Pre-scientific-review intake checklist
Preflight checklist for laboratory result files
A browser-local intake checklist for recording whether an exact laboratory result package can move safely from quarantine through manifest, file, schema and identifier checks into separate scientific review.
SingularCell Research. Reviewed for primary-source scope, intake safety, structural validation and unsupported claims. Technical preflight remains separate from scientific review and result acceptance.
How to use this resource
Use this checklist against one exact received package, return-specification and ruleset version. Record only non-confidential working notes, preserve every quarantine or warning state, and transfer approved findings into your controlled intake system.
Entries stay in this browser page and are not submitted to SingularCell. Download or storage is not implied.
Laboratory result-package preflight
Work from exact receipt bytes to a bounded routing decision. Each checked item records technical intake coverage only and cannot approve the experiment or its results.
Working preflight finding
Draft one technical finding here, then move approved information into the controlled intake, security or study-record system used by your organisation.
Name exact receipt, package, specification, file, ruleset, scanner, parser, schema and validator versions in scope.
Record the named property checked, exact inputs, tool and configuration, outcome, warnings and errors without scientific interpretation.
Describe the expected, declared and actual values and the affected files, schemas, identifiers, units or mappings.
Record the neutral routing state, responsible security or data owner, requested correction and predecessor or successor relationship.
Bind any classification or waiver to the exact finding and package versions, rationale, reviewer, time and remaining scientific-review boundary.
Neutral preflight routing outcomes
Use these states to route exact packages without turning technical intake into safety, authenticity, scientific-validity or result-acceptance claims.
| Outcome | Exact meaning | Required next step |
|---|---|---|
| QUARANTINED_SECURITY_REVIEW | A detection, unsafe container or path, scan error or policy condition blocks parsing | Security review or provider resubmission |
| TECHNICAL_RESUBMISSION_REQUIRED | Required files, hashes, formats, schemas, mappings or access material block intake | Issue an exact discrepancy list |
| TECHNICALLY_READABLE_WITH_WARNINGS | Approved parsers read the files but non-blocking technical or context gaps remain | Show every warning to reviewers |
| TECHNICAL_PREFLIGHT_COMPLETE | Configured intake checks completed without blocking findings | Release this exact package version to scientific review |
| HUMAN_CLASSIFICATION_REQUIRED | A file role, schema, unit, mapping or correction meaning cannot be resolved safely | Route to the named accountable reviewer |
| PREFLIGHT_BLOCKED_ACCESS | Encryption, passwords or permissions prevent inspection | Obtain authorized access or request resubmission |
Passing technical preflight means only that the exact package completed the configured intake checks and can be routed for scientific review. It does not mean the files are safe, authentic, correct, scientifically valid or accepted.
Receive and inspect without trusting
Bind the receipt to exact package bytes, a submission event, the expected return specification and a versioned preflight ruleset. Preserve the received package in restricted quarantine and prevent active content from executing during inventory or readability checks.
A malware scanner can report no detection, a detection, an error or that a scan was not run. No detection is a result from one mechanism at one time; it must never be translated into safe, benign or authentic.
- Record the receipt, sender declaration, channel and exact package version
- Calculate a receipt digest without modifying the bytes
- Keep the original received package in restricted quarantine
- Record scan engine, version, update time, scope and outcome
- Apply bounded archive size, count, nesting, path and time limits
Reconcile the package before parsing
Compare three separate inventories: what the return specification expected, what the laboratory manifest declared and what safe enumeration found in the package. Report missing, unexpected, duplicated, conflicting, inaccessible and encrypted entries individually.
For each file, preserve logical identity, role, path, size, declared and detected type, schema version and supplied versus calculated digest. Reconciliation proves only that this package matches the named inventory rules; it does not establish universal completeness or authenticity.
- Keep expected, declared and actual inventories separate
- Normalize paths without accepting traversal, links or device entries
- Compare size, type, role, schema and digest declarations
- Preserve unexpected and inaccessible files for explicit routing
- Never overwrite a mismatched or superseded receipt copy
Route technical structure to scientific review
Approved parsers and validators can record readability, file warnings, schema conformance, row or object counts, identifier closure, declared units and required context fields. They should not silently repair scientific fields, infer missing units or decide whether laboratory-declared QC is adequate.
The strongest automated outcome is technical preflight complete: the exact package can proceed to scientific review under the configured ruleset. Security, data-steward, laboratory and scientific queues remain separate, and every waiver binds the exact finding and package versions.
- Record parser, schema, vocabulary and validator versions
- Expose duplicates, orphans and cardinality conflicts
- Keep declared native, raw, processed and QC states source-labelled
- Create successor versions for corrected or resubmitted packages
- Use neutral routing outcomes instead of accepted, valid or approved
Primary sources
- NIST — Research Data Framework, Version 2.0 ↗National Institute of Standards and Technology · Data lifecycle, ingest, formats, metadata, checksum, security, versions, derivatives and provenance fields for a bounded intake design.
- NIST — NERDm: A Reader's Guide ↗National Institute of Standards and Technology · An official implementation example that separately records locator, media type, format, checksum and byte size in structured metadata.
- NIST — SP 800-53 Rev. 5, Update 1 ↗National Institute of Standards and Technology · A bounded security-control reference for scanning external files and applying organisation-defined blocking, quarantine or alert responses.
- NIST — FIPS 180-4 Secure Hash Standard ↗National Institute of Standards and Technology · Approved hash algorithms produce message digests that can detect whether compared messages changed after digest generation.
- NIH — Elements of a Data Management and Sharing Plan ↗National Institutes of Health · Within NIH policy context, declarations can cover data types, formats, metadata, documentation, tools, identifiers, definitions, preservation and access.
- NIH — Selecting a Data Repository ↗National Institutes of Health · Repository-selection guidance distinguishes identifiers, metadata, curation, common formats, provenance, retention and access controls.
- The FAIR Guiding Principles for scientific data management and stewardship ↗Wilkinson et al., Scientific Data · The original FAIR principles describe persistent identifiers, linked metadata, standard retrieval, formal representations, qualified references and provenance.
- W3C — PROV Data Model ↗World Wide Web Consortium · Machine-readable semantics for checking whether declared entity, activity, agent, source, generation, derivation and revision links resolve.
- FDA — Data Integrity and Compliance With Drug CGMP ↗United States Food and Drug Administration · A bounded drug-CGMP example for retaining metadata, audit context, original records, invalidated results and reprocessing history.
- NCBI GEO — Submission validation ↗National Center for Biotechnology Information · A bounded sequencing-repository example of metadata, file-existence, decompression, integrity, truncation, format-content, duplicate and consistency checks.
Limitations
- This preflight records technical intake checks for exact received bytes; it does not establish that a file is safe, authentic, complete, correct or scientifically valid.
- A malware no-detection result, hash match, parser success, schema conformance or closed identifier graph verifies only the named property under the recorded tool and configuration.
- The checklist does not determine biological acceptance, laboratory quality or competence, method or site equivalence, provenance truth, regulatory compliance, acceptance thresholds or whether a result should be accepted.
- NIST, NIH, W3C, FAIR, FDA and NCBI material remains bounded to its technical, security, policy, regulatory, repository or reuse context and does not endorse SingularCell or the result package.
- Do not enter confidential, personal, proprietary, regulated or customer result information into this public browser page.