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.

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.