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authorBryan Newbold <bnewbold@robocracy.org>2018-09-12 11:06:57 -0700
committerBryan Newbold <bnewbold@robocracy.org>2018-09-12 11:06:57 -0700
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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
+