public
Created

  • Download Gist
run_geo_reuse_collection.py
Python
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240
import os
import time
import re
import nose
from nose.tools import assert_equals
from collections import defaultdict
import EUtils
from EUtils import HistoryClient, ThinClient
import dataset
import datasources
from datasources import pubmedcentral
from datasources import pubmed
from datasources import affiliation
from datasources import geo
from datasources import urlopener
import utils
from utils.cache import TimedCache
import pickle
 
EMAIL_CONTACT = "hpiwowar@gmail.com"
VERBOSE = False
 
#base_query = """(GEO[text] OR omnibus[text]) NOT "pmc gds"[filter]"""
#base_query = """(GEO[text] OR omnibus[text]) NOT "pmc gds"[filter] AND ("1900"[PubDate] : "2009"[PubDate])"""
base_query_reuse = """("1900"[PubDate] : "2009"[PubDate]) NOT "pmc gds"[filter]"""
base_query_submit = """("1900"[PubDate] : "2009"[PubDate]) AND "pmc gds"[filter]"""
 
#url_for_gse = """http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gds&term=GSE[ETYP]&retmax=10000&usehistory=n"""
#url_for_gds = """http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gds&term=GDS[ETYP]&retmax=10000&usehistory=n"""
 
 
def test_get_accession_in_pmc_fulltext():
response = get_accession_in_pmc_fulltext("GSE", "200008514", base_query_reuse)
assert_equals(response, ['2785812', '2620272'])
 
response = get_accession_in_pmc_fulltext("GSE", "200008478", base_query_reuse)
assert_equals(response, ['2223695'])
 
response = get_accession_in_pmc_fulltext("GSE", "200007778", base_query_reuse)
assert_equals(response, [])
 
response = get_accession_in_pmc_fulltext("GDS", "2643", base_query_reuse)
assert_equals(response, ['2715883', '2781753'])
def test_get_accession_variants():
response = get_accession_variants("GSE", "200008514")
assert_equals(response, ['GSE200008514', '"GSE 200008514"', 'GSE8514', '"GSE 8514"'])
def get_accession_variants(id_type, id):
variants = []
variants.append(id_type + id)
variants.append('"' + id_type + ' ' + id + '"')
id_stripped = geo.get_stripped_accession(id)
if (id_stripped != id):
variants.append(id_type + id_stripped)
variants.append('"' + id_type + ' ' + id_stripped + '"')
return(variants)
def get_accession_in_pmc_fulltext(id_type, id, pmc_query):
pmc_ids = []
accession_variants = get_accession_variants(id_type, id)
for variant in accession_variants:
query = variant + "[text] AND " + pmc_query
pmc_ids += pubmedcentral.search(query)
return(pmc_ids)
def test_get_authors_and_submittors_from_accession():
response = get_authors_and_submittors_from_accession([u'17911395'], [u'Ye P', u'Rainey W'])
assert_equals(response, ['Mariniello', 'Shibata', 'Ye', 'Rainey', 'Mantero'])
 
def get_author_last_names(pmids):
last_names_list = []
for pmid in pmids:
authors = pubmed.authors([pmid])
authors_list = authors[0].split(";")
last_names = [author.split(" ")[0] for author in authors_list]
last_names_list += last_names
return(last_names_list)
def get_authors_and_submittors_from_accession(pmids, contributors=None):
last_names_list = get_author_last_names(pmids)
if contributors:
contributor_last_names = [author.split(" ")[0] for author in contributors]
last_names_list += contributor_last_names
last_names_set = set(last_names_list)
return(list(last_names_set))
def test_get_dict_submit_reuse_of_accession_in_pmc_fulltext():
response = get_dict_submit_reuse_of_accession_in_pmc_fulltext("GSE", ["200008514", "200008478"], base_query_reuse)
assert_equals(response.items()[0:2], [(('GSE200008514', '2785812'), ('200008514', [u'17911395'], ['2785812', '2620272'], [u'19917117'], ['Mariniello', 'Shibata', 'Ye', 'Rainey', 'Mantero'], ['Kroll', 'Barkema', 'Carlon'], [], ['Algorithms Mol Biol'], ['2009'], [], [], [])), (('GSE200008478', '2223695'), ('200008478', [u'17977147', u'17951393'], ['2223695'], [u'17993534'], ['Moser', 'Fischer', 'Friberg', 'Pessi', 'Lindemann', 'Hauser', 'Rehrauer', 'Hennecke', 'Ahrens'], ['Hacker', 'Aktas', 'Narberhaus', 'Sohlenkamp', 'Geiger'], [], ['J Bacteriol'], ['2008'], [], [], ['deposited', 'accessed', 'published']))] )
def test_get_author_intersect_submit_reuse():
response = get_author_intersect_submit_reuse(['Pessi', 'Ahrens', 'Rehrauer', 'Lindemann', 'Hauser', 'Fischer', 'Hennecke', 'Lindemann', 'Moser', 'Pessi', 'Hauser', 'Friberg', 'Hennecke', 'Fischer', u'Pessi', u'Ahrens', u'Rehrauer', u'Lindemann', u'Hauser', u'Fischer', u'Hennecke'], ['Hacker', 'Sohlenkamp', 'Pessi', 'Aktas', 'Geiger', 'Narberhaus'])
assert_equals(response, ['Pessi'])
def get_author_intersect_submit_reuse(submit_authors, reuse_authors):
intersect = multi_intersection([submit_authors, reuse_authors])
return(intersect)
 
meshes = """"Algorithms"[mesh]
"Databases, Genetic"[mesh]
"Gene Expression Profiling/methods"[mesh]
"Computational Biology/methods"[mesh]
"Oligonucleotide Array Sequence Analysis/methods"[mesh]
"Genomics/methods"[mesh]
"Reproducibility of Results"[mesh]
"Software"[mesh]
"Computer Simulation"[mesh]
"Internet"[mesh]
"Data Interpretation, Statistical"[mesh]""".split("\n")
 
metaquery = "(meta-analysis [pt] OR meta-analysis [tw] OR metanalysis [tw]) OR meta-analysis [mh])"
 
words = """submitted
deposited
user*
public
accessed
downloaded
published""".split("\n")
def get_dict_submit_reuse_of_accession_in_pmc_fulltext(id_type, ids, pmc_query):
response_dict = defaultdict(str)
num_ids = len(ids)
id_counter = 0
geo_instance = geo.GEO()
for accession in ids:
id_counter += 1
pmc_reuse_pmcids = get_accession_in_pmc_fulltext(id_type, accession, pmc_query)
if not pmc_reuse_pmcids:
continue
stripped_accession = geo.get_stripped_accession(accession)
try:
submit_pmids = geo_instance.pmids(id_type + stripped_accession)
except Exception:
continue
submit_contributors = geo_instance.contributors(id_type + stripped_accession)
submit_authors = get_authors_and_submittors_from_accession(submit_pmids, submit_contributors)
 
for reuse_pmcid in pmc_reuse_pmcids:
reuse_pmids = pubmedcentral.pmcids_to_pmids(reuse_pmcid)
reuse_authors = get_authors_and_submittors_from_accession(reuse_pmids)
submit_affiliation = affiliation.institution(submit_pmids) if submit_pmids else []
reuse_affiliation = affiliation.institution(reuse_pmids)
intersect = get_author_intersect_submit_reuse(submit_authors, reuse_authors)
journal = pubmed.journal(reuse_pmids)
year = pubmed.year_published(reuse_pmids)
medline_status = pubmed.medline_status(reuse_pmids)
metaanal = pubmed.filter_pmids(reuse_pmids, metaquery)
biolink_filter = pubmedcentral.filter_pmcids([reuse_pmcid], '(geo OR omnibus) AND microarray AND "gene expression" AND accession NOT (databases OR user OR users OR (public AND accessed) OR (downloaded AND published))')
basic_filter = pubmedcentral.filter_pmcids([reuse_pmcid], '"gene expression omnibus" AND (submitted OR deposited)')
mesh_filters = [term for term in meshes if pubmed.filter_pmids(reuse_pmids, term)]
word_filters = [term for term in words if pubmedcentral.filter_pmcids([reuse_pmcid], term + "[text]")]
response_dict[(id_type+stripped_accession, reuse_pmcid)] = (id_type+stripped_accession, submit_pmids, reuse_pmcid, reuse_pmids, submit_authors, reuse_authors, submit_affiliation, reuse_affiliation, intersect, journal, year, medline_status, metaanal, biolink_filter, basic_filter, mesh_filters, word_filters)
print response_dict[(id_type+stripped_accession, reuse_pmcid)]
print id_counter, "of", num_ids, ":", stripped_accession, "--", (submit_pmids), "; ", len(pmc_reuse_pmcids)
return(response_dict)
def authors_in_common_from_pmids():
pmids = ["20349403", "18998887", "18767901"]
response = authors_in_common_from_pmids(pmids)
assert_equals(response, ["Piwowar"])
 
def multi_intersection(xs):
inter = reduce(set.intersection, [set(x) for x in xs])
return list(inter)
def authors_in_common_from_pmids(pmids):
last_names_list = []
for pmid in pmids:
authors = pubmed.authors([pmid])
authors_list = authors[0].split(";")
last_names = [author.split(" ")[0] for author in authors_list]
last_names_list.append(last_names)
authors_intersection = multi_intersection(last_names_list)
return(authors_intersection)
def get_from_query_gds_in_pmc_fulltext_dict(id_type, pmc_query, geo_year=None):
ids = geo.get_ids_by_year(id_type, geo_year)
(response_dict) = get_dict_submit_reuse_of_accession_in_pmc_fulltext(id_type, ids, pmc_query)
return(response_dict)
 
 
def print_accession_pmcids(prefix, accession_dict):
for accession in accession_dict:
pmcid_list = accession_dict[accession]
if pmcid_list:
for pmcid in pmcid_list:
print "%s\t%s%s\t%s" %(prefix, prefix, accession, pmcid)
else:
print "%s\t%s%s\t%s" %(prefix, prefix, accession, "")
 
#print_accession_pmcids("GDS", gds_dict)
#print_accession_pmcids("GSE", gse_dict)
 
def test_estimate_pmc_coverage():
response = estimate_pmc_coverage("arrayexpress[title]")
assert_equals(response, (6, 14, 0.42857142857142855))
 
response = estimate_pmc_coverage('"gene expression profiling"[mesh]')
assert_equals(response, (11038, 47384, 0.23294783049130507))
 
def test_estimate_pmc_coverage_given_years():
response = estimate_pmc_coverage('"gene expression profiling"[mesh]', "2007", "2009")
assert_equals(response, (6311, 21569, 0.29259585516250175))
def estimate_pmc_coverage(query, start_year="1800", end_year="3000"):
pubmed_query = query + ' AND ("' + start_year + '"[pdat] : "' + end_year + '"[pdat])'
pubmed_ids = pubmed.search(pubmed_query)
num_pubmed = len(pubmed_ids)
 
pmc_query = query + ' AND ("' + start_year + '"[PubDate] : "' + end_year + '"[PubDate])'
pmc_ids = pubmedcentral.search(pmc_query)
num_pmc = len(pmc_ids)
ratio = num_pmc / (num_pubmed + 0.0)
return(num_pmc, num_pubmed, ratio)
 
def run_stats():
if False:
(num_pmc, num_pubmed, ratio) = estimate_pmc_coverage('"gene expression profiling"[mesh]', "2007", "2009")
 
geo_year = "2007"
id_types = ["GDS", "GSE"]
response_dict = {}
for id_type in id_types:
response_dict[(id_type, geo_year)] = get_from_query_gds_in_pmc_fulltext_dict(id_type, base_query_reuse, geo_year)
pkl_file = open("scienceplot/results/" + id_type + "_dict" + geo_year + ".pkl", "wb")
pickle.dump(response_dict[(id_type, geo_year)], pkl_file)
pkl_file.close()
fh = open("scienceplot/results/" + id_type + geo_year + ".csv", "w")
header = "id_type+stripped_accession, submit_pmids, reuse_pmcid, reuse_pmids, submit_authors, reuse_authors, submit_affiliation, reuse_affiliation, intersect, journal, year, medline_status, metaanal, biolink_filter, basic_filter, mesh_filters, word_filters"
fh.write(header + "\n")
dataset.csv_write_to_file(fh, response_dict[(id_type, geo_year)].values())
fh.close()
 
return(response_dict)

Please sign in to comment on this gist.

Something went wrong with that request. Please try again.