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-rw-r--r--extra/extid_map/README.md109
-rwxr-xr-xextra/extid_map/load_core.py42
-rwxr-xr-xextra/extid_map/load_pmc.py47
-rwxr-xr-xextra/extid_map/load_wikidata.py43
4 files changed, 241 insertions, 0 deletions
diff --git a/extra/extid_map/README.md b/extra/extid_map/README.md
new file mode 100644
index 00000000..d972ae25
--- /dev/null
+++ b/extra/extid_map/README.md
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+
+Process for generating a sqlite3 database file mapping between:
+
+- DOI
+- Wikidata QID
+- CORE database id
+- PubMed Central id
+- PubMed id
+
+This fast/indexed local database file, which is about a gigabyte compressed, is
+useful for optimizing some fatcat 'release' entity imports and operations.
+
+There is an example database at <https://archive.org/details/ia_journal_pid_map_munge_20180908>
+
+## Data Sources
+
+EuropePMC mapping (more works than the USA PubMedCentral mapping)
+- <ftp://ftp.ebi.ac.uk/pub/databases/pmc/DOI/PMID_PMCID_DOI.csv.gz>
+- <https://archive.org/details/europepmc-id-map-2018-08-31>
+
+Wikicite data snapshot
+- <https://archive.org/details/wikicite-biblio-data-20180903>
+
+CORE dataset
+- <https://core.ac.uk/services#api>
+- <https://archive.org/download/core_oa_metadata_20180301>
+
+## Wikidata Extract
+
+Early query:
+
+ zcat wikidata-20180806-publications.ndjson.gz.crdownload | rg '"P356"' | jq '{qid: .id, doi: .claims.P356[0]}' -c | pv -l | head
+
+Polished:
+
+ zcat wikidata-20180903-publications.ndjson.gz | rg '"P356"' | jq '[(.claims.P356[0] | ascii_downcase), .id] | @tsv' -cr | pv -l > doi_wikidata.20180903.tsv
+
+ # 13.6M 0:26:13 [8.65k/s]
+
+Hrm, got this but seemed to continue:
+
+ jq: error (at <stdin>:455616): explode input must be a string
+
+## CORE Extract
+
+ xzcat core_json/*.json.xz | jq -rc 'select(.doi != null) | [(.doi | ascii_downcase), .coreId] | @tsv' | pv -l > doi_core.20180301.tsv
+
+ # bnewbold@bnewbold-dev$ wc -l doi_core.20180301.tsv
+ # 28210779 doi_core.20180301.tsv
+
+## PMCID/PMID
+
+In a nice CSV format, no extract needed.
+
+ bnewbold@bnewbold-dev$ zcat PMID_PMCID_DOI.csv.gz | rg doi.org | wc -l
+ 19441168
+
+## sqlite schema
+
+ CREATE TABLE ids (doi text not null, core int, pmid int, pmcid text, wikidata text);
+ CREATE UNIQUE INDEX ids_doi on ids (doi);
+
+Run CORE import first (largest mapping, thus fewest exception/update paths),
+then pubmed, then wikidata.
+
+## Run import
+
+ cat doi_core.20180301.tsv | ./load_core.py release_ids.db
+ => read 28210000, wrote 28210000
+ => overnight? but seemed to run fast
+
+ zcat doi_wikidata.20180903.tsv.gz | ./load_wikidata.py release_ids.db
+ => uhoh, seems very slow. lots of IOWAIT. switching to host with SSD
+ => wow, like 5-10x faster at least. sigh.
+ => ran in a few hours
+
+ zcat PMID_PMCID_DOI.csv.gz | ./load_pmc.py release_ids.db
+ => read 29692000, wrote 19441136
+
+
+ sqlite> select count(*) from ids;
+ 24831337
+
+ # only 2.3 million works have all IDs
+ sqlite> select count(*) from ids where wikidata not null and core not null and pmid not null;
+ 2314700
+
+ # almost (but not all) PubMedCentral items are PubMed items
+ sqlite> select count(*) from ids where pmid not null;
+ 19328761
+ sqlite> select count(*) from ids where pmcid not null;
+ 3739951
+ sqlite> select count(*) from ids where pmcid not null and pmid not null;
+ 3682486
+
+ # wikidata DOIs seem to mostly come from pmid mapping
+ sqlite> select count(*) from ids where wikidata not null;
+ 13608497
+ sqlite> select count(*) from ids where pmid not null and wikidata not null;
+ 13179156
+
+ # core IDs are more independent (?)
+ sqlite> select count(*) from ids where core not null;
+ 7903910
+ sqlite> select count(*) from ids where core not null and wikidata not null;
+ 2372369
+ sqlite> select count(*) from ids where core not null and pmid not null;
+ 2783344
+
diff --git a/extra/extid_map/load_core.py b/extra/extid_map/load_core.py
new file mode 100755
index 00000000..a6a09e8a
--- /dev/null
+++ b/extra/extid_map/load_core.py
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+#!/usr/bin/env python3
+"""
+Run like:
+
+ zcat CORE_FILE | ./load_core.py release_ids.db
+"""
+
+import sys
+import csv
+import sqlite3
+
+def run(db_path):
+ #db = sqlite3.connect("file:{}?mode=ro".format(db_path)
+ db = sqlite3.connect(db_path)
+ c = db.cursor()
+ count = 0
+ inserted = 0
+ for row in sys.stdin:
+ row = row.strip().split("\t")
+ if len(row) != 2:
+ continue
+ (doi, coreid) = row[:2]
+ if count % 1000 == 0:
+ print("read {}, wrote {}".format(count, inserted))
+ db.commit()
+ count = count + 1
+ coreid = int(coreid)
+ doi = doi.lower()
+ # UPSERTS were only added to sqlite3 in summer 2018 (not in xenial version)
+ try:
+ c.execute("""INSERT INTO ids (doi, core) VALUES (?, ?)""", (doi, coreid))
+ except sqlite3.IntegrityError:
+ c.execute("""UPDATE ids SET core = ? WHERE doi = ?""", (coreid, doi))
+ inserted = inserted + 1
+ db.commit()
+ db.close()
+
+if __name__=="__main__":
+ if len(sys.argv) != 2:
+ print("Need single argument: db_path")
+ sys.exit(-1)
+ run(sys.argv[1])
diff --git a/extra/extid_map/load_pmc.py b/extra/extid_map/load_pmc.py
new file mode 100755
index 00000000..5454541e
--- /dev/null
+++ b/extra/extid_map/load_pmc.py
@@ -0,0 +1,47 @@
+#!/usr/bin/env python3
+"""
+Run like:
+
+ zcat PMID_PMCID_DOI.csv.gz | ./load_pmc.py release_ids.db
+"""
+
+import sys
+import csv
+import sqlite3
+
+def run(db_path):
+ #db = sqlite3.connect("file:{}?mode=ro".format(db_path)
+ db = sqlite3.connect(db_path)
+ reader = csv.reader(sys.stdin)
+ c = db.cursor()
+ count = 0
+ inserted = 0
+ for row in reader:
+ (pmid, pmcid, doi) = row
+ if count % 1000 == 0:
+ print("read {}, wrote {}".format(count, inserted))
+ db.commit()
+ count = count + 1
+ if not doi.startswith("http"):
+ continue
+ doi = doi.replace("https://doi.org/", "").lower()
+ if pmcid == '':
+ pmcid = None
+ if pmid == '':
+ pmid = None
+ else:
+ pmid = int(pmid)
+ # UPSERTS were only added to sqlite3 in summer 2018 (not in xenial version)
+ try:
+ c.execute("""INSERT INTO ids (doi, pmid, pmcid) VALUES (?, ?, ?)""", (doi, pmid, pmcid))
+ except sqlite3.IntegrityError:
+ c.execute("""UPDATE ids SET pmid = ?, pmcid = ? WHERE doi = ?""", (pmid, pmcid, doi))
+ inserted = inserted + 1
+ db.commit()
+ db.close()
+
+if __name__=="__main__":
+ if len(sys.argv) != 2:
+ print("Need single argument: db_path")
+ sys.exit(-1)
+ run(sys.argv[1])
diff --git a/extra/extid_map/load_wikidata.py b/extra/extid_map/load_wikidata.py
new file mode 100755
index 00000000..8d29a58a
--- /dev/null
+++ b/extra/extid_map/load_wikidata.py
@@ -0,0 +1,43 @@
+#!/usr/bin/env python3
+"""
+Run like:
+
+ zcat doi_wikidata.20180903.tsv.gz | ./load_wikidata.py release_ids.db
+"""
+
+import sys
+import csv
+import sqlite3
+
+def run(db_path):
+ #db = sqlite3.connect("file:{}?mode=ro".format(db_path)
+ db = sqlite3.connect(db_path)
+ c = db.cursor()
+ count = 0
+ inserted = 0
+ for row in sys.stdin:
+ row = row.strip().split("\t")
+ if len(row) != 2:
+ continue
+ (doi, qid) = row[:2]
+ if count % 1000 == 0:
+ print("read {}, wrote {}".format(count, inserted))
+ db.commit()
+ count = count + 1
+ if not doi.startswith("10.") or not qid.startswith('Q'):
+ continue
+ doi = doi.lower()
+ # UPSERTS were only added to sqlite3 in summer 2018 (not in xenial version)
+ try:
+ c.execute("""INSERT INTO ids (doi, wikidata) VALUES (?, ?)""", (doi, qid))
+ except sqlite3.IntegrityError:
+ c.execute("""UPDATE ids SET wikidata = ? WHERE doi = ?""", (qid, doi))
+ inserted = inserted + 1
+ db.commit()
+ db.close()
+
+if __name__=="__main__":
+ if len(sys.argv) != 2:
+ print("Need single argument: db_path")
+ sys.exit(-1)
+ run(sys.argv[1])
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-26 03:15:35 +0000