Journal Metadata

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Introduction

Integrated journals should send metadata regarding their manuscripts directly to Dryad, either through our email system or through the REST API. These notices allow Dryad to create and pre-populate a record for the data, greatly facilitating the author's process of data deposit. These messages also allow journals to communicate the status of manuscripts to Dryad, allowing us to move the corresponding packages through our curation process along with the journal's editorial process.

Although notices may be sent in batches, it is best for Dryad to receive information as soon as the information is available, so we prefer to receive metadata in individual notifications as the status of the manuscript is changed.

Required Metadata

Mandatory information about the article

In order for Dryad to know how to uniquely associate a manuscript with a data package, the article's metadata must include some minimal information about the journal and the manuscript:

  • Journal Name is the full publicationname of the journal.
  • Journal Code is the journal-specific abbreviation that Dryad uses for internal management. This should have been specified during the integration process. This field must be the first listed in the email block.
  • MS Reference Number is the number that will be used to identify an article within Dryad during the submission process. This typically corresponds to the journal's internal manuscript number. If your submission system changes the manuscript number during the editorial process, please make sure that Dryad is aware of this.
  • MS Title will be displayed to the author during the submission process, allowing the author to verify that the correct article has been selected. The title of the Dryad data package will be identical to this title, with the words "Data From:" prepended.
  • MS Authors: Dryad can accommodate several formats for the author list, as long as there is a clear way to distinguish the author names. The most common formatting is to list each author name in the format "Last, First" (without quotes) and separate authors with semicolons. 
  • Article Status specifies how Dryad will handle data submitted in relation to the article. See values below.

Article status

An article can have one of several statuses; these statuses trigger different components of the Dryad workflow.

  • accepted: The article has been accepted for publication. Data submitted to Dryad will be made available subject to the embargo status chosen by the author. If data had been submitted while the article was under review, this data will now become publicly available (again, subject to the author's embargo selection). A DOI will be assigned, and will resolve.
  • submitted: The manuscript has been submitted by an author, and is being processed/reviewed by the journal. A provisional DOI will be assigned, but the DOI is not registered, and will not resolve. The data can only be accessed by others using a Dryad-provided reviewer URL.
  • needs revision: Reviewers have requested that more experiments be performed, or more data be supplied. If data had been submitted while the article was under review, the data package will be moved into the user's workspace, and remain available for future submissions.
  • rejected: The journal has either rejected the article, and/or the entire data package has been deemed inappropriate for publication in Dryad. If data had been submitted while the article was under review, the data package will be moved into the user's workspace, and remain available for future submission to another journal.

Timing of notices

  • Journals using the Basic workflow usually send a single notice to Dryad at the time a manuscript is accepted, using the accepted status, but they may occasionally also use the needs revision or rejected status in a subsequent notice.
  • Journals using the Review workflow, making data available for editorial oversight or peer review prior to article acceptance, send Dryad two notices regarding each manuscript: the first one with Article Status: "submitted," and a subsequent one with Article Status: either "accepted" or "rejected." They may also use the status needs revision.

Proposed value for transferring articles to other journals. This value is under discussion, and is not yet used by Dryad.

  • rejected and referred to X - The article has been rejected by the target journal, but the author has been directed to resubmit the article to another integrated journal. The value of X should be the Dryad Journal Code for the other journal. Currently, Dryad will treat this status as equivalent to the rejected status.

Optional Metadata

The required metadata fields must be included in every metadata email, but additional metadata may be included along with the required metadata. Dryad parses all fields up to the delimiter EndDryadContent.

Common fields

Many journals send the following fields to Dryad:

  • Print ISSN
  • Online ISSN
  • Journal Admin Email
  • Journal Editor
  • Journal Editor Email
  • Contact Author
  • Contact Author Email
  • Contact Author Address 1
  • Contact Author Address 2
  • Contact Author Address 3
  • Contact Author City
  • Contact Author State
  • Contact Author Country
  • Contact Author ZIP/Postal Code
  • Publication DOI

If your journal plans to include other fields, please contact Dryad to make sure that our system will process them correctly.

Special cases

Some optional fields are handled in a special manner.

Keywords

Keywords for the manuscript can be included as a comma- or semicolon-delimited list.

Abstract

If the abstract is included in the email, it must be the last field in the email block, followed by EndDryadContent. This is because many abstracts have complex formatting needs, and the simple key:value parsing that the system uses for most fields is turned off to process the Abstract.

Dryad Data DOI

This field is typically used by journals who have authors deposit data in Dryad prior to manuscript submission. In this case, the author first submits data in Dryad and receives a provisional data DOI. The author then submits their manuscript to the journal and communicates the data DOI to the journal. When the journal sends subsequent metadata to Dryad, the Dryad Data DOI is included, allowing Dryad to match the metadata email with the already-existing data package. This DOI can be formatted either as a doi (e.g. doi:10.5061/dryad.abc123) or as a CrossRef URL (e.g. http://dx.doi.org/10.5061/dryad.abc123).

Metadata Submission via Email

Most journals send metadata to Dryad via email. Email is simple and human-readable. It is also the easiest communication method for many journals, since their manuscript processing systems already send many templated email messages.

Dryad metadata can be parsed from a plaintext email as long as it occurs in a single block in the email, starting with the Journal Code and ending with EndDryadContent (or the end of the email itself).

Notices to the Dryad system can be generated as separate items from a manuscript submission system, or alternatively the Dryad system address can be copied on existing routine notices to authors, as long as the content needed by the Dryad system is in a self-contained section of the email. Some journals add the Dryad notice to their standard emails to authors, prefacing the Dryad content with a statement like: "Below is the information about your manuscript that we are relaying to the Dryad repository to facilitate your data archiving."

For journals that use Manuscript Central/Scholar One, the general format and content of the email is specified in the Manuscript Central template for Dryad created by Tim Vines.

Header

From: XXX
To: journal-submit@datadryad.org
Subject: Prepopulation data email

Sample message body

Note that the sample codes enclosed in hashes are the codes used by ScholarONE. For other manuscript processing systems, different codes will be required, but the basic format of the message should be the same.

Journal Name: ##JOURNAL_NAME##
Journal Code: XXXX
Print ISSN: XXX
Online ISSN: XXX
Journal Admin Email: ##EMAIL_CONTACT_ADMIN_CENTER_EMAIL##
Journal Editor: ##PROLE_MANAGING_EDITOR_FIRSTNAME## ##PROLE_MANAGING_EDITOR_LASTNAME##
Journal Editor Email: ##PROLE_MANAGING_EDITOR_EMAIL##
MS Reference Number: ##DOCUMENT_ID##
Article Status: accepted
MS Title: ##DOCUMENT_TITLE##
MS Authors: ##DOCUMENT_AUTHORS##
Contact Author: ##PROLE_AUTHOR_FIRSTNAME## ##PROLE_AUTHOR_LASTNAME##
Contact Author Email: ##PROLE_AUTHOR_EMAIL##
Contact Author Address 1: ##PROLE_AUTHOR_ADDRESS1##
Contact Author Address 2: ##PROLE_AUTHOR_ADDRESS2##
Contact Author Address 3: ##PROLE_AUTHOR_ADDRESS3##
Contact Author City: ##PROLE_AUTHOR_CITY##
Contact Author State: ##PROLE_AUTHOR_STATE##
Contact Author Country: ##PROLE_AUTHOR_COUNTRY##
Contact Author ZIP/Postal Code: ##PROLE_AUTHOR_POSTALCODE##
Keywords: ##ATTR_KEYWORDS##
Abstract: ##DOCUMENT_ABSTRACT##
EndDryadContent

NOTE: the email block must end with EndDryadContent. If the Abstract is present, it must be the last field in the block.

Metadata Submission via REST API

Dryad also accepts submission of manuscript metadata via a REST API. The API accepts metadata in JSON format. A sample JSON item is shown below. Although the information is largely the same as in the Email format, the field names and their arrangement differs from the email format. A copy of the REST API is available for viewing and (minimal) testing in the documentation at apiary.

Sample metadata JSON document

{
"abstract":"This is the abstract of the article",
"authors":{
"author":[
{
"familyName":"Smith",
"givenNames":"John",
"identifier":"0000-0000-0000-0000",
"identifierType":"orcid"
},
{
"familyName":"Jones",
"givenNames":"Sally"
}
]
},
"correspondingAuthor":{
"address":{
"addressLine1":"123 Main St",
"addressLine2":"Box 40560",
"addressLine3":"",
"city":"Anytown",
"country":"United States",
"state":"North Carolina",
"zip":"27511"
},
"author":{
"familyName":"Smith",
"givenNames":"John",
"identifier":"0000-0000-0000-0000",
"identifierType":"orcid"
},
"email":"smith@example.com"
},
"dryadDataDOI":"doi:10.5061/dryad.abc123",
"keywords":{
"keyword":[
"Science",
"Data",
"Publishing"
]
},
"manuscriptId":"MS12345",
"publicationDate":"2014-10-17",
"publicationDOI":"doi:10.12345/987cba",
"status":"accepted",
"title":"Title of article"
}

Notes

  • Journal Code is specified in the URL path itself instead of as a field in the JSON.
  • Within author entries, the identifier and identifierType are optional.
  • If a correspondingAuthor is given, the author name must match one of the authors already in the author list.
  • Required fields are: manuscriptID, status, authors (though author identifiers are optional), and title. All other fields are optional.
  • Some characters need to be escaped in the metadata. This most commonly affects the title and the abstract. Quotes, newlines and other reserved characters should be escaped as described in the JSON specification.

Fields supported by the REST API that are not supported by the Email format

  • identifier and identifierType for authors
  • publicationDate: This is an expected date for an article to be published. It can be updated as publication nears. This date is used to time the release of data that is in "publication blackout" status, awaiting publication of the article.

Sending metadata to Dryad

Authorization

In order for a journal to send metadata to Dryad using the REST API, an access token is required. Please contact Dryad directly to set one up.

Sending a new manuscript

To create a new manuscript entry in Dryad, POST your JSON object to http://datadryad.org/api/v1/organizations/{journalCode}/manuscripts?access_token=xxxx. This is easiest to do using the curl command: 

curl --insecure --header "Content-Type:application/json" --request POST --data-binary @ms.json http://datadryad.org/api/v1/organizations/{journalCode}/manuscripts?access_token=xxxx

Updating a manuscript's status

To update the status of a manuscript entry in Dryad, PUT a JSON object containing the updated status to http://datadryad.org/api/v1/organizations/{journalCode}/manuscripts/{manuscriptId}?access_token=xxxx. Only the manuscriptId is required.

The equivalent curl command:

curl --insecure --header "Content-Type:application/json" --request PUT --data-binary @ms.json http://datadryad.org/api/v1/organizations/{journalCode}/manuscripts/{manuscriptId}?access_token=xxxx

See Also