Publications

Publications in MxLIVE are fetched automatically. There is no mechanism for manually adding depositions or articles at this time.

PDB depositions are fetched periodically from public online sources. New depositions are added to MxLIVE, along with any associated articles.

Publications

Icons in the toolbar give access to:

  • detailed list of PDBs, Subject Areas, and Journals, and

  • publications metrics (statistics).

Setup

The following variables can be added to your settings.py file to override the default values:

Publications Settings

Settings

Default

Usage

PDB_FACILITY_ACRONYM

‘CLSI’

Used to build a search query provided to the PDB_SEARCH_URL

CONTACT_EMAIL

‘cmcf-support@lightsource.ca

Contact email provided to CrossRef

CROSSREF_API_KEY

None

API key used for CrossRef calls

CROSSREF_THROTTLE

1

Time delay (seconds) between CrossRef calls

CROSSREF_BATCH_SIZE

10

Limit the number of publications fetched from CrossRef at a time

PDB_SEARCH_URL

https://www.rcsb.org/pdb/rest/search

Fetch all PDB codes related to PDB_FACILITY_ACRONYM

PDB_REPORT_URL

https://www.rcsb.org/pdb/rest/customReport

Fetch detailed report for codes fetched from PDB_SEARCH_URL

GOOGLE_API_KEY

None

API key used for calls to GOOGLE_BOOKS_API

GOOGLE_BOOKS_API

https://www.googleapis.com/books/v1/volumes

Fetch information about books related to PDBs

SCIMAGO_URL

https://www.scimagojr.com/journalrank.php

Fetch journal metrics which are then stored by year

Mentions and citations are fetched from https://api.eventdata.crossref.org/v1/events/distinct and https://www.crossref.org/openurl/.

Beamline Tags

To tag depositions and articles by beamline, define a PDB_TAG_FUNCTION in your settings.py file, mapping beamline acronyms from the source to the acronyms defined for your beamline(s) in MxLIVE:

def clsi_beamline_tags(entry):
    """
    Generate proper CLSI beamline tags for publications
    :param entry: the entry from the PDB report
    :return: a list of tag names
    """

    acronym = entry['diffractionSource'].split()[-1]
    acronyms = {
        '08ID-1': ['CMCF-ID'],
        '08ID-2': ['CMCF-ID'],
        '08B1-1': ['CMCF-BM'],
        'CLSI': ['CMCF-ID', 'CMCF-BM',],
    }
    return acronyms.get(acronym, [])

PDB_TAG_FUNCTION = clsi_beamline_tags

Statistics

Publications metrics can be filtered by year and beamline.

Publication Metrics