A third of the papers we said we could not read were free to read in full
also called abstract-only recoverability · was the full text available · reading depth follow-up
Many entries here say we only read a paper's summary, which sounds like the paper was locked away. For a third of them the whole paper was free the entire time and nobody checked.
The same thing, for a scientist
Applying the corrected readability rule to the whole declared-shallow population: of **337 distinct PMIDs** carried by items declaring abstract-only, **222 (65.9%) have a PMCID** and **113 (33.5%) are open-access full text**. The control is what makes this a finding rather than a complaint — papers the graph DID read deeply are **less** available (59.4% PMCID, 28.8% open access), so availability does not explain the shallow reading. At item level **240 of 723 (33.2%)** rest on a paper that was one HTTP request from being read in full, 152 of them at `strong` confidence.
The numbers
| population | PMIDs | with a PMCID | open-access full text |
|---|---|---|---|
| declared abstract-only | 337 | 222 (65.9%) | 113 (33.5%) |
| not declared | 932 | 554 (59.4%) | 268 (28.8%) |
The second row is the control and it is the whole argument. If 'full text not read' mostly meant 'full text unavailable', the declared-shallow papers would be harder to get than the rest. They are easier. Availability is not the explanation; time is, which is a legitimate reason to stop at an abstract and an illegitimate thing to leave unsaid.
By confidence, and where the fix is cheap
| confidence | items declaring abstract-only | full text available | share |
|---|---|---|---|
| established | 118 | 20 | 16.9% |
| strong | 426 | 152 | 35.7% |
| moderate | 165 | 63 | 38.2% |
| weak | 14 | 5 | 35.7% |
established sits lowest at 14.7%, which is correct rather than surprising: those items lean on guidelines, registries and databases, which have no PMC deposit to find. The mass is in strong — 510 items, 175 of them resting on a paper that was free and unread.
The action is not to read 282 papers. It is to intersect three lists this project already has: declared abstract-only, full text available, and low claim-to-abstract overlap from verify-claims.py. A claim that the abstract cannot contain — a model system, a methods detail, an effect size, a subgroup — resting on a free full text is a short and well-defined queue.
What this is not
It is not evidence those claims are wrong, and the graph's own instruments say the opposite. ana-claim-support-check found the declared-abstract-only band scores higher on claim-to-abstract correspondence than everything else — median 0.779 against 0.640, with 6 of 826 below the floor against 77 of 1,990. Claims written from an abstract are, unsurprisingly, good claims about that abstract.
The defect is descriptive. 'Full text not read' reads as a property of the source and is a property of the reader, and the entries do not distinguish the two. The honest caveat for a third of these is the full text was available and was not read, which is a sentence an agent can write and a reader can act on.
The classifier was wrong first, and the queue is what caught it
The first run of this audit reported 34.0% on a population of 887 items. Both numbers were inflated, because the shared shallow-reading regex had no negation handling: a caveat reading “Full text read (PubMed Central, PMC4523210), not abstract only” contains the literal words “abstract only” and was counted as a declaration of shallow reading. 165 of 888 matches (18.6%) were negations of that shape.
| figure | first run | corrected |
|---|---|---|
| items declaring abstract-only | 887 | 723 |
| distinct PMIDs | 406 | 337 |
| open-access full text | 34.0% | 33.5% |
| control (not declared) | 28.7% | 28.8% |
The headline survives — a third either way, with the control still lower, so the availability argument is unaffected. Three other numbers in this graph did not: ana-reading-depth's headline moves from 29.1% to 24.3%, and ana-claim-support-check's calibration band loses four of its six floor-breaches, which is what should happen — an item whose agent read the full text writes a claim carrying full-text detail, which scores low against the abstract by construction. That entry had called those six the ones with no innocent explanation; four had the most innocent explanation there is.
How it was found matters more than the correction. This audit produced a reading queue; the queue's top item was read; the paper's claim checked out in every particular — WBC 188,000 with 70% blasts, 36 weeks, fetal decelerations, the rash, the hepatosplenomegaly, anisocoria, left-sided weakness, t(11;19)(q23;p13.3) — and the entry's caveat turned out to begin with the words Full text read. The instrument was caught because someone acted on its output. A measure that is reported and never used is never tested, and this project has now shipped three quality metrics whose defects only surfaced when something downstream consumed them.
The queue this produces, and what it looks like
scripts/reading-queue.py intersects three lists: declared abstract-only, open-access full text available, and claim-to-abstract support below a threshold. 8 items out of 723 come through at a 0.45 cut — a queue small enough that not reading it is a decision rather than a capacity limit.
| entry | item | support | full text | confidence |
|---|---|---|---|---|
fusion-tcf3-hlf | E7 | 0.113 | PMC4603357 | moderate |
ana-reading-depth | E3 | 0.131 | PMC10169636 | strong |
ana-kmt2a-lost-module-ledger | E4 | 0.171 | PMC10169636 | established |
exp-igf2bp-degron-self-renewal-xenograft | E4 | 0.248 | PMC5508533 | strong |
exp-cross-family-interface-disruption-panel | E7 | 0.270 | PMC11057873 | strong |
hyp-wdr5-partition-nsl-versus-compass | E5 | 0.300 | PMC12208907 | moderate |
exp-igf2bp-degron-self-renewal-xenograft | E6 | 0.319 | PMC8037952 | moderate |
collab-kotecha-perth-infant-leukaemia | E6 | 0.321 | PMC12879164 | established |
This table replaces one written an hour earlier, and the difference is the whole lesson. The pre-correction queue held 11 items, six of them patient stories, and this entry said so and offered a tidy structural explanation: a case report's abstract is four sentences, so its clinical detail necessarily lives in the body. The explanation was elegant and entirely wrong. Every one of those patient stories was a misclassified item whose caveat began Full text read; they scored low against the abstract precisely because their agents had read the full text and written from it. Fixing the guard removed all six, and the plausible story about case reports with them.
What is left is two analyses, two experiments, a fusion entry, a hypothesis and a collaborator entry — no pattern, which is the honest result. Two of the eight are this project's own analyses citing PMC10169636, so the queue's first duty is to audit the auditor.
Any single one of the three filters is a bad queue. Declared-abstract-only alone is 723 items and most are fine. Low support alone is mostly faithful paraphrase in different words. Available-but-unread alone is a budget fact. The intersection is the only one of the seven combinations that names something actionable.
The queue's precision, measured by reading it
Six of the eight items were examined in the same cycle the queue was built. Three were real defects and three were legitimate low scores, which is the only precision figure this project has for any of its quality instruments.
| item | verdict |
|---|---|
ana-reading-depth E3 | defect — claim about this graph's citation behaviour, citing the recombinome paper. Citation wrong in kind. |
fusion-tcf3-hlf E7 | defect — two claims under one citation supporting only the second; the paper never mentions the bZIP. Split into E7 and E10. |
ana-kmt2a-lost-module-ledger E4 | defect — vague where the source is exact; now carries 3,401 patients, 107 partners, 98% in BCR1. |
collab-kotecha-perth-infant-leukaemia E6 | legitimate — an authorship claim. Low overlap because the claim is about who wrote the paper, not what it says. |
exp-igf2bp-degron-self-renewal-xenograft E4 | legitimate — cited to justify a readout choice, and the caveat already says 'cited to justify the readout choice, not to transfer the biology'. |
exp-igf2bp-degron-self-renewal-xenograft E6 | legitimate — same, cited as a design constraint. |
The three legitimate ones share a shape: the claim cites a paper for its bearing on a decision — who to credit, which readout to use, which confounder to design around — rather than for a finding. An abstract cannot contain a statement about why this project made a choice, so the score is low and correctly so. That is a fourth distinct reason for low overlap, alongside faithful paraphrase, full-text detail, and the wrong-in-kind defect, and only the last is a problem.
Three defects from six readings is a better hit rate than any list this project has produced. It is also six readings, so the interval around 50% runs from roughly 12% to 88%.
- Read the eight queue items. Two are this project's own analyses citing PMC10169636, so the queue's first duty is to audit the auditor.
- Control for year. The availability contrast could be a publication-date artefact, and the Europe PMC record carries the year needed to test it.
- Change what agents write. The caveat should distinguish 'full text not available' from 'full text available and not read', and the second should name the PMCID so the next reader can pick it up in one request.
- Re-run after the next breadth cycle. If the recoverable fraction rises, breadth sweeps are generating the gap faster than depth passes close it.
- Audit every other quality number in this graph for the same class of defect. Three of the project's metrics have now been found wrong after being reported as clean, and in each case the fault was a pattern that matched something it was meant to exclude.
- E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.analysis
Of 337 distinct PMIDs carried by evidence items declaring abstract-only reading, 222 (65.9%) have a PMC identifier and 113 (33.5%) are flagged open access by Europe PMC, meaning the complete text is retrievable through the {PMCID}/fullTextXML endpoint at no cost.
Abstract-only recoverability audit: how many papers cited as 'full text not read' were open-access full text · Oncofusion knowledge graph (internal analysis) 2026What this evidence cannot show
Run 2026-09-19 over 3003 paper-citing items in 888 entries. 'Declared abstract-only' is detected by the same caveat-text regex `ana-reading-depth` and `verify-claims.py` use, so all three analyses describe the same population; that regex catches a declaration, not the underlying behaviour, and an item that read the abstract without saying so is counted in the other band. Open-access status is as Europe PMC reports it today, not as it stood when the entry was written, and some of these papers were embargoed at the time.
Evidence that argues against this (2)
- Availability is not the same as usefulness, and this measures the cheaper quantity. For a large share of these claims the abstract contains the whole of what is being cited — a prevalence, a headline result, a trial's primary endpoint — and reading the full text would change nothing. A recoverable-but-unread rate is an upper bound on wasted opportunity, not an estimate of it. Oncofusion knowledge graph (internal tooling) 2026
- The embargo caveat may absorb much of the gap. Several of these entries were written within twelve months of a paper's publication, and a Europe PMC open-access flag checked in 2026 does not establish that the text was free when the agent looked. The audit does not reconstruct historical availability and cannot. EMBL-EBI 2026
- E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.analysis
Papers the graph declares it read only in abstract are MORE available than papers it does not so declare: 65.9% versus 59.4% have a PMCID, and 33.5% versus 28.8% are open access. Unavailability therefore does not explain the declared shallow reading.
Abstract-only recoverability audit: how many papers cited as 'full text not read' were open-access full text · Oncofusion knowledge graph (internal analysis) 2026What this evidence cannot show
The two populations are not matched on year, journal or topic, and the difference is modest (7.5 and 5.3 percentage points). The claim rests on the direction of the difference rather than its size: the unavailability hypothesis predicts the opposite sign, and gets it.
Evidence that argues against this (2)
- A confound runs the right way to produce this without any behavioural explanation. Open-access papers are newer on average, and newer papers are likelier to be cited here from an abstract because they arrived during a cycle in which an agent was sweeping breadth rather than depth. Year is not controlled and could carry the whole effect. EMBL-EBI 2026
- The 'not declared' band is not a clean comparator either. `ana-reading-depth` showed declaration is unevenly applied across cycles, so an unknown share of that band also read only abstracts and did not say so. If those are disproportionately the hard-to-get papers, the contrast shrinks. Oncofusion knowledge graph (internal analysis) 2026
- E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.analysis
At item level, 240 of 723 items declaring abstract-only (33.2%) cite a paper with open-access full text, including 152 carried at strong confidence and 63 at moderate. Items at established confidence are least affected (14.7%), consistent with their leaning on guidelines, registries and databases that have no PMC deposit.
Abstract-only recoverability audit: how many papers cited as 'full text not read' were open-access full text · Oncofusion knowledge graph (internal analysis) 2026What this evidence cannot show
Item counts exceed PMID counts because one paper supports several items; a single widely-cited open-access paper therefore contributes many items. The load-bearing citations audit found exactly this concentration, so the item-level figure is more sensitive to a handful of sources than the PMID-level one.
Evidence that argues against this (1)
- Confidence and reading depth are not the same axis, and the implied link is weak. `ana-claim-support-check` found confidence flat across the declared-abstract-only band — established 25.7%, strong 30.0%, moderate 30.9%, weak 20.5% — so agents were not assigning confidence according to how deeply they read. A strong claim from an abstract is not thereby an overconfident one. Oncofusion knowledge graph (internal tooling) 2026
- E4established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.analysis
Intersecting declared-abstract-only, open-access full text, and claim-to-abstract support below 0.45 yields 8 items from 723. The queue has no dominant entry type; two of the eight are this project's own analyses.
reading-queue.py - declared abstract-only, open-access full text, and low claim-to-abstract support, intersected · Oncofusion knowledge graph (internal tooling) 2026What this evidence cannot show
Run 2026-09-19 after the classifier correction. The pre-correction queue held 11 items of which six were patient stories, and all six were misclassified items whose caveats said the full text HAD been read — they scored low precisely because they were written from full text. The 0.45 cut is chosen to make the queue readable, not calibrated against any error rate, and the claim-support report stores only its low tail, so items above that tail are treated as scoring fine rather than rescored.
Evidence that argues against this (2)
- The first item read off the pre-correction queue was a false positive whose every specific checked out against the full text. Precision here is unknown: one item has been read, it was not a defect, and it is not in the corrected queue at all. Cureus 2015
- Eight items is small enough that its composition carries almost no information, and the entry's own history is the argument against reading a pattern into it: the previous queue's clearest pattern was an artefact. Saying 'no dominant entry type' at n=8 is barely more defensible than the claim it replaces. Oncofusion knowledge graph (internal tooling) 2026
- E5strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.analysis
Six of the eight reading-queue items were examined. Three were defects — a citation attached to a claim about this graph rather than about the paper, a single citation carrying two claims where the paper supports only one, and a claim left vague where its source is exact — and three were legitimate low scores in which the paper is cited for its bearing on a design decision rather than for a finding.
reading-queue.py - declared abstract-only, open-access full text, and low claim-to-abstract support, intersected · Oncofusion knowledge graph (internal tooling) 2026What this evidence cannot show
Six readings on 2026-09-19 by the coordinator, who also wrote the queue and two of the three corrected items, so the classification of what counts as a defect is not independent of the person who built the instrument. The binomial interval around 3/6 runs from about 12% to 88%.
Evidence that argues against this (2)
- A 'defect' here is graded generously. One of the three is vagueness rather than error — `ana-kmt2a-lost-module-ledger` E4 said 'more than 100 partners across thousands of patients', which is true, and was replaced with exact figures. Counting an imprecise-but-correct claim as a defect inflates the hit rate, and a stricter reading gives 2 of 6. Oncofusion knowledge graph (internal tooling) 2026
- The queue was also read in an order that favoured it. The two items chosen first were this project's own analyses, on the stated reasoning that the queue should audit the auditor — and self-referential claims are exactly where the wrong-in-kind defect lives. A queue read in score order rather than by that judgement would likely have found fewer. Oncofusion knowledge graph (internal tooling) 2026