checklists with trips - its not the most pleasant user experience to do so, but its possible to store and render out the exact same data formats. Notice I said presence/absence not abundance as a major caveat is that eBird checklists accomodate counts and trips accomodate presence/absence only.

As for wheth

Posted by ahospers over 1 year ago (Flag)

er this feature will be supported, I think we’re still in the exploratory phase trying to understand the use case more than the exact user interface. For example, at the moment one thing that I think is cool about trips is that you can put a clade like ‘Reptiles’ on your target list and then even if you only saw zero, one, or two species etc. the trip still can be used to generate absence data for every other reptile species. Contrast this with having to put Reptile A, Reptile B, Reptile C etc explicitly on your target list. But after looking at the trips people are posting, it seems like there’s a lot of potential for people to create ‘false-absences’ from this tool. For example:

alot of people seem to be putting things like ‘Plants’ on their target list but ignoring things like mosses which are covered by Plants (thus creating data that could be misinterpreted as absences for alot of moss species)
if you have Ferns on your list (e.g. 1) but post an obs ID’d to genus ( 1) the trip is recording this as an absence for every species in the genus (because there were no obs of any species in that genus) but clearly at least one species was present.
One option might be to make it so that only species can go on the target list, to trade off ‘power’ for correctness of the data. You could also imagine a ‘without taxon’ filter added to the target list (e.g. Ferns without Horsetails), etc.

There also remains a lot of unclarity about how this kind of tool would work well with other issues that have been discussed a lot on the forum like obscured observations or captive/cultivated observations etc.

I’m definitely interested in bug reports but not so much UI optimization at this point. One thing I’d love is to get a little pile of data that we can play with in validating distribution modeling analogous to how we’ve been using eBird data for a non-bird group such as amphibians and reptiles. I’ll try in the next week or two to put together a little ‘call to action’ that describes the structure of a trip that would be most useful for this exercise (e.g lets each spend ~30m making a trip surveying for reptiles and amphibians) along with a little demo of how we’ve been using eBird presence/absence data to validate bird distributions and then assuming we get enough of the right kind of data we can do the same exercise with the trip data we collect and get a sense for whether this data is even that useful for distribution modeling and if not what need to change to make it more useful. Sound ok?

Posted by ahospers over 1 year ago (Flag)

already mentioned the Tatzpiteva project led by @ariel-shamir and @oarazy. One thing thats very interesting is that most people interact with this project, not through but through which is an app build on top of the iNaturalist API. Along with, these are the longest running external web apps built on the iNaturalist back end that we're aware of.

Posted by ahospers over 1 year ago (Flag)

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