DOI

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Introduction

DOIs refer to Digital Object Identifiers. Reactome began issuing DOIs in Reactome version 25, released on June 30, 2008.

From CrossRef:

The Digital Object Identifier (DOI®) System is for identifying content objects in the digital environment. DOI® names are assigned to any entity for use on digital networks. They are used to provide current information, including where they (or information about them) can be found on the Internet. Information about a digital object may change over time, including where to find it, but its DOI name will not change.

In Reactome DOI instances are generated by concatenating a constant prefix (the string that identifies Reactome to CrossRef; 10.3180) followed by the event's stable ID (including its version).

So for Reactome, DOIs take this form:

  • doi:10.3180/REACT111111.1
    • 10.3180 - The Reactome source identifier
    • REACT111111 - The Reactome event stable ID
    • .1 - The Reactome event stable ID, version suffix

The Reactome StableID insures that the specific event that the DOI is tagged to will always be traceable.

Identification of new DOI-worthy events.

For versions 1-15 of Reactome a historical search was conducted to determine when modules were first released. Modules from versions 15 through 24 were entered in bulk. There were two lists that were generated during this effort, a master and review list of events. These lists are available here:

Starting with release 25, DOIs have been assigned with each release.

To date DOI tagging is a straight forward process. DOIs are assigned to events that have a modified doi slot. Using the curator tool, the managing editor adds the text "needs DOI" to the doi slot value. During the release process a script generates the a DOI for these events at the time stable ID's are generated.

Identifying such events require manual work by curators and editors. Each event that receives a DOI represents a discrete contribution to Reactome. When issuing DOIs curators and editors consider:

  • The minimum content required. In theory a single event (reaction) could have a DOI assigned to it. Though our practice thus far has favored only issuing DOIs to pathways.
  • Novelty of The material covered.
  • Expert interest. Contributors may want to have a DOI that can be used to cite their contribution to Reactome.
  • The minimum amount of change needed to justify issuing a new DOI for an existing event. Journals do not make this sort of use of DOI's, though it is permissible. We substantially revise events on a regular basis as part of our topic review process. In these cases if the material is revised we issue a new DOI. See #DOI Assignment & Revision.

CrossRef maintains our DOI's as a flat list, not a hierarchy. Reactome maintains a pathway hierarchy that roots to a small number of top level pathways/concepts. Multiple authors, editors, and reviewers are involved in the creation of top level and sub-pathways. Therefore there is nothing to prevent both a parent event and some or all of its child events from all having DOI's if they were produced at different times by different authors.

DOI Assignment & Revision

A discreet piece of work has a stable identifier that links to the top level event of the work. This stableID is used to generate a DOI that is linked to that discreet piece of work, generated for a specific release of Reactome, at a specific time. Reactome is committed to regularly reviewing curated material and updating that material. When a Reactome event is updated with new information the StableID that links to that event is "stepped". A stepped event will have its version suffix incremented by 1. A stepped StableID will go from REACT111111.1 to REACT111111.2. As there is no automatic connection between StableID generation, StableID stepping, and DOI creation the curator and editorial staff must agree that a revised topic requires a new DOI. This process is not automated, requiring human review to confirm that there has been a substantial change to the the material.

  • A substantial change the work that would warrant the assignment a new DOI could include:
    • change in authorship
    • change in reviewer
    • change in topology of pathway
    • A major change in literature cited
    • A major change in the event summation

Creating a Digital Object Identifier Links

A digital object identifier (DOI) can be used to cite and link to electronic documents. A DOI is guaranteed not to change, so you can use it to link permanently to the Reactome module.

To find a document using a DOI

1. Copy the DOI of the module that you want to reference. Reactome modules with a DOI can be identified from our Table of Contents page here. The correct format for citing a Reactome DOI is:

doi:10.3180/REACT_1059.1

2. Open the following DOI site in your browser:

   http://dx.doi.org

3. Enter the entire DOI citation in the text box provided, and then click Go.

The document that matches the DOI citation will display in your browser window.

The DOI scheme is administered by the International DOI Foundation. Many of the world's leading publishers have come together to build a DOI-based document linking scheme known as CrossRef.

Reactome DOI Generation

The steps required for DOI generation with each Reactome release are detailed on the development wiki here.

DOI QA

See the internal page on the development wiki here.


Reactome DOIs

If you would like to see the DOIs that have been issued by pathway, CrossRef has an API for that.

API DOI retrieval examples:

To retrieve the first 1000 rows (we don't have that many DOIs at this time) from January 2002 (our first entries) till December 2014 use this:

http://api.crossref.org/prefixes/10.3180/works?filter=from-pub-date:2002-01,until-pub-date:2014-012&rows=1000

Note: Reactome DOI prefix is: 10.3180

Here is a cleaned up excel file with the result from that query: Media:CrossRef DOI Dump.xlsx