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About

This file serves to collect thoughts on how to stimulate the reuse of open data, and on how to quantify such reuse. Reuse is to be understood here as non-primary use, i.e. use in a way that was not the primary purpose of collecting the respective data. This blog post considers some of the conditions that have to be met for reuse to happen, and the importance of generativity in the systems involved. Another blog post highlighted

Open tools, open media, and syndication

as key factors on how to achieve that. There are others, and the precise mixture probably depends much on context.

Research questions

  • How are research objects being used?
  • What kinds of reuses are there?
  • What are useful ways to track these kinds of reuses?
  • How is reuse distributed over time, space, discipline, application sector, user populations, operating systems?
  • How can reuse be encouraged?

Examples

General

Klosneuviruses

Examining the genomes within a sample from a wastewater treatment plant in Austria, Schulz et al. assembled a previously undiscovered giant virus genome, which they used to mine genetic databases for related viruses.

Here we report the discovery of a group of giant viruses (Klosneuviruses) in metagenomic data.

Diffuse intrinsic pontine glioma

  • From the abstract of Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma (emphasis added):

    • We collated data from 157 unpublished cases of pediatric high-grade glioma and diffuse intrinsic pontine glioma and 20 publicly available datasets in an integrated analysis of >1,000 cases. We identified co-segregating mutations in histone-mutant subgroups including loss of FBXW7 in H3.3G34R/V, TOP3A rearrangements in H3.3K27M, and BCOR mutations in H3.1K27M. Histone wild-type subgroups are refined by the presence of key oncogenic events or methylation profiles more closely resembling lower-grade tumors. Genomic aberrations increase with age, highlighting the infant population as biologically and clinically distinct. Uncommon pathway dysregulation is seen in small subsets of tumors, further defining the molecular diversity of the disease, opening up avenues for biological study and providing a basis for functionally defined future treatment stratification.

H1N1 viral sequences

  • From the abstract of Novel antigenic shift in HA sequences of H1N1 viruses detected by big data analysis (emphasis added):

    • The influenza virus H1N1 has been prevalent all over the world for nearly a century. Many studies on its evolutionary history, substitution rate and antigenicity-associated sites have been done with small datasets. To have a complete view, we analysed 3171 full-length HA sequences from human H1N1 viruses sampled from 1918 to 2016, and discovered a new clade has formed with sequences isolated in Iran.

Visualization of wind speeds in an area

JATS

PubMed Central (PMC) is a repository for scholarly literature in the biomedical field. Some of its content is available under terms that allow for Reusing, Revising, Remixing and Redistributing Research, e.g. to extract audio and video materials from these articles and upload them to Wikimedia Commons, as the Open Access Media Importer does.

The bot's activity has revealed a number of inconsistencies in the XML at PMC, since the XML standard in use at PMC (JATS) is by design not very prescriptive and leaves lots of room for interpretation.

This sparked the formation of the JATS for Reuse (JATS4R) Working Group that now elaborates recommendations on how best to tag articles in JATS, so as to facilitate reuse (overview).

Improving reusability

Stats

Wikimedia Commons

OPENi

  • OPENi is a searchable collection of images from PubMed Central and other sources

ImageJ

British Library's Mechanical Curator collection

Data Documentation Initiative

Te Papa Tongarewa/ Museum of New Zealand

Repurposed media files

See also