Issues

• Trim trailing whitespace from article_title at export

  TranslatorSRI/pubmed2db#60 · Filter by author gaurav opened on Sep 28, 2026

• validate: efetch serves issue, abstract and DOI values the archival XML never had

  TranslatorSRI/pubmed2db#59 · Filter by author gaurav opened on Sep 28, 2026

• Report the corpus cutoff: the date of the last update file a build loaded

  TranslatorSRI/pubmed2db#57 · Filter by author gaurav opened on Sep 28, 2026

• Upstream's type_mesh_ids sorts publication types and drops their names

  TranslatorSRI/pubmed2db#56 · Filter by author gaurav opened on Sep 25, 2026 · Upstream

• Check whether serfile deltas predating the baseline should be skipped

  TranslatorSRI/pubmed2db#52 · Filter by author gaurav opened on Sep 4, 2026 · Not urgent

• Decide whether the serfile baseline year should roll over automatically

  TranslatorSRI/pubmed2db#51 · Filter by author gaurav opened on Sep 4, 2026 · Needed later

• Expose serfile's cancelled ISSNs as resolver aliases

  TranslatorSRI/pubmed2db#50 · Filter by author gaurav opened on Sep 4, 2026 · Needed soon

• Investigate process_catalog()'s duplicate records and download size before reporting upstream

  TranslatorSRI/pubmed2db#49 · Filter by author gaurav opened on Sep 4, 2026 · Upstream

• Consider dropping journal.abbreviation_iso, which duplicates abbreviation_medline

  TranslatorSRI/pubmed2db#48 · Filter by author gaurav opened on Sep 4, 2026 · Needed soon

• Add PubMed publication type

  TranslatorSRI/pubmed2db#46 · Filter by author gaurav opened on Aug 24, 2026 · pubmed2db v1.1

• Export per-version publication status (retracted/updated/latest) for Babel

  TranslatorSRI/pubmed2db#45 · Filter by author gaurav opened on Aug 21, 2026
  1

• Confirm DocumentMetadataAPI consumers accept a pub_month that carries a year

  TranslatorSRI/pubmed2db#43 · Filter by author gaurav opened on Aug 20, 2026
  2

• Re-baseline the JSON export's peak RSS and wall time after the COPY rewrite

  TranslatorSRI/pubmed2db#42 · Filter by author gaurav opened on Aug 20, 2026
  1

• Add a 06-parquet.sbatch once the Parquet export has been measured

  TranslatorSRI/pubmed2db#41 · Filter by author gaurav opened on Aug 20, 2026 · Not urgent

• Add ruff and rumdl to enforce style on this repo

  TranslatorSRI/pubmed2db#40 · Filter by author gaurav opened on Aug 20, 2026 · pubmed2db v1.2

• Tune PUBMED2DB_DUCKDB_MEMORY_LIMIT against a real corpus load

  TranslatorSRI/pubmed2db#37 · Filter by author gaurav opened on Aug 20, 2026 · pubmed2db v1.1
  1

• Read ELocationID DOIs as a fallback when ArticleIdList carries none

  TranslatorSRI/pubmed2db#35 · Filter by author gaurav opened on Aug 20, 2026
  1

• Report pubmed-downloader's ReferenceList-scope bugs upstream (or decide to keep the workarounds local)

  TranslatorSRI/pubmed2db#34 · Filter by author gaurav opened on Aug 20, 2026

• Settle the CURIE prefix for PMCIDs in the JSON export's identifiers

  TranslatorSRI/pubmed2db#33 · Filter by author gaurav opened on Aug 20, 2026

• Decide whether validate's journal fields should be able to fail

  TranslatorSRI/pubmed2db#31 · Filter by author gaurav opened on Aug 19, 2026

• Distinguish deleted from merged records in validate's deletion check

  TranslatorSRI/pubmed2db#30 · Filter by author gaurav opened on Aug 19, 2026

• Run the Parquet export at corpus scale and record its cost

  TranslatorSRI/pubmed2db#29 · Filter by author gaurav opened on Aug 18, 2026 · Not urgent

• Decide what to do with <PubmedBookArticle> records, which parse_file silently ignores

  TranslatorSRI/pubmed2db#27 · Filter by author gaurav opened on Aug 18, 2026

• Overlap parsing with insertion in load_files (~2s of every ~6s per file is idle)

  TranslatorSRI/pubmed2db#26 · Filter by author gaurav opened on Aug 18, 2026

• Stream the XML with iterparse: parse_file holds the whole DOM (~1.2 GiB/file)

  TranslatorSRI/pubmed2db#25 · Filter by author gaurav opened on Aug 18, 2026