Identity
DOI, PMID, or another persistent identifier; complete authorship; ORCID iDs; ROR organization identifiers.
Report the joins, not just the layers.
Genomics, metabolomics, microbiomics, and metallomics become useful together only when samples, methods, units, uncertainty, and causal limits survive publication in a form others can connect.
Ingestibility standard
This page describes the information that helps WikiBiome evaluate and connect a work. Completing it does not guarantee citation, visibility, acceptance, or favorable treatment.
Keystone editorial designation
Keystone remains a separate graph-based judgment applied only after acceptance. It cannot be purchased or claimed by an author or institution.
Read the Keystone criteria →Make every finding inspectable.
Study frame
Structured abstract, study design, cohort and sample definitions, controls, exclusions, timepoints, and covariates.
Reproducibility
Methods, pipeline and database versions, quality controls, data and code links, and reuse license.
Results
Effect sizes, uncertainty, units, negative findings, missingness, and multiplicity handling—not significance alone.
Transparency
Funding, conflicts of interest, protocol or registration links, data restrictions, and known limitations.
Add every module your study touches.
Microbiome module
Make the biological observation traceable through the entire assay pipeline.
- Sampling site, method, timing, storage conditions, and freeze–thaw history
- Extraction method, kit or reagent lots where material, sequencing or assay platform
- Reference database and version, taxonomic resolution, normalization and filtering
- Negative and positive controls, batch effects, contamination identification and handling
- Bioinformatics pipeline, software versions, thresholds, and deposited reads or feature tables
Metallomics module
Treat the element measurement as a first-class biological layer, not a background covariate.
- Biological matrix and collection materials, including tubes, needles, closures, and potential metal contamination
- Digestion or preparation method; analytes; oxidation state, binding form, or chemical species where measured
- Instrument and acquisition mode; calibration range; reference materials; internal standards
- Procedural and field blanks, recovery, drift, carryover, matrix effects, and contamination controls
- Reported units, wet/dry-weight basis, dilution, detection and quantification limits, and censoring treatment
- An explicit statement of whether metal speciation was measured; total-element concentration must not be presented as speciation
Cross-omics module
Preserve the joins that make interdisciplinary interpretation possible.
- Shared, pseudonymized sample identifiers and aligned timepoints across every assay
- Covariate definitions and transformations applied consistently across layers
- Integration method, model assumptions, validation strategy, and multiplicity correction
- Direction and scale of cross-layer associations with uncertainty
- Mechanistic hypothesis separated from observation, plus explicit causal limitations
- A machine-readable map of samples, assays, features, units, and provenance
At least three of five graph-based criteria.
Evaluation happens after editorial acceptance and asks whether the work changes the structure or interpretation of WikiBiome’s evidence graph.
- Cross-domain bridgeConnects otherwise separate biological domains.
- Structural dependencyMultiple important claims depend on the work.
- Cross-condition reachProvides evidence relevant across conditions.
- Mechanistic explanationExplains a pathway or interaction rather than only correlating features.
- Interpretive changeMaterially changes how the surrounding evidence is understood.
Submission packet template
Copy this checklist into a README, repository, supplementary file, or data dictionary and replace every bracketed prompt.
# WikiBiome-Ready Research Packet ## Persistent identity - DOI / PMID / preprint: [identifier] - Complete authors: [names + ORCID iDs] - Institutions: [names + ROR identifiers] - License: [metadata, text, data, code] ## Study frame - Design and registration: [details] - Cohort / sample / controls / exclusions: [definitions] - Timepoints and covariates: [table or data dictionary] - Funding and conflicts: [complete disclosure] ## Methods and results - Methods, software, databases, and versions: [links] - Quality controls and negative findings: [details] - Effect sizes, uncertainty, units, missingness: [details] - Data and code: [persistent links + access conditions] ## Domain modules - Microbiome: [sampling → storage → extraction → assay → pipeline → contamination controls] - Metallomics: [matrix → materials → preparation → analytes/species → instrument → calibration/QC → units/LOD/LOQ] - Cross-omics: [shared sample IDs/timepoints → aligned covariates → integration → multiplicity → causal limits] ## Editorial context - Main claims supported: [claims] - Limitations readers must retain: [limitations] - Related work: [persistent identifiers]