From a00eaaefa5d67bb1a0bb58905a63fe59456c3932 Mon Sep 17 00:00:00 2001
From: Ivan Pavlovich <ivan.pavlovic@hes-so.ch>
Date: Fri, 14 Mar 2025 02:11:40 +0100
Subject: [PATCH] Calculated number of published pubmed articles for ncds with
keywords
---
dataSources/PubMed/data_num_locale.py | 295 +++++---
.../PubMed/doc/locale_articles_count.json | 632 ++++++++++++++++++
2 files changed, 847 insertions(+), 80 deletions(-)
create mode 100644 dataSources/PubMed/doc/locale_articles_count.json
diff --git a/dataSources/PubMed/data_num_locale.py b/dataSources/PubMed/data_num_locale.py
index 618b4d196..35aad2e52 100644
--- a/dataSources/PubMed/data_num_locale.py
+++ b/dataSources/PubMed/data_num_locale.py
@@ -8,10 +8,34 @@ sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "../../"
from variables.pubmed import NCDS_MESH_TERM, KEYWORDS_MESH_TERM, KEYWORDS_MESH_SUBHEADING, KEYWORDS_MESH_SITE_PROPOSITION, KEYWORDS_MESH_PROPOSITION
+CATEGORIES = [
+ "KEYWORDS",
+ "SUBHEADINGS",
+ "SITE PROPOSITION",
+ "PROPOSITION"
+]
+
+INTERVALS = [
+ "day",
+ "week",
+ "month"
+]
+
DATA_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), "./data"))
file_path = f"{DATA_DIR}/save_3_years.json"
+def lower_keywords(mesh_terms):
+ res = []
+
+ for _, mesh_term in mesh_terms.items():
+ if isinstance(mesh_term, list):
+ res.append([part.lower() for part in mesh_term])
+ else:
+ res.append(mesh_term.lower())
+
+ return res
+
def get_date_indices(date, start_date):
delta_days = (date - start_date).days
day_index = delta_days
@@ -37,26 +61,149 @@ def match_mesh_terms(article_mesh_terms, ncd, keyword):
else:
return False
+def init_index(category, counts, ncd, article_date):
+ start_date = datetime(2022, 1, 1)
+ day_index, week_index, month_index = get_date_indices(article_date, start_date)
+
+ if day_index not in counts[ncd][category]["day"]:
+ counts[ncd][category]["day"][day_index] = []
+
+ if week_index not in counts[ncd][category]["week"]:
+ counts[ncd][category]["week"][week_index] = []
+
+ if month_index not in counts[ncd][category]["month"]:
+ counts[ncd][category]["month"][month_index] = []
+
+def add_article(article, category, counts, ncd, article_date):
+ start_date = datetime(2022, 1, 1)
+ day_index, week_index, month_index = get_date_indices(article_date, start_date)
+
+ if article["PMID"] not in counts[ncd][category]["day"][day_index]:
+ counts[ncd][category]["day"][day_index].append(article["PMID"])
+
+ if article["PMID"] not in counts[ncd][category]["week"][week_index]:
+ counts[ncd][category]["week"][week_index].append(article["PMID"])
+
+ if article["PMID"] not in counts[ncd][category]["month"][month_index]:
+ counts[ncd][category]["month"][month_index].append(article["PMID"])
+
+
with open(file_path, "r", encoding="utf-8") as file:
data = json.load(file)
print(len(data))
ncds_mesh_terms = [mesh_term.lower() for ncd, mesh_term in NCDS_MESH_TERM.items()]
-keywords_mesh_terms = [mesh_term.lower() for keyword, mesh_term in KEYWORDS_MESH_TERM.items()]
-keywords_subheading_mesh_terms = keywords_mesh_terms + [mesh_term.lower() for mesh_term in KEYWORDS_MESH_SUBHEADING]
-keywords_site_proposition_mesh_terms = keywords_subheading_mesh_terms + [mesh_term.lower() for mesh_term in KEYWORDS_MESH_SITE_PROPOSITION]
-keywords_proposition_mesh_terms = keywords_site_proposition_mesh_terms + [mesh_term.lower() for mesh_term in KEYWORDS_MESH_PROPOSITION]
+keywords_mesh_terms = lower_keywords(KEYWORDS_MESH_TERM)
+keywords_subheading_mesh_terms = lower_keywords(KEYWORDS_MESH_SUBHEADING)
+keywords_site_proposition_mesh_terms = lower_keywords(KEYWORDS_MESH_SITE_PROPOSITION)
+keywords_proposition_mesh_terms = lower_keywords(KEYWORDS_MESH_PROPOSITION)
counts = {}
+
+for ncd in ncds_mesh_terms:
+ counts[ncd] = {
+ "KEYWORDS" : {
+ "day": {},
+ "week": {},
+ "month": {}
+ },
+ "SUBHEADINGS" : {
+ "day": {},
+ "week": {},
+ "month": {}
+ },
+ "SITE PROPOSITION" : {
+ "day": {},
+ "week": {},
+ "month": {}
+ },
+ "PROPOSITION" : {
+ "day": {},
+ "week": {},
+ "month": {}
+ },
+ }
+
+ start_date = datetime(2022, 1, 1)
+ end_date = datetime(2024, 12, 31)
+ current_date = start_date
+
+ while(current_date < end_date):
+ day_index, week_index, month_index = get_date_indices(current_date, start_date)
+
+ for category in CATEGORIES:
+ counts[ncd][category]["day"][day_index] = []
+ counts[ncd][category]["week"][week_index] = []
+ counts[ncd][category]["month"][month_index] = []
+
+ current_date += timedelta(days=1)
+
+counts["ALL"] = {
+ "KEYWORDS" : {
+ "day": {},
+ "week": {},
+ "month": {}
+ },
+ "SUBHEADINGS" : {
+ "day": {},
+ "week": {},
+ "month": {}
+ },
+ "SITE PROPOSITION" : {
+ "day": {},
+ "week": {},
+ "month": {}
+ },
+ "PROPOSITION" : {
+ "day": {},
+ "week": {},
+ "month": {}
+ },
+}
+
start_date = datetime(2022, 1, 1)
+end_date = datetime(2024, 12, 31)
+current_date = start_date
+
+while(current_date < end_date):
+ day_index, week_index, month_index = get_date_indices(current_date, start_date)
+
+ for category in CATEGORIES:
+ counts["ALL"][category]["day"][day_index] = []
+ counts["ALL"][category]["week"][week_index] = []
+ counts["ALL"][category]["month"][month_index] = []
+
+ current_date += timedelta(days=1)
for article in data:
mesh_terms = [mesh_term.lower() for mesh_term in article["MeshTerms"]]
+ article_date = datetime(int(article["Date"]["Year"]), int(article["Date"]["Month"]), int(article["Date"]["Day"]))
if "ALL" not in counts:
- counts["ALL"] = {}
+ counts["ALL"] = {
+ "KEYWORDS" : {
+ "day": {},
+ "week": {},
+ "month": {}
+ },
+ "SUBHEADINGS" : {
+ "day": {},
+ "week": {},
+ "month": {}
+ },
+ "SITE PROPOSITION" : {
+ "day": {},
+ "week": {},
+ "month": {}
+ },
+ "PROPOSITION" : {
+ "day": {},
+ "week": {},
+ "month": {}
+ },
+ }
for ncd in ncds_mesh_terms:
if ncd not in counts:
@@ -85,104 +232,92 @@ for article in data:
for keyword in keywords_mesh_terms:
- if match_mesh_terms(mesh_terms, ncd, mesh_terms):
+ if match_mesh_terms(mesh_terms, ncd, keyword):
+ init_index("KEYWORDS", counts, ncd, article_date)
+ init_index("SUBHEADINGS", counts, ncd, article_date)
+ init_index("SITE PROPOSITION", counts, ncd, article_date)
+ init_index("PROPOSITION", counts, ncd, article_date)
- article_date = datetime(int(article["Date"]["Year"]), int(article["Date"]["Month"]), int(article["Date"]["Day"]))
+ add_article(article, "KEYWORDS", counts, ncd, article_date)
+ add_article(article, "SUBHEADINGS", counts, ncd, article_date)
+ add_article(article, "SITE PROPOSITION", counts, ncd, article_date)
+ add_article(article, "PROPOSITION", counts, ncd, article_date)
- day_index, week_index, month_index = get_date_indices(article_date, start_date)
+ init_index("KEYWORDS", counts, "ALL", article_date)
+ init_index("SUBHEADINGS", counts, "ALL", article_date)
+ init_index("SITE PROPOSITION", counts, "ALL", article_date)
+ init_index("PROPOSITION", counts, "ALL", article_date)
- if day_index not in counts[ncd]["KEYWORDS"]["day"]:
- counts[ncd]["KEYWORDS"]["day"][day_index] = []
-
- if week_index not in counts[ncd]["KEYWORDS"]["week"]:
- counts[ncd]["KEYWORDS"]["week"][week_index] = []
-
- if month_index not in counts[ncd]["KEYWORDS"]["month"]:
- counts[ncd]["KEYWORDS"]["month"][month_index] = []
-
- if article["PMID"] not in counts[ncd]["KEYWORDS"]["day"][day_index]:
- counts[ncd]["KEYWORDS"]["day"][day_index].append(article["PMID"])
-
- if article["PMID"] not in counts[ncd]["KEYWORDS"]["week"][week_index]:
- counts[ncd]["KEYWORDS"]["week"][week_index].append(article["PMID"])
-
- if article["PMID"] not in counts[ncd]["KEYWORDS"]["month"][month_index]:
- counts[ncd]["KEYWORDS"]["month"][month_index].append(article["PMID"])
+ add_article(article, "KEYWORDS", counts, "ALL", article_date)
+ add_article(article, "SUBHEADINGS", counts, "ALL", article_date)
+ add_article(article, "SITE PROPOSITION", counts, "ALL", article_date)
+ add_article(article, "PROPOSITION", counts, "ALL", article_date)
for keyword in keywords_subheading_mesh_terms:
- if match_mesh_terms(mesh_terms, ncd, mesh_terms):
-
- article_date = datetime(int(article["Date"]["Year"]), int(article["Date"]["Month"]), int(article["Date"]["Day"]))
-
- day_index, week_index, month_index = get_date_indices(article_date, start_date)
-
- if day_index not in counts[ncd]["SUBHEADINGS"]["day"]:
- counts[ncd]["SUBHEADINGS"]["day"][day_index] = []
-
- if week_index not in counts[ncd]["SUBHEADINGS"]["week"]:
- counts[ncd]["SUBHEADINGS"]["week"][week_index] = []
+ if match_mesh_terms(mesh_terms, ncd, keyword):
+ init_index("SUBHEADINGS", counts, ncd, article_date)
+ init_index("SITE PROPOSITION", counts, ncd, article_date)
+ init_index("PROPOSITION", counts, ncd, article_date)
- if month_index not in counts[ncd]["SUBHEADINGS"]["month"]:
- counts[ncd]["SUBHEADINGS"]["month"][month_index] = []
+ add_article(article, "SUBHEADINGS", counts, ncd, article_date)
+ add_article(article, "SITE PROPOSITION", counts, ncd, article_date)
+ add_article(article, "PROPOSITION", counts, ncd, article_date)
- if article["PMID"] not in counts[ncd]["SUBHEADINGS"]["day"][day_index]:
- counts[ncd]["SUBHEADINGS"]["day"][day_index].append(article["PMID"])
+ init_index("SUBHEADINGS", counts, "ALL", article_date)
+ init_index("SITE PROPOSITION", counts, "ALL", article_date)
+ init_index("PROPOSITION", counts, "ALL", article_date)
- if article["PMID"] not in counts[ncd]["SUBHEADINGS"]["week"][week_index]:
- counts[ncd]["SUBHEADINGS"]["week"][week_index].append(article["PMID"])
-
- if article["PMID"] not in counts[ncd]["SUBHEADINGS"]["month"][month_index]:
- counts[ncd]["SUBHEADINGS"]["month"][month_index].append(article["PMID"])
+ add_article(article, "SUBHEADINGS", counts, "ALL", article_date)
+ add_article(article, "SITE PROPOSITION", counts, "ALL", article_date)
+ add_article(article, "PROPOSITION", counts, "ALL", article_date)
for keyword in keywords_site_proposition_mesh_terms:
- if match_mesh_terms(mesh_terms, ncd, mesh_terms):
-
- article_date = datetime(int(article["Date"]["Year"]), int(article["Date"]["Month"]), int(article["Date"]["Day"]))
-
- day_index, week_index, month_index = get_date_indices(article_date, start_date)
-
- if day_index not in counts[ncd]["SITE PROPOSITION"]["day"]:
- counts[ncd]["SITE PROPOSITION"]["day"][day_index] = []
+ if match_mesh_terms(mesh_terms, ncd, keyword):
+ init_index("SITE PROPOSITION", counts, ncd, article_date)
+ init_index("PROPOSITION", counts, ncd, article_date)
- if week_index not in counts[ncd]["SITE PROPOSITION"]["week"]:
- counts[ncd]["SITE PROPOSITION"]["week"][week_index] = []
+ add_article(article, "SITE PROPOSITION", counts, ncd, article_date)
+ add_article(article, "PROPOSITION", counts, ncd, article_date)
- if month_index not in counts[ncd]["SITE PROPOSITION"]["month"]:
- counts[ncd]["SITE PROPOSITION"]["month"][month_index] = []
+ init_index("SITE PROPOSITION", counts, "ALL", article_date)
+ init_index("PROPOSITION", counts, "ALL", article_date)
- if article["PMID"] not in counts[ncd]["SITE PROPOSITION"]["day"][day_index]:
- counts[ncd]["SITE PROPOSITION"]["day"][day_index].append(article["PMID"])
-
- if article["PMID"] not in counts[ncd]["SITE PROPOSITION"]["week"][week_index]:
- counts[ncd]["SITE PROPOSITION"]["week"][week_index].append(article["PMID"])
-
- if article["PMID"] not in counts[ncd]["SITE PROPOSITION"]["month"][month_index]:
- counts[ncd]["SITE PROPOSITION"]["month"][month_index].append(article["PMID"])
+ add_article(article, "SITE PROPOSITION", counts, "ALL", article_date)
+ add_article(article, "PROPOSITION", counts, "ALL", article_date)
for keyword in keywords_proposition_mesh_terms:
- if match_mesh_terms(mesh_terms, ncd, mesh_terms):
+ if match_mesh_terms(mesh_terms, ncd, keyword):
+ init_index("PROPOSITION", counts, ncd, article_date)
- article_date = datetime(int(article["Date"]["Year"]), int(article["Date"]["Month"]), int(article["Date"]["Day"]))
+ add_article(article, "PROPOSITION", counts, ncd, article_date)
- day_index, week_index, month_index = get_date_indices(article_date, start_date)
+ init_index("PROPOSITION", counts, "ALL", article_date)
- if day_index not in counts[ncd]["PROPOSITION"]["day"]:
- counts[ncd]["PROPOSITION"]["day"][day_index] = []
+ add_article(article, "PROPOSITION", counts, "ALL", article_date)
- if week_index not in counts[ncd]["PROPOSITION"]["week"]:
- counts[ncd]["PROPOSITION"]["week"][week_index] = []
+for ncd in ncds_mesh_terms:
+ for category in CATEGORIES:
+ for interval in INTERVALS:
+ counts[ncd][category][interval] = [len(tmp) for key, tmp in counts[ncd][category][interval].items()]
- if month_index not in counts[ncd]["PROPOSITION"]["month"]:
- counts[ncd]["PROPOSITION"]["month"][month_index] = []
+ counts[ncd][category][interval] = {
+ "min": min(counts[ncd][category][interval]),
+ "max": max(counts[ncd][category][interval]),
+ "mean": statistics.mean(counts[ncd][category][interval])
+ }
- if article["PMID"] not in counts[ncd]["PROPOSITION"]["day"][day_index]:
- counts[ncd]["PROPOSITION"]["day"][day_index].append(article["PMID"])
+for category in CATEGORIES:
+ for interval in INTERVALS:
+ counts["ALL"][category][interval] = [len(tmp) for key, tmp in counts["ALL"][category][interval].items()]
- if article["PMID"] not in counts[ncd]["PROPOSITION"]["week"][week_index]:
- counts[ncd]["PROPOSITION"]["week"][week_index].append(article["PMID"])
+ counts["ALL"][category][interval] = {
+ "min": min(counts["ALL"][category][interval]),
+ "max": max(counts["ALL"][category][interval]),
+ "mean": statistics.mean(counts["ALL"][category][interval])
+ }
- if article["PMID"] not in counts[ncd]["PROPOSITION"]["month"][month_index]:
- counts[ncd]["PROPOSITION"]["month"][month_index].append(article["PMID"])
+with open(f"{DATA_DIR}/locale_articles_count.json", "w") as json_file:
+ json.dump(counts, json_file, indent=4)
\ No newline at end of file
diff --git a/dataSources/PubMed/doc/locale_articles_count.json b/dataSources/PubMed/doc/locale_articles_count.json
new file mode 100644
index 000000000..cb2b3056f
--- /dev/null
+++ b/dataSources/PubMed/doc/locale_articles_count.json
@@ -0,0 +1,632 @@
+{
+ "noncommunicable diseases": {
+ "KEYWORDS": {
+ "day": {
+ "min": 0,
+ "max": 3,
+ "mean": 0.20639269406392693
+ },
+ "week": {
+ "min": 0,
+ "max": 6,
+ "mean": 1.4394904458598725
+ },
+ "month": {
+ "min": 2,
+ "max": 12,
+ "mean": 6.277777777777778
+ }
+ },
+ "SUBHEADINGS": {
+ "day": {
+ "min": 0,
+ "max": 3,
+ "mean": 0.20639269406392693
+ },
+ "week": {
+ "min": 0,
+ "max": 6,
+ "mean": 1.4394904458598725
+ },
+ "month": {
+ "min": 2,
+ "max": 12,
+ "mean": 6.277777777777778
+ }
+ },
+ "SITE PROPOSITION": {
+ "day": {
+ "min": 0,
+ "max": 3,
+ "mean": 0.2328767123287671
+ },
+ "week": {
+ "min": 0,
+ "max": 6,
+ "mean": 1.624203821656051
+ },
+ "month": {
+ "min": 2,
+ "max": 14,
+ "mean": 7.083333333333333
+ }
+ },
+ "PROPOSITION": {
+ "day": {
+ "min": 0,
+ "max": 4,
+ "mean": 0.34885844748858447
+ },
+ "week": {
+ "min": 0,
+ "max": 8,
+ "mean": 2.43312101910828
+ },
+ "month": {
+ "min": 4,
+ "max": 17,
+ "mean": 10.61111111111111
+ }
+ }
+ },
+ "diabetes mellitus": {
+ "KEYWORDS": {
+ "day": {
+ "min": 0,
+ "max": 5,
+ "mean": 0.7497725204731575
+ },
+ "week": {
+ "min": 1,
+ "max": 11,
+ "mean": 5.248407643312102
+ },
+ "month": {
+ "min": 3,
+ "max": 31,
+ "mean": 22.27027027027027
+ }
+ },
+ "SUBHEADINGS": {
+ "day": {
+ "min": 0,
+ "max": 5,
+ "mean": 0.7497725204731575
+ },
+ "week": {
+ "min": 1,
+ "max": 11,
+ "mean": 5.248407643312102
+ },
+ "month": {
+ "min": 3,
+ "max": 31,
+ "mean": 22.27027027027027
+ }
+ },
+ "SITE PROPOSITION": {
+ "day": {
+ "min": 0,
+ "max": 8,
+ "mean": 1.0454959053685169
+ },
+ "week": {
+ "min": 2,
+ "max": 15,
+ "mean": 7.318471337579618
+ },
+ "month": {
+ "min": 3,
+ "max": 44,
+ "mean": 31.054054054054053
+ }
+ },
+ "PROPOSITION": {
+ "day": {
+ "min": 0,
+ "max": 10,
+ "mean": 1.4249317561419472
+ },
+ "week": {
+ "min": 3,
+ "max": 20,
+ "mean": 9.97452229299363
+ },
+ "month": {
+ "min": 5,
+ "max": 57,
+ "mean": 42.32432432432432
+ }
+ }
+ },
+ "neoplasms": {
+ "KEYWORDS": {
+ "day": {
+ "min": 0,
+ "max": 16,
+ "mean": 2.692447679708826
+ },
+ "week": {
+ "min": 2,
+ "max": 33,
+ "mean": 18.727848101265824
+ },
+ "month": {
+ "min": 14,
+ "max": 101,
+ "mean": 79.97297297297297
+ }
+ },
+ "SUBHEADINGS": {
+ "day": {
+ "min": 0,
+ "max": 16,
+ "mean": 2.692447679708826
+ },
+ "week": {
+ "min": 2,
+ "max": 33,
+ "mean": 18.727848101265824
+ },
+ "month": {
+ "min": 14,
+ "max": 101,
+ "mean": 79.97297297297297
+ }
+ },
+ "SITE PROPOSITION": {
+ "day": {
+ "min": 0,
+ "max": 16,
+ "mean": 2.735213830755232
+ },
+ "week": {
+ "min": 2,
+ "max": 33,
+ "mean": 19.025316455696203
+ },
+ "month": {
+ "min": 14,
+ "max": 101,
+ "mean": 81.24324324324324
+ }
+ },
+ "PROPOSITION": {
+ "day": {
+ "min": 0,
+ "max": 21,
+ "mean": 3.5281818181818183
+ },
+ "week": {
+ "min": 2,
+ "max": 43,
+ "mean": 24.563291139240505
+ },
+ "month": {
+ "min": 17,
+ "max": 127,
+ "mean": 104.89189189189189
+ }
+ }
+ },
+ "respiratory tract diseases": {
+ "KEYWORDS": {
+ "day": {
+ "min": 0,
+ "max": 1,
+ "mean": 0.02281021897810219
+ },
+ "week": {
+ "min": 0,
+ "max": 2,
+ "mean": 0.15822784810126583
+ },
+ "month": {
+ "min": 0,
+ "max": 3,
+ "mean": 0.6756756756756757
+ }
+ },
+ "SUBHEADINGS": {
+ "day": {
+ "min": 0,
+ "max": 1,
+ "mean": 0.02281021897810219
+ },
+ "week": {
+ "min": 0,
+ "max": 2,
+ "mean": 0.15822784810126583
+ },
+ "month": {
+ "min": 0,
+ "max": 3,
+ "mean": 0.6756756756756757
+ }
+ },
+ "SITE PROPOSITION": {
+ "day": {
+ "min": 0,
+ "max": 1,
+ "mean": 0.02281021897810219
+ },
+ "week": {
+ "min": 0,
+ "max": 2,
+ "mean": 0.15822784810126583
+ },
+ "month": {
+ "min": 0,
+ "max": 3,
+ "mean": 0.6756756756756757
+ }
+ },
+ "PROPOSITION": {
+ "day": {
+ "min": 0,
+ "max": 1,
+ "mean": 0.0364963503649635
+ },
+ "week": {
+ "min": 0,
+ "max": 2,
+ "mean": 0.25316455696202533
+ },
+ "month": {
+ "min": 0,
+ "max": 3,
+ "mean": 1.0810810810810811
+ }
+ }
+ },
+ "cardiovascular diseases": {
+ "KEYWORDS": {
+ "day": {
+ "min": 0,
+ "max": 5,
+ "mean": 0.6584699453551912
+ },
+ "week": {
+ "min": 0,
+ "max": 13,
+ "mean": 4.575949367088608
+ },
+ "month": {
+ "min": 3,
+ "max": 40,
+ "mean": 19.54054054054054
+ }
+ },
+ "SUBHEADINGS": {
+ "day": {
+ "min": 0,
+ "max": 5,
+ "mean": 0.6584699453551912
+ },
+ "week": {
+ "min": 0,
+ "max": 13,
+ "mean": 4.575949367088608
+ },
+ "month": {
+ "min": 3,
+ "max": 40,
+ "mean": 19.54054054054054
+ }
+ },
+ "SITE PROPOSITION": {
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\ No newline at end of file
--
GitLab