WeDigBio: Closing thoughts and appreciation

It was a very exciting past few days as Notes From Nature participated in WeDigBio. The event was a great success and you can see lots of photos and reports from the event on Twitter and Facebook. The WeDigBio site also has some really nice visualizations showing where people were working during the event and the overall transcription progress.

A Crab Shack participant's eye view of digitizing a crab specimen, one of dozens of digitized at the Marine Biodiversity Center of the Natural History Museum of Los Angeles County's event for the WeDigBio digitizing blitz.

A Crab Shack participant’s eye view of digitizing a crab specimen, one of dozens of digitized at the Marine Biodiversity Center of the Natural History Museum of Los Angeles County’s event for the WeDigBio digitizing blitz.

We want to offer our sincere appreciation for all those that made this event possible and especially to the volunteers who stepped up and helped us meet not one, but two challenge goals for the event! The WeDigBio team started out with a goal of completing 25,000 transcriptions for the entire event using all the transcription platforms. After that milestone was met the goal was raised to 30,000 transcriptions. The event ended with well over 34,000 transcriptions!

The official count for transcriptions completed using Notes From Nature was 9,980! This is simply incredible and the Notes From Nature team is so very thankful for these efforts. The number could actually be as many as 1,500 transcriptions higher since there were some glitches that prevented some transcriptions from getting counted on the first day. The transcriptions themselves are saved, it was a glitch with the visualizations on the WeDigBio page.

Adam Wall, of the Crustacea Section at the Natural History Museum of Los Angeles County, orients participants in the Crab Shack digitizing event on what they'll see inside the research storage facility.

Adam Wall, of the Crustacea Section at the Natural History Museum of Los Angeles County, orients participants in the Crab Shack digitizing event on what they’ll see inside the research storage facility.

While these numbers are amazing, we are also thrilled with many of the less tangible aspects of the event such the interactions between the museum curators and citizen scientists that occurring during the onsite gatherings. We hope to see you all for the second annual WeDigBio event in 2016!

UC Berkeley Museum and WeDigBio

For centuries, scientists have explored and documented the natural world, collecting the billions of specimens housed in museums, universities, and field stations worldwide. And now, UC Berkeley and other institutions across the globe want to help make that information available to the general public.

But they need your help.

UC Berkeley’s Essig Museum of Entomology invites members of the public to one of the many transcription parties that will be held this week during the Worldwide Engagement for Digitizing Biocollections (WeDigBio) Event. The WeDigBio event will transform the cryptic data sequestered on the labels of plant, insect, fish, and fossil specimens into an open, globally accessible, digital resource with the help of the public.

“Between California’s extended drought, extensive wildfires, and other assaults on our environment, it is now more important than ever to understand how these pressures are changing insect communities and the ecosystem services they provide,” says local event organizer and collections manager, Dr. Peter Oboyski. “There is no better way to convey this message than by inviting the public behind the curtain to help us collect the data we need to document these patterns.”

The Essig Museum contains nearly 6 million specimens of insects, spiders, and their relatives, representing over 35,000 species. These specimens also represent the past 100 years of California’s climate, terrestrial habitats, and waterways in the form of distribution records of native and invasive species. “California is a biodiversity hotspot and a world leader in conservation, research conducted at the University of California over this time span allows us to map the past and give us a glimpse of our environmental future,” says Oboyski.

The WeDigBio event emerged within the museum community to accelerate the rate of digital data creation about the historical what, when, and where of the perhaps 9 million species on Earth. The major online transcription platforms include the U.S.-based Notes from Nature, Smithsonian Transcription Center, and Symbiota; the Australia-based DigiVol; the UK-based Herbaria@Home; and the France-based Les Herbonautes.

This one-of-a-kind event will be held from October 22-25 at 30 locations across the globe. While the local event at UC Berkeley offers a social setting where people can contribute and learn about the entomology museum and local insect diversity, members of the public can contribute at anytime from anywhere during the event at one of the participating online transcription platforms.

Essig Museum ”CalBug” specimens will be available for transcriptions at More information about the WeDigBio event can be found at

The UC Berkeley transcription blitz will take place from 9 a.m. to 2 p.m. on Saturday, October 24th, in the BioScience Library of the Valley Life Science Building. More information is available at RSVP to

Student feedback from Day 1 of WeDigBio

The following is a collection of comments and reactions from students that used Notes From Nature as part of their classroom activities on the first day of WeDigBio. The is an innovative example of service learning and community engagement being used in the classroom. The NFN team is always excited to see these kinds of activities being integrated into the classroom setting!

“I really enjoyed the WeDigBio Blitz; there is something about contributing to digitizing important records that are so vital to botanists and other researchers that is satisfying. Of interest: I found two plants of the twenty-five I did that were collected on the day of my dad’s birth!”

“This Notes from Nature transcription activity was quite valuable. I felt like I was legitimately helping and contributing to the scientific community; the WeDigBio experience is super important.”

“This morning we contributed to science in wedigbio. I enjoyed converting the old data sheets into a database and felt good that I contributed to humanity.”

“Wedigbio is a very well designed website. It was easy to use and I felt like I accomplished something for the greater good of our world. The blitz itself was cool to think about when looking at it from an outside point of view. There are thousands of people around the world working together to transcribe the world’s flora! That is amazing to think about.”

“The experience of transcribing for Notes from Nature was very rewarding. The idea that I am contributing to the study of scientific specimens from around the world is very exciting and I was happy to be a part of it. “

“Notes From Nature is a fun and easy way to transcribe plants into the online system. I didn’t experience any glitches with the system. Some of the plants are difficult to transcribe because the herbarium notes aren’t very detailed, especially those from out of the country.“

“My experience today with transcribing for Notes From Nature was fulfilling in that I felt like I was contributing to a bigger picture for further discoveries and enabling those in the field to continue to collect and document specimens.”

“I really enjoyed this assignment and the idea that all of us could make an impact in the scientific community. My favorite discovery was hearing that each label/specimen is transcribed four times in an attempt to minimize errors. While I think more activity on the site might get rid of transcribing jobs, this is a really innovative project. I liked being able to see how botany is transitioning into the modern age with everything at our finger tips.”   

“This morning’s Notes from Nature experience was fun and informative especially hearing more information about how it works behind the scenes. It also gave a different perspective of how this work is done, I work in the herbarium on campus where digitization is being done and it is not greatly different which was curious. I wish there was a bit more time to go in depth and discuss and reinforce the importance of digitizing plant collections.”

“I found it very helpful to move from material data to technological data since we are in the era of technology. Making this ability to help out public is a very good idea and motivated students will be sure to help out, I know I will. The experience overall was hit or miss with the transcribing, some handwriting is hard to read and some information is omitted, regardless, this is a great idea to make available to the public.”

“I really enjoyed being able to transcribe for the Notes From Nature. It is very easy to access and fun to see different types of plants that are found in different areas of the world. I also felt like I was doing my part by being able to transcribe something so important that a computer could not. Overall it was a wonderful experience.”

“It was an interesting experience for the limited amount of time that I was in class. This is something that I would probably do for fun on my spare time.”

“The blitz was really fun, I was more into it than I thought I was going to be. I think the fact that the whole class was doing it at the same time made it much more exciting. “

“I transcribed 9 specimens. I chose to do them from the University of South Florida Herbarium. I liked that I was already familiar with most of the plants I had the chance to look at. Most of them where approximately 40 years old. However the oldest specimen was from1959 and the newest was collected in 2012. Very interesting to look at specimens that old.”

“When transcribing the labels on WeDigBio, I realized for the first time how unstandardized the labeling system is. Some collectors put all necessary information with plant facts, others put the bare minimum and didn’t do a very good job on describing the location of the specimen.”

“Transcribing for Notes from Nature was simple and interesting and certainly a productive experience. Even doing something as easy as typing the records of a particular plant specimen feels like a significant contribution to the scientific community. It also provides an example of what details should be recorded about plants for other scientists and helps users take one more step on the road to becoming a botanist.”

“WeDigBio was a good way to spend my class time. I was able to learn how to digitize records really easily. The entire process was quick, painless and very straightforward.”

“This was a fun experience, and I felt like I was making a positive contribution to science. Fortunately my specimens were very clear, and easy to decipher the information. It made me confident in my submission and that I was able to supply accurate information. I also noticed there were different types of specimens such as crabs to be transcribed, and I would like to do those as well.”

“It was hard to read a lot of the labeling. Also, I noticed that for the SLU records, if a record from found on campus, it just said “on campus” and didn’t say the county. So this part I’m sure will be missing for a lot of their records. The activity went more or less smoothly, although I am not a huge plant person, so I didn’t personally enjoy the activity very much, although I understand the scientific value in it.”

“Learning about how the notes from nature website was developed was interesting. Doing more label identifications were helpful to learn how the pressed plant labels should be. Doing the label identification is also fun to do, and a great citizen science website that is user friendly.”

“Transcribing Notes from Nature was cool because we got to help science as citizens by helping create an online database for plants. We viewed pictures of plants and labels and transferred the information to the online database by filling out the proper information. I think it would be interesting to see how many people participated so far and I will definitely participate in the future.”

“One of my specimens had an incorrect scientific name. Thankfully we had a subtle pencil correction on the specimen to go off of. All of my specimens were collected by Olga Lakela, who evidently was an influential female botanist in the 60’s. “

“I really enjoyed the concept of the transcription event. Being a little competitive myself, I viewed it as a challenge to get as many done in the time we had. I do actually feel like I am providing a valuable service by transcribing for Notes From Nature. Learning that what I transcribe will be transcribed by 3 other people removed any stress that I might get something wrong and prevent me from wanting to participate. I would participate in a future transcription event if I found out about it.”

“It was a really interesting event to take part of (WeDigBio). Notes From Nature was an easy site to do this through, as it walked you through what to look for in separate steps and provided examples. However, the specimen navigation (zooming in and moving to different areas) was a little difficult. Additionally, the specimen label was missing information sometimes, such as county or habitat.”

“Transcribing through Notes From Nature was a interesting experience. It was neat to see such a variety of specimens, some that were many decades old. I liked being able to do something that benefits the scientific community. WeDigBio seems like it is and will continue to be a huge event.”

“I think that notes from nature is a great way to start developing museums labels for herbariums. I sometimes could not find all the information and some of the labels were a bit hard to read but that comes with the territory I suppose. The site was nicely made and easy to navigate. I would definitely use it again!”

“I think the Notes From Nature activity was a really cool activity we did in class today because it was a world-wide effort. There were a few issues I found with using the website that were kind of confusing when it came to transcribing. Some specimens had more than one label with different information on each, two specimens popped up at once a few times, and not all the information needed to transcribe was given for each specimen. Overall fun and cool class activity!”

“My experience transcribing for Notes from Nature was quite interesting. For the most part I had species that were found in Florida except for one that was a herbarium sheet from Finland. It was interesting to transcribe for a species from a different country. I was also thankful that all the herbarium sheets I transcribed had typed information rather than handwritten information.”

“My experience transcribing for Notes from Nature was quite interesting. For the most part I had species that were found in Florida except for one that was a herbarium sheet from Finland. It was interesting to transcribe for a species from a different country. I was also thankful that all the herbarium sheets I transcribed had typed information rather than handwritten information.”

“I enjoyed the class this morning, I transcribed around 10 plants. The website itself runs great, although I had a few problems throughout with the picture freezing when trying to zoom in or out but refreshing the page seemed to be a quick fix. Hearing the guest speakers side of the story to the beginning of the site gave me more respect for the site and for the cause. I now see why the website is necessary to preserve herbarium specimens because some I transcribed were beginning to fade and wrinkle (granted they were added to the collection during 1968).”

Slicing up SERNEC

As many of you may already know, the herbarium interface (or collection as its called on NFN) is comprised of images related to the SERNEC initiative. This is a very large consortium of herbaria that is interested in bringing more data about plants online for everyone to use. When I say more, I mean a lot more – millions of records! The geographic focus of these efforts is the southeastern United States, which is an extremely rich and unique global biodiversity hotspot.

Since NFN began, volunteers were only able select one set of herbarium images to work on. These have been preselected by the science team for a variety of different reasons. We have realized that there are limitation of this approach and have wanted to make these sets of images even more meaningful to everyone involved, especially our volunteers.

We have taken a step in this direction this week, by offering up four different collections to work on. These sets of images were selected and separated because they are from museums that are hosting onsite events this week as part of WeDigBio. The thought is that people have come to these events, in order to specifically help the museum that they are visiting. The new page allows volunteers to do just that.

This is a great test for the NFN team to see how this works out and will inform our plans for the future. For example, we are planning to allow for the subsetting of images by geography (e.g., North Carolina) and taxon (e.g., sunflower family). This has not been possible in the past mostly because this kind of information was not being collected when the specimens were imaged. The SERNEC group has changed it’s imaging protocol to allow for these kinds of selections to be made in the future. We are also interested in exploring other methods such as creating word clouds by using OCR methods to automatically extract all the words from the image and allow users to select them. After all, one of our main goals is to make coming to NFN a valuable experience for our volunteers.

Newfound Gap Rd near Clingman's Dome Rd - Great Smoky Mountains National Park. Photo by Timothy Wildey

Newfound Gap Rd near Clingman’s Dome Rd – Great Smoky Mountains National Park. Photo by Timothy Wildey

The Crab Shack at the Natural History Museum of Los Angeles County

We’re incredibly excited to have the opportunity to work with you through WeDigBio so that we can move forward with digitizing our crabs! And a large part of our excitement is because of you.

So what are these crabs? And who are “we”?


Immodestly, we’ll start with “we”: we’re the Marine Biodiversity Center (MBC) at the Natural History Museum of Los Angeles County (LACM). Despite the provinciality of “county” in our name, LACM has some of the world’s largest specimen collections in numerous disciplines. The MBC began its life over fifteen years ago as an initiative to sweep up many of the “orphan” subcollections that had accumulated in LACM’s marine section. Because of its intrinsically cross-taxon nature, the MBC has matured into a center for integrative biodiversity studies, sidestepping the classical taxon stovepipes of the traditional museum world.


But back to the crabs. One of LACM’s largest collections is of marine Crustacea — one of the biggest in the U.S. and the world. Crustacea are a subphylum that also includes shrimp, lobsters, crayfish and barnacles to name a few. For this project, we’ve chosen to focus on crabs of the family Cancridae, of which there are thousands in the LACM collection.

Why the Cancridae? OK, let’s be honest here: they’re cute. And they taste great. (Always choose a research subject you can eat. [Of course, no one is suggesting that museum specimens are edible — particularly not ones that may have been in formalin. But I digress.].) More objectively, there are a number of reasons that make the family Cancridae a compelling target group. Our current phylogenetic understanding (e.g., evolutionary history) of the family comes mostly from fossil evidence, and it would be fascinating to explore those hypotheses with extant specimens. Extant organism are ones that are still living, while many fossils represent organisms that have gone extinct some time in the past. The Cancridae include a number of commercially important species, such as Dungeness Crab and Rock Crabs. On the west coast of the United States, different states regulate fisheries of these crabs in radically different ways: some states individually regulate the species, while some lump them all together. That’s a situation that could be better informed using museum specimen data.

LACM’s collection of Cancridae dates back to the early twentieth century. A significant proportion of the specimens came from the massive collecting efforts of Captain Allan Hancock, a Los Angeles oil magnate early in the last century, who had a deep interest in marine collections. Key qualifications for biologists on his expeditions included musical talent — Hancock was unwilling to be trapped on a ship without entertainment. With this digitization project, we will learn just how much of this subcollection is Eastern Pacific, and how much has been added from the rest of the world.

But there’s a problem: if these specimens are so important and interesting, why haven’t we digitized them already? The short answer: it’s hard.


The problem is common to many “wet collections” (specimens in jars of alcohol): it’s ludicrously time-consuming to get the labels out so that the data on them can be captured. Over the years, researchers have added supplementary information to the specimens, hence many jars have multiple labels, any or all of which may be critical for understanding the importance of the specimen. Each label has to be removed, laid out, and imaged before data capture can begin.

Even after the labels have been imaged, the text that has been printed or written on them needs to be captured in machine-readable form. The combined effort needed to get the labels out of the jars, image them, and then enter the data just isn’t something we have the staff to tackle.

Enter WeDigBio.

Having the opportunity to engage a broader public gave us the incentive to get started. Over the last few months, we’ve designed and implemented a label (and specimen jar) imaging system, developed software to process the label images, and prepared ourselves for label data analysis.

Now that we know you’ll jump in to help us do the actual data capture from the labels, we’ve been able to get the preparatory work done.

That’s the magic of unfolding our institutional box to the public in a project like this: we get to give you a peek into some of life’s coolest specimens, and your help gives us the ability to achieve digitization that we wouldn’t (couldn’t!) achieve without your help.

Thank you for your work with our collection and all the other WeDigBio-associated collections — not only are you contributing to projects that are describing the scope of life on earth, you’re making those projects possible.

Many thanks to Rafe LaFrance, our Notes From Nature developer, for his help making Crab Shack come to life under a short deadline!

Notes From Nature participation in WeDigBio

The Notes From Nature team is really excited to be involved in the WeDigBio event that is taking place this week!

masthead-bgWeDigBio stands for Worldwide Engagement for Digitizing Biocollections. It is a global event that focuses on digitizing of natural history museum specimens, which is something we care very deeply about. Notes From Nature is not the only transcription tool that is being used. There are others such as the DigiVol in Australia and Les herbonautes in France making this a truly global event.

The focus of the WeDigBio event is on onsite digitization gatherings that will take place around the world over the next few days. Many of these events will include fun activities and tours of the museums. Notes From Nature has been primarily a distributed group of people working towards a common goal. We are excited to see how bringing people together in one place will go and we certainly hope it will be an engaging and fun experience.

Even though most of the events are onsite, you can still participate from wherever they are! You can track the progress on the very cool dashboard on the WeDigBio site. We will also be using the hashtag #WeDigBio on Twitter and Facebook, along with some blog updates during the event, which runs from tomorrow Oct. 22 to Sunday the 25th.

CalBug Expeditions is online! Welcome to the Wood Boring Beetle Campaign.

Buprestis (Knulliobuprestis) confluenta

Buprestis (Knulliobuprestis) confluenta

Welcome everyone, to a CalBug expedition exploring part of one of the most stunning groups of beetles, the jewel beetles. We have pulled together a set of 15,416 images of these beetles from the holdings of the CalBug institutions to be transcribed. The data from these specimens will help us better understand where the beetles live, their habitats, ecology, and other fundamental data for researchers working on the group.

The family Buprestidae, are also commonly called “metallic wood boring beetles,” but this captures only one of the life histories found in the group. Many are herbaceous plant stem-borers or leaf-miners. Some feed on living trees, while others on dead or dying trees.  Some are well-known fire followers, showing up in vast numbers while the logs are still smoldering after a wildfire.

Jewel beetles have a life history that includes eggs laid by the female on a host plant, larvae that feed on the host plant and, a pupal stage where the very plain, grub-like larva transforms into the ostentatious adult. Many adults are not frequently seen unless one is specifically looking in places they hide. However, there are some that are conspicuous on flowers during the day, where they feed on pollen. At least some of these species are capable pollinators, assisting bees and flies with that important work.

When it comes to natural beauty, many jewel beetles, rival or surpass birds and butterflies. Their stunning colors make them pure entomological eye-candy. Their color patterns have been the inspiration for art and their shiny metallic bodies have been used in art and jewelry itself.

Though adults have the looks, it’s the unassuming, grub-like larvae that have the greatest economic impact. When they are a larva they can feed on a wide range of agricultural, ornamental, and forest trees. In North America species like the Emerald Ash Borer and Goldspotted Oak Borer have been introduced or are spreading and now causing serious damage, sometimes killing trees.

It’s important for scientists, foresters and control managers to have information on the distribution of these species, both native and introduced, so that harmless native species can be protected and potentially harmful species can be managed.  This expedition focuses on two subfamilies of jewel beetles, Agrilinae and Buprestinae. Your transcription efforts will be a critical part of this expedition’s goals to transcribe a major collection – 15,416 imaged specimens. Thank you!

For more information on the wood-borers:

Goldspotted Oak Borer:

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