New phenology themed badges

The NfN team is excited to announce that we have a new set of badges. As many of you have likely noticed we have been experimenting in our Labs group with some new kinds of expeditions. So far these have all been related to Phenology. For this reason, we thought it would be fun to have a set of phenology themed badges. These badges can be earned by scoring 2, 10 and 100 specimens. Here is the first one called the Blossoming Badge.

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The Blossom Badge

Instead of showing you all the badges here, we thought we would create some suspense (and maybe motivation!) by letting you see the rest of them once you reach each threshold. Score 10 specimens for the Multi-blossoming badge and 100 for the Fruiting Badge.

Please take a look at the phenology themed expeditions and let us know what you think. We have one running now and expect to launch another very soon.

The NfN Team

Danke schön

The Botanic Garden and Botanical Museum Berlin says “Danke schön” – “Thank you”

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Herbarium and the biodiversity informatics staff at the Botanischer Garten und Botanisches Museum Berlin

Thanks a lot to the Notes from Nature Community for completing the Amaranthaceae expedition. Your transcriptions are very helpful for the Caryophyllales (an order of flowering plants that includes the cacti, carnations, amaranths, etc.) research group at the Berlin Botanical Museum. We’ll include the results into information systems to make them available for further research queries. You classified 444 specimens which is great! Many labels on these specimens were handwritten and not easy to read. All the more we appreciate your enthusiasm and endurance!

 

The results of the Amaranthaceae Expedition help our team to track back distribution patterns of this plant family and are important for biogeographical analyses and dynamic monographs of the group.

Dr. Sabine von Mering, Coordinator, Caryophyllales Research Group

 

Kind regards,

Agnes Kirchoff, Botanischer Garten und Botanisches Museum Berlin

New expedition: Microbe Mutualists!

Introducing a new ecologically-themed expedition from Plants of Virginia: Microbe Mutualists!  An overwhelming number of plants rely on beneficial microbes – microscopic fungal mycorrhizae and bacteria – to improve their access to mineral nutrients, such as nitrogen, phosphorous and potassium, in the soil.

Jump into the expedition to learn more about the taxonomic breadth of these interactions, which are occurring under our feet in our backyards every day. In this edition, over fifty of the most common microbe mutualistic genera residing in the state of Virginia are highlighted.

Introducing WeDigFlowering

When do plants flower across time and space, and how does this change with temperature, precipitation, and species? These are the questions that inspired me to work with biodiversity informatics: using the “big data” of herbarium specimen records to answer pertinent ecological and evolutionary questions. Herbarium specimens are like time capsules, capturing a snapshot of the phenological (i.e., reproductive) status of a plant at a particular point in time and space. From these aggregated data, we can discover patterns that help us explain the natural world.

Herbarium specimens have already helped us discover that many plants flower early in response to warmer temperatures, but some phenological responses are not so predictable (Willis et al. 2017). The U.S. Southeastern Gulf Coastal Plain is a particularly interesting place to further study this phenomenon because of its unique biodiversity and warm, humid climate. The many different species could be responding to different cues, and understanding these cues could help us predict future shifts with climate change.

The WeDigFlowering project provides a unique opportunity for interested volunteers, students, and citizen scientists to contribute to the study of phenological shifts. In it, participants estimate the percentage of buds, flowers, and fruits on an herbarium sheet, and these data help determine the approximate “phenophase” of the specimen. I hope you join us for this exciting, new project, and that you enjoy the flowers as you go!

Katie Pearson, Graduate Student and Curator, R. K. Godfrey Herbarium, Florida State University

http://mastlab.org/people/katelin-d-pearson

Cited study: Willis CW, Ellwood ER, Gallinat A, Mazer S, Nelson G, Pearson K, Primack R, Rossington N, Sparks T, Yost J. Old plants, new tricks: phenological research using herbarium specimens. Trends in Ecology and Evolution. 32(7):531-546.

What we’ve been learning thanks to your help and participation – a museum view.

This past month I seem to be in reporting mode, with a number of Conferences all lined up in a row. It’s been a great opportunity to meet many other scientists and researchers with Natural History collections and compare notes about our efforts to fully digitise those and get them online for anyone in the world to research or explore.

As we wait on the final few images in the Miniature Lives Magnified (MLM) expedition to be fully retired (don’t let that 100% complete fool you ), I thought it would be a nice moment to report back to you what we’ve been learning so far, thanks to your help!!

The slideshow below is the one that I presented to my SYNTHESYS consortium partners at a two-day meeting in the Natural History Museum to share all of our outcomes with each other. This is the source of my own funding up until this coming August, and all of us in the consortium have natural history collections that we have been digitising.

I always try not to put too many words on the slides themselves, so I’ve replicated my voice-over for you below, following the slides numerically.

(There is something going wrong with embedding that slideshow in the post here – so please open up the presentation in another tab, and read my notes below at the same time: https://www.slideshare.net/MobileMaggie/setting-collections-data-free-with-the-power-of-the-crowd-synthesys3 to open it.

  1. The title of my talk
  2. Where my work has fit into the total SYNTHESYS project (WP = Work Package, Obj = Objective)
  3. The context of my work here at the Natural History Museum London, it’s a pretty big collection, so a very ambitious project to digitise it all!
  4. We have a huge variety of types of specimens, that all have their own unique photography challenges
  5. And we’ve got some unique specimen label challenges as well!
  6. Not the least of which is, reading handwritten labels – and this is the main reason that we can’t use Optical Character Recognition software to let computers digitise it for us.
  7. Because of the scale of the challenge, we’ve been asking people’s help by donating some of their ‘down-time’ to transcribe these labels – that’s YOU! 🙂 Did you know that you were using your cognitive surplus? 😉  The reason I like this example of how many hours people have spent watching Gangnam Style on YouTube, is that time could have built Wikipedia a time and a half over again. This relates pretty closely to what we’re trying to do – we want to make the data in our collections available for anyone in the world online, and our even longer term goal is to link that to research, curators, scientists, etc…
  8. …getting a giggle from the audience…
  9. We started by scanning all of the things in our collection that are small and flat – because they are the easiest to start with – and that’s why you are seeing so many microscope slides from us!
  10. This is our Open Data Portal, where everything that you help us process will be published. I’m really looking forward to sending you a link to the final data there by the end of the summer (fingers crossed).
  11. As we get better at the scanning work, we’re starting to be able to handle large volumes. This is my colleague Louise, who is currently scanning our Louse collection, both imaging the microscope slides AND making lovely enlarged images of the specimen itself. We’re hoping that this might become an expedition, and it will be FAR more enjoyable to be able to see the specimens up close like that.
  12. And this is what your volunteer effort has helped us to accomplish so far. YAY!
  13. These are the two expeditions that the Natural History Museum London has on Notes from Nature, both in Magnified
  14. Introducing Notes from Nature to the SYNTHESYS audience, with thanks to NfN for their support in being able to use this great platform, and to be working closely with the NfN community – that’s YOU! 🙂
  15. This is what your pattern of contribution has been looking like for the three batches of the MLM expedition.
  16. Those big spikes are the days that we’ve had a group of volunteers in the Museum with us for the whole day on the expedition – it’s been wonderful to be able to give them face-to-face training and support, and once they get the hang of it, some of them have been stellar super-transcribers. This slide is our record holder day 🙂
  17. This is an event format that we call “Visiteering” because it is both volunteer work with us for the day, but also visiting the museum and meeting the curator. If you’re ever in London (yes, I’ve got your name on my list GH!!) please do tell me so that you can join one of these days!!
  18. Some of you are really super 🙂  – super-transcribers that have made a HUGE contribution as an individual – but the whole picture of lots of little contributions also absolutely adds up to something very valuable. (This is the data from our first batch of Chalcid slides).
  19. The first data that we got from the first batch showed us what we already new to a degree – telling the difference between the scientific name of the Chalcid specimen itself, and the host insect it had parasitised, and the host plant on which that was found – is pretty tough!! The errors we were finding were mostly related to that. But your transcription work isn’t lost in those cases – where it looks like a piece of data is in the wrong field, we’ll simply move it over to a catch-all notes section so that it is still fully searchable.
  20. Two of our partners in the SYNTHESYS consortium also have an expedition on Notes from Nature, which I helped them put together and launch.
  21. The Amaranthacae were still not done yet at that time, and they have been more slow going. They are completely transcribed now though – HUGE thanks! We look forward to sharing information with you about what that partner (The Botanisher Garten in Berlin) learns from the collection.
  22. We think (thanks to your comments in Talk and Chat), that this has been more difficult partially because there is such a wide range of label styles, such as this one
  23. and this one.
  24. And we (I) made the mistake of trying to capture all of the possibilities – which resulted in a pretty long workflow, that can be confusing.
  25. Going back up to the other project
  26. The Primulacae from Kew Gardens are still not completed yet, and are similarly slow going.
  27. Once again we think that the wide variety of labels is one of the factors
  28. as well as a more complicated workflow that is trying to capture all of the possibilities
  29. And then the most recent Natural History Museum London expedition is the Fossil slides.
  30. This is the display table that I had out at the Lyme Regis Fossil Festival where we launched that project. The pyramid is made out of the same sandstone that the real pyramids are built out of, and they contain Nummulites, a Formanifera fossil that is shown in the specimen beside it. On the smooth side of the pyramid you can see what these fossils look like as a ‘slice’ – which is how they appear on the Miniature Fossils Magnified (MFM) microscope slides!
  31. Here is how the MFM project is going so far
  32. There are a number of things I’ve been learning from your feedback in the Talk forums, and from the data you’ve been generating for us – such as Drop Down menus making the workflows much easier, and lowering the risk of error.
  33. And this is the latest project that I’ve helped a SYNTHESYS partner to launch – the Exploring Tropical Sweden expedition that was built directly onto the Zooniverse platform instead of Notes from Nature, because we were offering both an english and a swedish-language workflow for the local audience of Swedish Museum of Natural History fans. Luckily they needed less information from their labels, so the workflow is very easy!
  34. This project got a huge boost when it first launched, thanks to the communications from the Museum in Stockholm, and the Zooniverse community of testers for new projects built on Panoptes (the open project builder that we used to launch this).
  35. The Museum in Stockholm held an in-house Citizen Science day where they invited the public to take part in helping to transcribe their Brachiopod labels, and they really enjoyed speaking to volunteers like yourselves.
  36. Their Talk forums have been very active, and you can see a few peaks when a person really dove in and did lots of transcribing, and also had lots of interesting questions!
  37. So coming back to the context of the SYNTHESYS project, as this presentation is being given to my consortium partners (21 institutions from all over Europe, who all have natural history collections). In particular I wanted them to know that the value of the effort you’ve been making on our behalves is not just about the volume of transcriptions – there are all sort of other ‘non-quantifiable’ benefits of institutions doing projects like this together with the public.
  38. I shared an example of one of you lovely people who went diving into a thorough research of the web to discover the exact location of Wema Island (with apologies again from me for mis-reporting the country, after an in-house volunteer also did a deep search for this) – I know from the Talk forums that many of you have been enjoying finding out more and are really great detectives for these collections!
  39. I shared the example of our favourite ‘nature blogger’ in the Talk forums 🙂 sharing so many lovely observations of the plants and flowers in her immediate environment, and how she is encouraging others to share their observations as well.
  40. And I shared some of my own examples of a computer-room session I ran at my daughter’s primary school here in England, with a group of 10 and 11 year olds doing the Tiger Beetles. Through this project they learned the names of the provinces of Canada, which we wrote on the whiteboard along with their abbreviations. They learned what ‘altitude’ meant. We talked about why collectors write down all of this information on labels, and why it is important. They had great questions for me, such as ‘Are there any Tiger Beetles in England?’ – so we did some internet searching together. And these quotes are what they told me at the end :).
  41. There are sometimes some lovely little surprises in these collections. For example, some of the Brachiopod fossils in the Swedish Museum of Natural History collection were collected by the then King of Sweden!
  42. And although this example is from someone who works with collections in Ontario, and is not related to one of these projects, it does show that sometimes there is some quite poignant history captured in these collections as well.
  43. From our point of view at the Natural History Museum in London, providing more awareness of our collections behind the scenes is an important part of our public outreach. (That is our Chalcids curator Natalie showing our Visiteers her specimen work space, and some of the pinned Chalcids in her collection)
  44. This is the Data Portal where all of your hard work will be published, and made available for anyone in the world to research. As a Museum we hold these specimens in trust for the public. They don’t belong to us. And that is why it is so important that they are truly available to anyone – which includes folks without research & accommodation budgets to come and spend time physically studying our collections, as well as those who are just generally curious.
  45. We’ve been showcasing this data, via our Data Portal and the Application Programming Interface (API) through which you can access that data, to the developer community as well. This is a ‘Hack Day’ event that I ran with 200+ developers, where we invited them to explore our collections data and do interesting things with it.
  46. This is the team that won our Natural History Open Data Challenge‘, by creating a wonderful interface into our Bioaccoustica data, that allows you to listen to them ‘spatially’.
  47. I then had a moment for our audience to ask any questions.
  48. These are spare photos that I had ready in case anyone had questions about our efforts to digitise all of our collections.
  49. Here you see a contraption that one of my colleagues invented to hold an ancient folio of bound herbarium sheets open for photographing, in a way that won’t tear the pages or break the spine. He built it using LEGO Mechanics, with the cut-off fingers of surgical gloves on their tips to protect the pages!
  50. This is what the first photo looks like, using this method (on the left), and then with software we’re able to straighten that image out a bit better (on the right).
  51. And this is our set-up for photographing the pinned-insects, that not only need to be captured from more than one angle to study them properly, but also to capture the labels that are pinned underneath the insect itself.

And that’s a wrap 🙂 Do let me know if you have any questions!! You can contact me at any time at m.gold@nhm.ac.uk.

If you’re interested in finding out more about our digisitsation work at the Natural History Museum in London, you can read our own blog here: https://blog.nhm.ac.uk/tag/digital-collections-programme/, and you can find out more about the Digital Collections Programme itself here: http://www.nhm.ac.uk/our-science/our-work/digital-museum/digital-collections-programme.html

Happy Anniversary

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It has been a year since we launched the new version of Notes from Nature or what we sometimes call “NfN 2.0.” The new platform has been a big improvement for us, providing the opportunity to really bring a range of new expeditions up and online, and to connect to more people than ever before. We hope NFN2.0 has been something in which you’ve been excited to take part!

In the past year, over 281,000 images have been transcribed by 3,641 registered volunteers. We have completed 64 expedition from a variety of expeditions groups. We added fossils, butterflies, aquatic insects and even brought back fungi to the site.  We hope to have new and exciting expeditions to bring forward in the next year, including more phenology exhibits and new groups.  There are some exciting new developments on transcription improvements, field book contents, and how we organize our expeditions, that should also come online in the next year.  We can’t wait for Y2 for NFN2.

We would like to take this opportunity to thank the Zooniverse team and all of the specimen image providers that we work with, but most of all the site wouldn’t be a success without a dedicated group of volunteers. We sincerely hope that you all find value in working with us and we remained committed to providing a valuable experience for you.

Sincerely,

The NfN Team

BOON herbarium thanks you!

Our “Plants have all the anthers! Pt 1” was a great success! We appreciate everyone’s hard work. This first expedition contained over 780 specimens, which is no small feat. As the title suggests, this was is just the beginning! Soon our new expedition will launch so keep an eye out for “Plants have all the anthers! Pt 2”. Feel free to follow the BOON Herbarium on Facebook or Twitter to keep track of all the exciting discoveries and events we have going on. The BOON Herbarium thanks everyone for their time and effort for making Notes from Nature such a success for all herbaria!

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A botany class out exploring at Appalachian State University

— Jordan Willet, Appalachian State University, Boone, North Carolina, U.S.A.

Editor’s Note: BOON is the official acronym for the herbarium at Appalachian State University. A resource called Index Herbariorum compiles the acronyms for the over 3,000 herbaria around the world.

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