dryad curation practices august 2012. dryad package/file structure data package metadata data...
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Dryad Curation Practices
August 2012
Dryad Package/File Structure
DATA PACKAGEMETADATA
BITSTREAM (DATA)
PUBLICATION/ARTICLE
BITSTREAM (README)
BITSTREAM (DATA)
DATA FILEMETADATA
DATA FILEMETADATA Scholarly
publication/article associated with Dryad data package, not stored in Dryad
A Dryad data package is a conceptual and metadata object. It contains a summary description of all the constituent data files and creates the link with the associated publication. Each data file has a metadata description and at least one bitstream (additional bitstreams, such as readme files, are optional). Metadata pertaining to the publication (citation, publication date, article DOI) is stored in the data package. Metadata pertaining to each file and its embargo period is stored in each file record.
Important Curation Documents
• Curation manuals– http://wiki.datadryad.org/Curation
• [email protected]– Notifications of new submissions, newly published articles, other
assignments– Correspond with authors using this account, send as [email protected]
• Curator office whiteboard– Google doc shared with dryadassistant google account– Includes login information for Dryad user accounts, EZID, etc.
• Submission tracking spreadsheet– Google doc shared with dryadassistant google account
• Integrated journal metadata emails– Access via [email protected]
• Templates for correspondence– http://wiki.datadryad.org/Templates_for_Correspondence
Integrated and Non-Integrated Journals
• Non-Integrated– No coordination between journal and Dryad (no metadata
emails, journal contact addresses for reporting, etc.)• Integrated
– Metadata emails send info ahead of submission– May use review workflow or only archive data after
manuscript acceptance– May require ‘blackout’ of Dryad submission until article
publication– Journal contacts are notified upon submission for review
(if using review workflow), acceptance to blackout queue, approval/archiving, and weekly summary
The original integrated workflow is represented to the right. Some journals now also use a review workflow with additional steps or require the Dryad data package to remain hidden until after article publication (what we call “blackout”).
Further integration details are available in the following presentation:http://wiki.datadryad.org/wg/dryad/images/c/c6/DryadIntegrationOverview.pdf
Basic Integrated Workflow (no review)
Review Workflow
• Journal sends manuscript information to Dryad before manuscript acceptance and invites authors to upload data.
• Dryad submission is routed to private review workspace, not main curation and publication queue. Passkey link is sent to journal for editor/reviewer access to Dryad submission.
• Author may continue to add files while submission is in review workspace.
• Journal sends second metadata email to Dryad with manuscript acceptance notification, triggering any associated submission to move from review to curation.
• Curator inspects and approves, queues, or rejects submission, as in basic workflow.
Review Workflow
Navigation
• Notifications of new tasks go to [email protected]
• Log in to Dryad site with [email protected] and [email protected], as appropriate– http://datadryad.org/password-login
• Dryad site left sidebar:– My Submissions are submissions you have created– My Tasks are submissions you can act on as a curator– Workflow Overview provides a way to search for items
before or after archiving, and to force changes in their status that aren’t always available in the interface
Overview of New Submission Processing
JOURNAL
SETTINGS ARTICLE STATUS
ARTICLE STATUS
FILES FILES
FILES FILES
SETTINGS
REJECTAPPROVE
REJECT
REJECT
REJECT
APPROVE
APPROVEQUEUE
QUEUEERROR
INTEGRATED NON-INTEGRATED
PUBLISHEDNOT PUBLISHEDREVIEW? BLACKOUT?
METADATA EMAIL?SPREADSHEET ENTRY?
REVIEW PUBLISHEDACCEPTEDAPPROPRIATE
NOT APPROPRIATE
APPROPRIATE
NOT APPROPRIATE
NOT APPROPRIATE
NOT APPROPRIATE
APPROPRIATEAPPROPRIATE
BLACKOUT NO BLACKOUT
Journal Settings
• See JournalSubmissionTracking spreadsheet shared in google docs.
• First tab (“Notes”) lists each integrated journal and its review and blackout settings.
• Also search for duplicate submissions or notes in appropriate sheet.
Article Status• If integrated submission, should be indicated in
metadata email (not stated = accepted manuscript)• Look for article DOI or volume information in the
submitted metadata.• Google search and/or visit publisher website.
1. New submissions will be listed on the My Tasks page in the list labeled In Curation: Unclaimed
2. Choosing account with which to claim submissionA. If item is going to be approved/rejected (publication blackout is
not required = integrated journal that does not require blackout OR any journal if the article has been published) Claim with Dryad Assistant account
B. If item is going to publication blackout queue (integrated journals requiring publication blackout OR non-integrated journals ahead of article publication) Claim with Dryad Queue account
3. Once claimed, submission will appear in In Curation: Claimed list on My Tasks page
4. Click Edit item(s) button (lower right when viewing the claimed submission) and open package and all files in tabs to inspect files and edit all metadata
Claiming Submissions
Inspecting Files
• Check for technical problems, corrupt files, files that won’t open in expected software, etc.
• Files should contain something that looks like data, with a very broad definition of data (supplementary figures, multimedia, etc., are ok, the manuscript itself is not).
• Look for copyright statements and licenses (not good).
• Look for identifiable human subject data (err on the side of caution).
• Look for duplicated files, data files uploaded in place of readme files, etc., and clean these up.
Rejecting Submissions
• The most common reasons for rejection are inappropriate files, submissions associated with integrated journals for which we have no metadata email, and integrated submissions that should have been directed to the review workspace but the author did not use the integrated process. A submission might also be rejected because a journal is out of scope, but always consult a senior curator before rejecting for this reason.
• When rejecting a submission, you must enter a reason. This reason will be sent to the submitter; it should be courteous and should explain clearly to them what the problem was and how they can fix it if they wish to resubmit.
• See Templates for Correspondence wiki page for common rejection explanations.
Editing Metadata• REMEMBER: some metadata, such as author names, is repeated on the package and
files and will need to be edited in both places.• Scan over all metadata to see if it looks reasonable and identify problems.• Strip any formatting tags or mangled characters. International or special characters
can often be copied and pasted from metadata email or other source on the web.• Check the journal name, especially for non-integrated journals. It should match
exactly the name already in use in the repository. If it’s a new journal, ask a senior curator about establishing a new name.
• Author names should be formatted as – LastName, FirstName M. I. – remove any titles, such as “PhD”
• Data package title should be formatted as – Data from: Article title in sentence case
• Add specialized keywords (geographic, temporal, scientific name), moving them from/to general subject keywords, as appropriate. Scientific names should be Latin (common names go in dc:subject instead) and should be recognized by http://eol.org/.
• Look for line breaks, especially in article abstract and file descriptions and edit these fields as needed for clarity when the content is displayed without line breaks.
• Check for inappropriate embargoes (custom when we have no info from journal, untilArticleAppears when article is out) and adjust as needed. If custom embargo, add embargo period (from journal) as dryad:curatorNote in file metadata.
Approving/Archiving (no blackout)
1. Check for duplicates and notes in tracking spreadsheet, if you haven’t already done so.
2. Click Approve (will need to click twice if item is going through blackout first, based on settings). Email notification is sent automatically.
3. Visit Dryad homepage and find item in Recently Published list (if not there, look for it on My Tasks page or track down any error).
4. Check for duplicated package DOI and delete, if needed. If there is a duplicated package DOI the link from the homepage to the package won’t work, and you’ll need to manually modify the link to reach the package page.
5. Check that package DOI resolves correctly (may be a few minutes delay). Log in to EZID and check/fix, if needed.
6. Update submission tracking spreadsheet.
Placing Submission in Publication Blackout Queue
You should have already claimed the item with Dryad Queue account, inspected files, edited metadata, and checked for duplicate submissions at this point.
1. Register package DOI in EZID. Go to Create IDs -> Advanced in order to specify your DOI. Use http://datadryad.org/publicationBlackout as the location and leave all other description blank.
2. Send acceptance email to submitter (and journal contacts, if integrated journal). Template is saved as a draft in dryadassistant gmail account. Journal contact emails should appear in package metadata and Dryad journal config file.
3. Add entry to submission tracking spreadsheet.4. Leave task claimed in Dryad Queue account.
Updating Archived Items Once Article is Published
You have made a match between a published article and a Dryad data package that needs to be updated.
1. Check author names, article title, and article abstract against published article and update if needed.
2. Edit package dc:date.issued to match earliest (online) publication date of article (format as YYYY-MM-DD)
3. Add article DOI to package dc:relation.isreferencedby (format as doi:####)4. Add article citation to package dc:identifier.citation or updated existing citation (if
advance access online article now print citation). Format as:LastName F, LastName FM (YYYY) Article title in sentence case. Journal Name Vol(Num): page-page.
orLastName F, LastName FM (YYYY) Article title in sentence case. Journal Name, online in advance of print.
5. Lift embargoes or set embargo end dates for each file, as appropriate. Go to the Item Embargo pane in Edit Item to work with embargoes.
6. Visit public view of package page (leave Edit Item) and verify article citation, resolvable article DOI, and updated embargoes.
7. Update submission tracking spreadsheet.
Approving Submission out of Publication Blackout
1. Update metadata as described in Updating Archived Items Once Article is Published. Because this submission isn’t archived yet, dates won’t have been added to the metadata by the system, so you will add the article publication date to package as dc:date.issued, instead of editing an exisiting value.
2. Click Approve. Find item in Publication Blackout list on My Tasks page. Claim the task and click Approve again.
3. Visit Dryad homepage and find item in Recently Published list (if not there, look for it on My Tasks page or track down any error).
4. Check for duplicated package DOI and delete, if needed. If there is a duplicated package DOI the link from the homepage to the package won’t work, and you’ll need to manually modify the link to reach the package page.
5. Update package DOI in EZID (use Lookup function) and change location to point to public item URL.
6. Update file embargoes (lift or set end date, appropriate). Go to the Item Embargo pane in Edit Item for each file to work with embargoes.
7. Update submission tracking spreadsheet.
PACKAGE METADATA GUIDEAuthors dc:contributor.author repeatable required LastName, FirstName M.
Corresponding author dc:contributor.correspondingAuthor
not repeatable required LastName, FirstName M.
Spatial coverage dc:coverage.spatial repeatable optional place names, geographic coordinates, etc
Temporal coverage dc:coverage.temporal repeatable optional intended for geologic timespans, but years and other values are accepted
Approval timestamp dc:date.accessioned not repeatable required system-generated upon submission approval
Approval timestamp dc:date.available not repeatable required system-generated upon submission approval
Article publication date dc:date.issued not repeatable required system-generated to match approval date, later edited by curator to article publication
Data package DOI dc:identifier not repeatable required doi:10.5061/dryad.####
Article citation dc:identifier.citation not repeatable optional modified PLoS citation style
Journal’s manuscript ID
dc:identifier.manuscriptNumber
not repeatable optional only for integrated submissions
Data package handle dc:identifier.uri not repeatable required http://hdl.handle.net/10255/dryad.####, system-generated upon submission approval
Abstract dc:description not repeatable optional article abstract
Component data file DOIs
dc:relation.haspart repeatable required doi:10.5061/dryad.####/1, doi:10.5061/dryad.####/2, etc
Article volume, issue, year
dc:relation.ispartofseries
not repeatable optional only present if entered by depositor during submission
Article DOI dc:relation.isreferencedby
not repeatable optional doi:####
Keywords dc:subject repeatable optional
Data package title dc:title not repeatable required Data from: Article title
Record type dc:type not repeatable required system-generated, now set to “Article”
Curator note dryad.curatorNote repeatable optional rarely used
Scientific names dwc:ScientificName repeatable optional Latin taxon names
Journal name prism:publicationName not repeatable required use authorized form of name only
FILE METADATA GUIDEAuthors dc:contributor.author repeatable required LastName, FirstName M.
Spatial coverage dc:coverage.spatial repeatable optional place names, geographic coordinates, etc
Temporal coverage dc:coverage.temporal repeatable optional intended for geologic timespans, but years and other values are accepted
Approval timestamp dc:date.accessioned not repeatable required system-generated upon submission approval
Bitstream availability timestamp
dc:date.available not repeatable required system-generated upon availability of bitstreams for download (will not appear if file is embargoed)
Approval date dc:date.issued not repeatable required system-generated upon submission approval
Data file DOI dc:identifier not repeatable required doi:10.5061/dryad.####/#
Data file handle dc:identifier.uri not repeatable required http://hdl.handle.net/10255/dryad.####, system-generated upon submission approval
File description dc:description not repeatable optional brief file description entered by depositor
Associated data package DOI
dc:relation.ispartof not repeatable required doi:10.5061/dryad.####
Rights information dc:rights.uri not repeatable required CC0 URI for all items except a few legacy items under Original License
Keywords dc:subject repeatable optional
Data file title dc:title not repeatable required
Record type dc:type not repeatable required system-generated, now set to “Dataset”
Curator note dryad.curatorNote repeatable optional rarely used, mostly to specify custom embargo dates
Scientific names dwc:ScientificName repeatable optional Latin taxon names
Embargo end date dc:date.embargoedUntil not repeatable optional YYYY-MM-DD, will have value 9999-01-01 for embargoed items when the article has not yet been published then edited by curator to real date, not present for items that were never embargoed or after embargo has been lifted (see dc:date.available for embargo lifting timestamp)
Embargo type dc:type.embargo not repeatable required controlled list of values: none, untilArticleAppears, oneyear, custom