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Diffstat (limited to 'proposals/2021-10-28_grobid_refs.md')
| -rw-r--r-- | proposals/2021-10-28_grobid_refs.md | 82 |
1 files changed, 72 insertions, 10 deletions
diff --git a/proposals/2021-10-28_grobid_refs.md b/proposals/2021-10-28_grobid_refs.md index 3a17af3..ff835d4 100644 --- a/proposals/2021-10-28_grobid_refs.md +++ b/proposals/2021-10-28_grobid_refs.md @@ -13,18 +13,61 @@ in Crossref, and include them in refcat. ## Schema and Semantics -Follows that of `grobid_tei_xml` version 0.1. +The output JSON/dict schema for parsed references follows that of +`grobid_tei_xml` version 0.1.x, for the `GrobidBiblio` field. The +`unstructured` field that was parsed is included in the output, though it may +not be byte-for-byte exact (see below). One notable change from the past (eg, +older GROBID-parsed references) is that author `name` is now `full_name`. New +fields include `editors` (same schema as `authors`), `book_title`, and +`series_title`. + +The overall output schema matches that of the `grobid_refs` SQL table: + + source: string, lower-case. eg 'crossref' + source_id: string, eg '10.1145/3366650.3366668' + source_ts: optional timestamp (full ISO datetime with timezone (eg, `Z` + suffix), which identifies version of upstream metadata + refs_json: JSONB, list of `GrobidBiblio` JSON objects + +References are re-processed on a per-article (or per-release) basis. All the +references for an article are handled as a batch and output as a batch. If +there are no upstream references, row with `ref_json` as empty list may be +returned. + +Not all upstream references get re-parsed, even if an 'unstructured' field is +available. If 'unstructured' is not available, no row is ever output. For +example, if a reference includes `unstructured` (raw citation string), but also +has structured metadata for authors, title, year, and journal name, we might +not re-parse the `unstructured` string. Whether to re-parse is evaulated on a +per-reference basis. This behavior may change over time. + +`unstructured` strings may be pre-processed before being submitted to GROBID. +This is because many sources have systemic encoding issues. GROBID itself may +also do some modification of the input citation string before returning it in +the output. This means the `unstructured` string is not a reliable way to map +between specific upstream references and parsed references. Instead, the `id` +field (str) of `GrobidBiblio` gets set to any upstream "key" or "index" +identifier used to track individual references. If there is only a numeric +index, the `id` is that number as a string. + +The `key` or `id` may need to be woven back in to the ref objects manually, +because GROBID `processCitationList` takes just a list of raw strings, with no +attached reference-level key or id. -Not all references are necessarily included for GROBID processing. They should -identified and mapped using the entire unstructured string. -When present, `key` or `id` is woven back in to the ref objects (GROBID -`processCitationList` doesn't ever see the keys). `index`, returned by -`grobid_tei_xml`, may not be accurate (because not all references were passed), -and may be removed (TBD). +## New SQL Table and View +We may want to do re-parsing of references from sources other than `crossref`, +so there is a generic `grobid_refs` table. But it is also common to fetch both +the crossref metadata and any re-parsed references together, so as a convience +there is a PostgreSQL view (virtual table) that includes both a crossref +metadata record and parsed citations, if available. If downstream code cares a +lot about having the refs and record be in sync, the `source_ts` field on +`grobid_refs` can be matched againt the `indexed` column of `crossref` (or the +`.indexed.date-time` JSON field in the record itself). -## New SQL Table and View +Remember that DOIs should always be lower-cased before querying, inserting, +comparing, etc. CREATE TABLE IF NOT EXISTS grobid_refs ( source TEXT NOT NULL CHECK (octet_length(source) >= 1), @@ -35,8 +78,7 @@ and may be removed (TBD). PRIMARY KEY(source, source_id) ); - CREATE OR REPLACE VIEW crossref_with_refs - doi, indexed, record, source_ts, refs_json AS + CREATE OR REPLACE VIEW crossref_with_refs (doi, indexed, record, source_ts, refs_json) AS SELECT crossref.doi as doi, crossref.indexed as indexed, @@ -61,3 +103,23 @@ locally on the machine with sandcrawler-db. Another tool will support taking large chunks of Crossref JSON (as lines), filter them, process with GROBID, and print JSON to stdout, in the `grobid_refs` JSON schema. + + +## Task Examples + +Command to process crossref records with refs tool: + + cat crossref_sample.json \ + | parallel -j5 --linebuffer --round-robin --pipe ./grobid_tool.py parse-crossref-refs - \ + | pv -l \ + > crossref_sample.parsed.json + + # => 10.0k 0:00:27 [ 368 /s] + +Load directly in to postgres (after tables have been created): + + cat crossref_sample.parsed.json \ + | jq -rc '[.source, .source_id, .source_ts, (.refs_json | tostring)] | @tsv' \ + | psql sandcrawler -c "COPY grobid_refs (source, source_id, source_ts, refs_json) FROM STDIN (DELIMITER E'\t');" + + # => COPY 9999 |