 I am Kelsey Yule. I am the project manager for the neon biorepository that's located at Arizona State University. And a quick overview of what I want to talk about is just what the biorepository is, what biodiversity occurrence records are, because that's the kind of data that we work with. With the biorepository that is overlapping but not the same as the type of ecological data you would find in the main neon data portal. Show our biorepository portal and how you would find or download samples. Really quickly, just bring up how you can access our samples and acknowledge biorepository samples and publish your own data through the biorepository portal, which is unique. The main neon portal does not typically pull in data from external researchers in the way that we can. So it's a more unique way to get some visibility for your own research within an official neon data portal, which I think is particularly cool. And kind of a demo slash scavenger hunt where I will actually use the portal to go find a couple of different things like a typical user might do. So first, we all probably know what neon is. Of course, there are these 81 terrestrial and freshwater sites. And the main thing I want to say about them is that in addition to all of the amazing data that neon is taking, they are also collecting samples at all of those sites. And we at the neon biorepository consider ourselves like a turntable that pulls in neon samples and data and then provides them out again to researchers to do novel things with neon samples. And then come back to the neon biorepository portal and further, you know, enrich the ecological data community. So we operate using fair principles so in keeping with neon's main data portal we are also, you know, concerned with the findability accessibility interoperability and reusability of data so that's something we just always keep in mind. As we are working with biorepository data and samples we have the same kind of outlook for the samples themselves physically as well as the data. So as I said, physical samples are collected at the neon field sites. They go are brought into the neon domain facilities. Then they might either go to external contractors who do all sorts of interesting like genetic or genomic or biogeochemical analysis on them or they'll go directly to the biorepository. Pretty much all samples end up being curated at the neon biorepository at ASU. We then publish the sample associated data on the neon biorepository data portal which is connected to but separate from the main neon data portal. We then push our data, our organismal sample associated data out to the global biodiversity information facility. So this is important because it is what makes neon sample data fully integrated into the overall biodiversity occurrence record data that is available globally and interoperable with that data. So I'll talk about how we do that a bit more in a moment. And then of course, we give the data and the samples to researchers so they come to us or receive a shipment of samples in the mail, or they get the data from our data portal and then they turn that into research that then we share and give additional visibility to through our portal. So we get a variety of different samples every year, about 80 to 100 plus thousand samples each year, they have a wide taxonomic spread, some of them look like typical natural history collections, specimens like oppressed or variant voucher or pinned insect. And then some are quite different, they might be environmental samples like dried soils, they might be a bulk community sample like the bycatch from neon pitfall trapping, or actually 65 ish percent of the neon samples are cryo samples so they are either chemical organisms or tissues or microbial samples that are frozen, according to the best practices for making their data potential available in the long term. So we have over 421,000 samples that represent over 3400 identified taxa. Of course we have these bulk samples that have a lot of unlocked diversity within them as well so there's more taxonomic spread in our collections then can be represented by the names that you'll see attached to an individual on the portal. So, we trade in biodiversity occurrence records in the natural history collections community. These, these data follow Darwin core standards, which is a standard that is developed and voted on by the biodiversity information standards group or TEDWIG. And it means that all of the records associated with neon samples have are following this stable straightforward and flexible framework for compiling biodiversity data from a variety of different sources. The data associated with a collecting event in the field might will look really different, depending on the protocol that it comes from, but we translate all of that at the sample level into these well defined fields that really represent, you know, taxonomically what is this thing who identified it as that where and when was it collected. If when relevant, you know what life stage was it what was its reproductive condition, the habitat that it lives in, but all of those are kind of standardized across all of the different collections that we publish. The one by repository data portal is a symbiota software based collections portal. This is a really commonly used software for managing and publishing biodiversity occurrence records, and it's an aggregator that brings in data, often from different sources, and then allows collections to both manage it within the portal and then it's published out to the community. I just want to point out that symbiota. There are many of these portals and they will represent different taxonomic groups or locations or research projects associated with samples and biodiversity records. So pretty much everything I'm going to talk about with using the neon buyer repository data portal would apply to how you would interact with any symbiota portal. So, this is a broad data skill to be learning. This is what an example of what a full record that you might see in the portal would look like. And just those those kinds of Darwin core fields that I brought up earlier are all present there. This is what it will look like when you pull up a record on the site, but then you can also download the data in the standardized version for many, many samples or specimens at once. So how you use the portal. I'll go really quickly through this because we'll actually demo it later on. So the portal looks like this like I've already shown this is the homepage for it. The primary way that someone might want to use the portal is through this sample search option in the menu. And then a what we call a search form that has a bunch of different criteria that you can use to then filter the search results. So if you just went to the sample search and then said click that search button on the right you would get every single sample that we actually have at the buyer repository in those results but then of course you can filter that in a bunch of different ways before you get yourself search results. All of these menus or criteria in the portal are in these accordion menu so you can open or close those depending upon what criteria you're interested in looking for. And then whatever you are searching for will show up as chips on the side there as criteria and you can, you know, X out of those if you don't want that criteria anymore, etc. So when you are, you know, the first often most common way that someone might want to filter your results is by the actual tax on. When you start typing into the tax on box, the suggestions will show up and so you know that if you're clicking on one of those suggestions, you're actually choosing a tax on that is indexed in our taxonomic thesaurus so this prevents spelling errors which is really nice for, yeah, searching for complicated scientific names and it will also have common names when those are available. And just going back real fast I want to point out that here in this example we have algae which is not an actual, you know, evolutionary tax on its. But it is like an ecological type of pseudo tax on and we do have those available in the neon biorepository to match the types of ecological collections and ecological data products that neon collects. And so that's kind of unique to this portal. So there are three different types of collections in our portal. The first is the neon collections that are actually at the biorepository then there are additional neon collections. These are legacy collections from before the biorepository existed, or or something like the like the soil mega pits that were collected at the beginning of the neon project are not located at ASU and so those are something that you can also find in the portal, but they're in these additional neon collection section and then there's other collections from neon sites. So this is where we've actually pulled in these interoperable data sets from other biodiversity portals but it's for samples and specimens that were actually collected at neon localities prior to the existence of neon. So this is a way that you can kind of look at baseline diversity that's been studied at neon in the past. So, this is a collapsible menu that you can open to look at these different collections and you can filter them by taxonomic group. The neon theme that the collections are associated with or the sample type this is typically like how the sample is preserved or if it's a DNA sample versus preserved in fluid, etc. So you can, you know, again expand or collapse these options and select collections you're interested in. So you can click on any of the links for those collections you'll be taken to the collection description page. This is really useful gives a summary of what's in the collection photos of example samples in that collection links to the neon protocols and the associated with neon data products and also a link out to that global biodiversity information facility portal and all of the different publications that have actually used those samples, the data associated with those samples and their work. So, yeah, again, the collections that you select will be represented in the chips and under criteria on the right hand side of that form. You can filter the samples in other ways like if they have genetic data or images. And then we have a menu for locality. And this is where you can search by neon domain or neon site. You can click on any of those links and you'll be brought to the actual neon site description page. There's also geographic criteria where you can draw a bounding box in a map or actually type in latitudes and longitudes to search for samples geographically. Once you click search, then you will get the results. And these will be presented in a long list like this you can also look at them, the basic data in table view. And then of course you can download that data, and you'll have two options a symbiota native or a Darwin core native. So Darwin core is that that data standard that I talked about before symbiota native follows that data standard but then also add some additional fields. And then, right, that's what that says. And then when you download the data, if you choose to download the full zip file, you will get this, this folder you can open that will then have a number of CSV files in it. Most often you'll be interested in this one that's called occurrences that's where you have a single row in your spreadsheet for each sample or specimen, but you could have downloaded just that occurrences file or one of these other files like one that represents just the images for these samples. And then there is the option there to copy the URL for the exact search that you did. And this is useful if you want to make the exact search based on all of the criteria again or send these search results to to someone else. As you see there's these three tabs at the top of this list, and we're looking at the occurrence records one here, you can also look at a species list that lists all of the taxa that were included in the search. And then there's the maps tab, where you can actually plot all of these samples on Google Maps, or download a KML file. Quickly just, I want to really plug that these samples are available for use. And for many different purposes, even consumptively or destructively. Sometimes reach out to the technical working group for approval to make sure that we aren't depleting the spatio temporal and taxonomic diversity of the collection. But they're meant to be used very frequently and so we approve most things as long as researchers agree to share after publication of the sample associated data for use by the rest of the research community. And then you can find on our portal, the sample use policies and ways to acknowledge and cite us in your publications. And there is a form that you can fill out to request samples, or also, you know, I recommend just reaching out directly to buy a repo at asu.edu. If you're in the process of preparing a proposal that would use neon samples, you would typically need a letter of support from us and please reach out as early as possible in the process of that proposal of preparation. We'll provide those letters as quickly as we can but sometimes we do need to reach out to the technical working group to make sure we can improve destructive uses. In the end, I want to note that there can be a cost if there is an especially large request or one that requires us to do a lot of special handling or processing of the samples. So that's another thing we'll need to evaluate for in any research proposal situation so another reason to reach out. And you can also always come to Arizona State to look at and work on the samples. Like I said before, a really cool thing is that we do actually publish the value added data collected by researchers on our site. We publish these as public data sets on the site. So there is information about publications. Those are linked to the sample records so the publication is available directly within the sample record and then we also have this page for each paper that will have the paper abstract and links out to the paper as well as links to all of the samples that were used in it. So it's a way that we hope you can get additional visibility for your work. And then we can also publish those data sets out to the environmental data initiative portal for you as well. I want to quickly acknowledge the team that works at the Biorepository. We have collection managers, biodiversity informaticians and sample preparators who work really hard to make all of this available. And so with that, I want to actually just move to using the portal. So I am going to stop sharing this page and actually go to the portal. And you cannot now see what I said that I wanted to find because I'm going to actually go to the portal. But the first one I wrote as wanting to find is a description of the neon soil microbes sampling protocols and links related to the neon data products for soil microbes. And so how I would do that is I would go to our portal. And I'll just point out that our portal homepage also has those nice summary statistics that are always kept up to date and you can actually click on these as links. And then there that was a very easy way to see every single environmental sample that we have. So those would be like soils and aquatic sediments, etc. But if I want to find those soil micro protocols, what I would do is go to find the soil microbes. So what I did here again was I went to the sample search form under search. I wanted to expand the list of available neon collections. I am interested in microbes, so I expanded the microbes option. And then I'm going to go to the description page for one of these soil micro collections. So here, there's two different soil micro associated collections we have the bulk frozen soils samples. We also have DNA extracts from soils. So I'll just go for example to the bulk soil micro collection. Here you can see a description of what these samples are, then pictures of what samples look like this is different. These are the types that neon has used over the years. Back in the early years, they use these world packs but now they're in these nicer vials, but scrolling down. So here we have a link out to the sampling protocol document for these samples, as well as links out to some of the neon data products that are associated with the samples so you could cross reference sample IDs or sample barcodes found in our portal with associated data records in the neon data products. The second thing on my list to find was all perimuscus lucopus voucher specimens. So that is the white footed mouse. And how I would find all of our perimuscus lucopus vouchers is I would again go to this sample search form, and I would find perimuscus lucopus. And again, the search form has helped me not spell that wrong, because it's available in the drop down menu. So here's an interesting thing to consider we have this include synonyms check mark. And so if I uncheck that that I will only get the samples or specimens that are associated with this name verbatim. If I include synonyms, then I will get any other taxonomic names that are determined to be the same so if the tax on name has changed over time because the group has been revised, then those samples or specimens will come up as well. Also, sometimes we'll get samples from neon where they have got this mouse in the field, and it is not possible to distinguish these two species in the field based on the external morphological characters that this particular individual had. The neon field staff will indicate that it may be one of two species and they will do that in this way. And if we include synonyms then we'll make sure to get samples associated with either one of these names. So we won't miss potential perimuscus lucopus. Just because there was some uncertainty in the ID. So we want all perimuscus lucopus. I'm going to include synonyms because I do want them all. And then we want vouchers only. So like I said, this is a mouse. So we're going to go to vertebrates. I'm going to click on all of the available mammal voucher collections. So we get mammal vouchers that come as incidental mortalities from neon small mammal capturing protocol. We also get those from outside of standard sampling. So this is if a mortality is found outside of typical protocols that is also archived for research. And then occasionally a small mammal will fall into the pitfall traps that are put out for beetle sampling. And we also prepare and archive those individuals. So I'm going to look across all three collections here. And yeah, I wanted them all. So I am going to do that search. We have 75 of these vouchers. You can see in some of these cases we have these ones where these are from the ground beetle sampling, where they are this uncertainty. And then we have basically the rest of them. The ID is certain. If we went to the species list, we would see this these two different options. And so I want to look, because I also put on my scavenger hunt that you can't see anymore. So how do I find the determination history for an individual. So we now know that this one is paramuscus leucopus did the field technician know that originally or is that something that has been found out later. And so here we can go to the full record details. Oh, you probably can't see this because this came up in a new window. I'm sorry I will bring that over. Okay. Here we have that individual. And it, we can see the full details for this individual. And we can see that it is determined as paramuscus leucopus. And it was determined here by Laura Steger who actually works at the bio repository. And she has given this reference where she has. After the specimen came to the bio repository she has actually followed the protocol in this paper to actually genotype this specimen. So we can see the identification history. And here it actually was also determined to be paramuscus leucopus based on the field work, as well as the, the sequence in bold. So this one we are very sure of. But we may not have had that certainty for some of these specimens. Well, I've found two good ones, but often there is this field uncertainty that then may later be corrected and the new identification information can be found in the bio repository portal. And I also want to point out that you can see here in the records like this, that we also have material samples associated with the specimen. And here, this specimen was prepared by Laura Steger at the bio repository. And not only do we have the steady skin for the specimen but we also have a number of different tissues or organs that have been pulled out of that specimen and frozen and are also available for research. Okay, the next thing I wanted to, I put in the scavenger hunt is how to find a list of specimens that were used in a recent publication that is documenting vile diversity in rodents. So I mentioned before that we create public data sets associated with publications that use neon biorepository samples. So we can find that here in the research data sets and special collections page and we're looking for viral diversity. So there is this 2023 paper that I've found in this list that actually studied viral diversity and used a few of our neon mammal vouchers like those I just showed in the previous search. And here is an abstract for that paper, the link out to the paper, and then we can actually see the three voucher specimens that were used in this paper. When we look at one of those specimens, we can see that that reference is associated with it. And this reference will also be published in the data download for these specimens. And just as a reminder, it is this download button kind of in the top right hand corner of the search results. That is what allows you to actually download that specimen data and those biodiversity occurrence records, as well as other files like the image records and the determination history is also available in a separate file, as well as the list of all of those, what we call material samples like those organs and tissues associated with the vouchers. Next thing on my scavenger hunt was all DNA samples associated with organisms collected at the CP or Central Plains experimental range neon site. So, again, we would go do a sample search. We would want to find all DNA samples. So, we could go through and select only our DNA extract collections like this but there's a much more efficient way to do that of course which is to go over to sample type and just select all DNA samples. And so you'll see that these are either typical DNA extracts or they are pathogen extracts. So there's a different protocol that's used and those samples are used for pathogen testing, but they are essentially a genomic extract as well. So we will select all of those and then the easiest way to find all of the CP or samples would be to go search by locality. You could go find them in a map or put in the latitude and longitude if you knew it. I certainly don't know that for CP or so I am going to actually find the individual site. I do happen to know that it is located in D 10 Central Plains, which is easy for this one because this is called the Central Plains experimental range but you might have to search through if you wanted to select it like this. It is also quite nice that the neon biorepository search form does allow you to search in the locality field by site codes so we could also put CPER right in the locality but either one will work in this case. So as you see in the chips over here we have everything that is a DNA sample and CPER site and that's the filtering that we're doing. We've got 1454 of these samples. Again we could look at all of the record details for these and we could download the data, we could map the data, we could see our species list here. And so we have a lot of species represented here across mammals and mosquitoes and beetles. There are also microbial DNA extracts that would be included in this search result, but they do not have a defined tax on of course because they're a bulk sample so they won't show up in the tax account but they are here in our search results overall list. And then the last thing I wanted to do is another search, but this time I am asking what the number of unique taxa within the asteraceae family is collected at neon sites in the western continental US and you might be able to see how you would do that already using the search form, but I thought I would not want to miss out on at least showing what the map search would look like where you could do this same sort of search. So this brings up a Google map view of the whole world, but we want to filter it. And then let's say we want this western half of the continental US of course my my prompt here is not an exact thing, but we'll say that this is the western US, we want all asteraceae. This is the sunflower family of plants. And then let's search for that. So these are all of the sunflower family samples that were collected by neon in the western continental US and if we want to see those taxa. We can go over to this taxa list tab. So there are 325 different taxa that meet these criteria that were collected by neon and are available in the neon by repository data portal. And in the same way as with the regular sample search, you can download all of these records directly from the map search. So that's just an alternative way of searching for neon samples using our data portal. So that was what I had to share today and I'm really happy to answer any questions about how to use our portal or how to access samples, whatever folks might be interested in. Yeah.