sebotic
sebotic
/ wd_query_issue.py
Created
July 14, 2016 22:07
View wd_query_issue.py
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| import requests | |
| query = ''' | |
| select distinct ?p1 where { | |
| VALUES ?pd { | |
| <http://www.wikidata.org/entity/Q423026> | |
| <http://www.wikidata.org/entity/Q616005> | |
| <http://www.wikidata.org/entity/Q7644128> | |
| <http://www.wikidata.org/entity/Q898273> | |
| <http://www.wikidata.org/entity/Q898362> |
sebotic
/ wikidata_mygene_wrapper.py
Created
March 18, 2016 23:11
a script to retrieve a mapping from entrez id to Wikidata QID and English Wikipedia pages
View wikidata_mygene_wrapper.py
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| import requests | |
| import urllib | |
| import json | |
| __author__ = 'Sebastian Burgstaller' | |
| __license__ = 'AGPLv3' | |
| prefix = ''' | |
| PREFIX schema: <http://schema.org/> | |
| PREFIX wd: <http://www.wikidata.org/entity/> |
sebotic
/ gene_ontology_evidence_codes.py
Created
March 18, 2016 04:26
Gene Ontology evidence codes to determine how a certain annotation came into existance
View gene_ontology_evidence_codes.py
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| # instance of Gene Ontology Evidence code (Q23173209) | |
| go_evidence_codes = { | |
| 'EXP': 'Q23173789', | |
| 'IDA': 'Q23174122', | |
| 'IPI': 'Q23174389', | |
| 'IMP': 'Q23174671', | |
| 'IGI': 'Q23174952', | |
| 'IEP': 'Q23175251', | |
| 'ISS': 'Q23175558', | |
| 'ISO': 'Q23190637', |
sebotic
/ latest_rev.py
Created
February 18, 2016 06:22
Retrieves the latest revision for all Wikidata items which are retrieved by a SPARQL query
View latest_rev.py
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| import requests | |
| import PBB_login | |
| import sys | |
| import pprint | |
| __author__ = 'Sebastian Burgstaller-Muehlbacher' | |
| __license__ = 'AGPLv3' | |
| def exec_wd_query(y): | |
| rev_id_block = [x[1] for x in y] |
sebotic
/ WD_WP_disease_mapping.py
Created
July 25, 2015 00:49
maps the labels of Wikidata QIDs to the appropriate Wikipedia pages
View WD_WP_disease_mapping.py
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| #!/usr/bin/env python | |
| # -*- coding: utf-8 -*- | |
| __author__ = 'Sebastian Burgstaller' | |
| __licence__ = 'GPLv3' | |
| import PBB_Core | |
| import pandas as pd | |
| import requests | |
| import os |
View test.py
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| eferences = { 'P279': [ { 'ref_properties': ['P248', 'P143', 'TIMESTAMP'], | |
| 'ref_values': ['Q17939676', 'Q20641742', 'TIMESTAMP']}], | |
| 'P351': [ { 'ref_properties': ['P248', 'P143', 'TIMESTAMP'], | |
| 'ref_values': ['Q17939676', 'Q20641742', 'TIMESTAMP']}], | |
| 'P353': [ { 'ref_properties': ['P248', 'P143', 'TIMESTAMP'], | |
| 'ref_values': ['Q17939676', 'Q20641742', 'TIMESTAMP']}], | |
| 'P703': [ { 'ref_properties': ['P248', 'P143 | |
| 9;, 'TIMESTAMP'], | |
| 'ref_values': ['Q17939676', 'Q20641742', 'TIMESTAMP']}]} |
sebotic
/ wd_write_test2.py
Created
July 6, 2015 23:48
View wd_write_test2.py
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| __author__ = 'Sebastian Burgstaller' | |
| __licence__ = 'GPLv3' | |
| """ | |
| Test retrieval and construction of a WD json representation | |
| """ | |
| import PBB_Core | |
| import pprint | |
| import time | |
| from PBB_login import WDLogin |
sebotic
/ wikidata_write_test.py
Created
June 29, 2015 18:24
View wikidata_write_test.py
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| __author__ = 'Sebastian Burgstaller' | |
| from PBB_login import WDLogin | |
| import requests | |
| import json | |
| import pprint | |
| user = '' | |
| pwd = '' |
sebotic
/ WikiData_to_Wikipedia.py
Last active
August 29, 2015 14:20
View WikiData_to_Wikipedia.py
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| __author__ = 'sebastian' | |
| __license__ = 'GPLv3' | |
| import pywikibot | |
| import pywikibot.login | |
| gene_list = ['BRCA1', 'REELIN', 'MYL2', 'TP53', 'INS'] | |
| hgid = ['Q1232', 'Q1235', 'Q1236', 'Q1234', 'Q1233'] | |
| mgid = ['Q1238', 'Q1239', 'Q1240', 'Q1237', 'Q1241'] | |
| pages = ['Template:PBB/672', 'Template:PBB/5649', 'Template:PBB/4633', 'Template:PBB/7157', 'Template:PBB/3630'] |