Leveraging publication metadata to help overcome the data ingest bottleneck
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Leveraging publication metadata to help overcome the data ingest bottleneck

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A talk on Dryad given at the ORCID Participant Meeting in Boston, 5/18/2011

A talk on Dryad given at the ORCID Participant Meeting in Boston, 5/18/2011

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  • Full Name Full Name Comment goes here.
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  • The idea is that an ORCID (or, more likely, a cluster of ORCIDs) can be equated to a researcher identity. This would a repository to recognize different records to which the same researcher has contributed using an exact match between ORCIDs rather than approximate matching of names, institutions, and other identifiable information.
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  • The relationship between ORCIDs and identities is confusing to me. But this is only a slide deck -- more research req'd.
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  • 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
  • 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.
  • 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.
  • Two aspects of the way Dryad works that merit more detailed explanation, both of which contribute to lowering the burden on data submission.
  • Integrated manuscript submission described in more detail, since this is more relevant to how Dryad data records get populated with ORCIDs
  • 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)
  • An example of an email sent to Dryad from an integrated journal (Molecular Ecology) with author names highlighted.
  • 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.
  • 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.
  • Dryad Metadata Application Profile 3.0

Leveraging publication metadata to help overcome the data ingest bottleneck Leveraging publication metadata to help overcome the data ingest bottleneck Presentation Transcript

  • Leveraging publication metadata to help overcome the data ingest bottleneck
    Todd J. Vision
    National Evolutionary Synthesis Center
    Department of Biology
    University of North Carolina at Chapel Hill
    ORCID Participant Meeting, Harvard, May 2011
  • The End
    To make data archiving integral to scientific publishing.
    The scope
    Data underlying findings in the peer-reviewed biological literature.
    The Means
    Integrated submission of data with the manuscript
    Low barrier to submission (at the datafile level)
    Free reuse of data (free as in both speech & beer)
    Journals share responsibility for governance and sustainability
  • The long tail of orphan data in “small science”
    after B. Heidorn
    Specialized repositories
    (e.g. GenBank, PDB)
    Volume
    Orphan data
    Rank frequency of datatype
  • The long tail of orphan data in “small science”
    after B. Heidorn
    Specialized repositories
    (e.g. GenBank, PDB)
    Volume
    Bumpus HC (1898) The Elimination of the Unfit as Illustrated by the Introduced Sparrow, Passer domesticus. A Fourth Contribution to the Study of Variation.pp. 209-226 in Biological Lectures from the Marine Biological Laboratory, Woods Hole, Mass.
    Orphan data
    Rank frequency of datatype
  • A publication package
  • A publication package
    1
    1. Integrated manuscript and data submission
  • A publication package
    2
    1
    1. Integrated manuscript and data submission
    2. Handshaking with specialized repositories
  • Integrated
    Submit manuscript
  • Integrated
    Submit manuscript
    Manuscript metadata
  • Integrated
    Submit manuscript
    Submit data
    Manuscript metadata
  • Integrated
    Submit manuscript
    Submit data
    Manuscript metadata
    Review passcode
    Peer review
  • Integrated
    Submit manuscript
    Submit data
    Manuscript metadata
    Review passcode
    Peer review
    Acceptance notification
    Curation
    Data DOI
    Production
  • Integrated
    Submit manuscript
    Submit data
    Manuscript metadata
    Review passcode
    Peer review
    Acceptance notification
    Curation
    Data DOI
    Production
    Article metadata
    Curation
  • Integrated
    Submit manuscript
    Submit data
    Manuscript metadata
    Review passcode
    Peer review
    Acceptance notification
    Curation
    Data DOI
    Production
    Article metadata
    Curation
    Article
    Publication
    Data publication
  • Non-integrated
    Integrated
    Submit manuscript
    Submit data
    Manuscript metadata
    Review passcode
    Peer review
    Submit data
    Acceptance notification
    Curation
    Data DOI
    Production
    Article metadata
    Curation
    Article
    Publication
    Data publication
  • Non-integrated
    Integrated
    Submit manuscript
    Submit data
    Manuscript metadata
    Review passcode
    Peer review
    Submit data
    Acceptance notification
    Curation
    Data DOI
    Production
    Author adds DOI
    Data DOI
    Article metadata
    Curation
    Article publication
    Article
    Publication
    Article metadata
    harvested
    Data publication
  • Article
    Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA (2011) Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in phylogenetic trees of phylogenetic marker genes. PLoS ONE 6(3): e18011. doi:10.1371/journal.pone.0018011
    Dryad data package
    Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA (2011) Data from: Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in phylogenetic trees of phylogenetic marker genes. Dryad Digital Repository. doi:10.5061/dryad.8384
  • Integrated submission
    Currently integrated or in process: 20
    All journals with Dryad content: >70
    A minority require data prior to review
    Journals published by a variety of organizations
    Traditional (incl. Oxford University Press, Wiley-Blackwell)
    Open Access (incl. BMC, BMJ Open)
    Society publishers (e.g. with Allen Press, or independent)
  • Dryad vs. Supplementary Online Materials
  • 612 downloads
  • Member nodes
    • Dryad, ORNL DAAC, Knowledge Network for Biocomplexity, etc.
    Coordinating nodes
    Investigator toolkit
  • Why Dryad yearns for ORCIDs
    Replace name strings with identities
    Disambiguation of like names
    Clustering of synonymous names
    Confidently recognizing different data packages that share an author
    Enabling
    Accurate author searches
    Internal and external author hyperlinks
    Aggregation of author contributions
    Inclusion of data records in the profiles of coauthors
    Propagation of ORCIDs with Dryad metadata
    Manual curation of names not feasible
    Only ~20% of Dryad authors in Library of Congress name auth. file
    Manual control would explode curation costs
  • How to get ORCIDs into Dryad
    Ideally sent to Dryad by integrated journals
    Pre-review/Pre-production: allows coauthors to edit data packages
    Post-production: works for all other uses
    Non-integrated journals
    Lookup API based on article or affiliation data
    To be avoided
    Authors required to enter ORCIDs during submission
    Authors required to register during submission
  • What do we know about authors?
    Names
    Often abbreviated except for corresponding or submitting author
    At least one article they have written
    Title, journal, volume, pages, DOI, abstract
    Other identifiable information
    An email for submitting authors
    Sometimes: institutional affiliation and contact information for corresponding authors
  • Some requirements
    Recognizing ORCIDs for authenticated users
    Mapping to InCommon Silver profiles
    ORCIDs for organizations (e.g. consortia)
    Dspacesupport
    Curator interface for ORCID lookup/verification
    Lookup/registration option from submission interface
    Allowing metadata relationships (e.g. of an ORCID with a name)
    Mechanisms for curator to
    Flag duplicates and errors
    Register provisional ORCIDs
    Map to other profiles (e.g. InCommon)
  • Business model issues
    Dryad is (will be) supported by subscriptions and deposit charges, primarily from journals.
    With a not-for-profit budget
    Feasibility requires wide adoption by publishers
    And manuscript-submission system developers!
    Favored model
    Pay for use of automated lookup services, with costs scaled by usage level
    Credit for curator contributions
  • "Cherish old knowledge that you may acquire new"
    The Analects of Confucius
    Special thanks to
    Elena Feinstein
    Jane Greenberg
    Ryan Scherle
    For more information:
    http://datadryad.org
    http://blog.datadryad.org
    http://datadryad.org/wiki
    http://code.google.com/p/dryad
    dryad-users@nescent.org
    Facebook: Dryad
    Twitter: @datadryad
  • Dryad Metadata Profile (v3.0)
    Article
    Data Package
    • dc.identifier = doi of article
    • bibo.status = article publication status
    • dc.creator = authors of article
    • dc.issued = article publication date
    • dc.title = title of article
    • bibo.journal = journal title
    • bibo.issn and bibo.eissn
    • bibo.volume
    • bibo.issue
    • bibo.pageStart and bibo.pageEnd
    • dc.abstract = article abstract
    • dc.isReferencedBy = data package doi
    • dc.identifier = doi of data package
    • dc.relation.hasPart = dois of data files
    • dc.references = handle of article description record
    • dc.title = title of data package
    • dc.description (not article abstract, optional)
    • dc.creator = authors of data package
    • dc.date (with refinements – dates associated with submission to Dryad and archiving in the repository)
    • dryad.external = GenBank accession number, TreeBASE identifier
    • dc.relation = URL of related resource
    • dc.subject = general keywords
    • DarwinCore.ScientificName = taxon keywords
    • dc.spatial = geographic keywords
    • dc.temporal = timespan keywords
    • dryad.curatorNote
    Datafile
    • dc.identifier = doi of data file
    • dc.relation.isPartOf = doi of data package
    • file-specific description: keywords, authors, format, size, checksum, etc.
    • embargo information (type, end date)