Difference between revisions of "Journal Metadata"

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(Metadata Submission via API)
(Metadata Submission via API)
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== Metadata Submission via API ==
 
== Metadata Submission via API ==
  
Dryad is in the process of implementing an API for metadata submission. The API will accept metadata in JSON format. The JSON format contains the same fields as the email format. A sample JSON item is shown below:
+
Dryad is in the process of implementing an API for metadata submission. The API will accept metadata in JSON format. A sample JSON item is shown below. Although the information is the same, the field names and their arrangement differs from the email format. For more details, see the [http://docs.dryad.apiary.io/ documentation at apiary].
 
<pre>
 
<pre>
 
{
 
{
"Journal_Name": "Journal of Dryad Examples",
+
  "abstract": "This is the abstract of the article",  
"Journal_Code": "JDryadEx",
+
  "authors": {
"Print_ISSN": "XXX",
+
    "author": [
"Online_ISSN": "XXX",
+
      {
"Journal_Admin_Email": "admin@jdryadex.org",
+
        "familyName": "Smith",  
"Journal_Editor": "Editorius Edmunton",
+
        "givenNames": "John",  
"Journal_Editor_Email": "editorius@jdryadex.org",
+
        "identifier": "0000-0000-0000-0000",  
"Article_Status": "accepted",
+
        "identifierType": "orcid"
"Publication_DOI": "doi:10.12345/987cba",
+
      },  
"Dryad_Data_DOI": "doi:10.5061/dryad.abc123",
+
      {
"MS_Reference_Number": "ABC1234",
+
        "familyName": "Jones",  
"MS_Title": "Amazing Sample Research",
+
        "givenNames": "Sally"
"MS_Authors": [
+
      }
"Darwin, Charles",
+
    ]
"Newton, Isaac"
+
  },  
],
+
  "correspondingAuthor": {
"Contact_Author": "Darwin, Charles",
+
    "address": {
"Contact_Author_Email": "charles@downhouse.org",
+
      "addressLine1": "123 Main St",  
"Contact_Author_Address": [
+
      "addressLine2": "Box 40560",  
"Luxted Road",
+
      "addressLine3": "",  
"Downe",
+
      "city": "Anytown",  
"Kent BR6 7JT",
+
      "country": "United States",  
"United Kingdom"
+
      "state": "North Carolina",  
],
+
      "zip": "27511"
"Keywords": [
+
    },  
"example",
+
    "author": {
"dryad",
+
      "familyName": "Smith",  
"submission"
+
      "givenNames": "John",  
],
+
      "identifier": "0000-0000-0000-0000",  
"Abstract": "This abstract is abstract."
+
       "identifierType": "orcid"
}
 
</pre>
 
 
 
Proposed alternate format (dleehr) - I transformed our internal XML format to JSON and added the DOI fields. This way the structure should match what we store on disk, so we just need to validate it and save it.
 
<pre>
 
{
 
  "DryadEmailSubmission": {
 
    "Abstract": "This is the abstract of the article",  
 
    "Address_Line_1": "123 Main St",  
 
    "Address_Line_2": "Box 40560",
 
    "Address_Line_3": "",  
 
    "Article_Status": "accepted",
 
    "Authors": {
 
       "Author": [
 
        "Smith, John",
 
        "Jones, Susan"
 
      ]
 
 
     },  
 
     },  
     "City": "Anytown",  
+
     "dryadDataDOI": "doi:10.5061/dryad.abc123",
     "Classification": {
+
    "email": "smith@example.com",  
 +
     "keywords": {
 
       "keyword": [
 
       "keyword": [
 
         "Science",  
 
         "Science",  
Line 163: Line 147:
 
       ]
 
       ]
 
     },  
 
     },  
     "Corresponding_Author": "Smith, John",  
+
     "manuscriptId": "MS12345",  
     "Country": "United States",
+
     "publicationDate" : "2014-10-17",
    "Dryad_Data_DOI": "doi:10.5061/dryad.abc123",
+
     "publicationDOI": "doi:10.12345/987cba",  
    "Email": "smith@example.com",
+
     "status": "accepted",  
    "ISSN": "0000-0000",
+
     "title": "Title of article 1"
    "Journal": "Journal Name",
 
    "Journal_Admin_Email": "admin@journal.com",
 
    "Journal_Code": "JournalName",  
 
     "Journal_Editor": "Ed Itor",
 
    "Journal_Editor_Email": "editor@journal.com",
 
    "Journal_Embargo_Period": "0",
 
    "Online_ISSN": "0000-0000",
 
    "Publication_DOI": "doi:10.12345/987cba",  
 
     "State": "North Carolina",  
 
     "Submission_Metadata": {
 
      "Article_Title": "Title of Article",
 
      "Manuscript": "ABC-1234567"
 
    },
 
    "Zip": "27511"
 
 
   }
 
   }
 
}
 
}
Line 187: Line 157:
  
 
Notes about the JSON format:
 
Notes about the JSON format:
* The JSON content may be a single object or an array of objects.
+
* 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 [http://www.ietf.org/rfc/rfc4627.txt JSON specification].
* Some characters need to be escaped in the metadata. This most commonly affects the MS_Title and the Abstract. Quotes, newlines and other reserved characters should be escaped as described in the [http://www.ietf.org/rfc/rfc4627.txt JSON specification].
 
  
 
== Seeking author consent to send metadata to Dryad ==
 
== Seeking author consent to send metadata to Dryad ==

Revision as of 18:35, 8 August 2014

This page documents the details of the metadata that journals send to Dryad. Journals should send a message notifying Dryad of each new manuscript and each change in status for a previously reported manuscript. These notices allow Dryad to create and pre-populate a record for the data, greatly facilitating the author's process of data deposit.

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.

Timing of notices

  • Journals using the Basic workflow usually send a single notice 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.

Critical information

The following fields are mandatory, or the email will not be correctly processed by the Dryad system:

  • Journal Name or Journal Code - These fields are used to determine where the message goes within Dryad, and what version of the processing system is used. A Journal Name the the full publication name of the journal. A Journal Code is the journal-specific abbreviation that Dryad uses for internal management. Since Journal Names may change, it is preferred to use the Journal Code. If both Journal Name and Journal Code are present in the message, Dryad will use the Journal Code.
  • MS Reference Number - The manuscript 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. 
  • MS Title - The manuscript's title. This 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 - A list of 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. This is the default format produced by ScholarOne.
  • Article Status - Specifies how Dryad will handle data submitted in relation to the article. See values below.

All other fields are optional. Any field that is blank should not be included in the message. Optional fields include:

Article Status

The Article Status field is mandatory. It specifies how Dryad will handle data submitted in relation to the article. Acceptable values and their meanings are below.

  • 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. Data submitted to Dryad will only be available to users who have the "reviewer PIN". A provisional DOI will be assigned, but the DOI is not registered, and will not resolve.
  • 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.

Data DOI

The field Dryad Data DOI may be used to indicate that a particular manuscript already has a data deposit in Dryad.

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 emails to Dryad, the Dryad Data DOI is included, allowing Dryad to match the metadata email with the already-existing data package.

An example of this field is shown below:

Dryad Data DOI: doi:10.5061/dryad.abc123

The Dryad Data DOI may be included at any point in the metadata email, as long as it is before the indicator EndDryadContent.

Publication DOI

The field Publication DOI may be used to indicate that a manuscript has been assigned a DOI. This DOI will not necessarily be registered with CrossRef, but it is the DOI that will eventually be registered for the target publication.

Publication DOI: doi:10.12345/987cba

The Publication DOI may be included at any point in the metadata email, as long as it is before the indicator EndDryadContent.


Metadata 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.

  • 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 the last part 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

Message Body

Note the 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

NOTES:

  • the Abstract should always be the last item in the email, with no text following it. If this is not possible (e.g., if the journal email system automatically adds a footer), the message must be terminated with the tag EndDryadContent.
  • in testing, please send at least one test message with multiple authors, so we can be sure that the Dryad system correctly interprets the separator used between names.

Metadata Submission via API

Dryad is in the process of implementing an API for metadata submission. The API will accept metadata in JSON format. A sample JSON item is shown below. Although the information is the same, the field names and their arrangement differs from the email format. For more details, see the documentation at apiary.

{
  "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"
    }, 
    "dryadDataDOI": "doi:10.5061/dryad.abc123", 
    "email": "smith@example.com", 
    "keywords": {
      "keyword": [
        "Science", 
        "Data", 
        "Publishing"
      ]
    }, 
    "manuscriptId": "MS12345", 
    "publicationDate" : "2014-10-17",
    "publicationDOI": "doi:10.12345/987cba", 
    "status": "accepted", 
    "title": "Title of article 1"
  }
}

Notes about the JSON format:

  • 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.

Seeking author consent to send metadata to Dryad

If the journal wishes to seek author consent before sending manuscript details to Dryad, they may use this template which adds a checkbox to the initial manuscript submission phase, asking if the author would like deposit data in Dryad. This Scholar One template was created by Tim Vines for use with Molecular Ecology.