Crossref Search

class habanero.Crossref(base_url='https://api.crossref.org', api_key=None)[source]

Crossref: Class for Crossref search API methods




Includes methods matching Crossref API routes

Also:

What am I actually searching when using the Crossref search API?

You are using the Crossref search API described at https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md. When you search with query terms, on Crossref servers they are not searching full text, or even abstracts of articles, but only what is available in the data that is returned to you. That is, they search article titles, authors, etc. For some discussion on this, see https://github.com/CrossRef/rest-api-doc/issues/101

Doing setup:

from habanero import Crossref
cr = Crossref()
# set a different base url
Crossref(base_url = "http://some.other.url")
# set an api key
Crossref(api_key = "123456")

Rate limits

See the headers X-Rate-Limit-Limit and X-Rate-Limit-Interval for current rate limits. As of this writing the limit is 50 requests per second, but that could change. In addiiton, it’s not clear what the time is to reset. See below for getting header info for your requests.

Verbose curl output:

import requests
import logging
import httplib as http_client
http_client.HTTPConnection.debuglevel = 1
logging.basicConfig()
logging.getLogger().setLevel(logging.DEBUG)
requests_log = logging.getLogger("requests.packages.urllib3")
requests_log.setLevel(logging.DEBUG)
requests_log.propagate = True
from habanero import Crossref
cr = Crossref()
cr.works(query = "ecology")

Field queries

One or more field queries. Field queries are searches on specific fields. For example, using query_title searches titles instead of full search across all fields as would happen by default. Acceptable set of field query parameters are:

  • query_title - Query title and subtitle
  • query_container_title - Query container-title aka. publication name
  • query_author - Query author first and given names
  • query_editor - Query editor first and given names
  • query_chair - Query chair first and given names
  • query_translator - Query translator first and given names
  • query_contributor - Query author, editor, chair and translator first and given names



funders(ids=None, query=None, filter=None, offset=None, limit=None, sample=None, sort=None, order=None, facet=None, works=False, cursor=None, cursor_max=5000, **kwargs)[source]

Search Crossref funders

Note that funders without IDs don’t show up on the /funders route, that is, won’t show up in searches via this method

Parameters:
  • ids – [Array] DOIs (digital object identifier) or other identifiers
  • query – [String] A query string
  • filter – [Hash] Filter options. See examples for usage. Accepts a dict, with filter names and their values. For repeating filter names pass in a list of the values to that filter name, e.g., {‘award_funder’: [‘10.13039/100004440’, ‘10.13039/100000861’]}. See https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md#filter-names for filter names and their descriptions and filter_names() and filter_details()
  • offset – [Fixnum] Number of record to start at, from 1 to 10000
  • limit – [Fixnum] Number of results to return. Not relavant when searching with specific dois. Default: 20. Max: 1000
  • sample – [Fixnum] Number of random results to return. when you use the sample parameter, the limit and offset parameters are ignored. This parameter only used when works requested. Max: 100
  • sort – [String] Field to sort on, one of score, relevance, updated (date of most recent change to metadata. Currently the same as deposited), deposited (time of most recent deposit), indexed (time of most recent index), or published (publication date). Note: If the API call includes a query, then the sort order will be by the relevance score. If no query is included, then the sort order will be by DOI update date.
  • order – [String] Sort order, one of ‘asc’ or ‘desc’
  • facet – [Boolean/String] Set to true to include facet results (default: false). Optionally, pass a query string, e.g., facet=type-name:* or facet=license=*
  • works – [Boolean] If true, works returned as well. Default: false
  • kwargs – additional named arguments passed on to requests.get, e.g., field queries (see examples)
Returns:

A dict

Usage:

from habanero import Crossref
cr = Crossref()
cr.funders(ids = '10.13039/100000001')
cr.funders(query = "NSF")

# get works
cr.funders(ids = '10.13039/100000001', works = True)

# cursor - deep paging
res = cr.funders(ids = '10.13039/100000001', works = True, cursor = "*", limit = 200)
sum([ len(z['message']['items']) for z in res ])
items = [ z['message']['items'] for z in res ]
items = [ item for sublist in items for item in sublist ]
[ z['DOI'] for z in items ][0:50]

# field queries
res = cr.funders(ids = "10.13039/100000001", works = True, query_container_title = 'engineering', filter = {'type': 'journal-article'})
eds = [ x.get('editor') for x in res['message']['items'] ]
[ z for z in eds if z is not None ]
journals(ids=None, query=None, filter=None, offset=None, limit=None, sample=None, sort=None, order=None, facet=None, works=False, cursor=None, cursor_max=5000, **kwargs)[source]

Search Crossref journals

Parameters:
  • ids – [Array] DOIs (digital object identifier) or other identifiers
  • query – [String] A query string
  • filter – [Hash] Filter options. See examples for usage. Accepts a dict, with filter names and their values. For repeating filter names pass in a list of the values to that filter name, e.g., {‘award_funder’: [‘10.13039/100004440’, ‘10.13039/100000861’]}. See https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md#filter-names for filter names and their descriptions and filter_names() and filter_details()
  • offset – [Fixnum] Number of record to start at, from 1 to 10000
  • limit – [Fixnum] Number of results to return. Not relavant when searching with specific dois. Default: 20. Max: 1000
  • sample – [Fixnum] Number of random results to return. when you use the sample parameter, the limit and offset parameters are ignored. This parameter only used when works requested. Max: 100
  • sort – [String] Field to sort on, one of score, relevance, updated (date of most recent change to metadata. Currently the same as deposited), deposited (time of most recent deposit), indexed (time of most recent index), or published (publication date). Note: If the API call includes a query, then the sort order will be by the relevance score. If no query is included, then the sort order will be by DOI update date.
  • order – [String] Sort order, one of ‘asc’ or ‘desc’
  • facet – [Boolean/String] Set to true to include facet results (default: false). Optionally, pass a query string, e.g., facet=type-name:* or facet=license=*
  • works – [Boolean] If true, works returned as well. Default: false
  • kwargs – additional named arguments passed on to requests.get, e.g., field queries (see examples)
Returns:

A dict

Usage:

from habanero import Crossref
cr = Crossref()
cr.journals(ids = "2167-8359")
cr.journals()

# pass many ids
cr.journals(ids = ['1803-2427', '2326-4225'])

# search
cr.journals(query = "ecology")
cr.journals(query = "peerj")

# get works
cr.journals(ids = "2167-8359", works = True)
cr.journals(ids = "2167-8359", query = 'ecology', works = True, sort = 'score', order = "asc")
cr.journals(ids = "2167-8359", query = 'ecology', works = True, sort = 'score', order = "desc")
cr.journals(ids = "2167-8359", works = True, filter = {'from_pub_date': '2014-03-03'})
cr.journals(ids = '1803-2427', works = True)
cr.journals(ids = '1803-2427', works = True, sample = 1)
cr.journals(limit: 2)

# cursor - deep paging
res = cr.funders(ids = '10.13039/100000001', works = True, cursor = "*", limit = 200)
sum([ len(z['message']['items']) for z in res ])
items = [ z['message']['items'] for z in res ]
items = [ item for sublist in items for item in sublist ]
[ z['DOI'] for z in items ][0:50]

# field queries
res = cr.journals(ids = "2167-8359", works = True, query_title = 'fish', filter = {'type': 'journal-article'})
[ x.get('title') for x in res['message']['items'] ]
licenses(query=None, offset=None, limit=None, sample=None, sort=None, order=None, facet=None, **kwargs)[source]

Search Crossref licenses

Parameters:
  • query – [String] A query string
  • offset – [Fixnum] Number of record to start at, from 1 to 10000
  • limit – [Fixnum] Number of results to return. Not relavant when searching with specific dois. Default: 20. Max: 1000
  • sort – [String] Field to sort on, one of score, relevance, updated (date of most recent change to metadata. Currently the same as deposited), deposited (time of most recent deposit), indexed (time of most recent index), or published (publication date). Note: If the API call includes a query, then the sort order will be by the relevance score. If no query is included, then the sort order will be by DOI update date.
  • order – [String] Sort order, one of ‘asc’ or ‘desc’
  • facet – [Boolean/String] Set to true to include facet results (default: false). Optionally, pass a query string, e.g., facet=type-name:* or facet=license=*
  • kwargs – additional named arguments passed on to requests.get, e.g., field queries (see examples)
Returns:

A dict

Usage:

from habanero import Crossref
cr = Crossref()
cr.licenses()
cr.licenses(query = "creative")
members(ids=None, query=None, filter=None, offset=None, limit=None, sample=None, sort=None, order=None, facet=None, works=False, cursor=None, cursor_max=5000, **kwargs)[source]

Search Crossref members

Parameters:
  • ids – [Array] DOIs (digital object identifier) or other identifiers
  • query – [String] A query string
  • filter – [Hash] Filter options. See examples for usage. Accepts a dict, with filter names and their values. For repeating filter names pass in a list of the values to that filter name, e.g., {‘award_funder’: [‘10.13039/100004440’, ‘10.13039/100000861’]}. See https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md#filter-names for filter names and their descriptions and filter_names() and filter_details()
  • offset – [Fixnum] Number of record to start at, from 1 to 10000
  • limit – [Fixnum] Number of results to return. Not relavant when searching with specific dois. Default: 20. Max: 1000
  • sample – [Fixnum] Number of random results to return. when you use the sample parameter, the limit and offset parameters are ignored. This parameter only used when works requested. Max: 100
  • sort – [String] Field to sort on, one of score, relevance, updated (date of most recent change to metadata. Currently the same as deposited), deposited (time of most recent deposit), indexed (time of most recent index), or published (publication date). Note: If the API call includes a query, then the sort order will be by the relevance score. If no query is included, then the sort order will be by DOI update date.
  • order – [String] Sort order, one of ‘asc’ or ‘desc’
  • facet – [Boolean/String] Set to true to include facet results (default: false). Optionally, pass a query string, e.g., facet=type-name:* or facet=license=*
  • works – [Boolean] If true, works returned as well. Default: false
  • kwargs – additional named arguments passed on to requests.get, e.g., field queries (see examples)
Returns:

A dict

Usage:

from habanero import Crossref
cr = Crossref()
cr.members(ids = 98)

# get works
res = cr.members(ids = 98, works = True, limit = 3)
len(res['message']['items'])
[ z['DOI'] for z in res['message']['items'] ]

# cursor - deep paging
res = cr.members(ids = 98, works = True, cursor = "*")
sum([ len(z['message']['items']) for z in res ])
items = [ z['message']['items'] for z in res ]
items = [ item for sublist in items for item in sublist ]
[ z['DOI'] for z in items ][0:50]

# field queries
res = cr.members(ids = 98, works = True, query_author = 'carl boettiger', limit = 7)
[ x['author'][0]['family'] for x in res['message']['items'] ]
prefixes(ids=None, filter=None, offset=None, limit=None, sample=None, sort=None, order=None, facet=None, works=False, cursor=None, cursor_max=5000, **kwargs)[source]

Search Crossref prefixes

Parameters:
  • ids – [Array] DOIs (digital object identifier) or other identifiers
  • filter – [Hash] Filter options. See examples for usage. Accepts a dict, with filter names and their values. For repeating filter names pass in a list of the values to that filter name, e.g., {‘award_funder’: [‘10.13039/100004440’, ‘10.13039/100000861’]}. See https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md#filter-names for filter names and their descriptions and filter_names() and filter_details()
  • offset – [Fixnum] Number of record to start at, from 1 to 10000
  • limit – [Fixnum] Number of results to return. Not relavant when searching with specific dois. Default: 20. Max: 1000
  • sample – [Fixnum] Number of random results to return. when you use the sample parameter, the limit and offset parameters are ignored. This parameter only used when works requested. Max: 100
  • sort – [String] Field to sort on, one of score, relevance, updated (date of most recent change to metadata. Currently the same as deposited), deposited (time of most recent deposit), indexed (time of most recent index), or published (publication date). Note: If the API call includes a query, then the sort order will be by the relevance score. If no query is included, then the sort order will be by DOI update date.
  • order – [String] Sort order, one of ‘asc’ or ‘desc’
  • facet – [Boolean/String] Set to true to include facet results (default: false). Optionally, pass a query string, e.g., facet=type-name:* or facet=license=*
  • works – [Boolean] If true, works returned as well. Default: false
  • kwargs – additional named arguments passed on to requests.get, e.g., field queries (see examples)
Returns:

A dict

Usage:

from habanero import Crossref
cr = Crossref()
cr.prefixes(ids = "10.1016")
cr.prefixes(ids = ['10.1016','10.1371','10.1023','10.4176','10.1093'])

# get works
cr.prefixes(ids = "10.1016", works = True)

# Limit number of results
cr.prefixes(ids = "10.1016", works = True, limit = 3)

# Sort and order
cr.prefixes(ids = "10.1016", works = True, sort = "relevance", order = "asc")

# cursor - deep paging
res = cr.prefixes(ids = "10.1016", works = True, cursor = "*", limit = 200)
sum([ len(z['message']['items']) for z in res ])
items = [ z['message']['items'] for z in res ]
items = [ item for sublist in items for item in sublist ]
[ z['DOI'] for z in items ][0:50]

# field queries
res = cr.prefixes(ids = "10.1371", works = True, query_editor = 'cooper', filter = {'type': 'journal-article'})
eds = [ x.get('editor') for x in res['message']['items'] ]
[ z for z in eds if z is not None ]
random_dois(sample=10, **kwargs)[source]

Get a random set of DOIs

Parameters:
  • sample – [Fixnum] Number of random DOIs to return. Default: 10. Max: 100
  • kwargs – additional named arguments passed on to requests.get, e.g., field queries (see examples)
Returns:

[Array] of DOIs

Usage:

from habanero import Crossref
cr = Crossref()
cr.random_dois(1)
cr.random_dois(10)
cr.random_dois(50)
cr.random_dois(100)
registration_agency(ids, **kwargs)[source]

Determine registration agency for DOIs

Parameters:
  • ids – [Array] DOIs (digital object identifier) or other identifiers
  • kwargs – additional named arguments passed on to requests.get, e.g., field queries (see examples)
Returns:

list of DOI minting agencies

Usage:

from habanero import Crossref
cr = Crossref()
cr.registration_agency('10.1371/journal.pone.0033693')
cr.registration_agency(ids = ['10.1007/12080.1874-1746','10.1007/10452.1573-5125', '10.1111/(issn)1442-9993'])
types(ids=None, query=None, filter=None, offset=None, limit=None, sample=None, sort=None, order=None, facet=None, works=False, cursor=None, cursor_max=5000, **kwargs)[source]

Search Crossref types

Parameters:
  • ids – [Array] Type identifier, e.g., journal
  • query – [String] A query string
  • filter – [Hash] Filter options. See examples for usage. Accepts a dict, with filter names and their values. For repeating filter names pass in a list of the values to that filter name, e.g., {‘award_funder’: [‘10.13039/100004440’, ‘10.13039/100000861’]}. See https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md#filter-names for filter names and their descriptions and filter_names() and filter_details()
  • offset – [Fixnum] Number of record to start at, from 1 to 10000
  • limit – [Fixnum] Number of results to return. Not relavant when searching with specific dois. Default: 20. Max: 1000
  • sample – [Fixnum] Number of random results to return. when you use the sample parameter, the limit and offset parameters are ignored. This parameter only used when works requested. Max: 100
  • sort – [String] Field to sort on, one of score, relevance, updated (date of most recent change to metadata. Currently the same as deposited), deposited (time of most recent deposit), indexed (time of most recent index), or published (publication date). Note: If the API call includes a query, then the sort order will be by the relevance score. If no query is included, then the sort order will be by DOI update date.
  • order – [String] Sort order, one of ‘asc’ or ‘desc’
  • facet – [Boolean/String] Set to true to include facet results (default: false). Optionally, pass a query string, e.g., facet=type-name:* or facet=license=*
  • works – [Boolean] If true, works returned as well. Default: false
  • kwargs – additional named arguments passed on to requests.get, e.g., field queries (see examples)
Returns:

A dict

Usage:

from habanero import Crossref
cr = Crossref()
cr.types()
cr.types(ids = "journal")
cr.types(ids = "journal-article")
cr.types(ids = "journal", works = True)

# field queries
res = cr.types(ids = "journal-article", works = True, query_title = 'gender', rows = 100)
[ x.get('title') for x in res['message']['items'] ]
works(ids=None, query=None, filter=None, offset=None, limit=None, sample=None, sort=None, order=None, facet=None, cursor=None, cursor_max=5000, **kwargs)[source]

Search Crossref works

Parameters:
  • ids – [Array] DOIs (digital object identifier) or other identifiers
  • query – [String] A query string
  • filter – [Hash] Filter options. See examples for usage. Accepts a dict, with filter names and their values. For repeating filter names pass in a list of the values to that filter name, e.g., {‘award_funder’: [‘10.13039/100004440’, ‘10.13039/100000861’]}. See https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md#filter-names for filter names and their descriptions and filter_names() and filter_details()
  • offset – [Fixnum] Number of record to start at, from 1 to 10000
  • limit – [Fixnum] Number of results to return. Not relavant when searching with specific dois. Default: 20. Max: 1000
  • sample – [Fixnum] Number of random results to return. when you use the sample parameter, the limit and offset parameters are ignored. Max: 100
  • sort – [String] Field to sort on, one of score, relevance, updated (date of most recent change to metadata. Currently the same as deposited), deposited (time of most recent deposit), indexed (time of most recent index), or published (publication date). Note: If the API call includes a query, then the sort order will be by the relevance score. If no query is included, then the sort order will be by DOI update date.
  • order – [String] Sort order, one of ‘asc’ or ‘desc’
  • facet – [Boolean/String] Set to true to include facet results (default: false). Optionally, pass a query string, e.g., facet=type-name:* or facet=license=*
  • cursor – [String] Cursor character string to do deep paging. Default is None. Pass in ‘*’ to start deep paging. Any combination of query, filters and facets may be used with deep paging cursors. While rows may be specified along with cursor, offset and sample cannot be used. See https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md#deep-paging-with-cursors
  • cursor_max – [Fixnum] Max records to retrieve. Only used when cursor param used. Because deep paging can result in continuous requests until all are retrieved, use this parameter to set a maximum number of records. Of course, if there are less records found than this value, you will get only those found.
  • kwargs – additional named arguments passed on to requests.get, e.g., field queries (see examples)
Returns:

A dict

Usage:

from habanero import Crossref
cr = Crossref()
cr.works()
cr.works(ids = '10.1371/journal.pone.0033693')
dois = ['10.1371/journal.pone.0033693', ]
cr.works(ids = dois)
x = cr.works(query = "ecology")
x['status']
x['message-type']
x['message-version']
x['message']
x['message']['total-results']
x['message']['items-per-page']
x['message']['query']
x['message']['items']

# Get full text links
x = cr.works(filter = {'has_full_text': True})
x

# Parse output to various data pieces
x = cr.works(filter = {'has_full_text': True})
## get doi for each item
[ z['DOI'] for z in x['message']['items'] ]
## get doi and url for each item
[ {"doi": z['DOI'], "url": z['URL']} for z in x['message']['items'] ]
### print every doi
for i in x['message']['items']:
     print i['DOI']

# filters - pass in as a dict
## see https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md#filter-names
cr.works(filter = {'has_full_text': True})
cr.works(filter = {'has_funder': True, 'has_full_text': True})
cr.works(filter = {'award_number': 'CBET-0756451', 'award_funder': '10.13039/100000001'})
## to repeat a filter name, pass in a list
x = cr.works(filter = {'award_funder': ['10.13039/100004440', '10.13039/100000861']}, limit = 100)
map(lambda z:z['funder'][0]['DOI'], x['message']['items'])

# Deep paging, using the cursor parameter
## this search should lead to only ~215 results
cr.works(query = "widget", cursor = "*", cursor_max = 100)
## this search should lead to only ~2500 results, in chunks of 500
res = cr.works(query = "octopus", cursor = "*", limit = 500)
sum([ len(z['message']['items']) for z in res ])
## about 167 results
res = cr.works(query = "extravagant", cursor = "*", limit = 50, cursor_max = 500)
sum([ len(z['message']['items']) for z in res ])
## cursor_max to get back only a maximum set of results
res = cr.works(query = "widget", cursor = "*", cursor_max = 100)
sum([ len(z['message']['items']) for z in res ])
## cursor_max - especially useful when a request could be very large
### e.g., "ecology" results in ~275K records, lets max at 10,000
###   with 1000 at a time
res = cr.works(query = "ecology", cursor = "*", cursor_max = 10000, limit = 1000)
sum([ len(z['message']['items']) for z in res ])
items = [ z['message']['items'] for z in res ]
items = [ item for sublist in items for item in sublist ]
[ z['DOI'] for z in items ][0:50]

# field queries
res = cr.works(query = "ecology", query_author = 'carl boettiger')
[ x['author'][0]['family'] for x in res['message']['items'] ]