Advanced Analytics for Fish & Habitat Relationships Webinar Recording

by elsa.macdonald@merck.com | Jun 30, 2021 | Biological Services, Webinar 

Understanding what features comprise high quality habitat is critical to endangered species recovery. Ecological datasets often incorporate nonlinear relationships, correlated variables, and substantial noise: all of which make establishing the relationship between species and their habitat challenging. Biomark researchers have developed advanced analytical tools that pair abundance and habitat characteristics data to define these elusive relationships. Leveraging a suite of modeling techniques such as habitat suitability (HSI), habitat preference, and quantile random forest (QRF) allow for a comprehensive approach to evaluating habitat quantity and quality.

This webinar recording showcases how generating near real-time estimates of carrying capacity by species and life stage, can provide actionable information for habitat restoration and recovery planning.

Biomark Applies Novel Methodology to Endangered Salmon Populations in the Pacific Northwest

by elsa.macdonald@merck.com |  Jun 23, 2021  | Biological Services, New from Biomark  

Biomark Applies Novel Methodology to Endangered Salmon Populations in the Pacific Northwest

Research Study Demonstrates Robust, Efficient Approach for Salmonid Conservation

NEWS RELEASE

FOR IMMEDIATE RELEASE    

Media Contacts:         

Elsa MacDonald                                                         

+1 (208) 985-4452 | Elsa.macdonald@merck.com

Jeanette Lewis                                                           

+1 (973) 937-5508 | Jeanette.lewis@merck.com

BOISE, Idaho, March 9, 2020 – Biomark today announced the publication of a research study designed to estimate the carrying capacity for juvenile salmon using quantile random forest models, which demonstrate the viability of guiding habitat restoration efforts that could de-list salmon from the endangered species list.

The research study, entitled “Estimating Carrying Capacity for Juvenile Salmon using Quantile Random Forest Models,” [manuscript number ECS20-0483.R1]  was published in Ecosphere, a journal of ecological science and interdisciplinary studies relating to ecology.  

Endangered salmon populations in the Pacific Northwest are facing the loss or degradation of their stream habitat throughout the interior Columbia Basin. Recent published studies have suggested that their recovery may be constrained by a lack of capacity or a lack of high-quality habitat. However, understanding what habitat characteristics define high-quality habitat is confounded by large, convoluted datasets with non-linear relationships, correlated variables and outliers.

“In our research study, a quantile random forest (QRF) model was developed using fish and habitat data from seven watersheds in the Columbia River Basin to estimate life-stage specific habitat-based carrying capacity. This new approach leveraged nearly a decade of detailed habitat data from the Columbia Habitat and Monitoring Program (CHaMP) to determine habitat characteristics that best explain salmon abundance and density, which is used to predict contemporary capacity at those sites and extrapolated throughout the basin,” said primary author Kevin See, Senior Biometrician, Biomark.

While stream habitat rehabilitation actions are taking place in many watersheds within the Columbia River Basin, the potential improvements to carrying capacity for an individual action may not be reflected in observed fish abundances for many years. This research study demonstrates one way to infer the effect restorative actions have in near real time by focusing on how habitat restoration translates  directly to fish capacity. Historically, the response to capacity changes by fish populations may take years or even decades to manifest, making the evaluation of those actions difficult.

As more ecological datasets become available, and the ability to sample large areas of habitat becomes more feasible (e.g., aerial imagery, LiDAR), the QRF framework demonstrated in this study provides a robust structure for using a capacity-based approach to prioritization, implementation and evaluation of habitat rehabilitation actions.

View the Full Publicaiton Here

About Biomark

Biomark is a worldwide supplier of electronic identification and related monitoring systems to the fish and wildlife conservation communities and aquaculture industry. Biomark is an Aquaculture portfolio of digital products within Merck Animal Health.

Biomark specializes in low frequency RFID (radio-frequency identification) tags also referred to as Passive Integrated Transponder (PIT) tags and related monitoring equipment and services. They integrate these products by focusing on in-house design and manufacturing and providing installation services and maintenance. The monitoring systems collect identification data at specific and strategic locations to provide researchers valuable animal intelligence for management decisions. Biomark also provides specialized services including fish tagging, statistical analysis, software development, study execution, report writing and computational model development to support statistically robust solutions.

Founded in 1990, Biomark continues their specific focus on animal identification and monitoring that enables them to lead the way in product development, innovation and data solutions, positively impacting conservation, restoration and smart management.

For more information, visit www.biomark.com and connect with us on LinkedIn, Twitter, Youtube, Instagram, and Facebook.

Netherlands Workshop

by elsa.macdonald@merck.com |  Jun 21, 2021  | New from Biomark  

First of its Kind Spillway PIT Tag Detection System

by elsa.macdonald@merck.com | Jun 10, 2021 | Featured Projects

The lifetime of projects is not always a decade in the making, however that was the case for this Biomark project. It began in 2006, the National Oceanic & Atmospheric Administration (NOAA) Fisheries, with funding from the Bonneville Power Administration, initiated a research and development project to develop a spillway PIT tag detection system.

PIT tag detection systems were present at juvenile bypass systems and the majority of fishways in the Columbia River, but there was no way to detect PIT-tagged fish passing through the spill. Yuri Smirnov led the design of all antenna prototypes, the Biomark F3001 transceiver, as well as, the half-telegram tag or “Fastag” concept.

The final system: transceiver, antenna and tag, provided tag detection of nearly 50 inches above the antenna, far exceeding today’s standard low-profile or pass-by antennas where 24-30 inches is acceptable. Tests conducted at NOAA Fisheries facility in Pasco, Washington demonstrated that a standard 12-mm FDX-B tag could be detected at 30 inches above the antenna while traveling 70 feet per second, that’s almost 48 miles per hour. This past December, personnel from Biomark, NOAA Fisheries and the Pacific States Marine Fisheries Commission tested antennas at different points of the spillway and found that performance exceeded the figures from the initial install tests. The system will begin full operation in April 2020 and the region is anxious for this first of a kind spillway PIT tag detection system.

Recording of Sea Turtle Tagging Database: The Dedicated Repository for Sea Turtle PIT Tag Data Webinar

by elsa.macdonald@merck.com |  Jun 4, 2021 | Webinar | Comments

Biomark and Loggerhead Marinelife Center have partnered to develop a free, password protected data repository and sharing platform for sea turtle tagging data. 
Video transcript:

00:00

All of you for joining us today. My name is Chris Beasley, I’m the director of the applied biological Services Division at Biomark. So my coworker Dr. Sarah Hoffmann will present today on a collaborative initiative to launch a unified database for sea turtle mark identification and metadata. So unfortunately, Sarah and I were looking forward to launch this initiative at the ISTS meeting scheduled in Cartagena, Colombia earlier this year, but COVID changed those plans for I think, all of us. So instead, I’m transmitting live today from my really cold, decidedly dirty and certainly unorganized garage here in Meridian, Idaho. So this is my temporary workstation as we’re trying to maintain social distancing at Biomark. With that said, I hope all of you and your loved ones and colleagues and friends and family are safe. And just wanted to say that I really respect you guys and appreciate your participation in this webinar today. I think it’s just a testament to the dedication that have received to continue to advance science despite all of the challenges that are thrown at us. So, guess I’d like to introduce Dr. Justin Perrault, director of research for Loggerhead Marine Life Center. He will act as our moderator today. Despite the fact that we can’t meet together in person right now, we want this to be an interactive presentation. So please take advantage of the chat feature and send questions. And Dr. Perrault will interject those questions during Sarah’s presentation. So with that, I will turn it over to Justin. Oh, one other thing I guess I would mention that all the panelists will stay online after the conclusion of this presentation for anyone who wants to stick around and talk about other ideas or get a bit more information on this initiative. So Justin, please take it away.

 01:51

Yeah, thank you guys all for joining like Chris said, We I will be the moderator. So any questions that you guys have, you can just direct them to me and then Sarah Hoffmann will be doing the majority of the presentation. So I’ll kind of interrupt her as we go along here and throw those questions out here as you guys come up with them. And we’re also joined today by one of my co workers, Sarah Hirsch, who’s the senior manager of research and data at loggerhead Marine Life Center. So we kind of started this partnership with Biomark, all of you are in the turtle world that are on here now, and you know about all of the tags and numbers that we all use and try to figure out where these turtles came from. So this partnership kind of developed really naturally. And we’re excited to get this database going and off the ground, and we hope that it’s successful. And with that, I’m happy to let Sarah Hoffmann take it away.

 02:44

Thanks Justin, and thank you everybody for tuning in today. I want to preface this with the fact that I am a shark biologist by training so I will rely very heavily on Sarah and Justin to help me out with the turtle part of things. But I really got involved in this type of program after doing some work and acoustic telemetry and seeing how effective these cooperative telemetry databases are for different types of research. And then, through my involvement in Biomark and the PIT tagging world, we saw the need to figure out a way to more efficiently share data and put researchers in communication with each other to track down these mystery tags and really leverage the re-sight data to their fullest potential.

So with that, I just wanted to start with a little bit of information about sea turtle tagging, and I won’t belabor it too much since I’m sure we are all here because we are interested in either sea turtles or tagging. The earliest record that I could find, though, of tags being used in sea turtle conservation was back in 1917, a mark recapture study, and they had a remarkable a 166 recaptures with the longest time at liberty of five months. So I know that we’ve come a long way since then. But we are continually looking at ways to be able to identify individuals as we go about scientific studies. So since the time of rubber bands on flippers, our technology has advanced quite a bit.

So we have a number of different of different tagging technologies these days, both in the form of visible external IDs as well as these implantable or transmittable tags. So perhaps one of the most ubiquitous tagging options are flipper tags, which are cost efficient. They’re very conspicuous, and they don’t require any additional technology to decipher the code. So at that point, it’s just being able to get in contact with whoever the original tagger was. Living tags are another conspicuous tagging mechanism that have been used. However, it’s a little more invasive. Oftentimes, a turtle has to remain in captivity to ensure healing, and there is more information that would need to come through the original tagging organization. The final conspicuous tagging method that I can think of is the either chalk or paint markers. However, we know that those are a relatively short term tagging option, but arguably the least invasive. And what I really wanted to demonstrate with this image is that oftentimes tagging mechanisms are used in concert to leverage more information we can provide given one individual, the greater that we can leverage these sampling opportunities. So as you can see in this image as well, this is an acoustic tag that has been attached to the carapace. So we have here multiple examples of tagging that are occurring on one individual. And then another transmitting tag that we can think of would be, of course, the satellite tags. So for turtles, fortunately, they surface enough that you are able to transmit some of those data or for other species that don’t come to the surface, we have that pop off opportunity with a galvanic time release mechanism. But again, just another opportunity to follow these long lived migratory animals.

And that brings us kind of back around to the PIT tag world, which is where we as Biomark play a little bit more in this community. So PIT tags are a great opportunity to provide unique ID, they’re really ideal when we think about the longevity of a tag, so there is no battery associated with a PIT tag. And it doesn’t really have the opportunity to fall off. So they do have a great longevity. They also have a relatively high retention rate. And then compared to some other tagging mechanisms such as internal implantation along the body cavity, or added tag burden on the carapace, we can consider them relatively minimally invasive. So, for these reasons, we have seen that PIT tags have been a good tool for the sea turtle community, and hope to figure out ways to continue the spread of their use.

 07:49

And with that we lend we’ve been leaning towards this idea of a cooperative telemetry platform. So the value of a tag is inherently tied to its re-sight potential. So whenever you can see an individual again and again, you’re always gaining more and more data about where that animal is being seen, how much that animal may have grown, and so on. So the ability to collect all of the data possible and share and tie all of that data to one individual is a really useful opportunity. And this has been recognized by a number of groups throughout the research community. I’m going to start by talking about PITAGIS, which is near and dear to our hearts in Boise, Idaho. So PTAGIS is the Columbia River Basin PIT tag data program. And this was created to track salmonid and other riverine fish throughout the Columbia River Basin back in 1995, and it was a way to standardize data collection as fish, particularly anadromous fish, were migrating throughout the system. To date, there have been over 48 million fish tagged with over 18 million unique detections. And there are 38 participating agencies in the region. Now, a lot of the success of the program came from mandated participation. So certain groups if you were to receive funding or permitting from some agencies, they would require you to enter your tag into PITAGIS. So this has been a really great regional effort to get a better understanding of how these populations are working at a larger scale, despite the fact that there are so many smaller scale projects operating within this umbrella.

Another great example of this type of data sharing platform is the Ocean Tracking Network or ONT, and all of their partner nodes. And OTN has really grown into this global repository for acoustic telemetry data. I know for example, when I was working in Florida, the Florida division, or FACT, was responsible for maintaining arrays along the coast of Florida, where data were openly shared between researchers that were getting other people’s tags on their receivers. And, according to OTNs more most recent report, they have over 58,000 tagged animals with over 170 species, over 180 participating agencies and over 326 publications. And particularly if you dive into this literature, you will notice that many of these movements are recorded throughout a number of different states or even countries. And so they’re entirely dependent on other people’s acoustic receivers in order to recapture that data, which I think you could argue is similar for turtles that are also highly migratory.

And then the last database that I really wanted to point to here is something that is very active and very helpful in the sea turtle community, which is the Archie Carr center for sea turtle research, their online flipper tag inventory, the sea turtle listerv, which is an immensely useful tool and then also the cooperative marine turtle tagging program. And as per their website, they’re issuing about 10,000 flipper tags per year. On the sea turtle listserv, they have over 1600 subscribers from over 50 countries and then over 340 publications. So just from at first glance alone, we can see that cooperative telemetry has a really big impact on getting researchers in contact with each other and sharing information that would otherwise be missed, especially beyond the scope of what can be recaptured within an individual project or an individual region.

 12:12

And so the data or the benefits that we see to these cooperative telemetry platforms are first of all, just increasing the scope of the data. So being able to locate these “mystery tags” that you may have come across in your regional study, or finding data on individuals that you tagged that have exited your regional study. And then putting the sharing of data directly into the hands of the researchers, is a way to foster global collaboration between groups you may not be familiar with, so opening up that line of communication and seeing where animals are moving may help the bridge of information and collaboration between groups. Similarly, we see that these data may benefit multiple kinds of studies, whether they be ecological, or age & growth, or movement studies, there are a number of multi disciplinary data that would benefit from increasing those re-sight potentials on tagging opportunities. All of these things together are also beneficial to our fourth point, which is the enhancement of funding opportunities. So, funding agencies may be more likely to fund multidisciplinary or multi collaborative studies that have the potential to or the infrastructure rather to gain all of the data potential from tagging opportunities. And as we’ve seen, through both the acoustic telemetry community as well as the PITAGIS community here in the Columbia River Basin, having some standardized method is a good way to ensure accuracy. And because consistency among studies, especially when there is a big push towards long term status and trend monitoring, so making sure that the data that we collect today are going to be beneficial down the line as well. Another benefit to hosting all of your data in one repository is that if something terrible happens, and you were to lose your data, you do have that cloud backups. So it’s just another insurance policy for that long term legacy data just in case bad things happen, which those of us who work in the field know is not that uncommon. And then finally, one of the last, or maybe greatest benefits to cooperative telemetry is that you’re expanding your spatial and temporal data. Which has big implications for global data management. So particularly as these migratory and long-lived species are moving through different regions, states, countries, we have the opportunity to provide evidence on this global scale.

So all of these reasons led us, being Biomark and Loggerhead Marinelife Center, to partner to build the sea turtle database. And what this is, is a free, open access platform for researchers to share their PIT tag data. And our mission is to facilitate integrative global collaboration through partnership and data sharing, stimulate advanced research and technological innovation for sea turtle and habitat conservancy, and then leverage you all this network of experts and data driven science to inform policy. So just expanding the conversation and leveraging all of the data that are available.

 16:06

We just had one question come in, it was just, you know, kind of explaining how this is different from some of the other sea turtle tagging databases that already exist, particularly with like the Archie Carr database?

 16:18

Yes, that’s a great question. And so the way that we have set up the sea turtle database is to put that communication directly into the hands of the researchers. So we’re going to walk through the website in just a second and you’ll be able to see where you can actually look up a tag, and it will provide you with that researchers contact information. So it’s sort of eliminating that third party, and we don’t see it as competing with, but rather in addition to the existing databases like the Archie Carr database and more focused on the PIT tag ID. So I think that it is going to add an additional layer of data, which already exists with the Archie Carr database.

Okay, and so when we developed the sea turtle database, one of the biggest things that we wanted to tackle was data privacy and sharing. So all of us working on this project, we are researchers ourselves, so we understand the importance of keeping your data private and secured, but then also working in collaboration to expand the breadth of your data application. So the way that we decided to tackle this was through an approved user registration system. So in order to gain access to the data side of the database, you do have to be an approved user. So when you go to register, registration is going to be contingent upon your affiliation, so either by email address, address, or some other form of evidence that you are an active sea turtle researcher that will be contributing data to the database. At that point, your data privacy is going to be established at the project level. And that’ll make a little more sense as we start walking through the database as well. But every researcher is going to have the ability to create a project and then associate tags and data to that project. And it’s that project level at which you will be able to decide whether somebody looking up your pet tag is going to be able to see either just your contact info if it’s a private data project, or more data associated if you choose to make it public. Additionally, we, the partners, agree not to use distribute or publish any data so nobody will be able to email us and ask for the dissemination of data. Well, I suppose they can ask but the answer will be no. And then we also agreed to not use any of that data for any meta analyses or anything like that. And this would be agreement to our data privacy and sharing policy is agreed upon with user registration.

Okay, and I suppose without further ado, we will start walking through the database and how it works. So the web address is www.seaturtledb.com. And what I will point out is that this is our first time demoing it. So what we’re really hoping for from this community is feedback on features that may or may not be useful things that you do or don’t want to see. So we’re still in that development process and we would love to hear from you as we walk through this about features that you may find useful. So the first thing that you see upon going to the sea turtle database website is our admission. And then it’s going to ask you to register for access. And what I’ll point out is that without registration, these are the four tabs that you see. So you see a history of our of our project, as well as our data policy. Within that, you will also see tabs for frequently asked questions, contact information, and then the ability to register.

 20:32

We have a list of frequently asked questions that have not been asked yet since this is day one of the demo. But I think the biggest thing here, or the biggest question that we anticipate is why would you need to register and again, the reason that we decided to make this an approved user forum is just for an added layer of data privacy, so ensuring that everybody in the community or everybody is active in the community and contributing to this resource. So if you then decide to register, you can click on this tab up here. And, again, the way that we are currently going about approving users is through their organization or affiliation. So for example, for loggerhead if you have an at marinelife.org email, we can assume that you’re associated with Loggerhead Marinelife Center, and that would give you access behind the registration wall. We are would also accept things like recommendations or if you have publications or presentations that demonstrate that you are actively working within the sea turtle community those would be accepted as registration material as well.

So once you are registered, it will open up additional tabs for you. So what you will see, once you have logged in after your registration has been approved, is first of all this lookup tag. So that is going to be where you would search a mystery tag that you came across. There’s also a forum, and then the ability to enter and edit any of your data. And so I wanted to start with the forum. We built this as a way for researchers to communicate with each other, potentially share publications or start community conversations. So for example, one of the things that we thought of being on the tag side of things is that if groups wanted to order tags together in order to achieve both bulk discounts, that’s an example of something that could be discussed or arranged in the forum. Other things that we see with potential within the forum is the ability to publications or collaborate on projects together? Or perhaps even hunt down mystery tags that aren’t available in that tag lookup.

 23:10

The benefits of those another question coming in at those bulk tag orders.

 23:16

Sorry, would you repeat that?

 23:17

Yeah. Can you like, what would be some of the benefits of like both tag ordering?

 23:23

Yeah, that’s a great question. Um, the way that we sell or we the way that we price tags at Biomark is based on volume. So if you increase the volume of your order, you’ll be receiving discounts on those tags. So for example, Justin, I’m going to use you as an example because you’re here but for example, if loggerhead wanted to partner with other tagging organizations in the area, you could all order those tags together and distribute amongst each other by using that bulk discount, just as an example.

Okay, now Moving on to the data side of things, one of the probably biggest uses once you are registered user is going to be to import your data. And as I had mentioned before, this really starts at the project level. So when you first register and you first go to the my data tab, it will look like this. You don’t have any projects created yet. So you click on that add a project button, and it will prompt you to enter some of your information. So for the sake of this demo, and not putting incorrect data into the database that could be misconstrued, we are going to be exploring the movement and behavior of inland sea turtles in an isolated lake of northern Idaho. So at the project level, you are going to name your project, give a start date, you’re welcome to give an end date if it’s a historic project, or you can leave that blank if it’s ongoing. And then you can also give a general location for the project as well as a description. And then here’s where you will have the option to either make all of the data associated to that project, either private or public. So for the sake of moving forward, I’m going to leave this as public and show you what that looks like in the tag lookup down the line. And it’s worth noting that at any point, you can go in and edit any of these fields, including your privacy, so you can turn your data from public to private or vice versa, once the project is already established.

 25:36

Sarah, we just had another question come in. It’s can you add data to an existing project that’s created by somebody else?

 25:46

That’s a great question. And yes, we are you do have the ability to add collaborators but you can only add data to a project if you are a collaborator on that project. So for example, if somebody else was wants to add data to your project, you would need to go in and add them as a collaborator to have access to that data.

 26:14

Another one just came in, if you wanna just hold on one more second. It’s a good one. If you’re associating people to an organization, how do you confirm that they’re actually part of that organization? Or if they leave the organization? How is that controlled for?

 26:30

That’s a great question. And that’s something that we would really be more reliant on the community for. So I think some groups have established a governing board for their data policy, which I think could be a really great option to manage that access. And I guess at this point, it would fall on either the user or the organization to let us know that they are no longer a part of that to remove that data access. And then as far as how if you have an active email address for the organization, that’s what we are basing, registration on at the moment.

 27:13

There’s a few more coming in, I’ll let you like go a little bit further. And I’ll ask a couple more. Okay.

 27:22

Okay, so here in once you have an established project, you will see that you have a number of actions over here on the right. So you can either edit the project, and that’s going to take you to that page that we were at last where you can edit any one of these fields as well as your data, public or private status. And then the more important part probably here is the ability to manage your data. So if you want to add or edit any data, this is how you’re going to do it. And there are two ways to upload data. I think one is probably more attractive, which will be the bulk upload. So I’m going to talk about that last actually. But what I wanted to do is walk you through how you can edit or add a tag manually. So if you wanted to add data, you would go into that edit data function and click add a tag, you then enter the ID species life’s age and sex. These are the only required fields within this current platform. And then once your record is created, you have the ability to go in and add any biological or ecological data that you want to associate. So for example, starting with capture info, in order to add anything, you just click this little plus button, and then you can add any information that you want within here. So for example, going back to our inland sea turtle station, We can say that we caught this turtle at Alice Lake, provide the lat and long in decimal format, and then have that in our capture history. The next thing we would want to do here would be to add any existing tags, there is an indefinite amount of tags that you can add. So, I’ll show you once we get to the bulk upload template, we have it a little bit different. But say you encountered a turtle that had 15 tags on it, you can go in here and add as many as you want. And then for the type, what we have listed so far, our pet tags flipper tags, acoustic and satellite, but we can modify that if there are requests for additional tagging types as well. The other thing that we know is particularly important for pet tags is the location. So we’ve added locations in for you to designate that.

 30:02

we got a couple more questions coming in a few. So it says, Can you specify data within a project as public or private? Or is it an all or none function?

 30:12

The way we have it set up right now is an all or none function. And in a few slides, I’ll show you what that looks like. Essentially, the data that you will receive upon tag lookup, if it is a public study, is the project metadata, so you would have to be in contact with that researcher to get any of the associated biological data with that tag.

 30:38

Yeah, I think you’re gonna get to some of these. I’m gonna hold off on some of these other questions until you get a little bit further in.

 30:46

So the next group of data that we have available are the standard measurements. So again, we’re still very much in development right now. So we can add or modify these as people see fit, but we pulled from the standard measurements that we have seen generally taken across the field with everything in centimeters, and then weight in kilograms, and we do have those instructions on the website as well. And then again, this would all be if you’re adding it manually, you can click in and modify or add any of those measurements by hand as well. All right, these next two fields are both available in the bulk import. But the added function that they have within the manual entry is the ability to add images. So for example, if you want to add a sea turtle injury, and the great thing that you can do within this individualized platform is add in an image. And again, this is kind of where we get to for example, if you are still wanting to bulk upload the majority of your data from a template you will be able to locate that tag record and go back and add a photo in. And then same thing with any other notes. So for example, with this turtle, we noted that you don’t typically find turtles, especially turtles with shark bites in isolated snow melt lakes at 8600 foot elevation, which we found to be a relatively odd occurrence. And yet, we have the photo evidence to document it. So you have to take that as you will. So once you have all of your data in there, this is what an individual tag record looks like. So if anybody if you were to go look up this turtle, again, this is going to be all of the data that you have input into this tag record, whether it’s public or private, only you the researcher who owns the project are ever going to see this screen.

 32:59

So that takes us to the bulk input. If you go to my data there will be and you click the drop down arrow, there will be an option to bulk import your data. I think a lot of people are probably familiar with this. This is just a CSV file that will open into Excel. And then you can add all of your data in that Excel file and then upload the whole file at once. So this is a list of everything that we have on the upload template. So this is everything we walked through. And then right now the only thing that is required is some sort of ID and the species. The biggest thing to think about, as you were uploading data is making sure everything is in text format. Sometimes Excel tries to be more clever than you are and reformat your numbers as dates or things like that. But as long as you have everything in text format and re upload it as a CSV, it should go together smoothly. As I have worked through this, trying to break it as often as I can, it’s always been the date, that’s been an issue for me. So we’ve included quite a few instructions on the website, as well as how to get all of these fields appropriately formatted for about bulk import.

 34:35

Okay, if you want to just yeah, real quick. And I think just this is important for people to know that this is still you know, it’s a work in progress. And we’re open to suggestions, but one that came in is, how are you managing the status of the tags if they’re present or lost at recapture, and I think that could you know, those are kind of suggested good suggestions that people can have to email you guys And let you know of, you know, things that can be modified within the database and you know, things that we may have missed and not thought about.

 35:08

Yes, that’s an absolutely good point. So, yeah, thank you for pointing that out. Justin Again, we were really hoping to have this be more of a conversation to figure out how we can make this as useful for your community as possible. So please don’t hesitate to contact us with suggestions like that. It’s a great point.

And I’m almost done talking, I promise. This is just to prove to you that the bulk import does work. So here are all of the turtles that I imported using the template. And now we have that within our project data record. And then the very last thing that I wanted to show you was how this tag lookup works and what it shows when a study is public versus private. So if you look up a tag and it is in the system, but that project is marked private, all you will receive is my contact info or the contact info associated with the tag. One thing that we are one way that we decided to structure with this was that if multiple organizations have encountered that tag, so say, loggerhead tagged at first, and then it made its way up to South Carolina, then you would have two emails listed here. So every encounter associated with an organization is associated with an email. So whenever you search that tag, you’ll have that full record of everyone who has ever encountered that tag. And then if the data were instead marked public, what you will, or the way that we’ve designed it right now is that you will receive all of the project data so you’ll receive the date that it was tagged the project and then the location of the project. This is something that we’ve been talking about, and we could very easily make this a tiered approach where you’re receiving some biological data or lat an long. But mainly we’re trying to get a gauge on how willing people are to share their data and how much data people would want to make public. So that’s, again, sort of the feedback that we’re looking from you guys, and what you think would be most useful. And that’s really all I have. So now I would really like to open it up for questions and conversation.

 37:39

Yeah, we’ve got a bunch of a couple of questions in the queue. One is, I think this is in there, but I may have glossed over it briefly. It was Will you be able to input FP data or fibropapillomatosis data and I believe the answer is yes on there.

 37:55

Yes. So we do have we have columns for injuries as well as tumors.

 38:01

And a couple other questions a couple people asked, Can you talk a little bit about the institutions that own the sea turtle database and how the database will be sustained over the long term?

 38:15

That’s a good point. Um, right now, so we developed this for free. And as I mentioned, we are not using any of the data or anything like that, and fortunately, the annual hosting costs are relatively minimal. What we’re really hoping to do is develop some sort of partnership with other organizations in order to help keep that aloft. And what that funding would also do is implement additional tools like the ability to download tag histories or the ability to format all of your annual tag history into your FWC reporting metrics or things like that. So right now the plan is just to, we’re looking for partners. But as of right now, it’s just us, Biomark and Loggerhead hosting and maintaining it. So that’s maybe not the best question for you, or the best answer for your question. But that’s kind of step one right now was just figuring out if this is something anybody would even use, I guess. And so as we move forward, and as we assess how many people are using it, if people are using it, then we will, we will figure out what to do in the long term.

I see on that question also is Do you have an app to collect data? And can you run the software offline? Right now, no, the software cannot be well, I guess it can be run offline in that you can download the template and import all of your data into that template offline and then maintain or you know, come back online in order to import it. But that search function is dependent on the cloud database. As far as the app to collect the data, we do. So Biomark has a data collection module application that we are working on modifying that if you use the DCM software, it will automatically push those data to the cloud. So that would be the app based form of that are of this data collection application.

 40:28

And some other ones or if you get notifications, if someone recaptures a turtle from your projects, let’s say someone looks up one of your tag numbers with you, that was tagged by us that LMC would we get like an email saying somebody looked up that tag?

 40:44

That’s a good question. And I don’t think that we have that in place, but I think that should be something that is in place. Yes, that your tag has been searched. So perhaps a mutual exchange of contact information at the very least

 41:00

Any plans for developing this and other languages?

 41:05

Oh, geez, yes, you’re right, we probably should. That’s a great question. And something I will add to our list. I think, you know, one of the biggest imperatives behind developing this was for that global collaboration. So, we’ll look into, I know that there are a couple like program add ins that can translate everything for you. So I will look into how we can get those running.

 41:32

Some others are if a turtle is found and entered into your system, will that be shared with the cooperative marine turtle tagging program so that they can update their files as well? Or will that just be will they need to contact them separately?

 41:47

I think right now, it would have to be a separate process. One thing that we really wanted to do as we as we develop this was put everything in the hands of the user. So we wanted to ensure everybody that the data that are entered into the database stay there, nobody is going to disseminate that data outside. So perhaps we can make, you know, add in a feature that would do so. But right now everything is researcher to researcher.

 42:19

That’s what kind of goes on. So if you’re encountered a Florida turtle in South Carolina, and you observe the tag there, are you able to see its original history? So say two people entered the same tag would there be? What would it just come up with everybody’s contact information to contact one another? Would you be able to see the full history of that tag?

 42:44

That’s a great question. And it’s totally dependent on the previous organization’s data privacy policy. So say that turtle was tagged in Juno, and then it was spotted again, in Jacksonville and then it was spotted again in South Carolina, if the group in Jacksonville had their data as private, then you would just get that email address. But below it would be the full history if the group in Juno decided to make that data public. So that’s kind of why we organized it that way in order to give different organizations different levels of data privacy.

 43:25

Going along with that this one just came in is so would the database prevent, like duplicate tag entries?

 43:32

No. So right now we don’t have where you can’t have duplicate tag entries. And again, that’s just to allow users the ownership over their encounter. So you even if so say you recapture a turtle that already has a PIT tag in it. You will put that PIT tag in if you want into the import function, and it will associate those histories together. But it won’t. So it’ll associate the records together, but they will be two separate capture records if make sense.

 44:17

There’s probably a few, four or five more, will you be able to change the contact information for a person who has left the program, but also may have collected the data? So I guess if somebody maybe leaves your facility and you don’t want them having access anymore, you know, is that an option?

 44:37

Yeah, that’s a great question. And maybe that’s a better question for those of you who work on an organizational level. I don’t know how data ownership is handled by organizations, do you Sarah Justin could you maybe speak to that?

 44:56

Sarah, you wanna have any you have anything to say on that?

 45:00

I do think that depending on the project and and depending on each organization, I think everybody kind of has a different agreement on what projects with the researcher versus stay at the institution, depending on what that relationship looks like after the person has left. I will say that because this is based on an email address, if that email address is no longer active at that organization, and that kind of provides some of that.It would be something that we would have to I guess, work with the community in terms of making sure that email addresses are kept up to date and that if you do change organizations, whatever projects you’re, you’re changing to and from have the appropriate access either through a collaboration with the individual so if I left one organization, but I still want access to that data, I could request that access through whoever is still at that organization I want that makes sense.

 46:17

So maybe one way to get around that is to have like data@marinelife.org be the governing email associated and then you can associate individual researchers as co-PIs on that account.

 46:38

So some other interesting questions. As you know, the use of this is not just specific to Biomark tags. So you could potentially enter ID tags that are other brands like a bid or some people are asking about entering you know, metal flipper tags as well.

 47:00

So we do have there are options for any type of flipper tag. So when you go to enter data, you have the option to enter flipper tag, PIT tag, acoustic tag or satellite tag. And again, we can modify that if you feel that there are additional tag types that would be useful to have in the database. And yeah, that’s a very good point. So it is not brand specific. So any tag from any manufacturer is welcome in the database. I know that, you know, one of the one of the benefits to potentially using tags that are made by an ISO or ICAR standard manufacturer is that you won’t have PIT  tag repeats. So that’s where having if you have a more or one tag show up in the database multiple times it can generally be assumed that it’s the same tag that has been recaptured multiple times. But certainly there are no manufacturer exclusion. Any data are welcome.

 48:11

I think this kind of goes along with just some suggestions that people are having to improve the functionality. But, you know, some another query or another input box might be, you know, how do you report the final sighting so you might have a disposition you know, drop down list that says, like, released alive or died in rehab or, you know, stranded dead or something like that.

 48:38

All right, couple more, I’m trying to keep up with all of them. So, um, so one, this is a good one. So as an individual user that would like to extract data, how robust are their functions for querying?

 48:51

That’s a great question. Do you mean data associated with a tag that has been recaptured by other groups? So I think those are going to be two different answers largely dependent on what those other groups have deemed their project or data privacy status as. And I think this is where we have really turned into the funding territory, right. So we were able to develop this database and we can certainly host it at a relatively low cost. But as we begin to add functions like that, we start to, we would need to be able to fund a data manager or somebody to develop these queries. So that’s kind of where we’re looking for partnerships if that’s the kind of things that people are interested in. But certainly, those are options that come with the time and funding to do so.

 50:00

I think a lot of these questions that are coming in are kind of suggestions or just, you know, ways to modify this and make it as user friendly as possible. So it may be best for us to kind of follow up with this with maybe some kind of survey or something where people can go in and, you know, give suggestions like a lot of these questions are having about, you know, just who has access and how to give access to multiple different people at an organization or certain things like that. Yeah. So somebody asked, Can you repeat what you said about the turtle ID? Is it created by the researcher or by the database? And if it’s created by the researcher, will that matter if that same idea is used for different projects?

 50:41

Yes, that’s a great question. The encounter ID is created by the database. But if you see the ID that is put into any of the tag ID fields that is created by the researcher so that’s why tags IDs that match will be associated to one another in the database, but they will have different encounter IDs.

 51:10

Yeah, there’s just some other a lot of these suggestions. So is there a way to designate like, nesting female like for us at loggerheads, you know, we have 1600 tags are something that are all nesting female, so that just maybe an additional like life stage or something to your drop down list.

 51:25

And that’s actually so how we have that right now is designated in the project stage if it’s a nesting project or an in water project, but we can certainly move that into one of the lower database levels.

 51:42

Will, the database be able to construct trends, graphs, or similarities among data points, or just specifically keep track of the data?

 51:52

So right now it’s designed to keep track of the data. I would really love to see it grow into doing something like being able to make more advanced queries, or even potentially add in some GIS functions to look at spatial movement, but again, those are all hopes and dreams. And ultimately, we’re really hoping, you know, there’s a lot of funding through like NSF, for example, that helps fund database work. And so we’re really hoping to partner with some groups who would be interested in helping us find the funding to be able to do that more advanced work. So that was really one of the big things that we wanted to talk to people at ISDS about is finding these collaborative partnerships. But we did want to demo the database as a place for data to live and connect researchers to one another, since that is the functionality that it does currently have.

 52:48

Um, there’s a couple good ones just came in, to add the manufacturer of the tag to possibly prevent duplication of the same tag numbers. I think would be particularly useful with maybe with flipper tags. You know, if you’re not getting it from directly from Archie Carr, there may be the possibility of getting a duplicate tag number.

 53:11

We can absolutely add in a field for a tag manufacturer.

 53:15

Nice one that came up maybe just to me that says would there be a recommendation timeframe for inputting data, for instance, fact otn likes one to two times per year minimum, similar for ACCSTR, but I get tagged returns from five years ago. So I think that’s a really great point. And that’s something that the acoustic community has done a really good job with because they are reliant on each other’s receivers to get their data. I think it would be really great to have a timeframe recommendation. Two times a year seems like a really achievable timeframe for us. I think that I don’t know how you would enforce participation since this is all totally voluntary. Any data that you put into the database is ultimately to help you if somebody recaptures your tag. But, you know, the enforcement of that is really upon the community. And those who are reliant on those recapture data.

 54:17

One more that I think it’s as kind of the overarching goal of this whole thing is, you know, what is the plan and this was a little bit thwarted by COVID, and not being able to go to ISTS. But what is the plan to roll this out and advertise internationally?

 54:33

Yep. Yeah, I think Justin, you pretty much hit the nail on the head is that we were really hoping to roll this out at ISTS. And I think that over the next year, we really look at the path forward as a learning opportunity to see how we can improve. And again, I think, personally, I’ve been blown away by how many people are just here attending so we really appreciate your attendance and this was really an opportunity for us to see if people are even interested in a database like this. So hopefully that’s a yes. And hopefully now we have some good suggestions for moving it forward. And I think that meetings are definitely going to be a good way to get this out to the international community. And as well as somebody else had mentioned, figuring out how to get this in multiple languages. I think it’s a really good starting point as well.

 55:26

We have a couple more questions coming in. But I know we’re kind of right at the time limit. So I’m not sure how you wanted to proceed.

 55:32

I’m happy to stay on and answer. I think this is really helpful for us.

 55:37

yeah. So I think we kind of chatted about this the other day when we were kind of running through this, but you know, the functionality of this as maybe a larger a lot of people just use Excel right now as their main kind of database. And would there be a way for a researcher to export all of their tag data from a specific just one specific project

 56:00

So our developer’s actually adding bulk export, probably right as we speak. So, yes, that would be an option.

 56:08

So this is kind of interesting, and I think would be, you know, as we get suggestions from people, and I think this would go along with that. But you know, there is just an example, if an injured turtle with tags is captured than Florida, sent to rehab in Georgia, would it be appropriate for one or both of the organizations to report the tag data? You know, because oftentimes, turtles that strand don’t have tags. And so the rehab facility in Georgia may put those tags on when the turtle was initially found in Florida. So that may just be kind of some of that location data that goes along with entering some of the data.

 56:47

Yeah, absolutely. And right now we do have options for you know, there’s capture information and release information. So that would be captured there, but I think that having a way to add a collaborator to a tag rather than a project may be useful as well.

 57:05

Um, someone wants to know how many people are on this call? I don’t know if you can tell us that. But, you know, just to see the level of interest.

 57:12

Yeah. So we had over 100 registered registrants.

 57:19

There’s one other one that I think might have come to me that says adding genetic data if genetics collaborators are interested would be a nice addition. I definitely agree. So definitely not just for physical tags. I know less about genetics than I know, sea turtles. So if you would want to reach out and collaborate I think that would be very helpful.

 57:44

I think I got pretty much everybody’s a couple of them were kind of duplicate or similar. But as of now, I’m not seeing anything new up on my end.

 57:55

That’s it. I think you had a really good idea to send out a survey. So we’ll see probably send out a survey to everybody who registered as well as maybe just the listserv in general. And as always, please don’t hesitate to contact us. Or if you have thoughts about how we could target some of those federal grants to get something up like this up and running. This is sort of a grassroots push right now. So we would also always really appreciate any feedback or collaboration.

Can we add necropsy data? Yeah, that’s an interesting one. I think that we can add pretty much any field under the sun that you want. We just have to decide what’s going to be most useful. And again, as we add functionality or fields or things like that, it’s totally dependent on funding opportunities.

 58:56

I think that’s pretty much it from what I’m seeing on my end. So, you know, thank you, everybody for your interest. This is more than we ever expected. And we’re really happy with the turnout with this. And we hope that this can be successful. I think this would alleviate some of the struggles that we have when we encounter these unknown tags and trying to you know,

 59:24

I think Justin might have frozen, but I will just continue to Oh, are you back?

 59:31

Cut out? Yeah. Just saying thank you to everybody. That’s it.

 59:36

And then we’ll stay on the call for just a couple minutes afterward if people have things that they want to ask us. But we did record the webinar, and we will send out the link to anybody who was registered. So feel free to pass that along. It will also live on our website. So with that, I think that we can probably end the recording and If you have any questions for us, we’ll stick around for a couple of minutes. Otherwise, thank you to everybody. We really appreciate your time and your feedback.

 60:26

Now we can go back to talking about our dogs

Please contact Sarah Hoffmann at sarah.hoffmann@biomark.com if you have questions.

We look forward to your thoughts and suggestions as we roll out this platform!