leveraging publication metadata to help overcome the data ingest bottleneck
DESCRIPTION
A talk on Dryad given at the ORCID Participant Meeting in Boston, 5/18/2011TRANSCRIPT
Todd J. VisionNational Evolutionary Synthesis Center
Department of Biology University of North Carolina at Chapel Hill
ORCID Participant Meeting, Harvard, May 2011
Leveraging publication metadata to help overcome the data ingest
bottleneck
• 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”
Volu
me
Rank frequency of datatype
Specialized repositories(e.g. GenBank, PDB)
Orphan data
after B. Heidorn
The long tail of orphan data in “small science”
Volu
me
Rank frequency of datatype
Specialized repositories(e.g. GenBank, PDB)
Orphan data
after B. Heidorn
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.
A publication package
1
1. Integrated manuscript and data submission
A publication package
1
1. Integrated manuscript and data submission
A publication package2
2. Handshaking with specialized repositories
Submit manuscript
Integrated
Manuscript metadata
Submit manuscript
Integrated
Submit data
Manuscript metadata
Submit manuscript
Integrated
Submit data
Manuscript metadata
Peer review
Review passcode
Submit manuscript
Integrated
Submit data
Manuscript metadata
Peer review
Review passcode
Acceptance notification Curation
Data DOIProduction
Submit manuscript
Integrated
Submit data
Manuscript metadata
Peer review
Review passcode
Acceptance notification Curation
Data DOIProduction
Article metadata Curation
Submit manuscript
Integrated
Submit data
Manuscript metadata
Peer review
Review passcode
Acceptance notification Curation
Data DOIProduction
Article metadata Curation
ArticlePublicatio
n
Data publicati
on
Submit manuscript
Integrated
Submit data
Manuscript metadata
Peer review
Review passcode
Acceptance notification Curation
Data DOIProduction
Article metadata Curation
ArticlePublicatio
n
Data publicati
on
Non-integrated
Submit data
Submit manuscript
Integrated
Submit data
Manuscript metadata
Peer review
Review passcode
Acceptance notification Curation
Data DOIProduction
Article metadata Curation
ArticlePublicatio
n
Data publicati
on
Non-integrated
Submit data
Author adds DOI
Data DOI
Article publicati
onArticle metadataharvested
Submit manuscript
Integrated
ArticleWu 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 packageWu 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
Dryad SOM
Article citations: reuse of data leads to article citations ✔ ✔
Identifiable: Data DOIs within articles serve as permanent, resolvable identifiers ✔ ✔/✗
Curated: quality control of data submissions and indexing metadata ✔ ✔/✗
Economy of scale: cost efficiency from shared infrastructure ✔ ✔/✗
Discoverable: indexed and exposed to both web and bibliographic search engines ✔ ✔/✗
Ease of deposit: streamlined deposit, allow large and complex datasets ✔/✗ ✔/✗
Formatted for reuse, i.e. not PDF ✔/✗ ✔/✗
Updatable: new versions of data files can be added, metadata can be enhanced ✔ ✗
Preservation planning: integrity audits, format migration, replication, etc. ✔ ?
Support for embargoes: can delay release of data in accordance with journal policy ✔ ?
Free reuse: no paywall, no unecessary IP restrictions/ambiguities ✔ ?
Data citations: reuse of data leads to data citations ? ✗
612 downloads
Investigator toolkit
Member nodes• Dryad, ORNL DAAC, Knowledge Network for Biocomplexity,
etc.
Coordinating nodes
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)
• Dspace support 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
For more information:http://datadryad.org
http://blog.datadryad.orghttp://datadryad.org/wiki
http://code.google.com/p/dryad
[email protected]: Dryad
Twitter: @datadryad
"Cherish old knowledge that you may acquire new" The Analects of Confucius
Special thanks toElena FeinsteinJane GreenbergRyan Scherle
Data PackageArticle
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)
• 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
• 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
Dryad Metadata Profile (v3.0)