"""Generate the human-facing documentation bundle from live pipeline results.""" from __future__ import annotations from datetime import datetime, timezone from common import human_bytes WORKS_COLUMNS = [ ("work_id", "string", "OpenAlex work ID (short form, e.g. W2146512944). Primary key."), ("doi", "string", "Normalized DOI (lowercase, no https://doi.org/ prefix). Null if absent."), ("title", "string", "Work title. Rows with empty titles are removed during cleaning."), ("publication_date", "string", "ISO date (YYYY-MM-DD). Null when OpenAlex has no exact date."), ("publication_year", "int16", "Publication year (2015-2025)."), ("publication_month", "int8", "Month extracted from publication_date."), ("type", "string", "OpenAlex work type (article, review, book-chapter, ...)."), ("primary_topic_id", "string", "OpenAlex topic ID of the work's primary topic."), ("primary_topic_name", "string", "Display name of the primary topic."), ("primary_topic_score", "float32", "OpenAlex confidence score for the primary topic."), ("field_id", "string", "OpenAlex field ID (top-level discipline) of the primary topic."), ("field_name", "string", "Field name, e.g. Medicine, Neuroscience."), ("subfield_id", "string", "OpenAlex subfield ID of the primary topic."), ("subfield_name", "string", "Subfield name, e.g. Oncology, Cardiology."), ("domain_id", "string", "OpenAlex domain ID (Life Sciences=1, Health Sciences=4)."), ("domain_name", "string", "Domain name."), ("topic_ids", "list", "All OpenAlex topic IDs assigned to the work (max 3)."), ("topic_names", "list", "Names aligned positionally with topic_ids."), ("topic_count", "int16", "Number of topics on the work."), ("author_count", "int32", "Number of authorships."), ("author_names", "list", "Author display names in authorship order."), ("author_ids", "list", "OpenAlex author IDs aligned with author_names."), ("author_orcids", "list", "ORCIDs aligned with author_names (null where absent)."), ("institution_count", "int32", "Number of distinct institutions on the work."), ("institution_ids", "list", "Distinct OpenAlex institution IDs."), ("institution_names", "list", "Institution display names."), ("institution_countries", "list", "Distinct ISO-3166 alpha-2 codes of institutions."), ("country_codes", "list", "All countries involved (authors + institutions)."), ("country_count", "int16", "Number of distinct countries."), ("source_id", "string", "OpenAlex source (journal/venue) ID."), ("source_name", "string", "Source display name."), ("source_type", "string", "Source type (journal, conference, repository, ...)."), ("issn_l", "string", "Linking ISSN of the source."), ("issns", "list", "All ISSNs of the source."), ("publisher", "string", "Host organisation / publisher name."), ("cited_by_count", "int32", "OpenAlex citation count at retrieval time."), ("recent_citations_3y", "int32", "Citations accrued in the last 3 years (2023-2025)."), ("referenced_works_count", "int32", "Number of references (per OpenAlex)."), ("referenced_work_ids", "list", "OpenAlex IDs of referenced works (short form)."), ("is_oa", "bool", "Open-access flag."), ("oa_status", "string", "OA status: gold, green, hybrid, bronze, diamond, closed."), ("oa_url", "string", "Best OA location URL."), ("license", "string", "License string of the primary/best OA location (e.g. cc-by)."), ("license_id", "string", "License identifier where provided."), ("language", "string", "Language code of the work."), ("abstract", "string", "Abstract reconstructed from OpenAlex's inverted index (null if none)."), ("has_abstract", "bool", "Whether an abstract could be reconstructed."), ("is_retracted", "bool", "Retraction flag."), ("is_paratext", "bool", "Paratext flag (front matter, editorials) - excluded by default."), ("fwci", "float32", "Field-Weighted Citation Impact (OpenAlex supplied)."), ("openalex_citation_percentile", "float32", "OpenAlex-supplied normalized citation percentile."), ("created_date", "string", "Date the record was created in OpenAlex."), ("updated_date", "string", "Date the record was last updated in OpenAlex."), ("mesh_terms", "list", "MeSH descriptor/qualifier terms where OpenAlex supplies them."), ("keywords", "list", "OpenAlex keyword tags."), ("paper_age_years", "float32", "DERIVED: reference_year - publication_year."), ("citations_per_year", "float32", "DERIVED: cited_by_count / max(paper_age_years, 1)."), ("citation_velocity", "float32", "DERIVED: recent_citations_3y / 3."), ("international_collaboration", "bool", "DERIVED: country_count >= 2."), ("multi_institutional", "bool", "DERIVED: institution_count >= 2."), ("publication_recency_score", "float32", "DERIVED: exp(-paper_age_years / halflife)."), ("citation_percentile", "float32", "DERIVED: percentile of cited_by_count within publication_year x field."), ("high_impact_flag", "bool", "DERIVED: citation_percentile >= configured threshold (default 90)."), ("research_growth_score", "float32", "DERIVED: late/early publication ratio of the work's field."), ("topic_growth_score", "float32", "DERIVED: late/early publication ratio of the primary topic."), ("emerging_topic_flag", "bool", "DERIVED: primary topic is emerging (growth ratio >= threshold, sufficient volume)."), ] RELATION_COLUMNS = { "work_authors.parquet": [ ("work_id", "FK to works.work_id"), ("author_id", "OpenAlex author ID"), ("author_name", "author display name"), ("orcid", "ORCID if available"), ("author_position", "first / middle / last"), ("is_corresponding", "corresponding-author flag"), ("institution_ids", "institutions for this authorship"), ("country_codes", "countries for this authorship"), ], "work_institutions.parquet": [ ("work_id", "FK to works"), ("institution_id", "OpenAlex institution ID"), ("institution_name", "name"), ("country_code", "ISO alpha-2"), ("institution_type", "education / company / government / facility / other"), ], "work_topics.parquet": [ ("work_id", "FK to works"), ("topic_id", "OpenAlex topic ID"), ("topic_name", "topic name"), ("score", "relevance score"), ("is_primary", "primary-topic flag"), ("subfield_id", "subfield"), ("subfield_name", "subfield name"), ("field_id", "field"), ("field_name", "field name"), ("domain_id", "domain"), ("domain_name", "domain name"), ], "citation_edges.parquet": [ ("citing_work_id", "work that cites"), ("cited_work_id", "work that is cited"), ("cited_in_dataset", "always true: edges are restricted to pairs inside this dataset"), ], "authors.parquet": [ ("author_id", "PK"), ("author_name", "name"), ("orcid", "ORCID"), ("works_count", "works in dataset"), ("first_year", "earliest year"), ("last_year", "latest year"), ("total_citations", "sum of citations"), ("mean_citations", "mean citations per work"), ("institution_ids", "affiliations seen"), ("country_codes", "countries seen"), ("primary_field_id", "most frequent field"), ("primary_field_name", "field name"), ], "institutions.parquet": [ ("institution_id", "PK"), ("institution_name", "name"), ("country_code", "ISO alpha-2"), ("works_count", "works in dataset"), ("first_year", "earliest year"), ("last_year", "latest year"), ("total_citations", "sum of citations"), ("mean_citations", "mean citations"), ("primary_field_id", "most frequent field"), ("primary_field_name", "field name"), ], "topics.parquet": [ ("topic_id", "PK"), ("topic_name", "name"), ("subfield_id", "subfield"), ("subfield_name", "subfield name"), ("field_id", "field"), ("field_name", "field name"), ("domain_id", "domain"), ("domain_name", "domain name"), ("works_count", "works in dataset"), ("first_year", "earliest year"), ("last_year", "latest year"), ("total_citations", "sum of citations"), ("mean_citations", "mean citations"), ], "sources.parquet": [ ("source_id", "PK"), ("source_name", "venue name"), ("source_type", "journal/conference/..."), ("issn_l", "linking ISSN"), ("issns", "all ISSNs"), ("publisher", "publisher"), ("is_oa", "venue OA flag"), ("works_count", "works in dataset"), ("total_citations", "sum of citations"), ("mean_citations", "mean citations"), ], } ANALYTICS_COLUMNS = { "topic_year_counts.parquet": [("topic_id", ""), ("topic_name", ""), ("publication_year", ""), ("works_count", "")], "topic_growth.parquet": [("topic_id", ""), ("topic_name", ""), ("first_year", ""), ("last_year", ""), ("early_count", "sum in first half of range"), ("late_count", "sum in second half"), ("growth_ratio", "(late+1)/(early+1)"), ("cagr", "compound annual growth of averages"), ("trend_slope", "OLS slope of yearly counts"), ("emerging_topic_flag", "growth and volume threshold")], "country_year_counts.parquet": [("country_code", ""), ("publication_year", ""), ("works_count", "")], "country_collaboration.parquet": [("country_a", ""), ("country_b", ""), ("collaboration_count", "co-authored works")], "institution_activity.parquet": [("institution_id", ""), ("institution_name", ""), ("country_code", ""), ("publication_year", ""), ("works_count", ""), ("total_citations", "")], } def _now(): return datetime.now(timezone.utc).strftime("%Y-%m-%d") def readme(cfg, stats, manifest) -> str: t = stats.get("totals", {}) yrs = stats.get("year_range") or [None, None] size = manifest.get("package_size_bytes", 0) cit = stats.get("citation_statistics", {}) return f"""# {cfg['project']['title']} A curated, normalized, enriched and packaged **biomedical research intelligence dataset** derived from OpenAlex metadata, provided in AI-ready formats (Parquet + JSONL) with full provenance and reproducible build tooling. This is a **derivative dataset**: it is not a re-upload of OpenAlex. The value added here is biomedical filtering by taxonomy, cleaning, normalization, relational restructuring, quality control and derived analytical features. ## What it is - **Source:** OpenAlex work metadata, retrieved through the OpenAlex REST API. - **Scope:** biomedical and health-related research only, selected by OpenAlex **taxonomy IDs** (fields 13, 24, 27, 28, 29, 30, 35, 36), not keyword search. - **Coverage:** publication years {yrs[0]}-{yrs[1]}. - **Selection:** stratified random sample drawn per (year x field) shard with a fixed random seed, so every year and every biomedical field is represented proportionally and the result is reproducible. - **Records:** {t.get('total_records', 0):,} works, {t.get('unique_works', 0):,} unique OpenAlex IDs, {t.get('unique_dois', 0):,} unique DOIs. - **Languages / OA:** see `metadata/dataset_statistics.json`. - **Package size (uncompressed):** {human_bytes(size)}. ## Intended uses Machine-learning and analytical research on the biomedical literature: trend and growth analysis, collaboration-network analysis, bibliometric modeling, topic classification, retrieval/ranking experiments, and as a ready-to-load table for LLM and data-science tooling. ## Formats and layout ``` data/ works + dimensions + relations (Parquet), JSONL exports, splits analytics/ pre-aggregated time-series and collaboration tables (Parquet) metadata/ manifest, statistics, schema, source queries, build info ``` Parquet is the primary format. JSONL exports (gzip) are provided for streaming/LLM use. See `DATA_DICTIONARY.md` for every column. ## Key derived features `paper_age_years`, `citations_per_year`, `citation_velocity`, `citation_percentile` (within year x field), `high_impact_flag`, `publication_recency_score`, `international_collaboration`, `multi_institutional`, `research_growth_score`, `topic_growth_score`, `emerging_topic_flag`. Definitions are in `METHODOLOGY.md`. ## Train / validation / test splits Chronological to avoid leakage: train <= {cfg['splits']['train_max_year']}, validation {cfg['splits']['validation_years']}, test >= {cfg['splits']['test_min_year']}. The complete unsplit dataset is retained separately. ## Limitations See `QUALITY_REPORT.md`. In short: metadata-only (no full text), citation counts are OpenAlex's at retrieval time, institutional/author disambiguation is inherited from OpenAlex, and derived growth signals are estimates that scale with sample size. ## Rights Base metadata originates from OpenAlex (CC0). Derived fields and packaging are original. No copyrighted full text, figures or supplementary files are included. See `LICENSE_AND_RIGHTS.md`. ## Reproduce ```bash pip install -r requirements.txt python run-all.py ``` Retrieval dates and exact filters are recorded in `PROVENANCE.md` and `metadata/source_queries.json`. _Generated {_now()} by pipeline v{cfg['project']['version']}._ """ def data_dictionary(cfg, stats) -> str: out = [f"# Data Dictionary - {cfg['project']['title']}", "", "All columns of every delivered table. Types are Arrow/Parquet types.", ""] out += ["## data/works.parquet", "", "| Column | Type | Description |", "|---|---|---|"] for name, typ, desc in WORKS_COLUMNS: out.append(f"| `{name}` | {typ} | {desc} |") out.append("") for fname, cols in RELATION_COLUMNS.items(): out += [f"## data/{fname}", "", "| Column | Description |", "|---|---|"] for name, desc in cols: out.append(f"| `{name}` | {desc} |") out.append("") for fname, cols in ANALYTICS_COLUMNS.items(): out += [f"## analytics/{fname}", "", "| Column | Description |", "|---|---|"] for name, desc in cols: out.append(f"| `{name}` | {desc} |") out.append("") out += ["## Splits", "", "`data/biomedical_works_train.jsonl.gz`, `..._validation.jsonl.gz`, " "`..._test.jsonl.gz` contain the same columns as `data/works.parquet`, " "split chronologically by publication year.", ""] return "\n".join(out) def methodology(cfg) -> str: f = cfg["features"] return f"""# Methodology ## 1. Collection Metadata is retrieved from the OpenAlex REST API (`/works`) using OAuth-free polite-pool access with a `mailto` identifier. Retrieval is resumable: each (year, field) shard keeps its own checkpoint, requests are retried with exponential backoff and jitter, and 429/5xx responses honour `Retry-After`. ## 2. Taxonomy filtering (no keyword search) The biomedical scope is defined by OpenAlex **field IDs**: | Field ID | Field | |---|---| | 13 | Biochemistry, Genetics and Molecular Biology | | 24 | Immunology and Microbiology | | 27 | Medicine | | 28 | Neuroscience | | 29 | Nursing | | 30 | Pharmacology, Toxicology and Pharmaceutics | | 35 | Dentistry | | 36 | Health Professions | These cover the requested areas (oncology, cardiology, public health, epidemiology, infectious disease, genetics, surgery, psychiatry, pediatrics, obstetrics & gynecology, radiology, anesthesiology, health policy, global health, and more) through their subfields and topics. The taxonomy snapshot is frozen under `metadata/taxonomy/` so normalization is deterministic. ## 3. Selection / sampling The scope is partitioned into (publication_year x field) shards. A global target row count is distributed across shards **in proportion to each shard's true size**, and works are drawn with OpenAlex's **seeded random `sample`** operator. Seeded sampling is essential: the default listing order returns the most-cited works first (median ~1,300 citations), whereas the seeded sample reproduces the true citation distribution (median 0-1). Each shard uses a deterministic seed, so re-running reproduces the identical set. No record is duplicated to inflate size. ## 4. Cleaning and normalization - **Deduplication** by OpenAlex work ID and by normalized DOI. - **DOI normalization**: lowercase, scheme/prefix stripped. - **Date normalization** to ISO `YYYY-MM-DD`; invalid dates dropped. - **Abstract reconstruction** from OpenAlex's inverted index into text. - **Author normalization**: names, OpenAlex IDs, ORCIDs (bare form), positions, corresponding flags; affiliations flattened. - **Institution normalization**: IDs, names, ISO-3166 alpha-2 country codes. - **Country normalization**: union of authorship and institution countries. - **Topic normalization** to a frozen topic index (topic/subfield/field/domain). - **Malformed removal**: rows without an ID or with empty titles are dropped. - **Missing values** represented consistently as null. ## 5. Derived metrics (deterministic, reproducible) Let `ref_year = max(publication_year)`, halflife = {f['recency_halflife_years']}y. - `paper_age_years = ref_year - publication_year` - `citations_per_year = cited_by_count / max(paper_age_years, 1)` - `citation_velocity = recent_citations_3y / 3` - `publication_recency_score = exp(-paper_age_years / halflife)` - `citation_percentile` = percentile rank of `cited_by_count` **within publication_year x field** (groups: {f['citation_percentile_group']}). - `high_impact_flag = citation_percentile >= {f['high_impact_percentile']}` - `international_collaboration = country_count >= 2` - `multi_institutional = institution_count >= 2` - Growth: each topic/field's yearly counts are split into an early and a late half of the year range; `growth_ratio = (late+1)/(early+1)`, `cagr` from the half-averages, `trend_slope` = OLS slope of yearly counts. - `emerging_topic_flag = growth_ratio >= {f['emerging_growth_threshold']} and late_count >= 50 and late > early`. No derived field is generated by a language model; all values are computed from OpenAlex metadata by the versioned code in `src/`. ## 6. Train / validation / test splitting Chronological, to prevent leakage: a work appears in exactly one split (works are unique and DOIs are deduplicated, so the same paper or DOI cannot cross splits). Train <= {cfg['splits']['train_max_year']}, validation {cfg['splits']['validation_years']}, test >= {cfg['splits']['test_min_year']}. The complete unsplit dataset is retained as `data/works.parquet`. ## 7. Validation and packaging Every Parquet table is validated against its canonical Arrow schema (column names, types, required-column nulls, primary-key uniqueness). SHA-256 checksums are written for all delivered files in `checksums.sha256`. """ def provenance(cfg, source_queries, stats, manifest) -> str: queries = source_queries or [] rows = [] for q in queries: rows.append(f"- retrieval started **{q.get('retrieval_started')}**, finished " f"**{q.get('retrieval_finished')}**, {q.get('rows_collected'):,} rows, " f"filters field IDs {q.get('field_ids')}, years {q.get('year_range')}, " f"endpoint `{q.get('endpoint')}`") qtext = "\n".join(rows) if rows else "- see metadata/source_queries.json" return f"""# Provenance ## Source The base metadata in this package originates from **OpenAlex** (https://openalex.org), an open scholarly-metadata catalogue. OpenAlex data is dedicated to the public domain under **CC0 1.0** (see `LICENSE_AND_RIGHTS.md`). - API base: `{cfg['source']['base_url']}` - Endpoint: `/works` (plus `/domains`, `/fields`, `/subfields`, `/topics` for taxonomy) - Access: polite pool via `mailto` - Selection operator: seeded random `sample` per (year x field) shard ## Retrieval records {qtext} ## Transformations 1. Raw JSON pages are streamed to gzip-JSONL shards per (year, field). 2. `normalize.py` flattens nested objects, reconstructs abstracts, normalizes identifiers and writes Parquet parts. 3. `derive_features.py` attaches derived metrics. 4. `build_relations.py` builds dimension tables and the internal citation graph. 5. `analyze.py` builds the analytics aggregates and statistics. 6. `validate.py` checks schemas; `package.py` writes the manifest, checksums and archive. Every stage is checkpointed and deterministic given the same config and seeds. ## Build - Pipeline version: {cfg['project']['version']} - Build timestamp: {manifest.get('build_timestamp')} - Config file: `config.yaml` (frozen values in `metadata/build_info.json`) ## Reproducibility Because sampling uses fixed seeds derived from shard keys, re-running the collection reproduces the same works (subject to OpenAlex's own record additions/updates between runs). Citation counts reflect OpenAlex at the retrieval date above. """ def license_and_rights(cfg) -> str: return f"""# License and Rights This document separates three layers of rights so that nothing is misrepresented. ## 1. Original OpenAlex metadata (source layer) The base bibliographic metadata is sourced from **OpenAlex**, which is made available under **CC0 1.0 Universal (Public Domain Dedication)**. OpenAlex aggregates metadata from Crossref, PubMed, MAG, institutional repositories and others; it publishes the aggregated metadata openly. - No exclusive ownership of OpenAlex source data is claimed. - The underlying public metadata is **not** proprietary. - Attribution to OpenAlex is given as a courtesy and is recorded in `PROVENANCE.md`. ## 2. Derived content (this package's contribution) The following are original to this project: the biomedical taxonomy-based selection and stratification, cleaning and normalization, relational restructuring, derived analytical features, quality control, documentation and packaging. This package is offered as a **curated, normalized, enriched and packaged derivative dataset**. It does not claim exclusive rights over the source data. ## 3. Content intentionally excluded The following are **not** included, because their redistribution rights are unclear or restricted: - Full-text articles, PDFs, HTML and publisher landing pages. - Figures, tables, images and supplementary files. - Any content flagged non-commercial or otherwise restricted. - Any dataset with unclear commercial reuse rights. Only OpenAlex metadata fields and abstracts that OpenAlex itself distributes through its API are included. Abstracts are reconstructed from OpenAlex's inverted-index metadata representation, which OpenAlex provides as part of its open API; no publisher scraping or access-control circumvention was performed. ## Practical guidance for downstream users - Cite OpenAlex as the metadata source. - Verify the licence of any individual work before redistributing its abstract, where a specific licence is required. - `works.license` / `works.license_id` record the OpenAlex-reported licence of the article's OA location where available. _This document is not legal advice._ """ def quality_report(cfg, validation, stats, norm_stats, derive_stats, files) -> str: t = stats.get("totals", {}) missing = stats.get("missing_value_percent", {}) worst = sorted(missing.items(), key=lambda kv: -kv[1])[:15] missing_rows = "\n".join(f"| `{k}` | {v}% |" for k, v in worst) tables = [] for rel, info in (validation.get("tables") or {}).items(): tables.append(f"| `{rel}` | {info.get('rows', 'n/a')} | {info.get('status')} |") tables_txt = "\n".join(tables) return f"""# Quality Report _Generated {_now()} by pipeline v{cfg['project']['version']}._ ## Schema validation Status: **{validation.get('status', 'unknown')}** ({len(validation.get('errors', []))} errors, {len(validation.get('warnings', []))} warnings) | Table | Rows | Status | |---|---|---| {tables_txt} ## Malformed records | Category | Count | |---|---| | Raw rows read | {norm_stats.get('raw_rows', 'n/a')} | | Malformed / dropped (no ID or empty title) | {norm_stats.get('malformed', 'n/a')} | | Duplicate work IDs removed | {norm_stats.get('dup_id', 'n/a')} | | Duplicate DOIs removed | {norm_stats.get('dup_doi', 'n/a')} | | Records kept | {norm_stats.get('kept', 'n/a')} | ## Missingness (top columns, by percent null) | Column | % null | |---|---| {missing_rows} ## Citation statistics `{stats.get('citation_statistics', {})}` ## International collaboration rate {stats.get('international_collaboration_rate')} ## Suspicious / notable values - Citation counts are OpenAlex's at retrieval time and can be 0 for recent works. - `citation_velocity` is null where OpenAlex supplies no `counts_by_year`. - `citation_percentile` is computed within (year x field); small shards in the least-populated (year, field) cells have coarser percentiles. - `emerging_topic_flag` requires >= 50 late-period works; small samples flag few topics. - OpenAlex primary-topic assignment is model-predicted and inherits its error. ## Coverage - Year range: {stats.get('year_range')} - Fields covered: {len(stats.get('works_per_field', {}))} - Subfields covered: {len(stats.get('works_per_subfield', {}))} - Countries covered: {len(stats.get('works_per_country', {}))} - OpenAlex-supplied citation percentile and FWCI retained for cross-checks. ## Known limitations 1. Metadata-only: abstracts where OpenAlex provides them; no full text. 2. Sampling: this is a proportional stratified sample, not the full corpus; rare cells are represented with fewer rows. 3. Author/institution identity is inherited from OpenAlex disambiguation. 4. Citation-based features are time-sensitive (snapshot at retrieval date). 5. Derived growth scores are estimates and scale with the sample size. ## Files validated {len(files)} delivered files hashed in `checksums.sha256`. """