Publication intake rules
Codified rules from publication discovery batches 1–4 (May 2026). These govern what enters the resource-map publications layer and what may appear in graph exports.
Related: publications-layer-plan.md · publication-data-intake-template.md · publications-quality-review.md
Registry baseline (after batch 4): 34 publications · 39 person–publication links · 6 publication–resource links (4 graph-included).
Purpose
The publications layer is not a DePaul bibliography. Records exist only when they help document facilities, equipment, labs, technical capability, or cross-unit hard-tech work tied to map entities. Authorship alone is insufficient for resource linkage.
Core principles
Person–publication links
Person–publication links are acceptable when authorship is verified against an official DePaul profile, lab page, publisher metadata (Crossref/DOI), or PMC author list with DePaul affiliation.
- One or two included publications per person per batch is the default cap.
- Pre-DePaul work may be retained in the registry when it documents a faculty member’s research program, but mark
pre_depaul_work: trueand do not infer current DePaul resource use from it alone. - Common names require explicit DePaul affiliation on the publication (see publications-quality-review.md §8).
Publication–resource links
Publication–resource links require explicit evidence connecting the publication to a specific resource already in the map. These edges are rare and high-confidence — not default edges created during person intake.
- Target: roughly one publication–resource link per 5–10 included publications at the current evidence bar (batches 1–4: 6 links across 34 publications; 4 remain graph-included after quality review).
- Default for a new publication: person–publication link only;
resource_link_allowed: falseuntil methods/acknowledgment text is reviewed.
What is not sufficient for resource use
| Inference | Rule |
|---|---|
| Profile method lists alone | Not sufficient. Example: PRL-PUB-004 (Grice profile method alignment without paper acknowledgment). |
| Center affiliation alone | Not sufficient. Example: PRL-PUB-003 (STEM Center contact page without proceedings text). |
| Author affiliation alone | Not sufficient. DePaul author on a paper does not link the paper to every lab the author directs. |
| Coauthorship | Not a collaboration edge. Person–publication records authorship; they do not create person–person or cross-unit collaboration edges. |
| Grant abstracts | May guide searches (e.g., GRA-010 manuscript pointer for Kozlowski) but are not resource-use evidence unless the grant or publication text explicitly names a facility. |
| Topical similarity | Not sufficient. Same research theme (e.g., fish physiology vs Poeciliid grant species) does not create a publication–resource link. |
Graph inclusion vs registry retention
| Situation | Action |
|---|---|
| Verified authorship, strong resource-map relevance | Add publication + person–publication link with include_in_graph: true |
| Verified authorship, weak or indirect relevance | Retain registry record if useful for audit trail; set person–publication include_in_graph: false (e.g., PPL-033 Wagner → PUB-028) |
| Verified authorship, medium relevance (scholarly book, bench paper without facility text) | Person–publication include_in_graph: true; no publication–resource link |
| Unclear identity or evidence | confidence: low, needs_review in notes; include_in_graph: false until resolved |
| Clearly wrong record | Prefer needs_review or include_in_graph: false over deletion unless duplicate or fabricated |
Weak or ambiguous records should be retained as registry records only when useful, but excluded from the graph when they would mislead (false hubs, cross-unit implications, or SPARK/instrumentation overclaims).
Hard exclusion rules for publication–resource links
Do not create publication–resource links when the only support is:
- Topical similarity alone — paper topic matches a lab’s research area but does not name the lab, instrument, or facility.
- A person’s general faculty profile — profile lists techniques, equipment, or “research interests” without tying this specific publication to a resource.
- Center membership alone — person directs SPARK, STEM Center, CyberLabs, etc.; paper does not acknowledge or document that center’s infrastructure.
- Author affiliation alone — “DePaul University” or school affiliation in the author block.
- Coauthorship with a lab member — shared authorship does not prove shared facility use.
- Grant abstract keywords — grant title/abstract mentions equipment or species but publication does not acknowledge the facility.
- Weak lab association — “methods align with profile techniques,” “center is coordination hub,” or “faculty lead on resource X.”
Required: Do not create a publication–resource link unless the publication text, abstract, acknowledgment, lab page, project page, or official source explicitly connects the work to the resource.
When in doubt, leave resource_link_allowed: false and document reason_resource_link_not_added in the intake template.
Allowed publication–resource evidence
Acceptable evidence types (with quoted or linked text in evidence_text):
| Evidence type | Example from batches 1–4 |
|---|---|
| Publication explicitly acknowledges a facility, lab, instrument, center, dataset, or project | PRL-PUB-001: APS trial run named in abstract (PUB-002 → EXT-003) |
| Official DePaul news or lab communication cites facility use for the work | PRL-PUB-002: DePaul news quotes APS data collection (PUB-010 → EXT-003) |
| Official lab page lists the publication as output of that lab for this work | PRL-PUB-005/006: Karver/Southern profiles name assay development for PUB-013 |
| Publication documents an instrument, method, software, facility, or deployed system already represented as a resource | Instrument papers where methods section names beamline, detector, or shop |
| Grant/project page explicitly connects the publication to a resource | Rare; quote required — grant abstract alone is insufficient |
| Thesis/project page explicitly identifies the facility or lab used | Acceptable for student work when facility is named |
Profile pages: A lab profile may support a publication–resource link only when it names this specific publication as output of that lab or quotes facility use for this work — not when it only lists generic methods the PI uses.
Person–publication intake criteria
Include a publication when all apply:
- Hard-tech or resource-map utility — instrumentation, sensing, imaging, HPC, fabrication, cyber-physical systems, GIS/analytics tied to mapped resources, bench methods, or documented technical capability (see publications-layer-plan.md §3).
- DePaul connection — at least one author matches a
people.yamlrecord with verified affiliation on the publication. - Evidence in intake — title, year, venue from allowed sources; DOI required when resolvable (verify via Crossref/ORCID against discovery source).
- Conservative per-person cap — 1–2 includes per person per batch unless quality review expands.
DOI verification and storage (source packets + refactors)
| Step | Rule |
|---|---|
| Discover | Faculty profile, lab page, Google Scholar, ORCID, or candidate link |
| Verify | Crossref (or ORCID/Web of Science) confirms title, year, venue, authorship |
| Store | publications.yaml: citation fields + abstract; evidence_url = https://doi.org/… |
| Do not store | Full-text PDF or publisher HTML in packet (403 publisher snapshots are audit-only) |
| Link | Resource prose and YAML use DOI links or PUB-### registry IDs |
| Person link | Add person_publication_links.yaml when DePaul authorship verified |
| Resource link | Add publication_resource_links.yaml only with explicit facility/instrument evidence |
See also Source Evaluation and Evidence Policy § Publication registry.
ORCID on people.yaml
| Field | Rule |
|---|---|
orcid |
Normalized iD when verified or probable |
orcid_url |
Must be https://orcid.org/{orcid} |
orcid_verification_status |
verified (Crossref on linked pubs), probable (ORCID API), needs_review, unresolved, not_applicable (staff) |
| Enrichment | Run scripts/enrich_scholarly_identifiers.py; review docs/reports/scholarly-identifiers-review.md |
| Scope | Identity and authorship cross-check only — not facility or equipment evidence |
Exclude or defer (candidate_status: maybe | exclude) when:
- No peer-reviewed scholarly output at current bar (e.g., PER-112 Binder — professional credits only).
- Teaching materials, op-eds, documentaries, or policy commentary without instrumentation.
- Pure qualitative health/social-science work with no hard-tech or mapped-resource signal (cohort 4 Wagner case).
- Pre-DePaul work when a DePaul-era paper exists (defer duplicate coverage).
- Bulk API harvest without per-record review.
Batch workflow (batches 1–4 pattern)
| Step | Action |
|---|---|
| 1 | Select 8–10 people from cohort plan; document search in cohort report |
| 2 | Search official DePaul profile / lab page first; Crossref/DOI for verification |
| 3 | Fill publication-data-intake-template.md per candidate |
| 4 | Set candidate_status: include | maybe | exclude |
| 5 | Add publications.yaml + person_publication_links.yaml for includes |
| 6 | Add publication_resource_links.yaml only when allowed evidence exists (usually zero per batch) |
| 7 | Run quality review pass; downgrade overclaimed edges |
| 8 | Run python3 scripts/refresh_all.py |
Expect ~1 weak inclusion per batch at current coverage; plan a quality review after each intake.
Lessons from batches 1–4
| Batch | People searched | Included | Pub–resource added | Key lesson |
|---|---|---|---|---|
| 1 (seed) | 9 | 8 | 1 | Official-page-first works; most papers get person–pub only |
| 2 (ISE/CSH/ID) | ~14 | 7 | 2 | APS/facility text in abstract or news is strong; profile inference is weak |
| 3 (hard-tech 10) | 10 | 9 | 0 | Grant-adjacent faculty yield person–pub without facility edges — correct |
| 4 (directors/grants) | 10 | 9 | 0 | Center directors need instrumentation/methods filter; zero pub–resource is success |
Downgraded in quality review: PPL-033 (weak person–pub), PRL-PUB-003 and PRL-PUB-004 (profile/affiliation inference for resource links).
Validation checks (automated)
scripts/refresh_all.py reports:
- Publication–resource links with
include_in_graph: trueand confidence belowhigh - Publication–resource links with vague
evidence_text - Person–publication links excluded from graph (
include_in_graph: false) - Publications with no resource links (informational count — not an error)
Full-text facility-evidence pass (opt-in, gated)
Metadata (title/abstract) rarely names the specific facility a paper used. This
pass optionally downloads full text for a narrow set of candidates and
extracts facility-use evidence, so that edges like PUB → APS (uses) are backed
by a quoted Methods/Acknowledgment line rather than co-authorship inference.
This pass is the only sanctioned exception to the "do not store full text" rule in source-evaluation-policy.md § Publication registry. It is scoped, human-gated, and never runs corpus-wide by default.
Script: scripts/fulltext_facility_pass.py (accepts an explicit DOI list or a
single --person; there is no "all publications" mode).
The funnel (each gate cheaper than the next)
| Gate | Input | Action | Advances when |
|---|---|---|---|
| 1 Hardware/author | OpenAlex/ORCID/Crossref metadata | existing discovery filter | DePaul map author + hardware relevance |
| 2 Facility candidacy | title + abstract only | score named vs generic vs affiliation-only | named or ambiguous (see below) |
| 3 Acquisition | DOI | tiered full-text fetch (OA → repo/PMC/arXiv → publisher → library) | any text retrieved (success/partial) |
| 4 Extraction | Methods / Experimental / Acknowledgments / Data Availability | gazetteer match + use-verb classifier | named facility and use language |
Gate 2 — facility candidacy (metadata only)
| Signal | Candidacy | Download? |
|---|---|---|
| Named facility in title/abstract ("Advanced Photon Source", "Pohang Light Source", "PAL-XFEL", "beamline 7-ID") | named |
Yes |
| Generic capability, no named facility ("X-ray free-electron laser diffraction", "synchrotron", "EXAFS") | ambiguous |
Yes — full text needed to disambiguate |
| Facility/partner appears only as a co-author affiliation | affiliation_only |
No — never triggers download or an edge |
Partner-institution co-authorship alone is never sufficient to download a paper or to create a facility edge. This is the standing lesson from the OpenAlex pass-2 trap (a co-author affiliated with a facility ≠ the work used that facility).
Gate 3 — tiered acquisition
Cheapest and most license-safe first; stop at first success:
| Tier | Source | Automation | Notes |
|---|---|---|---|
| 1 | Unpaywall / OpenAlex best_oa_location |
automated | free, legal |
| 2 | arXiv / PMC / institutional repository | automated | common in physics |
| 3 | Publisher via DOI | automated, best-effort | HTTP 403 stays partial; do not scrape around paywalls |
| 4 | DePaul library | curator-mediated | authenticated; drop retrieved file into packet uploads/ |
Every attempt records capture_status (success / partial / failed) and a
SHA-256, matching existing capture provenance. Full-text bodies are audit
evidence under the source packet (fulltext/ or uploads/), not registry
content, and are not committed to the public repo when the license forbids
redistribution.
Gate 4 — extraction and classification
Only evidence-bearing sections are read (Methods, Experimental, Acknowledgments, Data Availability). Each facility mention is classified:
| Text pattern | Classification | Edge |
|---|---|---|
| Named facility + use verb ("data collected at APS beamline 7-ID", "experiments at the Pohang Light Source", "beamtime at PAL-XFEL") | facility_use | propose uses / produced_by |
| Named facility with no use verb; generic technique only | ambiguous | no edge; flag for human |
| Facility name appears only in the author affiliation block | affiliation_only | no edge (hard exclusion) |
The classifier keys on named facility + use language, not co-occurrence. Prefer the specific sub-facility resource (e.g. EXT-003 APS) over the parent organization (EXT-015 Argonne) when the beamline/facility is named.
Output and review gate
Extraction emits proposed publication_resource_links rows with the quote
pre-filled and:
confidence: highonly forfacility_useextraction_method: fulltext_v1include_in_graph: false,needs_review: trueuntil a curator verifies the quote against the stored text
Proposed rows are written to a report / candidate file, never directly into
data/publication_resource_links.yaml.
Person-level rollup
Person→facility "uses" is derived from confirmed pub→facility edges, so a researcher's true facility portfolio emerges (e.g. Landahl → APS, PLS, PAL-XFEL) while affiliation-only facilities (e.g. European XFEL when never used) never appear.
Facility gazetteer and missing resources
The extractor maps facility names → resource IDs via data/facility_gazetteer.yaml.
When a named, used facility has no resource record yet (e.g. Pohang Light
Source, PAL-XFEL), the pass emits a "proposed new EXT resource" rather than
silently dropping the evidence — it must not be lost.
Regenerate counts: python3 scripts/refresh_all.py