Abstract: Interdisciplinary collaborations and data sharing are essential to addressing the long history of human-environmental interactions underlying the modern biodiversity crisis. Such collaborations are increasingly facilitated by, and dependent upon, sharing open access data from a variety of disciplinary communities and data sources, including those within biology, paleontology, and archaeology. Significant advances in biodiversity open data sharing have focused on neontological and paleontological specimen records, making available over a billion records through the Global Biodiversity Information Facility. But to date, less effort has been placed on the integration of important archaeological sources of biodiversity, such as zooarchaeological specimens. Zooarchaeological specimens are rich with both biological and cultural heritage data documenting nearly all phases of human interaction with animals and the surrounding environment through time, filling a critical gap between paleontological and neontological sources of data within biodiversity networks. Here we describe technical advances for mobilizing zooarchaeological specimen-specific biological and cultural data. In particular, we demonstrate adaptations in the workflow used by biodiversity publisher VertNet to mobilize Darwin Core formatted zooarchaeological data to the GBIF network. We also show how a linked open data approach can be used to connect existing biodiversity publishing mechanisms with archaeoinformatics publishing mechanisms through collaboration with the Open Context platform. Examples of ZooArchNet published datasets are used to show the efficacy of creating this critically needed bridge between biological and archaeological sources of open access data. These technical advances and efforts to support data publication are placed in the larger context of ZooarchNet, a new project meant to build community around new approaches to interconnect zoorchaeological data and knowledge across disciplines.
Category Archives: oa.paleontology
Open Science in Dinosaur Paleontology
Abstract: Research is in the midst of a period of global terraform, usually heralded under the banner of ‘Open Science’. Open Science is a response from communities to an increasingly digital ecosystem, enabling new practices to emerge. Three of the major pillars of Open Science include Open Access, Open Data, and Open Source. The global paleontological community is slowly adapting to each of these as part of its culture, raising new questions around scientific practices, data standards and interoperability, and the role of paleontological research in a modern society. This chapter discusses some of the progress that the paleontological community has made in shifting towards open practices, and considers some potential avenues for the future of the field.
Open Science in Dinosaur Paleontology
Abstract: Research is in the midst of a period of global terraform, usually heralded under the banner of ‘Open Science’. Open Science is a response from communities to an increasingly digital ecosystem, enabling new practices to emerge. Three of the major pillars of Open Science include Open Access, Open Data, and Open Source. The global paleontological community is slowly adapting to each of these as part of its culture, raising new questions around scientific practices, data standards and interoperability, and the role of paleontological research in a modern society. This chapter discusses some of the progress that the paleontological community has made in shifting towards open practices, and considers some potential avenues for the future of the field.
Mike Taylor | Szymon Górnicki
An interview with paleontologist and OA advocate, Mike Taylor.
“SG: You are a supporter of open access, open source and open data. Of course, science must be easily available for everyone. On the other hand, there are problems with funding research and paleoart, small number of jobs in paleontology. Do you have any thoughts on how to solve these problems?
MT: Well, first of all, open access, open source and open data do not threaten jobs in palaeontology at all. If anything, they create more of a market for research, as more can be done.
Palaeoart is a completely separate problem. Fundamentally, the compensation system is different. Academics are paid for doing their jobs, and the data-sets and papers they generate are in some sense by-products. Paying academics to use their data and papers would be ludicrous: they’ve already been paid. But (with maybe a very few exceptions) palaeoartists are not salaried. They get paid only in exchange for their services. For that reason, it’s morally defensible for them to use copyright to prevent their work from being copied, in a way that is not defensible for preventing copying of scholarly papers. It’s great when artists are able to work in ways that allow their work to be freely reproduced and modified, but that will always be the exception….
SG: Does PeerJ meet your expectations of academic publishing practices transformation?
MT: In almost all respects, absolutely. When I was putting together the Xenoposeidon-is-a-rebbachisaur paper, it literally didn’t even occur to me to send it anywhere but PeerJ. Their submission system is less painful than any other I’ve used, their editors are thorough, their peer-review system is efficient, effective AND transparent, their website is fine, their production is really careful, and of course they do all this at a superb low price. And they offer preprints, and an easy route to move from preprint to reviewed paper. I think that as things stand, they are BY FAR the best game in town: when I look at papers in traditional journals like JVP and Palaeontology now, with their hard-to-read two-column text and their tiny greyscale illustrations, they feel like relics of a bygone era.
If I have a reservation about PeerJ at all, it’s a rather churlish one: I wonder whether they could have been a bit MORE radical. But in reality, they probably hit the sweet spot: they’ve moved the Overton window now in a way that they couldn’t have done if they’ve been perceived as too left-field for the Big Names to publish in. But in fact, PeerJ is perceived now as one of the major venues for vertebrate palaeontology, in large part I think because established workers felt that it was recognisable enough as a journal that they were prepared to publish their work there.
There’s one other thing that does need to be mentioned: it worries me a little that PeerJ is privately owned. I know Pete Binfield and Jason Hoyt a little, and they are about the most principled and trustworthy owners a scholarly publishing operation could have. I am confident that they won’t sell out. But ultimately, anything that’s privately owned is to some degree vulnerable. Suppose they dilute their stock a bit more to bring in more investment. They become huge, Then Elsevier offers $500M for them, and the other shareholders group together and
force Pete and Jason to sell. It doesn’t seem likely, but it’s not impossible. I have grown increasingly convinced of the important of the https://cameronneylon.net/blog/principles-for-open-scholarly-infrastructures/ …”
Digitizing the vast “dark data” in museum fossil collections | Salon.com
“The uniqueness of each museum collection means that scientists routinely make pilgrimages worldwide to visit them. It also means that the loss of a collection, as in the recent heart-wrenching fire in Rio de Janeiro, represents an irreplaceable loss of knowledge. It’s akin to the loss of family history when a family elder passes away. In Rio, these losses included one-of-a-kind dinosaurs, perhaps the oldest human remains ever found in South America, and the only audio recordings and documents of indigenous languages, including many that no longer have native speakers. Things we once knew, we know no longer; things we might have known can no longer be known.
But now digital technologies — including the internet, interoperable databases and rapid imaging techniques — make it possible to electronically aggregate museum data. Researchers, including a multi-institutional team I am leading, are laying the foundation for the coherent use of these millions of specimens. Across the globe, teams are working to bring these “dark data” — currently inaccessible via the web — into the digital light….
The sheer size of fossil collections, and the fact that most of their contents were collected before the invention of computers and the internet, make it very difficult to aggregate the data associated with museum specimens. From a digital point of view, most of the world’s fossil collections represent “dark data.” …
The Integrated Digitized Biocollections (iDigBio) site hosts all the major museum digitization efforts in the United States funded by the current NSF initiative that began in 2011….
Our group, called EPICC for Eastern Pacific Invertebrate Communities of the Cenozoic, quantified just how much “dark data” are present in our joint collections. We found that our 10 museums contain fossils from 23 times the number of collection sites in California, Oregon and Washington than are currently documented in a leading online electronic database of the paleontological scientific literature, the Paleobiology Database….”
PaleorXiv Papers
“A preprint archive for Paleontology.”
DO NOT PUBLISH, or Sometimes, open data/open access not ideal – UC Berkeley Library News
“Some fields such as paleontology and archaeology have long maintained restrictions on the publication of site locations and promoted government policies and regulations to limit collection and trade in fossils, artefacts, and culturally sensitive and/or scientifically important material. Organizations such as the U.S. Forest Service do not disclose geospatial data in order to protect research sites. Other solutions include modification of research permits so that endangered species locations are not automatically uploaded into wildlife databases and masking such records on private land, as presently occurs in some states in the United States.
Is this relevant to any public health research? Other than personally identifiable information, what types of health data should not be made widely available?”
A database of all dinosaur specimens in the world | Sauropod Vertebra Picture of the Week
“Wouldn’t it be great if there was [an open-access] database of all dinosaur specimens?
Well, there is — or at least, it’s on its way. Gunnar Bivens, who we know from SV-POW! comments as bricksmashtv, in creaing a vast Google-Docs Spreadsheet ….”
Digging dinosaurs at ScienceOpen – ScienceOpen Blog
“Today, we’re happy to announce the integration of the Journal of Paleontological Techniques (JPT) onto our platform! This journal is all about sharing and opening up the methods that palaeontologists use in their day-to-day research.
So if you love Jurassic Park and dinosaurs, this collection is perfect for you! All articles are Open Access, which means they are free to read, share, and re-use by anyone.”
Fossilworks: Gateway to the Paleobiology Database
“Fossilworks provides query, download, and analysis tools that utilize the Paleobiology Database’s large relational database assembled by hundreds of paleontologists from around the world. The two websites and their predecessors have been used by professional researchers, students, and the public since 1998. The Fossilworks copy is refreshed daily. The data are owned by the contributors and the website and software were created by John Alroy. The site is housed at Macquarie University….”
Opening up the Natural History Heritage for Europeana
“Countless natural history treasures are deposited in museums across the world, many hidden away beyond easy access. The OpenUp! project creates a free access to these resources, offering over one million items belonging to the world’s biodiversity heritage. The objects made available through OpenUp! consist of high quality images, videos and sounds, as well as natural history artworks and specimens, and also include many items previously inaccessible to visitors. Information provided through OpenUp! is checked by scientists and made available through the Europeana portal at www.europeana.eu….”
Fossils preserved by Kansas chalk for eons will be digitized and shared via new NSF grant | The University of Kansas
“Not only will the digitization work make the Western Interior Seaway fossils more useful to scientists, but the grant will open up access to the fossil treasures for the public at large. “We’re going to be creating images and providing information about where fossils come from,” Lieberman said. “The public can look at the same resources as a museum researcher, to expand science out to the public more.” The public outreach will center on a new “Digital Encyclopedia of Ancient Life” intended as an open-access textbook of paleontology. The atlas will feature an online Cretaceous Atlas with at least 800 species from the Western Interior Seaway to be added to the existing Digital Atlas of Ancient Life for the web and an iPhone app. In addition to open-access resources, the researchers will develop K-12 curricular materials from the digitization project as well as providing 3-D scans of the fossils and 3-D models for some classrooms. Additionally, exhibitions based on the grant work are planned at the associated institutions….”
FASTR to be Considered by Senate Committee | SPARC
“After a month of intense conversations and negotiations, the Senate Homeland Security and Governmental Affairs Committee (HSGAC) will bring the ‘Fair Access to Science and Technology Research (FASTR) Act’ up for mark-up on Wednesday, July 29th. The language that will be considered is an amended version of FASTR, officially known as the ‘Johnson-Carper Substitute Amendment,’ which was officially filed by the HSGAC leadership late on Friday afternoon, per committee rules. There are two major changes from the original bill language to be particularly aware of. Specifically, the amendment Replaces the six month embargo period with ‘no later than 12 months, but preferably sooner’ as anticipated; and Provides a mechanism for stakeholders to petition federal agencies to ‘adjust’ the embargo period if the12 months does not serve ‘the public, industries, and the scientific community.’ We understand that these modifications were made in order accomplish a number of things: Satisfy the requirement of a number of Members of HSGAC that the language more closely track that of the OSTP Directive; Meet the preference of the major U.S. higher education associations for a maximum 12 month embargo; Ensure that, for the first time, a number of scientific societies will drop their opposition for the bill; and Ensure that any petition process an agency may enable is focused on serving the interests of the public and the scientific community …”
Impact of Social Sciences – Rather than narrow our definition of impact, we should use metrics to explore richness and diversity of outcomes.
“Impact is multi-dimensional, the routes by which impact occur are different across disciplines and sectors, and impact changes over time. Jane Tinkler argues that if institutions like HEFCE specify a narrow set of impact metrics, more harm than good would come to universities forced to limit their understanding of how research is making a difference. But qualitative and quantitative indicators continue to be an incredible source of learning for how impact works in each of our disciplines, locations or sectors.”
Wellcome Trust Launches Guide for Publishing Open Access Monographs and Book Chapters – OASPA
“Open access for monographs and book chapters is a relatively new area of publishing, and there are many ways of approaching it. With this in mind, a recent publication from the Wellcome Trust aims to provide some guidance for publishers to consider when developing policies and processes for open access books. The Wellcome Trust recognises that implementation around publishing monographs and book chapters open access is in flux, and invites publishers to email Cecy Marden at c.marden@wellcome.ac.uk with any suggestions for further guidance that would be useful to include in this document. ‘Open Access Monographs and Book Chapters: A practical guide for publishers’ is available to download as a pdf from the Wellcome Trust website.”