ICEDIG – glimpse on the diversity of European collections

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Take part in a European-wide experiment and help us discover the best methods to unlock the information stored within herbarium cupboards.

The ICEDIG project, “innovation and consolidation for large scale digitisation of natural heritage”, is funded by the European Union and aims to address many of the challenges that lie ahead to enable the mass digitisation of more than one billion specimens of natural history collections across Europe (https://icedig.eu/).

We need your help! We are experimenting with transcription on different crowdsourcing platforms using specimens from different herbaria, from many countries. Within this expedition you will find specimens from Botanic Garden Meise (BR), Botanischer Garten und Botanisches Museum Berlin-Dahlem (B), The Natural History Museum London (BM), Royal Botanic Gardens, Kew (K), Royal Botanic Gardens Edinburgh (E) and Muséum National d’Histoire Naturelle (P). The goal was to create an expedition with a good cross section of specimen characteristics, typed and handwritten labels, covering a wide range of collection dates, different countries and families. The aim is to try and discover if and why some specimens are harder to transcribe than others. We will share our findings with you.

Exceptionally, you will see the same specimens have been put up on several other crowdsourcing platforms. This is to allow us to analyse and compare transcriptions from different platforms.

If you like variety in your transcriptions, then this is the challenge for you. Thanks to all in advance from the ICEDIG team for trying the expedition. Happy transcribing!

— Sarah Phillips, Royal Botanic Gardens, Kew

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Calling all young people taking part in Notes from Nature!

Dear NfN Community,

You might notice an email coming from the Zooniverse team in the coming days, calling for young people to join a new research study, and we wanted to share a little more about this with you.

The Notes from Nature platform supports the transcription of data form many different Museum collections, including those from the Natural History Museum in London. Alongside participating in Notes form Nature, the Museum is responsible for a number of other citizen science projects relating to its collections and research and is taking part in an international collaboration to better understand how young people engage with projects of this nature.

The study is being carried out by researchers at the Open University and University of Oxford in collaboration with a range of other museums and academic institutions in the USA, funded by the National Science Foundation, Wellcome Trust & ESRC. The team aims to gain a better understanding of the experiences of people between the ages of 5-19 when taking part in Zooniverse projects, with the ultimate goal of designing better projects and tailoring learning experiences specifically for this age range.

As you might have guessed, Notes from Nature has been selected as one of the citizen science projects to be used in the study. The site and the classification process will remain exactly the same, however, if you’re one of our younger online-volunteers and would like to take part in the study you can find out more and sign up to be a part of it here [https://openuniversity.onlinesurveys.ac.uk/zooniverse].

Phenology at scale

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We have launched a number of recent phenology expeditions, as experiments and under our “Labs” section of Notes from Nature. We have gathered some great data from those efforts, and we are now excited to expanded further here, related to two ongoing on research projects. Our first attempt at expansion is now posted as a new expedition entitled, “Predicting Past and Present Phenology I”. So let’s talk about how your help can move forward some great science and informatics endeavors.

The first project is related to work to integrate phenological information coming from multiple sources. Over the past few years, we have been working on building data integration tools in order to bring together data from two different and major observation networks, the National Phenology Network (npn.org) here in the United States, and the Pan-European Phenology Network (http://www.pep725.eu/). Integrating these data is longer, neat story that involved building an ontology for plant phenology (https://www.frontiersin.org/articles/10.3389/fpls.2018.00517/full) and using a set of cool tools to end up with a new portal to find integrated phenology data (plantphenology.org). We are excited to now integrate herbarium data with the observation records as a next step. That will require some extra effort, since herbarium sheets only show parts of plants, not the whole plant, but we are working on the logic of how to do this. And we want to showcase citizen science efforts to help build these coordinated data resources, which is where you come in. We’ll be integrating the results of your efforts right into plantphenology.org!

But wait, there is more…

We are also working on a project looking at how regional urbanization along with climate change can both impact phenology. Urbanization can impact phenological timing of plants via especially increasing temperatures through the urban heat island effect. How such urbanization and overall climate changes impact phenology can be examined in the present looking at spatial patterns, but its very exciting to also be able to look at these questions temporally as well. How have trends over time in urbanization impacted phenology trends e.g. earlier flowering. Herbarium specimens can provide that critical look at the trends across time. We have explicitly chosen groups with relatively rich records in the 19th and 20th centuries that are also well studied today. We will presenting some of the results of this work over upcoming blog posts.

A couple notes about this expedition and the ones to follow. First, we are still experimenting with how to best capture phenology information from specimens, and feedback on how easy or hard you find the expedition(s) is much appreciated. Second, we have decided to present more than one taxa in the same expedition. We know this makes it challenging, and if you have issues, please let us know. We haven’t provided extensive help per species, but have tried to point you to some possible sources to check out more information.

Wading through Water Plants in Virginia

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Water plants are a diverse group of species that can be found in a number of unrelated families. We’re focusing on aquatic flowering plants in this expedition, although they can be found in other groups. Even ferns have aquatic members, like the nitrogen-fixing mosquito fern (Azolla).

Some aquatic plants can be large, showy, and easy to identify. Big, bright water lilies (Nymphaceae) are certainly hard to miss! Many of these water plants have converged on a similar morphology for ecological and evolutionary success. These plants frequently have very narrow (cattails; Typhaceae) or finely dissected leaves (water-nymphs; Najas) for life in the water.

These plants can often be quite common but they often pass under our radar. Sometimes we can’t access them out in a lake or in a mucky pond. And sometimes we might just pass them by without even noticing the smaller, less conspicuous species.

We would love to fully digitize our aquatic plants and make their collecting data available to students, researchers, artists, and others world-wide. So please help us with this expedition! You will get a chance to hone your ID skills for these diverse plants found across Virginia, U.S.A. Thank you!

— Jordan Metzgar, Virginia Polytechnic Institute and State University

Happy 2nd Anniversary!

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It has been two years since we launched the new version of Notes from Nature or what we sometimes call “NfN 2.0.” We wanted to take a moment to thank everyone and reflect on some events.

In the past two years, over 666,000 images have been transcribed by over 6,000 amazing volunteers. We have completed 124 expeditions from a variety of plant and animal groups. We have launched some mobile app based expeditions, and have been featuring more simple expeditions such as State Spotter and lots related to phenology. Our goal is to both facilitate science and provide a variety of rewarding volunteer experiences on the site.

There have been some milestones as well such as setting a new record of over 8,000 transcriptions in a single day!

Notes from Nature has also continued to have onsite events such as the one we organized on Earth Day this year called Take a Note. WeDigBio continues to be major yearly event for Notes from Nature and some of the team recently published a paper about it. Let’s not forget about museum kiosk event called Phenomuse!

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. We have some neat, new additions planned for Notes from Nature in the coming year, and can’t wait to share some of those soon.

Sincerely,

The NfN Team

NitFix Appreciation and Update

We wanted to take a moment to thank all that have helped with the NitFix expeditions. There has been a fantastic response to this project on Notes from Nature. The 5th expedition is currently at 17% complete and four expeditions have finished so far with over 15,000 transcriptions already completed!

Today there are researchers from the NitFix team collecting more samples at the Missouri Botanical Garden herbarium for analysis. This is one of the largest herbaria in the world with over 6.6 million specimens. To date the NitFix team has had 90% sequencing success meaning that they have been able to get genetic sequences from 90% of the samples collected. That is a really good considering that all of these samples have come from herbarium specimens as opposed to fresh plant tissue.

We expect about 6 more expeditions to come in the future as the NitFix team continues this ambitions project. You can continue to follow progress at the NitFix website and on Twitter @Nit_Fix

East Coast Versus West Coast Transcription Battle

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We are co-launching simultaneously two new expeditions that are part of our “Understanding A Critical Symbiosis: Nitrogen Fixing in Plants” series. These new expeditions are a departure from the previous ones as we are only asking for a subset of typical fields. This subset are almost all “drop down” fields, with one exception, and generally cover “higher geography” such as country, state and county, along with date. For our East Coast entrant (the New York Botanical Garden), we are also asking for “verbatim scientific name” as it is written on the label, because this is useful for curator purposes at the Garden and may differ from what we have recorded.

Our West Coast entrant is the California Academy of Sciences herbarium, who were kind enough to host us for three weeks in January for a marathon effort to sample herbarium sheets.  Our worked focused on the very strong collections of nitrogen fixers from Mexico and Central America.  

So its East Versus West in an epic transcription battle!  We’ll update how each expedition is doing in terms of weekly effort and see who will get the crown.  

Finally a very quick update that we are motoring through extracting DNA from all our samples, and have had excellent success so far getting DNA from most of our samples.  We’ll have more to report about sequencing efforts, which are now underway, in a follow-up post.

Rob Guralnick and Ryan Folk, Florida Museum of Natural History

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