Making progress in data sharing

A few useful tips on making progress in data sharing in a blog post "Data Sharing: Access, Language, and Context All Matter":

• To make the global data system less fragmented and disorganized, create data portals with good human-centered designs and support users with varying levels of expertise


• JSON and XML are great, but humans read data too. These formats are critical to fueling innovation, but make sure CSVs are available as well


• Responsible data use demands proper attention to metadata. Document datasets and don't ignore ReadMe files  while re-using them

Study: Biomedical data sharing and reuse

A recent publication in PLoS ONE "Biomedical Data Sharing and Reuse: Attitudes and Practices of Clinical and Scientific Research Staff" surveyed the Intramural Research Program at the US National Institutes of Health (NIH) with regard to data management, data sharing, and data re-use.  The authors received 190 responses and analyzed 135 (scientific and clinical staff). Below are the highlights from their findings:

• ~60% of respondents rated relevance of data re-use as high, while ~15% rated it as low


• ~25% rated their expertise in re-using data as high, while ~45% rated it as low


• ~61% reported that they had never uploaded a dataset into a repository, while ~71% said they had shared data directly with another researcher


• `30%  indicated that it took them more than 10 hours to prepare data for sharing


• Only 20 respondents provided reasons for not sharing data and their reasons were pretty scattered (see image below):

Image from the study (t016), responses to "...the reason(s) for not sharing your data"

The data from this study is available on Figshare, but it is not the full survey dataset, it's a subset to support the results of this publication. And for some reason it doesn't contain free text responses to the non-sharing question. It's always informative to see what people say beyond the provided standard categories (that is usually the most interesting story in my mind). Perhaps, there were no free text responses.

Citation: Federer LM, Lu Y-L, Joubert DJ, Welsh J, Brandys B (2015) Biomedical Data Sharing and Reuse: Attitudes and Practices of Clinical and Scientific Research Staff. PLoS ONE 10(6): e0129506. doi:10.1371/journal.pone.0129506

Archaeology meets modern scanning technology for preservation and re-use

Submitted by Annemiek van der Kuil, edited by Inna Kouper

Image from "The strange case of 60 frothy beads: puzzling Early Iron Age glass beads from the Netherlands" conference paper by D.J. Huisman et al.

Dr. Dominique Ngan-Tillard, a professor at the Faculty of Civil Engineering and Geosciences at Delft University of Technology, the Netherlands, has deposited a dataset into the 3TU.Datacentrum repository that contains tomography scans of early Iron Age glass beads found during the archaeological excavations in the Netherlands.

The dataset supports a conference publication by Dr. Ngan-Tillard and others “The strange case of 60 frothy beads: puzzling Early Iron Age glass beads from the Netherlands”. The micro-CT scans helped to identify gas bubbles and mineral and metal inclusions in the glass beads, which allowed the researchers to conclude that “the Zutphen glass beads are the result of local, inexpert, reworking of imported glass objects” (p. 231, conference paper).

In addition to the in-depth analysis of the beads’ structure, the scans serve as a form of virtual preservation of the ornaments. Stored in a data repository and made publicly available, they can help other archaeologists, as well as material scientists and museums in their research and educational activities. In the future 3D prints of the ornaments can be produced for a better understanding of the art of making glass and jewels.

According to Dr. Ngan-Tillard’ comment on the 3TU.Datacentrum website, storing digital collections of archaeological remains together with their meta-data and interpretation will help advance both arts and research and create more challenges for our knowledge.

Watch a short video about frothy beads or see the full story at http://datacentrum.3tu.nl/en/researchers-about-3tudatacentrum/showcase-ngan-tillard/

The International Polar Year 2007-2008 (IPY-4) and the importance ofdata management

The International Polar Year is an international collaboration that focuses on the Arctic and the Antarctic, or polar regions. The polar regions have many unique phenomena, but the cold harsh environment makes them expensive to visit and study. It takes a large multi-country collaborative effort to put together expeditions, install equipment, and collect data. The first three IPYs occurred in 1882–1883,1932–1933, and 1957–58 respectively. The fourth IPY took place between March 2007 and March 2009.

The fourth IPY was dramatically different from the previous efforts (Mokraine and Parsons, 2013). A $1.2 bln effort with participants from more than 60 countries, it had an ambitious vision to enable international sharing and reuse of multidisciplinary datasets and keep the data discoverable, open, linked, useful, and safe (Parsons, Godoy et al., 2011). The enormous efforts to initiate, coordinate, improve, and sustain IPY data stewardship have seen both successes and failures, with some components of the IPY infrastructure struggling to exist and be useful (Lessons and legacies..., 2012).

A fair amount of IPY data is available via such online portals as the IPY data page at the National Snow and Ice Data Center (NSIDC) in the US, the NASA Global Change Master Directory (GCMD) IPY portal, or the Global Cryosphere Watch portal. Some of it, such as a global IPY Data and Information System (IPYDIS)  or the Discovery, Access, and Delivery of Data for IPY (DADDI) are broken. Most importantly though, missing is a way to track and access all the IPY data via a federated or centralized catalog. There is no good consistent way of international polar data to “function locally and reach globally”, to use Mokraine and Parsons’ words.

The challenges of making heterogeneous data and metadata work together were exacerbated by the lack of focused international funding for planning data archiving post-IPY, differences in data policies and researchers “hoarding” data (Lessons and legacies..., 2012; Carlson, 2011). Despite many IPY projects adopting a free and open data-sharing policy, compliance with it and, ultimately, sharing was rather low. Additionally, the researchers in IPY-4 didn’t have access to data from the first IPY projects, some of the data were not available in the digital form, while others were scattered or lost. The data centers (WDCs) that were supposed to support the increasing IPY data streams, lacked mechanisms of working with heterogeneous data, e.g., they couldn’t support social and ecological data.

Despite the difficulties, the IPY data management experience is crucial to the advancement of global data services and the norms of data sharing and re-use. As Mark Parsons, Secretary General of the  Research Data Alliance and former Senior Associate Scientist and the Lead Project Manager at NSIDC put it,

“We were perhaps rather naive going in to IPY. Many of the organizers came from the geoscience background of earlier the IPYs and assumed data systems would exist that could handle IPY data. We weren’t prepared for the incredible diversity of IPY4 with data ranging from Indigenous knowledge to satellite remote sensing to genomic sequencing to cosmology. Although it is unclear what percentage of IPY data are available and much is surely lost, new data services were created and sustained, international coordination continues in sustained organisations, and we learned a lot about different disciplinary cultures and their attitudes to data sharing. The IPY Data Policy was aggressive and not fully honored, but it did drive changes in national policies towards more timely and open release of data. Most critically we saw a change in the conversation within polar science from whether to share to when to share and now how to share. We have a long way to go, but polar data are significantly more accessible than they were prior to IPY.”

Mark’s and others’ publications, some of which are listed below, are a good source of all the lessons learned from IPY data stewardship efforts, one important lesson being that “[e]xperts in data management are critical members of any team attempting internationally coordinated science ...” (Lessons and legacies..., 2012).

Resources

Carlson D. 2011. A lesson in sharing. Nature 469 (293).

Lessons and legacies of the International Polar Year 2007-2008. 2012.

Mokrane M and MA Parsons. 2014. Learning from the international polar year to build the future of polar data management. Data Science Journal 13.

Parsons MA, Ø Godøy, E LeDrew, TF de Bruin, B Danis, S Tomlinson, and D Carlson. 2011. A conceptual framework for managing very diverse data for complex interdisciplinary science. Journal of Information Science 37 (6): 555-569.

Parsons MA, T de Bruin, S Tomlinson, H Campbell, Ø Godøy, J LeClert, and IPY Data Policy and Management SubCommittee. 2011. The state of polar data—the IPY experience. In Understanding Earth’s Polar Challenges: International Polar Year 2007-2008. Ed. Krupnik I, I Allison, R Bell, P Cutler, D Hik, J López-Martínez, V Rachold, E Sarukhanian, and C Summerhayes. Edmonton, Canada: CCI Press.

Sharing in Paleontology leads to re-use

Submitted by Isabel Chadwick, Open University

This opinion piece on the PLOS Integrative Paleontology blog "And this is why we should always provide our data..." is about a  paleontologist who published data about dinosaur teeth in PLOS One, which was reused, leading to a new discovery about the evolution of small theropod dinosaurs.

Source: Andrew Farke. And this is why we should always provide our data. The Integrative PAleontologists (blog). January 25, 2013. Retrieved from http://blogs.plos.org/paleo/2013/01/25/and-this-is-why-we-should-always-provide-our-data/ 

(licensed under the CCBY Creative Commons Attribution 3.0 Unported License.)

Depositing in Netherlands repository adds value, researchers say

3TU.Datacentrum offers researchers within the technical and engineering sciences in the Netherlands several research data services. One of these services is a certified data repository.

A brochure describes good practices on some of the data sets in 3TU.Datacentrum. The brochure also contains a few good examples (stories), where researchers explain how depositing their research data to 3TU.Datacentrum, and making it openly available, has added value to their research.

Contributed by Annemiek van der Kuil, 3TU.Datacentrum