AUTHOR INDEX — Infant Gut Shotgun-Metagenome Catalog

Deterministic build (no LLM) of an author/organisation index for all 9,579 screened studies (389 included, 52 human_review, 9,138 excluded). Every name comes from a fetched record (Europe PMC authorString, NCBI BioProject XML) or an existing catalog table; nothing was typed from memory. Wall time ≈ 30.7 min; 495 HTTP calls (NCBI 199, EBI 296), all cached in harvest_cache/.

1. Sources

Studies with authors from both linked_paper and bioproject_publication: 78.

2. Coverage by catalog status

v1.2.1 correction: 9,513 of 9,579 studies have at least one displayable organisation (66 have only a submission id / username / placeholder: 3 included, 63 excluded). The original statement below is superseded — Every study has at least one organisation (submitter centre or BioProject owner), so no study is without any searchable entity. 103 included studies (26%) have no author at all — their BioProject carries no publication, no paper was linked, and ENA has no PubMed xref. These are the priority for a future literature back-link pass (title/accession search in Europe PMC full text), which is outside this deterministic track.

3. Counts

• Author rows: 28,367 (dedup on study + display name + PMID); distinct author keys 10,965, of which 36 are consortium/group names (is_group=True, e.g. "RESONANCE Consortium").
• Distinct papers behind the rows: 1,367; max authors on one paper 89; 120 (study, paper) pairs have ≥25 authors.
• Organisation rows: 18,888 over 9,886 distinct raw keys; v1.2.1 correction: 6,143 rows / 6,079 keys are not organisations (SRA submission ids SUB… 6,033, single lowercase usernames 93, placeholders 9, e-mail addresses 8); 3,747 displayable organisation keys remain after preferring the BioProject Organization over the ENA centre for PRJNA studies (organisations.parquet columns not_org_reason, is_organisation, display_eligible).
• Most-connected authors (studies): | author | studies | |---|---| | Ventura M | 244 | | Lugli GA | 244 | | Mancabelli L | 243 | | Turroni F | 243 | | Tarracchini C | 241 | | Milani C | 238 | | van Sinderen D | 215 | | Fontana F | 212 | | Alessandri G | 210 | | Viappiani A | 188 | (the Parma/Ventura group registers one BioProject per isolate genome — 240+ excluded single-genome projects.)

4. PMIDs / papers newly resolved

new_papers_from_bioproject.parquet: 881 Europe PMC records not present in papers_raw ({'bioproject_publication': 805, 'linked_paper': 75, 'ena_study_xref': 1}; sources {'MED': 848, 'PPR': 32, 'PMC': 1}), with authorString, title, journal, year, DOI, abstract and the study accessions they are registered for. Of the 955 BioProject publication refs only 55 were already in papers_raw — BioProject-registered publications are largely orthogonal to the literature-harvest channel (most belong to excluded, non-infant projects).

5. Failures / rate limits

• NCBI: 96 esearch + 96 efetch calls, 1 efetch batch failed on first pass (100 records) and was refetched successfully; no HTTP 429. 4 accessions are not in NCBI BioProject at all: ['PRJEB79367', 'PRJEB90452', 'PRJNA1163982', 'PRJNA448876'] (2 recent PRJEB not yet mirrored, 2 PRJNA suppressed/withdrawn) — organisation only from ENA.
• Europe PMC: 0 failed batches; 3 PMIDs registered on BioProjects (38298144, 34145447, 35559516) are absent from Europe PMC — NCBI structured-citation names used where present.
• 17 of 955 publication refs could not be resolved in Europe PMC (mostly MDPI Sci, Frontiers marine/plant, SSRN, Aquaculture Reports DOIs not indexed) — 15 used NCBI structured-citation authors, 2 have no authors.

6. Caveats

• String names only, no ORCID. Author identity = author_key = transliterated (ø→o, æ→ae, ß→ss, ł→l, đ→d, İ→i, Ð→d, Þ→th; v1.2.1) then ASCII-folded lowercase "surname initials" (e.g. van sinderen d). Homonyms are NOT disambiguated: 1,075 of 8,181 surnames (recomputed from authors.parquet v2, v1.2.1) occur with more than one initials set, and common East-Asian surname+initial combinations (e.g. wang y, zhang j) certainly merge distinct people. The site should present the index as "possible matches" and let the researcher confirm by study.
• 26 keys have >1 display spelling (accent/hyphen variants collapsed by the folding); the most frequent spelling is shown.
• Europe PMC authorString truncation ("et al."): 0 affected in papers_raw and 0 in the new records — both were fetched with resultType=core, which returns the full string (max observed 89 authors). The lite-endpoint truncation caveat therefore does not apply to this build.
• Initials parsing: 9 non-group rows have no initials (single-token names such as Indonesian mononyms); position/is_first/is_last follow the Europe PMC author order; NCBI structured citations may be incomplete or ordered differently.
• linked_paper rows inherit the link relation (own_data / reused_public_data / unsure / cited_only) and contested status — a "reused_public_data" author did not necessarily generate the deposit. bioproject_publication rows come from the submitter's own registration and are the strongest ownership signal.
• Organisation names are as deposited (case and abbreviation variants, e.g. "UNIVERSITY OF SOUTH FLORIDA"); only ASCII-folded lowercase keys are used for grouping — no institution normalisation.

7. Deliverables

• authors.parquet — 28,367 rows: study_accession, author_display, author_surname, author_initials, author_key, is_group, source, pmid, pmcid, doi, paper_title, pub_year, position, n_authors, is_first, is_last, paper_relation, link_method, catalog_status, reason_code, study_title.
• organisations.parquet — 18,888 rows: study_accession, organisation, abbr, role, org_type, source, organisation_key, catalog_status.
• authors_index.json (6.3 MB, single file, <15 MB) — {author_key: {display, group, n_studies, studies:[{acc, status, reason_code, title_short, pmid, src(L/B/E), pos}]}}.
• organisations_index.json (1.4 MB) — same shape for organisations.
• study_authors_summary.csv — one row per study: n_authors, first_author, last_author, n_papers, n_linked_papers, n_bioproject_pubs, organisations, has_any_author, has_any_organisation, in_ncbi_bioproject.
• new_papers_from_bioproject.parquet, bioproject_records.parquet (9,575 records: accession, title, publications JSON, publication_pmids, grants, external_links, organizations JSON, submitter_owner, center_id, submission dates), ena_study_xrefs.csv, harvest_bioproject_authors.py, bioproject_fetch_log.json.