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Viva la revolucion

Notes from Nature recently surpassed its 200,000th transcription!  Given this milestone, it seems like a good opportunity for the Notes from Nature team to do two things: 1)  We want to show a bit more where – geographically – we have filled in some data gaps; 2)  We want to talk a bit more about the Bigger Picture.  Where do these transcriptions go after they get done!?  We have talked a lot about the scientific uses of these data, and individual projects, but there is a bigger mission and one the Museum world is grappling with right now — how to simultaneously live in an analog and digital world.

Before we talk more about the Big Push to digitize records and get them mobilized for the good of society, lets do something a bit more close to home.  Below is snapshot of an intensity map which shows work done by transcribers state by state.  We focus on the United States here simply because we have had good dropdown list for USA states and could therefore easily get this map made without too much muxing.  We have gotten have gotten a lot of help from transcribers in other counties and you can see more about that in our previous post. You can explore the map in more detail:  click here to see the map .   We made this by simply tallying each record with a particular name of a state, and then linking those state names using a service provided by Google called Fusion Tables.   California (with 64,346 transcriptions) and Florida (with 21,283) make up a lion share of the transcriptions, but there is a lot of effort in the Southeast and West as well.  All things one might expect given the regional foci of CalBug and SERNEC.  Surprising, North Dakota has 1,518 transcriptions completed and Minnesota 2,109!  Go Upper Midwest!

Screen Shot 2013-07-17 at 4.08.53 PM

Merge of nfncountrystateCOUNT and US Regions State Boundaries

All this work really does feed into a larger effort that is happening here in the United States and around the world to make museum data available for broad use.  This isn’t just for scientists, but also for formal and informal science education and the broader public.  Museum specimens are obviously of great value — they even tell us more than the who, what, where, when which serves as a basis for documenting trends in changes in distribution and seasonal and yearly timing events such as emergence from hibernation.  Each specimen yields further secrets — whether it is DNA that can be extracted from the tissues, body size and relation to physiology, and so on.  They also tell stories about landscapes and peoples in the past, and about our own histories.  In this sense, natural history tie into the much larger picture of multiple cultures.

Up until recently, if you wanted to see this vast treasure trove of data, you had to get a special pass to enter the collections, and there under the watchful eyes of curators and collections managers, you could examine specimens.  Museums have always been places where visitors are most welcome, but physically moving around specimens, and figuring out which collection had what remained a challenge.  While access is critical, museum curators have to balance considerations related to the conservation of these precious objects.

In the last ten years, a revolution is unfolding and museums worldwide are digitizing their collections so that the contents can be discovered, searched, and used more effectively and by more people.  This work is very challenging.  Many folks involved in this endeavor have lamented that years of databasing and a lot of time and effort invested in building system to publish data and make them available… and still only 2-3% of the total number of records in museums (based on our best estimates) are digitally discoverable.  We have to hope there is a way to make this whole process more efficient.

So at some point, CalBug and SERNEC will take the hard work done by transcribers and make those digital records available to everyone.  You can see some of the progress that has already happened by checking out projects such as VertNet, GBIF, Map of Life and iDigBio. One of the goals of these projects is to bring together data from various sources in order to create a “one stop shop” for the discovery of biodiversity information.

In sum, the bigger story is that we are witnessing a revolution in how museums make their resources available.  Thanks for taking part and viva la revolucion!

-Rob Guralnick

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!”

“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
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