Bionomia, launched August 2018 with the aim of linking natural history specimen records to people who collected them and/or identified them to species. The two main goals are to:

(1) give credit to and improve the visibility of people who have contributed to the world’s natural history collections (see Thessen et al., 2019; McDade et al., 2011); and,

(2) encourage natural history collections data managers to incorporate these new digital annotations into their source data warehouses, which completes a round-trip of high-quality, curated annotations.

Zenodo is a key piece of infrastructure to help realize the first goal, especially for graduate students and early career researchers who desire a breadth of ways to illustrate their expertise and impact.

Bionomia uses data that is produced by the world’s natural history collections and subsequently shared with the Global Biodiversity Information Facility (GBIF). Linking specimen records to people in this data is however challenging because people names are typically expressed as free-text with considerable variability in the ordering of the parts of names, abbreviations, and according to local cultural practices in the used data exchange standard maintained by Biodiversity Information Standards (TDWG). Through Bionomia, authenticated users actively disambiguate these text-based “agent strings” as they are commonly called, into Uniform Resource Identifiers (URIs) from Wikidata or ORCID as declarations of unequivocal person identity. Thus, free-text strings for people are enhanced to become uniquely identifiable and are thus better participants in the exchange of data according to the FAIR principles (Wilkinson et al., 2016).

When a user first logs in to Bionomia via OAuth using their ORCID credentials, they are presented with an interface to claim the records of natural history specimens they collected or identified. Over 175M records are downloaded and refreshed from GBIF into Bionomia every few weeks, then processed and pre-indexed for a pleasing experience, which would ordinarily have been a daunting task for any user. The reason for this refresh cycle is to keep pace with the continuous activities that occur upstream in the world’s museums and collections in which researchers deposit their physical specimens. Each user has a “Settings & Integrations” section in their account in Bionomia where they have the option to archive their data to Zenodo. Behind the scenes, Bionomia makes use of Zenodo’s well-documented REST API for users to authenticate using OAuth – most often using their ORCID credentials once again – and then auto-deposits versioned archives of users’ claimed specimen records as both csv and JSON-LD files. The mechanics of this interaction is made seamless for users (Figures 1–4); they complete the process with a few clicks and no typing or form submission is required of them. Within moments, they have a new freely accessible (Creative Commons Zero v1.0 Universal) entry in Zenodo as a resource type “dataset” along with their ORCID ID clearly indicated, a handful of keywords, a formatted description, a title, a referenceable citation (Figures 5 & 6), and a DataCite DOI. Whenever specimen records are newly attributed to or claimed by users who have enabled this integration between Bionomia and Zenodo, their datasets are automatically constructed anew, pushed to Zenodo, and new versions appear (Figure 7). If a user additionally configures their ORCID profile to accept DataCite as a trusted party, their new dataset entry appears in ORCID soon afterward alongside their publications and affiliations (Figure 8).

To date, 84 users of Bionomia have integrated their account with Zenodo and are collectively archiving 552,659 specimen records. While this may seem like a small number of active integrations, this is a valuable service for each of them. Many researchers were newly introduced to this novel workflow – archiving specimen-based data is an uncommon practice in our domain – and are now appreciative of Zenodo’s mission, user-friendly design, flexibility, and openness. Why not join this growing open science movement, by claiming your specimen data?

Testimonial by Dr. Zoë Goodwin

As a tropical botanist, a lot of my effort goes into the fundamental aspects of natural history data: the collection, identification and naming of plant specimens. Without these actions we can have no understanding of the natural world around us. However, until now it has been virtually impossible to keep track of these actions, claim them as work and then see how my particular efforts have contributed to other scientists’ research. By using Bionomia to claim the specimens that I have collected and identified in GBIF, for the first-time others can see what I have done and see how I have contributed to our understanding of the natural world. Then, importantly as an early career researcher I can include all this information as a citation & DOI using Zenodo in my CV or on my personal webpage.

Goodwin, Zoë. 2022. Natural history specimens collected and/or identified and deposited. [Data set]. Zenodo. https://doi.org/10.5281/zenodo.3581428

Testimonial by K. Samanta Orellana

When I started studying insects in Central America, I had the opportunity to collect, process, and identify thousands of specimens in different entomological collections. However, I didn’t have the means or even know how to digitize and mobilize collection data and many of these activities went unnoticed. It wasn’t until I started my research as a PhD student in the US, that I was able to learn about the digitization workflows and the importance of sharing data in global aggregators such as GBIF. At the same time, I was able to learn about Bionomia and I was instantly engaged. Being able to see the details about my work in collections, and see how the specimens are connected to other collectors or taxonomists, became a strong motivation to continue digitizing and sharing data. Moreover, the ability to compile this information via Zenodo and make it citable has been a great way to make my contributions visible through my ORCID researcher profile, also allowing me to keep records of the progress made during my doctoral program.

Orellana, K. Samanta. 2022. Natural history specimens collected and/or identified and deposited. [Data set]. Zenodo. https://doi.org/10.5281/zenodo.3942155

References

McDade, L.A., D.R. Maddison, R. Guralnick, H.A. Piwowar, M.L. Jameson, K.M. Helgen, P.S. Herendeen, A. Hill, and M.L. Vis. 2011. Biology needs a modern assessment system for professional productivity. BioScience 61(8): 619–625. https://doi.org/10.1525/bio.2011.61.8.8

Thessen, A.E., M. Woodburn, D. Koureas, D. Paul, M. Conlon, D.P. Shorthouse and S. Ramdeen. 2019. Proper attribution for curation and maintenance of research collections: Metadata recommendations of the RDA/TDWG Working Group. Data Science Journal 18(1): 54. http://doi.org/10.5334/dsj-2019-054

Wilkinson, M., M. Dumontier, I. Aalbersberg et al. 2016. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3: 160018. https://doi.org/10.1038/sdata.2016.18

We’ve talked in the past about the challenges of running a service at the scale of Zenodo in the inhospitable environment of the modern internet. Over the past couple of years, we have experienced an exponential increase in our users, content, and traffic… and we couldn’t be happier that Zenodo is proving useful in so many different ways! For Open Science to flourish, researchers should feel empowered to share their data, software, and every part of their journey of publishing their work. We are proud to have done our part in lowering the barrier to share and preserve.

This year we crossed the threshold of 2 million records, we are closing in on storing our first PetaByte of data, and we’ve reached 15 million annual visits. To keep up with these challenging requirements, our team put their heads together with our colleagues here at the CERN Data Center. Their long-running expertise in handling PBs of data generated from the CERN experiments is one of the reasons why we can offer a reliable service to the world in the first place. Over the past year, we have tweaked and optimized our infrastructure to help solve a variety of scaling and performance issues that we’ve faced.

Improved file serving

One of the main culprits for our performance bottlenecks was the way we served files. Our web application was doing all the heavy-lifting, while the number of concurrent connections we needed to serve was increasing. The solution was simple: leave the heavy-lifting to the pros 💪. With the help of our CERN storage team, we now have a dedicated setup for offloading file downloads directly to our EOS storage cluster.

This change also came with a bonus side-effect: Zenodo file downloads now support HTTP Range requests! This means resumable file downloads, as well as the unlocking the possibility for a wide range of applications which depend on accessing small parts of large files (e.g. Cloud Optimized GeoTIFF, Zarr).

Dedicated space for crawlers and bots

Given our high content intake of almost 10k records on a weekly basis, it was natural that web crawlers and indexers had a tough time going through everything without stealing resources from normal users. There are conventions that instruct crawlers to slow down, but unfortunately, not all crawlers respect them. To minimize the impact crawlers have on the rest of the users, we’ve put up a dedicated space that serves them in a machine-friendly fashion. That means that regular users get a performant and snappy experience while browsing our pages, while crawlers still get to index Zenodo at their own pace.

Towards a stable future

This is of course not the end of the story. We expect Zenodo to continue growing at the same rate and we have many plans to further stabilize and scale our infrastructure. We have closely monitored our database and search cluster performance, and identified points of improvement based on industry best practices. We’re also eager to explore ways to provide cached versions of our pages.

Last, but not least, our efforts in building and rebasing Zenodo on top of InvenioRDM, a turn-key solution for digital repositories, come in the form of a bottom-to-top revamp of our software stack, based on the same pillars that made Zenodo what it is today: a resilient, top-of-the-class user experience, and scalable platform at the service of Open Science.

Cross posted at Dryad

The Dryad and Zenodo teams are proud to announce the launch of our first formal integration. As we’ve noted over the last years, we believe that the best way to support the broad scientific community in publishing their outputs is to leverage each other's strengths and build together. Our plan has always been to find ways to seamlessly connect software publishing and data curation in ways that are both easy enough that the features will be used but also beneficial to the researchers re-using and building on scientific discoveries.This month, we’ve released our first set of features to support exactly that.

Uploading to Zenodo Through Dryad

Researchers submitting data for curation and publication at Dryad will now have the option to upload code, scripts, and software packages on a new tab “Upload Software”. Anything uploaded here will be sent directly to Zenodo. Researchers will also have the opportunity to select the proper license for their software, as opposed to Dryad’s CC0 license.

Those familiar with Dryad may know that Dryad has a feature to keep datasets private during the peer review period, with a double blind download URL that allows for journal offices and collaborators to access the data prior to manuscript acceptance. Zenodo hosted software will be included in this private URL and will be held from the public until the dataset is ready to be published.

After curation and publication of the dataset, the Dryad and Zenodo outputs are linked publicly on each landing page and indexed with DataCite metadata. Versioning and updating of either package can happen at any time through the Dryad interface.

Elevating Software

Throughout our building together, we worked with researchers across scientific disciplines to both test the look and feel of the features but also to understand how data and software are used together. Through conversations with folks at Software Sustainability Institute (SSI), rOpenSci, Research Software Alliance (ReSA), US Research Software Sustainability Institute (URSSI) and leaders in the software citation space, we understood that while researchers may not always think of their R or Python scripts as a piece of software, integrations like this are essential to elevate software as a valued, published, and citable output.

This work between the organizations represents a massive win for open science and reproducibility. Besides the lack of incentives to share, a significant source of friction for researchers is the burden of preparing research artifacts for different repositories. By simplifying this process and linking research objects, Dryad and Zenodo are not only making it easier to share code and software, but also dramatically enhancing discoverability and improving data and software citation.

Karthik Ram, Director of rOpenSci & URSSI lead

Looking Forward

This release is the first set of features in our path ahead working together to best support our global researcher base. While we are building feature sets around Supporting Information (non-software and non-data files) for journal publishers, we know that this space is evolving quickly and our partnership will respond to both the needs of researchers as well as the development of best practices from software and data initiatives. We will keep the community apprised of our future developments and we are always looking to expand our reach and iterate on what we’ve built. If you believe there are ways that Dryad and Zenodo better support research data and software publishing, please get in touch.