Negative-Results Record, schema sketch v0.1

Overview

The core record is domain-agnostic. Domain profiles supply the identifiers, vocabularies, and evidence rules for a field. Two profiles are drafted: materials and biology.

One record equals one attempt on one path. A record is distilled, not raw: raw trajectories, logs, and instrument files may be attached, but the record is legible and useful without them.

The serialization is an RO-Crate 1.2 profile whose activity structure follows W3C PROV. Records are signed, immutable, and versioned: a correction produces a new version that points at the one it supersedes. Records are private by default, with an embargo the depositor sets, and become citable on release. Version and retraction status of everything a record cites is re-checked at read time, not frozen at write time.

Field names below are working names. Type is given as the JSON-LD range. Cardinality: 1 required, 0..1 optional, 0..n repeatable.

Core record (sections A to H)

These eight sections apply to every record, in every field. A profile may require more; it may not contradict what is here.

A. Identity and provenance

Who or what produced this record, with what software, and under whose authority.

B. Question

What the attempt was trying to establish, stated well enough that another agent can decide whether this record is about its question.

C. Path

What was actually done, in the stages that apply. Every stage is a PROV activity with start and end times.

C1. Literature stage (follows PRISMA-S)

C2. Computation stage

C3. Experiment stage

D. Screened items

One row per candidate considered and set aside: papers, structures, compounds, or prior results. This is the part a later agent queries first.

E. Outcome

F. Reuse guidance

The fields that make a dead end actionable instead of merely discouraging.

G. Relations

H. Integrity

Materials profile v0.1

The materials and chemistry profile. Records link to Materials Project, OPTIMADE, and ICSD identifiers, not only to papers, so that a novelty claim is checked against structured data rather than prose.

Starter vocabularies

Controlled and deliberately small. Additions go through the same review as the schema; a term nobody uses is removed.

Exclusion reasons (section D)

• out-of-scope
• duplicate
• superseded-by-newer-version
• retracted
• expression-of-concern
• corrected-materially
• preprint-not-peer-reviewed
• insufficient-detail-to-reproduce
• wrong-composition
• wrong-conditions
• no-full-text-available
• language-not-supported
• evidence-not-verifiable

Failure modes, materials and chemistry (section E)

• known-disordered-variant
• phase-separation
• decomposition-at-temperature
• precursor-impurity
• no-crystalline-product
• moisture-or-air-sensitive
• yield-below-threshold
• characterization-inconclusive
• irreproducible-across-replicates

Failure modes, computation (section E)

• unconverged
• unstable-above-hull
• imaginary-phonon-modes
• functional-inadequate
• cell-or-supercell-too-small
• basis-set-insufficient
• numerical-instability
• resource-exhausted
• input-structure-invalid

Example record (abridged)

Illustrative only. Identifiers are placeholders.

{
  "@context": ["https://w3id.org/ro/crate/1.2/context", {"prov": "http://www.w3.org/ns/prov#"}],
  "@graph": [
    {"@id": "ro-crate-metadata.json", "@type": "CreativeWork",
     "conformsTo": {"@id": "https://portolansoft.com/profile/nrr/0.1"}, "about": {"@id": "./"}},
    {"@id": "./", "@type": "Dataset", "name": "NRR: Li3MnCoO5 solid-state synthesis attempt",
     "datePublished": "2026-11-03", "visibility": "embargoed", "embargoUntil": "2027-11-03",
     "hasPart": [{"@id": "#attempt"}, {"@id": "#lit-search"}]},
    {"@id": "#lit-search", "@type": "SearchAction", "query": "(Li3MnCoO5 OR \"Li-Mn-Co oxide\") AND synthesis",
     "startTime": "2026-11-02T14:10:00Z", "result": [{"@id": "#cand-1"}]},
    {"@id": "#cand-1", "@type": "ScholarlyArticle", "identifier": "doi:10.1000/example",
     "decision": "excluded", "reason": "superseded-by-newer-version",
     "statusAtCheck": {"version": "AM", "integrity": "none", "assertedBy": "crossref-relation",
                       "checkedAt": "2026-11-02T14:11:30Z"}},
    {"@id": "#attempt", "@type": "CreateAction", "actionStatus": "FailedActionStatus",
     "object": {"@id": "optimade:mp/mp-000000"},
     "outcomeClass": "negative-not-novel", "failureMode": "known-disordered-variant",
     "nearestPriorResult": {"@id": "icsd:000000"},
     "applicabilityConditions": "solid-state route, 800-950 C, air",
     "invalidators": "a refinement showing cation ordering at these conditions",
     "cost": {"wetLabRuns": 3, "agentSeconds": 5400}}
  ]
}

Biology profile v0.1

A failed synthesis is a fact about a compound. A biological negative result is a claim that an effect was looked for and not found, and it is only informative if the assay could have detected the effect. The biology profile therefore adds three things the core record does not require: controls and sensitivity; persistent identity for reagents, strains, and cell lines; and evidence-synthesis screening decisions as first-class records. Four attempt types are recognized: wet-lab, computational, evidence-synthesis, hypothesis-generation.

Identifiers

Version and integrity status, extended

Beyond the core version terms, the biology profile adds preprint-v{n}; reviewed-preprint, with eLife assessment terms carried as structured fields (significance: landmark, fundamental, important, valuable, useful; strength of evidence: exceptional, compelling, convincing, solid, incomplete, inadequate); registered-report-stage1 and registered-report-stage2; trial-registered and trial-results-posted. Integrity adds post-publication-comment, with a PubPeer pointer carried as a signal, never a verdict. Every status carries assertedBy and checkedAt.

Outcome classes

• negative-no-phenotype
• negative-no-effect
• negative-no-association
• negative-not-replicated
• negative-not-novel
• negative-contradicted-by-vor
• inconclusive-controls-failed
• inconclusive-underpowered
• inconclusive-reagent-failed
• partial
• positive

Failure modes, wet-lab

• no-phenotype-single-allele
• lethal-or-sick-mutant
• off-target
• strain-background-effect
• reagent-nonspecific
• cell-line-misidentified
• contamination
• construct-failed
• transformation-failed
• no-expression
• dose-no-response
• batch-effect
• assay-out-of-range
• toxicity
• not-replicated-second-model

Failure modes, computational

• no-differential-signal
• not-significant-after-correction
• confounded
• model-did-not-generalize
• low-confidence-structure
• benchmark-contamination

Failure modes, evidence synthesis

• wrong-population
• wrong-intervention
• wrong-comparator
• wrong-outcome
• wrong-study-design
• duplicate-publication
• insufficient-data
• not-retrievable
• retracted
• preprint-superseded
• claim-not-supported-by-cited-source

Evidence block for experimental negatives

Applicability conditions

For a biological record the envelope is: organism and strain; genotype and allele; cell type and passage; developmental stage; sex; growth conditions; assay and readout; reagent lot; time point; dose range.

Governance rules specific to biology

• No human-subject data in records, only accessions. Human-derived records are embargoed by default, and outcomes are aggregate-only.
• Compliance identifiers (IACUC, IRB) are committed by hash and revealed only to authorized readers.
• A restricted visibility tier for select-agent or dual-use work, never public regardless of embargo.
• Reagent lot identifiers are public by default, because they are the most diagnostic field in the record.

Example: a Chlamydomonas ciliary-assembly negative

Placeholder identifiers.

{
  "@type": "CreateAction", "actionStatus": "FailedActionStatus",
  "attemptType": "wet-lab",
  "question": "Does loss of Cre00.g000000 shorten flagella or delay regeneration after deflagellation?",
  "organism": {"taxon": "NCBITaxon:3055", "strain": "CC-4533", "mutant": "LMJ.RY0402.000000"},
  "gene": {"id": "Cre00.g000000", "source": "Phytozome"},
  "assay": {"obi": "OBI:0000000", "protocol": "doi:10.17504/protocols.io.example",
            "readout": "flagellar length, DIC microscopy, 60 min post-deflagellation"},
  "controls": {"positive": {"genotype": "shf1", "expected": "short flagella", "observed": "short flagella", "pass": true},
               "negative": {"genotype": "CC-4533 parental", "observed": "wild-type length", "pass": true}},
  "sensitivity": "resolves 1.0 um difference in mean length at n=100 cells",
  "power": "80% for d=0.4 at n=100 per genotype",
  "replicates": {"biological": 3, "technical": 2},
  "statistics": {"test": "Welch t-test", "effect": "0.2 um", "ci95": [-0.3, 0.7], "n": 300},
  "outcomeClass": "negative-no-phenotype", "informativeness": "informative",
  "failureMode": "no-phenotype-single-allele",
  "applicabilityConditions": "TAP medium, 22 C, continuous light, single CLiP allele, steady-state and regeneration",
  "invalidators": "a second independent allele; complementation; a different readout such as IFT particle velocity",
  "untriedBranches": ["second allele", "double mutant with known IFT component", "proteomics of isolated flagella"],
  "screened": [{"identifier": "doi:10.1101/2026.00.00.000000v2", "decision": "included",
                "statusAtCheck": {"version": "reviewed-preprint", "eLifeStrength": "solid",
                                  "assertedBy": "eLife", "checkedAt": "2026-09-13T17:00:00Z"}}],
  "cost": {"wetLabDays": 6, "agentSeconds": 3200},
  "visibility": "embargoed", "embargoUntil": "2027-03-13"
}

Example: an evidence-synthesis exclusion

{
  "@type": "SearchAction", "attemptType": "evidence-synthesis",
  "question": "Systematic review: efficacy of intervention X in population Y (PROSPERO CRD0000000)",
  "sources": [{"name": "PubMed", "query": "(X[tiab]) AND (Y[MeSH]) AND randomized", "date": "2026-09-10", "retrieved": 412}],
  "screened": [{"identifier": "doi:10.1000/example", "decision": "excluded", "reason": "retracted",
                "statusAtCheck": {"version": "VoR", "integrity": "retracted", "assertedBy": "retraction-watch",
                                  "checkedAt": "2026-09-10T09:12:00Z"}}],
  "outcomeClass": "partial", "prismaCounts": {"identified": 412, "screened": 380, "excluded": 351, "included": 29}
}

Open questions for biologists

1. Is the informativeness rule the right minimum, or too strict for exploratory work?
2. Should a single-allele no-phenotype ever be informative, or always partial until a second allele or complementation?
3. Which reagent fields must be public for the record to be useful, and which will labs refuse to share?
4. Should each screening decision be its own record, or a review one record with many screened items?
5. What would make a lab deposit these at all?

Mapping to standards

Nothing here is a new standard. Each part of the record is carried by something that already exists.

Open questions

These are the decisions the draft does not make. Comments on any of them are the most useful thing a reader can send.

1. Granularity. Is one record one attempt, one campaign, or one decision point? Too fine and the registry is a log; too coarse and the applicability conditions stop being true.
2. Identity and keys. What identifies “the same path” across depositors, so that two labs failing the same way can be recognized as such?
3. Default embargo. What is the right default hold period, and should it differ for computation and wet-lab records?
4. Redaction. How are withheld conditions handled beyond hash commitment, and what is the minimum a redacted record must still disclose to be admissible?
5. Minimum record. What is the smallest set of required fields that is still worth depositing, given that capture must stay automatic?
6. Where the profile lives. Which body should hold the profile and its vocabularies long term, and under what governance? The draft assumes an operator independent of publishers and content platforms; whether that is a nonprofit, a consortium, or a national facility is open.

Comment on this draft

This document is draft v0.1 and open for comment. Corrections, objections, and field-level suggestions to contact@portolansoft.com.

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