Documentation

Overview

The Publications system stores references to publications and allows labelling them. It does not store PDFs of publications.

The Publications system is appropriate for keeping track of the publications for a group, a project, an institute, a department, or similar.

A publication reference ('publication' in short) may contain:

  • Title.
  • Author by name and with ORCID reference, if available.
  • Abstract.
  • Bibliographic data; publication date, volume, pages, etc.
  • References to external database entries (xrefs).
  • Labels; annotation added by the curators.

Publications are added by providing DOI (Digital Object Identifier) or PMID (PubMed identifier) which the Publications system then fetches the data for from the Crossref and/or PubMed web services.

User account

Only a user with a valid account may add and edit publications.

It is not possible to register an account by oneself in the system.To get an account one must contact the site admin; see the Contact page.

There are two user account roles in the Publications system: admin and curator.

The system admimistrator may change the role of an account. She may also disable and enable an account.

Admin

An admin (also called site administrator) is an account in the system with all available privileges, including creating, enabling and disabling curator accounts.

Only the admin can edit labels and assign them to curators. The admin can add, edit, delete and blacklist publication references.

Contact information for you admin is available in the Contact page.

Curator

A curator is an account in the system with the privileges to add, edit, delete and blacklist publication references, and to add the labels which it has been assigned by the admin.

A curator account requires login. It is created by the admin. It is not possible to register one's own account.

Add publication

Log in to your account

In order to add publications to this system, you have to be logged in to your account in the system. If you do not have one, request it by contacting the system administrator given in the Contact page.

Add publication by fetching data

This is the recommended procedure for adding a publication.

Publication references should be added using the Fetch data for publication page. In that page, do the following:

  • Enter the Digital Object Identifiers (DOI) and/or PubMed identifiers (PMID) of the publications to be added.
  • Use the checkboxes to denote which labels should be applied to the publications. Also select the applicable qualifier (if enabled in your site).
  • When clicking "Fetch", the system goes to the web services at Crossref and/or PubMed, respectively, to fetch the publication reference data.
  • This procedure checks whether the DOI or PMID already exists in the database, in order to avoid multiple copies. The labels and qualifiers will be applied to entries that already exist in the database, as if they had been added by the operation.

Add publication manually

Publication references can be added manually by filling in a form on the Add publication manually page. This is for publication that has neither a DOI nor a PMID, often preprints.

Edit publication

It is possible to edit the details of a publication. However, this is strongly discouraged. It is much more preferable to update contents from PubMed or Crossref.

If a publication as been wrongly marked using a label that you control, then do not delete the publication. Instead, edit the publication to remove the offending label.

Delete publication

A curator may delete any publication. Please note that this is a global operation, affecting the entire database.

This should therefore be done only if the publication is clearly irrelevant for the site as a whole, or if it is a duplicate.

Multiple copies

Multiple copies of a publication reference are, of course, bad news. The Publications system tries to avoid creating duplicates when performing fetch by checking for already loaded DOIs and PMIDs.

However, duplicates may nevertheless be created by mistake, for example when adding a reference manually that in fact has already been added.

A curator may view the Duplicates page, which uses a heuristic algorithm to identify possible duplicates.

A curator has to edit and/or delete the duplicated entries by hand to remove the offending entry. Note that labels may have to be transferred from the publication that is to be deleted to the one that is to be kept. This may require site administrator privileges.

Label

Labels are annotation tagged on to the publication references. They can be used to denote e.g. which facility unit or research group was involved in a publication, or what area the publication is in. The set of labels are controlled by the site administrator.

Note that the term "label" may be configured by the site administrator to be translated into some other term in your site. For example, the SciLifeLab Infrastructure Units Publications instance uses the term "Infrastructure Unit" instead of "label".

A curator account can have privileges for a set of labels. This means that she can add or remove those labels to a publication. She cannot change the labels for which she does not have privileges.

The site admin can add or remove a label from a set of publications listed in a CSV file produced by the subset feature.

Qualifier

Labels attached to a publication may have qualifiers, which can be used to denote e.g. what type of involvement a facility unit had with the publication.

The available qualifiers are part of the configuration of a site and are set by the site administrator, who may also disable the use if qualifiers entirely.

Xref

An xref is a reference to an external resource, most often a database entry. Ideally, the external reosuce should be accessible on the web. The reference consists of two parts: The external database and the accession code for the entry in it.

In those cases where the external database provides a URL template, the Publications system can be configured to allow the button in the interface to open a new browser tab for the database entry.

There is currently also an optional free-text description field associated with an xref. This may be used for a brief characterization of the data available in the database entry.

Researcher

The researcher entity records the ORCID for an author, if given in the PubMed or Crossref data. ORCIDs are increasingly becoming part of publication data since about 2020.

The extraction ORCID and association with an author is done automatically if the data is available. Unfortunately, the data from PubMed and Crossref, or from publishers themselves, rarely provide ORCIDs for every author of a paper.

It is possible to add a researcher manually. It is also possible to assign an author of a paper to a researcher manually.

Subset

A subset of publications may be obtained by executing a selection expression in the Subset page.

The selection expression works by using functions which select a subset of all publications currently in the system. Operators can be used to combine these subsets. Paranthesis are used to determine the order of evaluation if the operators. A selection expression may be arbitrarily complex.

The list of selected publications can be viewed or downloaded in different file formats.

The details of the subset feature are documented in the Subset page.

Blacklist

The blacklist is a list of PubMed identifiers and DOI's of publication references that should not be fetched into the database.

The idea is that a curator should be able to decide that a specific publication reference is clearly irrelevant for the database, delete the entry from the database, and simultaneously ensure that it does not get added at a later stage.

A curator may override a blacklist entry by explicitly checking an input box in the fetch page. This is to allow rescinding a previous decision, and should be used with care.

The list of current entries in the blacklist can be viewed in the Blacklisted page. A curator may delete entries from the blacklist.

API

The Python code examples below use the third-party package requests.

Fetch publication

  • URL: /publication
  • Method: POST
  • Payload: JSON
    {
   "identifier": "<PMID or DOI>",
   "labels": {"<labelname>": "<optional qualifier>"}
}
  • Description: The server is instructed to to fetch publication data from PubMed or Crossref given a PubMed identifier (PMID) or Digital Object Identifier (DOI). This API call fetches only one publication at a time. The labels item in the payload is optional.
  • Example code:
    import json
import requests

url = "http://your-server/api/publication"
headers = {'X-API-key': "my-API-key"}

data = dict(identifier="1557129",  # PMID identifier in this example.
            labels={"MyLab": "Collaboration"})

response = requests.post(url, headers=headers, json=data)

if response.status_code != 200:
    raise ValueError(f"Error {response.status_code}: {response.reason}")
else:
    print(json.dumps(response.json(), indent=2))

Change labels

  • URL: /publication/{iuid}/labels
  • Method: POST
  • Payload: JSON body
    {
   "labels": {"<labelname>": "<optional qualifier>"}
}
  • Description: Change the labels of the given publication. The labels provided must contain all labels to be set for the publication among those that the account specified by the API key can edit. That is, if the user account has three labels associated with it, and only two of those are specified, then the third will be removed if it was already present for the publication.
  • Example code:
    import json
import requests

url = "http://your-server/api/publication/{publication-iuid}/labels"
headers = {'X-API-key': "my-API-key"}

data = dict(labels={"MyLab": "Service"})

response = requests.post(url, headers=headers, json=data)

if response.status_code != 200:
    raise ValueError(f"Error {response.status_code}: {response.reason}")
else:
    print(json.dumps(response.json(), indent=2))
SciLifeLab Data Centre
Publications 9.5.1