Contamination Burden

Scientific meaning

What it measures

Assesses contamination burden using evidence appropriate to genomics and transcriptomics, distinguishing random uncertainty from systematic error.

Why it matters

Material weakness in contamination burden can change the direction, magnitude, certainty, or biological interpretation of the research conclusion.

Measurement criteria

Prespecified operational definition; appropriate comparator or reference; quantified uncertainty; independent or orthogonal corroboration; sensitivity analyses.

Typical methods of assessment

Structured critical appraisal; quantitative estimation with uncertainty; prespecified thresholds; independent replication; sensitivity and subgroup analyses.

Computation profile

Computation mode

RiskAssessmentComputation

Readiness

RubricOrModelRequired

Formula status

ContextSpecificProtocolRequired

Method family

risk assessment or calibrated probability estimation

Output datatype

xsd:string_or_decimal

Unit or scale

Ordinal risk rating or quantitative percentage/probability; lower is generally better

Numeric range

Context dependent

Directionality

LowerIsBetter

Required inputs

• risk_factors
• assessment_context
• rubric_or_model_version
• evidence_records

Optional inputs

• weights
• thresholds
• calibration_dataset

Machine-readable expression

{
  "language": "BEMO-Expression-JSON",
  "operator": "external_protocol",
  "protocolRef": "REQUIRED",
  "allowed_outputs": [
    "ordinal_risk_category",
    "probability",
    "percentage"
  ]
}

Computation policies

Aggregation

Not specified in source; must be defined and versioned before composite use.

Normalization

None by default; any normalization must be justified, versioned, and validated.

Missing data

Must be declared before computation; report missingness; no silent imputation; perform sensitivity analysis when material.

Uncertainty required

Yes

Uncertainty method

Confidence interval, credible interval, bootstrap distribution, inter-rater reliability, or sensitivity analysis as scientifically applicable.

Confidence interval required

Yes

Threshold policy

Prespecify, justify, version, and sensitivity-test thresholds; do not derive and evaluate on the same data without correction.

Decision thresholds

No universal threshold declared

Quality control

Source provenance; input validation; duplicate control; uncertainty reporting; independent or orthogonal validation where applicable.

Calibration

Required for probability outputs; rubric reliability required for ordinal outputs.

Applicability and validation

Evidence object

Result / experiment / study / body of evidence, as applicable

Evidence level

Result / experiment / study / body of evidence, as applicable

Study types

Whole-genome, exome, panel, bulk/single-cell/spatial transcriptomic studies

Domain

Genomics and Transcriptomics

Required data sources

Context-specific; use source references, registered studies, primary data, and authoritative biomedical resources as applicable.

Validation status

Source maturity: Established; BEMO computation profile requires independent validation.

Benchmark

A representative, versioned benchmark set is required before production use.

Reference standard

Use an independent reference standard when one exists; document expert-adjudicated alternatives.

External validation required

Yes

Interpretation safeguards

Common misinterpretations

Treating contamination burden as interchangeable with overall study quality, or interpreting a favorable value as proof that all other bias and validity domains are satisfactory.

Limitations

Depends on context, operational definition, thresholds, data quality, and evaluator judgment; it should not be used as a stand-alone summary score without domain-level evidence.

Dependency status

Not yet curated. Closely related metrics are represented; causal or computational dependencies require expert curation.

Source provenance

Source workbook

Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx

Source worksheet

Biomedical Evidence Metrics

Source row

249

Source record SHA-256

fc0cd98bc92235d469bf2bc025f0d327d8170dfb4df97b973710a8d887eff3f4

Definition source

Pure_Biomedical_Evidence_Research_Metrics_Part_2(3).xlsx row 249; see source_references

Ontology IRI

https://w3id.org/bemo/BEMO_2000242

Profile IRI

https://w3id.org/bemo/profile/BEMO_2000242

SHACL shape

https://w3id.org/bemo/shapes/BEMO_2000242_AssessmentShape

Scientific references (5)

1. https://www.fged.org/projects/miameSource framework, standard, guideline, or originSource-preserved; URL reachability not asserted by this package
2. https://www.fged.org/projects/minseqe/Source framework, standard, guideline, or originSource-preserved; URL reachability not asserted by this package
3. https://www.equator-network.org/reporting-guidelines/strobe-me/Source framework, standard, guideline, or originSource-preserved; URL reachability not asserted by this package
4. https://www.ga4gh.org/Source framework, standard, guideline, or originSource-preserved; URL reachability not asserted by this package
5. https://www.humancellatlas.org/Source framework, standard, guideline, or originSource-preserved; URL reachability not asserted by this package

Governance and FAIR status

Lifecycle

Candidate

Approval

Draft

Owner

BEMO Project

Curator

Unassigned

Reviewer

Unassigned

License

Pending owner approval; CC BY 4.0 recommended for OBO compatibility.

Findable

Provisional: stable local ID assigned; public namespace registration pending.

Accessible

Provisional: package is distributable; permanent public release location pending.

Interoperable

Yes: OWL 2, RDF, SKOS, SHACL, JSON-LD, CSV, and OBO-style identifiers.

Reusable

Provisional: rich metadata supplied; open-license owner approval pending.

Governance note

Candidate term pending scientific, ontology-engineering, and computation-method review.

Editor note

Source content preserved verbatim; computation metadata is a generated default and must be curated before normative use.