Dryad Cura)on Prac)ces. January 2014

Dryad Cura)on Prac)ces January 2014

Dryad Package/File Structure DATA PACKAGE METADATA PUBLICATION /ARTICLE DATA FILE METADATA BITSTREAM (DATA) BITSTREAM (README) DATA FILE METADATA BITSTREAM (DATA) Scholarly publicahon/arhcle associated with Dryad data package, not stored in Dryad A Dryad data package is a conceptual and metadata object. It contains a summary descriphon of all the conshtuent data files and creates the link with the associated publicahon. Each data file has a metadata descriphon and at least one bitstream (addihonal bitstreams, such as readme files, are ophonal). Metadata pertaining to the publicahon (citahon, publicahon date, arhcle DOI) is stored in the data package. Metadata pertaining to each file and its embargo period is stored in each file record.

Important Cura)on Documents CuraHon manuals hvp://wiki.datadryad.org/curahon dryadassistant@gmail.com NoHficaHons of new submissions, newly published arhcles, other assignments Integrated journal metadata emails Access via dryad.journal.submit@gmail.com Also correspond with authors using this account: send as help@datadryad.org Curator office whiteboard Google doc shared with dryadassistant google account Includes login informahon for Dryad user accounts, EZID, etc. Submission tracking spreadsheet Google doc shared with dryadassistant google account Templates for correspondence http://wiki.datadryad.org/templates_for_correspondence

Integrated and Non- Integrated Journals Non- Integrated No coordinahon between journal and Dryad (no metadata emails, journal contact addresses for reporhng, etc.) Integrated Metadata emails send info ahead of submission May use review workflow or only archive data a^er manuscript acceptance May require blackout of Dryad submission unhl arhcle publicahon Journal contacts are nohfied 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 addihonal steps or require the Dryad data package to remain hidden unhl a^er arhcle publicahon (what we call blackout ). Further integrahon details are available in the following presentahon: http://wiki.datadryad.org/wg/ dryad/images/c/c6/ DryadIntegrationOverview.pdf

Basic Integrated Workflow (no review) Author submits manuscript to journal Journal reports accepted manuscript to Dryad; Dryad creates provisional record Journal invites author to submit data to Dryad & provides link to provisional record Author submits data to Dryad & receives DOI Dryad curator approves submission & sends DOI to author & journal Dryad publishes data files with link to ar)cle; Journal adds Dryad DOI to all forms of ar)cle

Review Workflow Journal sends manuscript informahon to Dryad before manuscript acceptance and invites authors to upload data. Dryad submission is routed to private review workspace, not main curahon and publicahon queue. Passkey link is sent to journal for editor/reviewer access to Dryad submission. Author may conhnue to add files while submission is in review workspace. Journal sends second metadata email to Dryad with manuscript acceptance nohficahon, triggering any associated submission to move from review to curahon. Curator inspects and approves, queues, or rejects submission, as in basic workflow.

Review Workflow Author submits manuscript to journal Journal reports manuscript under review to Dryad; Dryad creates provisional record Journal invites author to submit data to Dryad & provides link to provisional record Author submits data to Dryad, using link sent by journal to provisional record Dryad sends review passcode and DOI to author & journal Upon ar)cle acceptance, journal no)fies Dryad Dryad publishes data files with link to ar)cle; Journal adds Dryad DOI to all forms of ar)cle

Naviga)on NoHficaHons of new tasks go to dryadassistant@gmail.com Log in to Dryad site your email and password http://datadryad.org/password-login Dryad site, nested under your account name: 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 a^er archiving, and to force changes in their status that aren t always available in the interface

Overview of New Submission Processing JOURNAL INTEGRATED NON- INTEGRATED SETTINGS REVIEW? BLACKOUT? METADATA EMAIL? SPREADSHEET ENTRY? ARTICLE STATUS NOT PUBLISHED PUBLISHED ARTICLE STATUS FILES FILES REVIEW ERROR ACCEPTED FILES PUBLISHED FILES APPROPRIATE BLACKOUT NOT APPROPRIATE REJECT NOT APPROPRIATE APPROPRIATE APPROPRIATE APPROPRIATE NOT APPROPRIATE SETTINGS APPROVE NOT APPROPRIATE REJECT APPROVE REJECT BLACKOUT BLACKOUT NO BLACKOUT APPROVE REJECT

Journal SeQngs See JournalSubmissionTracking spreadsheet shared in google docs. First tab ( Notes ) lists each integrated journal and its review and blackout seings. Also search for duplicate submissions or notes in appropriate sheet. Ar)cle Status If integrated submission, should be indicated in metadata email (not stated = accepted manuscript) Look for arhcle DOI or volume informahon in the submived metadata, as clues to published status. Google search and/or visit publisher website.

Claiming Submissions 1. New submissions will be listed on the My Tasks page under the heading In Cura)on: Unclaimed 2. Once claimed, submission will appear in In Cura)on: Claimed list on My Tasks page. 3. Click Edit item(s) buvon (lower right when viewing the claimed submission) and open package and all files in tabs to inspect files and edit all metadata

Inspec)ng Files Check for technical problems, corrupt files, files that won t open in expected so^ware, etc. Files should contain something that looks like data, with a very broad definihon of data (supplementary figures, mulhmedia, etc., are ok, the manuscript itself is not). Look for copyright statements and licenses (generally unacceptable). Look for idenhfiable human subject data (err on the side of cauhon, see guidelines arhcle at http://dx.doi.org/10.1136/bmj.c181). Look for duplicated files, data files uploaded in place of readme files, etc., and clean these up.

Rejec)ng Submissions The most common reasons for rejechon 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 rejechng for this reason. When rejechng a submission, you must enter a reason. This reason will be sent to the submiver; 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 rejechon explanahons.

Edi)ng 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 idenhfy problems. Strip any formaing tags or mangled characters. InternaHonal or special characters can o^en 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 formaved as LastName, FirstName M. I. Note the spaces between and periods a^er middle inihals remove any Htles, such as PhD Data package Htle should be formaved as Data from: ArHcle Htle in sentence case: no caps following colons, either. Add specialized keywords (geographic, temporal, scienhfic name), moving them from/to general subject keywords, as appropriate. ScienHfic names should be LaHn (common names go in dc:subject instead) and should be recognized by hvp://eol.org/. Look for line breaks, especially in arhcle abstract and file descriphons 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, unhlarhcleappears when arhcle 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. For submissions formerly in review, update Htle, authors, and abstract as necessary to match the acceptance nohce. 3. Click Approve. Email nohficahon is sent automahcally. 4. Visit Dryad Data Packages collec)on 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). 5. Check that the DOI resolves (there may be a few minutes delay a^er registering). DOIs should have been automahcally registered, check EZID if there is a problem. 6. 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. December 2013: We believe the problem is solved. Please alert the Senior Curator if you nohce a duplicated DOI.

Placing Submission in Publica)on 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. Add entry to submission tracking spreadsheet (or update exishng entry for submission that was previously in review). 2. Click Accept with Blackout buvon. Once file has successfully moved into the blackout queue, click send on the acceptance email.

Searching for items to update SomeHmes you will know to update entries because of journal alert emails (from integrated journals), and somehmes you will be searching by arhcle Htles to find published items (from nonintegrated journals). 1. Integrated Journals: Do a Htle search in the journal tracking spreadsheet for arhcles that are listed in the update mailers sent to the Dryad Assistant gmail account. Update as outlined on the next slide. If a newly published arhcle is listed in the spreadsheet as being in review, check the journal.submit gmail account for an acceptance email before asking for the item to be pushed to curahon. Never ask for a package in review to be pushed to curahon unless you have an acceptance email from the journal editor. 2. Nonintegrated Journals: Do google searches on Htles listed in the tracking spreadsheet. Be aware that Htles somehmes change between Dryad submission and publicahon. Update published arhcles as listed in the next slide.

Upda)ng Archived Items Once Ar)cle is Published You have made a match between a published arhcle and a Dryad data package that needs to be updated. 1. Check author names, arhcle Htle, and arhcle abstract against published arhcle and update if needed. 2. Edit package dc:date.issued to match earliest (online) publicahon date of arhcle (format as YYYY- MM- DD) 3. Add arhcle DOI to package dc:relahon.isreferencedby (format as doi:####) 4. Add arhcle citahon to package dc:idenhfier.citahon or updated exishng citahon (if advance access online arhcle now has print citahon). Format as: or LastName F, LastName FM (YYYY) ArHcle Htle in sentence case. Journal Name Vol(Num): page- page. LastName F, LastName FM (YYYY) ArHcle Htle in sentence case. Journal Name, online in advance of print. 5. Li^ 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 arhcle citahon, resolvable arhcle DOI, and updated embargoes. 7. Update submission tracking spreadsheet.

Approving Submission out of Publica)on Blackout 1. Find the package by searching My Tasks or Workflow Overview page. Claim the task. 2. Update metadata as described in Upda)ng Archived Items Once Ar)cle 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 arhcle publicahon date to package as dc:date.issued, instead of edihng an exishng value. 3. Click Approve and Archive. 4. Visit Dryad homepage and find item in Recently Published list or on the Data Packages CollecHon page if files are embargoed. (If not in either place, look for it on My Tasks page or track down any error.) 5. Check that the DOI resolves. 6. Update file embargoes (li^ or set end date, as appropriate). Go to the Item Embargo pane in Edit Item for each file to work with embargoes. 7. Update submission tracking spreadsheet.

Genomic Resources Notes (from MolEcolRes) These are a new (as of summer 2013) type of arhcle being submived to Molecular Ecology Resources. They are submived to Dryad with XXXX instead of dates. Once the arhcles have been accepted, change the X s to the accepted dates. Then add the citahon, which should look like this: Genome Resources Development ConsorHum et al. (2013) Genomic Resources Notes accepted 1 February 2013 31 March 2013. Molecular Ecology Resources 13(4): 759. doi:10.1111/1755-0998.12123

Adding data in review to the spreadsheet When data is submived associated with an arhcle in review, it must be entered into the spreadsheet. Refer to the email nohficahon forwarded from the senior curator for Htle, author, doi, and review workspace URL. Search the spreadsheet for the Htle and manuscript number to make sure that it isn't a duplicate. If it s a duplicate, enter in red in the Notes column of each duplicate: has dup Duplicate submission warnings are in the process of being created. Ideally, if someone has data in review and tries to re- submit it in the first- Hme submission area, they ll be taken to their exishng submission. Refer to the metadata email (dryad.journal.submit@gmail.com) to see if the submiver is the lead author. For submiver Smith and lead author Jones, write Jones (submived by coauthor Smith) In the final field, paste the reviewer key URL Make the row s background color light gray

PACKAGE METADATA GUIDE Authors dc:contributor.author repeatable required LastName, FirstName M. Corresponding author dc:contributor.correspo not repeatable required LastName, FirstName M. ndingauthor 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 dc:identifier.manuscript not repeatable optional only for integrated submissions ID Number 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 dc:relation.haspart repeatable required doi:10.5061/dryad.####/1, doi:10.5061/dryad.####/2, etc DOIs " Article volume, issue, dc:relation.ispartofserie not repeatable optional only present if entered by depositor during submission year s Article DOI dc:relation.isreference not repeatable optional doi:#### dby 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 dc:date.available not repeatable required system-generated upon availability of bitstreams for download (will not timestamp 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 dc:relation.ispartof not repeatable required doi:10.5061/dryad.#### package DOI " 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"