Archive by Author | mwdenslow

WeDigBio 2019 Day 2 summary

WeDigBio day 2 was another huge success! NfN received over 9,000 transcriptions (9,105 to be exact). That is our second most productive day ever. We are excited to see how the next two days unfold.

It’s not all about the numbers though. We’d love to hear about everyone’s experience at at an onsite event or participating online. Feel free to check in on NfN Talk.

We are so grateful to each and everyone who participated. Remember to check #WeDigBio on Twitter through out the event for more exciting developments!

— The Notes from Nature Team

How Weird is That?

Specimen collectors often have deep experience with the natural world, and occasionally they notice things that aren’t as they expected.  In a recent survey of over 220 collectors from across taxonomic disciplines (botanists, ornithologists, entomologists, etc.), over half (59%) reported documenting the anomalies that they observe on their specimen labels, which is great.  However, there is a huge diversity of ways in which they do this, which makes it hard to find their observations.  When asked to provide words that they use in those descriptions, survey respondents gave 170 unique words and phrases.  Most of these words and phrases can be used in ways that might not communicate an anomaly.  For example, “early” is a frequently cited word to describe a phenological anomaly (i.e., an anomaly related to the timing of life history events).  “Flowering early” is an observation of an anomaly; “specimen collected in early morning” is not.  Even words that might be thought straightforward, like “Strange”, appear in ways that are not documenting an anomaly (e.g., “Strange Road” as a place name).

With this new project, “How Weird is That?”, we are seeking help to classify specimen records as including an observation of an anomaly or not.  These classifications will then be used to train machines to differentiate between the two cases.  To ensure that some of the records being considered include observations of anomalies, we’ve searched the 120 million specimen records at iDigBio for each of 25 terms cited by collectors as useful in describing them.   In the project’s first Notes from Nature Expedition, we included all of the records that have images associated with them and that contain the terms “early”, “earlier”, or “earliest”.  The second expedition includes records that use the terms “late”, “later”, or “latest”.  After that, we will do a second late-later-latest set of specimens, then move on to other terms like “weird”, “abnormal”, and “odd”.  The further classification of statements of anomalies as being about phenology, distribution, or other things will be used in to refine the machine learning step.  Once the machines have been taught to flag assertions of an anomaly, it can be a much faster hand-off of that information to those who could use the information, such as those studying invasive species or mismatches in the arrival of migratory birds and emergence of the insects that they eat.

Finally, a few things to note.  We have the expectation that most images that are associated with specimen records will contain the specimen labels, but that is not always the case.  So as not to bias the sampling and diminish the utility of the machine learning rules that we arrive at, we have not removed any records from the datasets by acting on potentially faulty assumptions, such as “images of fossils don’t ever contain labels” or “bird images are only ever made in the field and not after specimen preparation is complete.”  This leads us to an important point: specimens are preserved plants, insects, birds, fish, etc.  If you think that viewing dead organisms, whether in the field (e.g., a photo of a beached whale) or after preservation (e.g., an insect on a pin), will trigger unpleasant reactions for you, we encourage you to contribute to science in a different Notes from Nature project.  Also, please note that some handwriting on labels is hard to read. If that’s the case for something you see, use “Uncertain” as a response, and we will check it later.  Finally, please be assured that classifications of specimen records as not containing an observation of an anomaly are as valuable to our process as finding those that do.  The machines need both to learn how to differentiate.

We are tremendously grateful to participants in this activity and hope to keep things interesting throughout this data creation campaign by remaining engaged in Talk and providing occasional blog updates.  Thank you and enjoy!

— Austin Mast, Florida State University


A new record and WeDigBio 2019 Day 1 summary!

WeDigBio 2019 got off to an amazing start! NfN received 9,865 transcriptions on day 1 of the 4 day event. That is our most productive day ever! This broke our previous record set back in 2017. We are beyond thrilled and can’t wait to see what happens with day 2.

Remember to check #WeDigBio on Twitter through out the event for more exciting developments!

— The Notes from Nature Team

Here we go!

WeDigBio 2019 is just starting to kick off around the world. Here at Notes from Nature we have lots of great content. There are over 20 expeditions in 9 different projects.

We hope everyone has an enjoyable event and that we see lots of transcription activity and chatter on Talk. Please take a moment to connect on the chat board to tell us about your event or anything else you want to share.

— The Notes from Nature Team

Introduction to the Notes from Nature Orange County Expedition

Just in time for WeDigBio 2019, the California Phenology Network introduces a brand new expedition of California treasures. This new expedition features specimens from the UC Irvine Herbarium (IRVC). Most specimens were collected in Orange County, California: from its highest point, Santiago Peak (5,678 ft) in the Santa Ana Mountains, to low lying wetlands and coastline. We will also encounter specimens from the broader Southern California region, Southwestern United States, and Baja California, Mexico — lands of arid deserts, foggy coasts, shrubby hills, and rocky mountain slopes.

Orange County is a small, densely populated county in coastal Southern California. At around 800 square miles, it is home to nearly 3.2 million people. Over half of the land area, and thus vegetation, of Orange County has been transformed by human use. However, good examples of almost every vegetation community that historically existed still exist today due to the county’s network of public and private protected areas. Old herbarium specimens can help us get a more complete picture of the historic vegetation of Orange County.

In terms of plant diversity, 1431 species and 1525 taxa, 953 of which are native, are recorded for the county (Roberts Jr, 2008). Dudleya stolonifera and Pentachaeta aurea subsp. allenii are the only county endemics, that is, plants that are limited in range solely to Orange County. The taxonomic focus of our first expedition are the plant families Adoxaceae (elderberries), Aizoaceae (carpet-weeds), Apiacae (carrots), Asteraceae (sunflowers/daisies), and Brassicaceae (mustards).

This expedition will be the focus of several WeDigBio on-site events in Orange County and beyond. Get ready to see its transcription numbers soar!

The end of an era

Notes from Nature made a big transition back in May. Even though NfN 3.0 has been up and running we still had some unfinished business in terms of expeditions that weren’t completed on the old system. A few days ago we completed our last expedition from the “old” platform. This also means that this particular project on Notes from Nature will be retired for good.

Not to worry though we have lots of fun and exciting expeditions on our current platform! NfN is now organized around Projects so look around and explore expeditions that are available within each one. Remember that these Projects can be filtered by tags such as Plants, Bugs, Butterflies and so on.

We have some mixed feelings about all these changes. We are thrilled to move forward and continue to make improvements to NfN 3.0 (our current platform), but we had so many great expeditions, events and memories over the time that NfN 2.0 was running. The amazing Notes from Nature community completed over 1 million transcriptions and was visited by over 8,000 volunteers. We are so happy that the community is continuing to help us build this resource.  Thanks as well to our network of providers and our hope is that 3.0 is ultimately an easier and better experience for all involved.

With all that said remember that we still have some more upgrades to complete on NfN 3.0. For example, this includes a unified Statistics page, improvements to Talk, etc.

— With gratitude the Notes from Nature Team

WeDigBio 2019!

The Notes from Nature team is very excited about WeDigBio 2019. The event will take place October 17 – 20.


To our amazing volunteers:

We hope you’ll save the dates and join us online or in person at one of the many events happening at that time.

To our collaborators and data providers:

It’s always a fun and exciting time for us as we get to work with lots of new and existing colleagues! If you plan to host an expedition this year let us know as soon as possible.

Note that Notes from Nature has recently gone through an upgrade. Previous data providers that we have worked with will utilize their existing Projects on our site. Other providers expeditions will go into a WeDigBio themed Project that we’ll start building very soon. We will plan to have all expeditions within the WeDigBio project complete within a month of the end of the event. We have lots of activity on the site and we always aim to keep our content fresh and have expeditions complete in a timely fashion.

— The Notes from Nature Team

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