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What happened to the transcription progress?

One of the questions we have been grappling with at Notes from Nature is how to add more specimen images to the application while still showing a clear path of overall transcription progress.  On the one hand, we have many more specimen images lined up from both CalBug and SERNEC, and need to keep expanding the pool of interesting and scientifically important collections being transcribed.  On the other hand, we don’t want Notes from Nature citizen science transcribers to become frustrated by a seemingly bottomless pool and confused by constantly increasing and decreasing progress bars.  In attempting to address this challenge, we’re going to do some small tests.  We’ve added some new specimen in recent days, and would like to hear what you think about these additions.  Among the new additions, we have about 74,000 new bugs, including many bombardier beetles, dragonflies, and damselflies, as well as about 13,500 new plant specimen.  Do you like that we’ve added these new specimen images?  Were you worried by the drop in transcription percentages?  Should we work to complete “missions” with smaller subsets before adding more content?  Whatever the case, check out the new specimen on Notes from Nature!”

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“What’s in bloom?”

Have you enjoyed contributing to scientific research by transcribing plant specimen labels in Notes from Nature?  If you like this, you may also be interested in the UVA Mountain Lake Biological Station’s “What’s in bloom” volunteer, citizen science wildflower bloom monitoring project.  You can find out details about it here:  http://mlbs.org/whatsinbloom .  This is another great opportunity to contribute to science, interact with researchers, and enjoy nature.

Tending Our Notes from Nature Garden

Sometimes in the shuffle of getting things done, we forget to explain the simplest things.   For example, where do all these images come from?  Are there more to do when these are done?   What the heck is a CalBug or a SERNEC?

So lets answer some of these questions as best we can.  As we mentioned in the “About” section of Notes from Nature, CalBug and SERNEC are both regional consortia of natural history collections — CalBug focused on western North American (predominately) insects and SERNEC on southeastern United States plant specimens.

Lets turn to the SERNEC records first.  Right now the following herbaria  (or single plant collection) are featured on the site:  The R. K. Godfrey Herbarium at Florida State University, with 8,368 specimen images available and the Mountain Lake Biological Station Herbarium at the University of Virginia with 6,990 specimen images.  Soon we plan to load a third collection of 13,511 images from the herbarium at the University of South Alabama.   This represents a small proportion of the millions of specimens found in southeastern United States herbaria, so there is still a LOT of work to do here.

CalBug has about 230,000 images already taken,of which ~33,000 have been already made available via Notes from Nature, with another 28,000 to be added shortly.  These mostly come from the Essig Entomology Museum at U.C. Berkeley but also from U.C. Riverside and the California Academy of Sciences.  CalBug will also be adding more images in the future.   The ones there now represent a select group of insect taxa including: bombardier beetles  (genus = ‘Brachinus’ or genus = ‘Metrius’), cuckoo wasps (family = ‘Chrysididae’), odonates or dragon flies,  (order = ‘Odonata’), skippers (family = ‘Hesperiidae’), and tiger beetles (genus = ‘Cicindela’ or genus = ‘Omus’ or genus =’Amblycheila’).

What to do about too much information?

If you’ve been working on transcribing labels in Notes from Nature, you may have run across some labels that have more information than you’d expect, or possibly what appears to be conflicting information.  Sometimes, this is the product of an original collector’s identification being reanalyzed and “determined” by a later collector or curator.  Take a look at this Notes from Nature discussion to see how you might deal with such discrepancies:  http://talk.notesfromnature.org/#/boards/BNN0000005/discussions/DNN00000j1

Profile of Notes from Nature Team Member: Mike Denslow

Name: Mike Denslow

Title: Assistant Director for Scientific Research Collections

Where do you work primarily? The National Ecological Observatory Network (NEON)

What you do in your day job? I am responsible for the archiving of biological samples collected as part of NEON’s field activities. Archiving is the act of safely saving and making available samples for use in research. NEON is an ecological observatory that will have 60 field sites across the Unites States (including Alaska, Hawaii and Puerto Rico) where ecological information will be collected for at least the next 30 years. These samples represent a range of organisms from mammals and plants to soils and zooplankton, just to name a few.   Now-a-days archiving not only deals with physical specimens and their safe keeping but also the digital information that goes along with them. For this reason, I am also concerned with capturing information about these sample in a digital format and making sure that it accessible on the internet for interested people to find and easily utilize.

What’s your role with NfN and what do you hope to gain from it?  If relevant, how will your research benefit?   My primary role at Notes From Nature is to bring in photographs of plant collections from various plant museums (called herbaria). I am also responsible for providing feedback on the design of the web interface for the project.   I am interested in developing new ways to make more information from museum specimens available for people to discover and use. My hope is that people will also appreciate the importance of museums in the process. There is a wealth of existing information about biodiversity that is not currently available in easily usable formats. It is critical that new ways of getting this information are developed and Notes From Nature is one exciting way that this is being done.

What’s the most exciting aspect of citizen science work from your point-of-view?  I really enjoy seeing the things that people notice about museum specimens and the questions that get generated from these observations. The contributors to Notes From Nature find all kinds of interesting things both on the labels and the specimens themselves. I am really enjoying interacting with people on the Talk page and it is helping me see museum specimens in a whole new way.

What to do about insufficient information?

Today’s post is going to highlight a recent conversation amongst Notes from Nature citizen scientists regarding what to do when a specimen doesn’t seem to have most of the necessary information.  Is it best to just leave fields blank?  Is it better to just skip it?  Is it a “Top Secret” specimen?  These are great questions, and ones which will likely come up over and over again throughout the life of Notes from Nature.  Here’s the conversation.  How would you deal with this?

  • by carolely

    The label has only the scientific name and a question about that. Should I create a record and leave all the other fields blank?

    Posted 4 days ago
  • by SandersClan

    I vote yes.

    Posted 4 days ago
  • by ghewson

    Yes, then it’ll be flagged as needing more information.

    Posted 3 days ago
  • by carolely

    Thanks for the help. It seems I lost this page when I started this discussion so I never got to enter it. However, I’ll know what to do next time.

    Posted 2 days ago
  • by nosenabook

    I’m glad to know what to do as well, when I saw one like this, I passed on to the next specimen.

    Posted a day ago
  • by nosenabook in response to ghewson’s comment

    Responding to ghewson, it sounds like it is better to leave a field blank than enter “none given” say, for the reference. I started doing that because it was easier than arguing with the form – YES skip this field – and because R. K. Godfrey rarely gives a reference.

    I’ll leave that field blank from here on out, unless or until I hear different.

    Posted 21 hours ago
  • by xairbusdriver

    I seem to have found a “Top Secret” specimen, twice! 😉 If you come across Image ANN000039x, you’ll see what I mean. The ‘Location’ info seems to te a test site for White Out(r)! “…N side of _ Creek Road (S of Rte _), ca. air mi ESE of _. __________ of Sec ” I sure hope L. C. Anderson didn’t get into any trouble finding that specimen! 8) LOL!

    Posted 18 hours ago
  • by ghewson in response to xairbusdriver’s comment

    Ah yes, I had that, and tagged it #redaction. But if you search for that tag, there are 0 results! Spookyyyyyyyyyyyyyyy!

    Posted 17 hours ago
  • by SandersClan in response to xairbusdriver’s comment

    I can’t decide whether this is a Roswell, thing, the MIB, or what!

    Posted 16 hours ago

Imaging the University of Virginia’s Mountain Lake Biological Station Herbarium

Notes from Nature has been a significant undertaking with many people involved, but the transcription work being completed through the project is only a slice of the entire process of increasing access to and use of research collections.  This guest post comes from Christina Deane, Head of Digitization Services in the University of Virginia Library.  Christina was intricately involved with the imaging of the University of Virginia’s Mountain Lake Biological Station Herbarium, which is one of the current featured collections.  Through this post, we hope you’ll gain an understanding of how all of the images in this collection were produced.  If you are interested in seeing more about the University of Virginia Library’s Digitization Services, see this video:  http://www.youtube.com/watch?v=7CRHyj-6syM (look to 3:24 for a photo of a herbarium sheet!).  This story is one of many ways, and we will likely touch on other imaging processes in the future.  – Andrew Sallans


We began a discussion of how this project would be carried out in late summer of 2005.  The conversations included biologists, librarians, and technologists, to make sure that we were covering our bases on _MG_0323technique, metadata, and consistency so we would only have to do this once!  Once we had ironed out some of the metadata issues, we were able to modify our scanning workflow to accommodate the different requirements for the herbarium specimen.   We agreed that we would create archival tiffs and deliverable jpegs at 300 dpi following UVa’s digitization guidelines, and our digital library workflows were already in place to programmatically extract technical metadata from the images.

We hired a student in the spring of 2006 to begin scanning images using our overhead, Hasselblad cameras with PhaseOne P45 Plus digital scan back cameras (capturing at 39 megapixels!).  These cameras are typically used for our rare print materials, including all varieties of rare books, Jefferson letters, and even copies for the Declaration of Independence.  We established a set way to position the ruler and color bar so we could achieve a consistent look for the images, and this was likely influenced by other herbarium digitization projects going on at the time.  It was definitely a different way to work than what we were doing for books and manuscripts.  When we began this work, we didn’t really know how many specimen there were to scan, as the estimates we were provided with were in the thousands.

Our workflow was to barcode the images before scanning them, create a folder name based on the folder the items_MG_0314 were housed in, and name each image based on the barcode.  Our cameras and digital backs were very slow back in 2006, and imaging took a lot longer then than it does now.  Once through the basic quality assurance steps (QA) we were to send jpegs to the librarians in charge of the project so they could facilitate the metadata creation with the team they had assembled to work on this part of the project.  We utilized multiple rounds of QA so at least 3 or 4 people examined each image.

Scanning continued from the spring of 2006 through the spring of 2007, at which point the student working on the project graduated.  Scanning resumed in the spring of 2008.  Over the course of the next year, DS digitized thousands more images.  This _MG_0317process went faster because DS had acquired new camera systems with autofocus lenses and faster digital backs for almost instantaneous capture of the images.  During 2008 we continued scanning specimen as they were delivered to us.  We made a big push in January of 2009 to finish the rest of the collection (over 4000 pieces), and we completed the project that month. Full-time staff involved in the project included Andrew Curley, Kristy Haney, Jeanne Pardee, and Christina Deane.  John Ruscher was the primary student worker in the early part of the project, and many student employees were involved in the second phase of scanning from 2008 to early 2009.  Over the course of the project, we scanned 8,935 images in all.

-Christina Deane, Head of Digitization Services, University of Virginia Library

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