From eb05234037c6cb165e548a43859b77f9d5421189 Mon Sep 17 00:00:00 2001
From: Bryan Newbold <bnewbold@robocracy.org>
Date: Wed, 12 Sep 2018 11:06:57 -0700
Subject: extid map generation scripts+README

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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
+
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