Leveraging publication metadata to help overcome the data ingest bottleneck

Editor's Notes

1. Demand from the user community (i.e. biologists) has led to a distributed network of sometimes inadequate, often unsustainable, generally non-interoperable, solutions, from personal websites to publisher hosted supplementary materials. Dryad, by contrast, is designed to be a self-sustainingservice that rationalizes the space and is responsive to multiple stakeholders:journals, publishers, societies, funders, authors, and data users
2. There is widely used infrastructure for certain well-defined “easy” biological datatypes like DNA sequences and protein structures. But these repositories are not adequate to capture all those many datasets that requires more context to be reusable. Dryad is designed specifically to enable archiving and reuse of this long tail of orphan data. Our civilization is not wealthy to ever support the variety specialized repositories that would be needed, and the curation that would be needed to standardize these data.
3. A classic example of orphan data is Bumpus’ (1898) sparrows " ... on February 1 of the present year, when, after an uncommonly severe storm of snow, rain, and sleet, a number of English [house] sparrows were brought to the Anatomical Laboratory of Brown University Seventy-two of these birds revived; sixty-four perished; ... “ Pages of his data on the measurements of birds that died versus those that revived, and the data has been used ever since to test statistical methods of measuring natural selection on multivariate traits, and for teaching evolutionary biology. This is not high-throughput biology. This is a single clever opportunistic, low-tech and idiosyncratic study by an individual investigator, who, by virtue of having published his data, enhanced the value of his science, and is still being read to this day. These data are nearly meaningless out of context. But even without elaborate machine-readable metadata, these data have been in 100s of papers, by many1000s of students, and is still being reused over a century later. The other lesson to take away from here is that publication related data is only the tip of the iceberg of the long tail, but it is the low-hanging fruit. It is the most consistently valuable, the most consistently reusable, and the easiest to archive in a systematic way, because there is a vast socio-technical-economic infrastructure of publication that can be leveraged.
4. Two aspects of the way Dryad works that merit more detailed explanation, both of which contribute to lowering the burden on data submission.
5. Integrated manuscript submission described in more detail, since this is more relevant to how Dryad data records get populated with ORCIDs
6. Canonical handshaking workflow: data files exchanged in a BagIttarball (files + manifest), completed submissions harvested via OAI-PMH updates.Future plans to use OAI-ORE for the manifest. Mechanism could be extended to allow deposit from research software (e.g. R, digital lab notebooks) or institutional repositories (e.g. withSWORD)
7. An example of an email sent to Dryad from an integrated journal (Molecular Ecology) with author names highlighted.
8. One can see these benefits action with a A 2009 data package compiled wood anatomy data from 8412 plant species. It has already been downloaded over 600 times! While some of these downloads may lead to citations, there is probably a good deal of data reuse for educational purposes, and exploration of analytical methods on this unique dataset.The inset from the corresponding Ecology Letters article shows the geographical distribution of wood density in North and South America. Each data point is the mean wood density value of all unique species occurrences in that cell. Wood density clearly varies in a very predictable way with temperature, precipitation, and seasonality. Dryad contains the data underlying this figure, but without Dryad, researchers would be unable to reconstruct the original data from this image for testing new hypotheses.
9. Dryad is one of many member nodes in the DataONE network, an NSF funded DataNet that includes federal labs, research stations, earth observatory networks, citizen science data archives, etc, which includes both earth science and life science data. Data is replicated across members nodes, while metadata and a layer of services are provided by a smaller number of redundant coordinating nodes. Dryad is the only member node that focuses on publication data, although many of the others are use in published literature. One of the technical goals is to support distributed authentication, so CRUD rights can be propagated from node to node for individuals, groups and organizations. DataONE has adopted InCommon, a single-sign on technology for US research and education, which is based on SAML-based authentication and authorization (e.g. Shibboleth). Specifically, DataONE uses InCommon Silver, which uses verified profiles allowing a high degree of trust.
10. Dryad Metadata Application Profile 3.0