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BITC / Biodiversity Inventories - Introduction to the BITC I

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Good morning and welcome everybody. Thank you Dr. Mafane and Dr. Fokam. And thank you in absentia to Moses for the welcome. I'm always in this strange position of welcoming you to somebody else's house and so I have to thank our hosts, and at the same time thank you for coming because I've always felt quite at home on all the previous courses and now on this course here in Cameroon. What I'd like to do in a couple of talks, is give you an introduction to the broader training curriculum program, give you a brief overview of the idea of biodiversity informatics, and then give you a specific introduction to this course. One flaw in my design of this morning is that I don't introduce the other instructors and you all until end of the end of the morning. That's not for lack of appreciation. It's just that it seems like it comes at the right time then. The Biodiversity Informatics Training Curriculum was born very slowly over the last decade and a half. It goes back to a series of training courses initially in Mexico and Brazil, and then, with global support, there was a series of courses mostly focused on ecological niche modelling. Those courses were held on 4 continents and had participants from 70 or 80 countries. Those were all, in many senses, a rehearsal. Partly because they were all on the same theme -which maybe some of us are now tired of doing courses on- so we're not doing that one anymore. But also, they were rehearsals technologically because they really reached the trainees in the room and not much farther. I think now with expanding reach of the Internet across the world, now we have the opportunity to make these courses go a bit farther. Dr. Mafane and Moses mentioned some things about biodiversity informatics. Let's go a little bit deeper into that. It is a new field, which is to say there is no textbook. You can find a textbook on population genetics or on phylogenetics or on systems ecology. This field is very different. In some senses, it's one of the oldest fields. You've heard of Carl Linnaeus and what he gave us was a wonderful information system by which to catalog and document the organization of life on earth. And museums, for literally centuries, have built information systems that allow people to access and retrieve data on biodiversity. So in one sense, the science of managing information about biological diversity is extremely old. And, then in another sense, it's extremely young. The digitization of biological collections began about 1980. That's probably older than most of you, but younger than some of us. The first collections digitized were done in a very skeletal fashion; that was because of storage space. Each of you has a laptop here that could hold easily everything that was a huge data file back in 1980 or 1985. So really, this field has been technology-limited from the outset of at least the new version of it. But suffice it to say there are no textbooks. There really are very few or no comprehensive graduate programs. There are a couple that I know of that are being designed, but a program that really crosses the entire spectrum -which we'll talk about in the next few minutes- doesn't really exist. You can't go somewhere and do a PhD in Biodiversity Informatics. Or a Masters. There are also quite a few training resources. There are not even informal, non-programmatic resources; that surprised me quite a bit as my colleagues and I scoped out this more comprehensive program. At the same time, as you all well know, this is a pressing field. This is not an esoteric field that we are involved in just because of its inherent interest. Rather, this is a field where, if biodiversity is not attended to in the short-term, it won't exist in the long-term. There are pressing economic, social, and natural resource related needs that derive very directly from good management, analysis, and interpretation about biodiversity. So again, it's not something we do just out of curiosity, but rather, there's a very specific need. We can go back to the roots of this field. These are pictures of natural history museums from around the world. A lot of these are very old buildings. That's my favorite. It looks like it's about to fall down. The building where several of us work is 100 years old. And that speaks to this elderly stature of biodiversity informatics. A lot of the things that we do today are pretty much the way they were done 50 or 100 years ago. These are pictures from the Division of Ornithology where Mark and I work. Preparation of skeletons. Everybody has a freezer full of dead birds. At least everybody who does birds. Preparation of skeletons. Specimens in formalin. That's a pretty ugly picture. It's the bones of a bird. But notice that we're already managing information here. Those seven characters on that aluminum tag -it's aluminum because the workers who cleaned the bones are little beetles who will eat anything else- but those seven characters are a unique identifier for this specimen which tie back to a whole world of data. If those data are lost -if that tag were to be lost- then we lose all of the data associated with that specimen. We have an elaborate, very 19th century system of data maintenance. These notebooks. You can look at notebooks that were prepared 100 years ago by our predecessors, predecessors, and they're really the same format. We're still using 100% rag paper. It's basically ground up cloth. And we're still using India ink which is essentially permanent. So, much of what we do in managing the information is very old. These are catalogs from bird collections. I'm not seeing from which country they come. But, this is somebody with very good handwriting. In the group, you will see people who have very readable handwriting and then you'll probably look over Mark's shoulder and see a counter example. When Mark and I arrived in the bird division at the University of Kansas, we were still cataloging in these old ledgers. There was a digital catalog of the collection our predecessors developed; but, when we arrived, nobody in the bird division knew how to get into those files and work with them. It took us about a year to be able to do that. At the close of that year, we said, 'okay, done with the ledgers.' And we eliminated one step in the process. But we haven't eliminated any more steps in the process. Later in the week, we'll talk about data replication and data security. That will be a repeated theme in this course. We're not just talking about how to record the data, or how to maximize the amount of data we record, but rather, what we're talking about is how to avoid losing any data. Next week, when we're out in Korup National Park, the data are there. The information is there. Then, the question is, how do you capture that information, preserve the information, systematize the information which is to say, make it organized in fields so people can search, access, and retrieve the information. But then also, how do we share that information globally so that these information gaps that we've talked about stop existing. There's a view into those ledgers. You can see there's not a lot of information in there; I think people were not wanting to copy all of the catalog data. So right there, there was only partial data replication. There was more information preserved in this system. Another information management system. These are catalogs and field notes; and, they come in threes. Each researcher in the field each night or day would do three things. One was the 'field catalog'. Specimen-by-specimen: specimen 1234 is this, this, this, this, this, and all the data. The second volume was what they called 'species accounts'. This was your notes on each species. Maybe some of those individuals of the species became specimens, but some were observations. So there is a richer quantity of information about each species. And, the third was the actual notes; basically a 'field diary'. Particularly, that includes an itinerary and descriptions of localities. Many times photographs and maps. This was another complicated information storage and retrieval system. Across all of these courses, there is repeated mention of Joseph Grinnell. He was the first director of the Museum of Vertebrate Zoology in Berkeley, California near San Francisco. And Grinnell invented this system of keeping field information. A lot of what we do right now is derived 100 years later, evolved out of the Grinnell system; and, we still keep those notes. They're in a bank vault in our building they're so valuable. Let's come a little bit more modern. Again, this is a bird view. In the course of this week, you'll see two other major taxa discussed; but, our specimens are usually these dried skins. We have two other major forms in which we preserve birds. You're going to hear a lot more about this from Mark; but, we have these very awkward tags that we use to keep our information. You can see they have a front and there is a back. There are these little details, like you have to be able to hold the tag and simply flip it like this, or Mark or I get very upset because there are these things that been done for centuries. Also, some of the data are in ink and some of the data are in pencil. That's because we want to be able to change species identifications because those do evolve through time. And, we also want the original data. Like, where and when and who. Those data should never change and so those are in permanent ink. These are egg specimens. These are new ones; and, those are old ones. You see, Mark, it's not just you that has bad handwriting. You can generally figure out the age of a specimen by how much data is on the tag. These are information rich systems. This is the best photograph I have of what these guys do for a living. We call them 'pickles'. But, they're specimens in formalin or ethanol. This is our nightmare. It's very hard to put that full tag on a specimen. So we do this. And that's something that we hate, and we'll talk about that. Why should we hate that? But it is something that I hate and you guys should hate because, what happens if you lose the other half? The catalog or the ledger that tells what P-1318 is. That's the danger. That's why we hate it. Most of our specimens end looking like this. And, they're stored in these cabinets. The cabinets are -allegedly- airtight, pest-proof, light-tight. That's mostly a true statement. So, that's where we stop being 19th-century. Up to here, what I've shown you, are things that would have been done in the 1920s. And, that's where then we see big opportunities opening for this field. For example, now we can capture data in a much more rapid form. This is a picture of data being captured from herbarium sheets. Some of you may know about an initiative in which Moses is involved which is the idea of

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Duration: 18 minutes and 1 second
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Language: English
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Posted by: townpeterson on Jun 22, 2016

This talk was presented in the course on Biodiversity Inventories, an advanced course focused on developing complete inventories of species present at sites. The workshop was held in Buea, Cameroon, during 2-5 March 2015. Workshop organized by the Biodiversity Informatics Training Curriculum, with funding from the JRS Biodiversity Foundation. Instructors included David Blackburn, Rafe Brown, Town Peterson, Mark Robbins, and Moses Sainge

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