Dryad Curation Practices - PowerPoint Presentation

Slide1

Dryad Curation Practices

March

2013

Dryad Package/File Structure

DATA PACKAGE

METADATA

BITSTREAM (DATA)

PUBLICATION/ARTICLE

BITSTREAM (README)

BITSTREAM (DATA)

DATA FILE

METADATA

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

dryadassistant@gmail.comNotifications of new submissions, newly published articles, other assignments

Integrated journal metadata emailsAccess via dryad.journal.submit@gmail.comAlso correspond with authors using this account, send as help@

datadryad.orgCurator office whiteboardGoogle doc shared with dryadassistant google accountIncludes login information for Dryad user accounts, EZID, etc.Submission tracking spreadsheet

Google doc shared with dryadassistant google accountTemplates for correspondencehttp://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.)

IntegratedMetadata emails send info ahead of submission

May use review workflow or only archive data after manuscript acceptanceMay require ‘blackout’ of Dryad submission until article publicationJournal 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 dryadassistant@gmail.com

Log in to Dryad site with dryadassistant@gmail.com and

dryad.queue@gmail.com, as appropriatehttp://datadryad.org/password-login

Dryad site left sidebar:My Submissions are submissions you have createdMy Tasks are submissions you can act on as a curatorWorkflow 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

REJECT

APPROVE

REJECT

REJECT

REJECT

APPROVE

APPROVE

QUEUE

QUEUE

ERROR

INTEGRATED

NON-INTEGRATED

PUBLISHED

NOT PUBLISHED

REVIEW? BLACKOUT?

METADATA EMAIL?

SPREADSHEET ENTRY?

REVIEW

PUBLISHED

ACCEPTED

APPROPRIATE

NOT

APPROPRIATE

APPROPRIATE

NOT

APPROPRIATE

NOT

APPROPRIATE

NOT

APPROPRIATE

APPROPRIATE

APPROPRIATE

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, as clues to published status.

Google

search and/or visit publisher website.

New submissions will be listed on the

My Tasks

page under the heading

In Curation: UnclaimedChoosing account with which to claim submission

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

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

Once claimed, submission will appear in In Curation: Claimed list on My Tasks page

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 to 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.Note the spaces between and periods after middle initials

remove any titles, such as “PhD”Data package title should be formatted as Data from: Article title in sentence caseAdd 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 (e.g., ‘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)

Check for duplicates and notes in tracking spreadsheet, if you haven’t already done so.

Click

Approve

(will need to click twice if item is going through blackout first, based on settings). Email notification is sent automatically.Visit Dryad Data Packages collection page <http://datadryad.org

/handle/10255/3> and find item in Recent Submissions list (if not there, look for it on My Tasks page or track down any error).Manually register the package DOI in EZID. Go to Create IDs -> Advanced in order to specify your

DOI. Check that the DOI resolves correctly by clicking the link on the package page (there may be a few minutes delay after registering).Update submission tracking spreadsheet.Spring 2013 update: do not delete DOIs that were duplicated in the metadata upon approval. These no longer create broken links, and leaving the duplicates in place may help the developers track down the underlying problem.

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.

Register package DOI

in EZID. Go to Create IDs -> Advanced in order to specify your DOI. Use http://datadryad.org/publicationBlackout as the location, Dryad Digital Repository as publisher, and (:tba

) for all other values.Send acceptance email to submitter (and journal contacts, if integrated journal). Templates are saved as drafts in dryad.journal.submit gmail

account. Journal contact email addresses should appear in package metadata and Dryad journal config file.Add entry to submission tracking spreadsheet (or update existing entry for submission that was previously in review).

Leave task claimed in Dryad Queue account. Do not click Approve at this time.

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.

Check author names, article title, and article abstract against published article and update if needed.

Edit package dc:date.issued to match earliest (online) publication date of article (format as YYYY-MM-DD)

Add article DOI to package dc:relation.isreferencedby (format as doi:####)Add article citation to package dc:identifier.citation or updated existing citation (if advance access online article now has print citation). Format as:

LastName F, LastName FM (YYYY) Article title in sentence case. Journal Name Vol(Num): page-page. or LastName

F, LastName FM (YYYY) Article title in sentence case. Journal Name, online in advance of print.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.

Visit public view of package page (leave Edit Item) and verify article citation, resolvable article DOI, and updated embargoes.Update submission tracking spreadsheet.

Approving Submission out of

Publication Blackout

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 existing value.Click Approve. Find item in Publication Blackout list on My Tasks page.

Claim the task and click Approve again.Visit Dryad homepage and find item in Recently Published

list or on the Data Packages Collection page if files embargoed. (If not in either place, look for it on My Tasks page or track down any error.)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.Update package DOI in EZID

(use Lookup function). Change location to point to public item URL and add real values for author, title, and year.Update file embargoes (lift or set end date, as appropriate). Go to the Item Embargo pane in Edit Item for each file to work with embargoes.

Update submission tracking spreadsheet.

PACKAGE

METADATA GUIDE

Authors

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 GUIDE

Authors

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