New Project Integration Pattern

Purpose

New completed projects should change the Atlas only where they improve synthesis, evidence, reuse, or review routing. The goal is not to mention every project everywhere; it is to decide which existing Atlas statements the project strengthens, weakens, redirects, or makes newly testable.

Intake Steps

1. Read the project report, review, and generated-data tables before editing Atlas pages.
2. Classify each project as one or more of: topic deepener, claim creator, claim modifier, conflict resolver, conflict creator, opportunity source, derived-product candidate, or data-gap evidence.
3. Update existing topic pages before creating new pages.
4. Create a claim only when the result is reusable outside the source project.
5. Update or create a conflict when the project complicates an existing story or exposes a necessary control.
6. Add project IDs to frontmatter only on pages where the project changes the synthesis.

Integration Map From This Pass

• lanthanide_methylotrophy_atlas: creates a reusable rare-earth biology claim and changes the critical-minerals synthesis from "REE data absent" to "direct REE fitness absent, but pangenome marker evidence is now substantial."
• prophage_amr_comobilization: creates a mobile-context AMR claim and strengthens AMR and mobile-element topics.
• microbeatlas_metal_ecology: creates a field-ecology claim that metal type diversity predicts niche breadth after phylogenetic control.
• metal_resistance_global_biogeography: supports global metal-resistance mapping but stays caveat-heavy because spatial validation and sampling-effort correction remain pending.
• soil_metal_functional_genomics: strengthens metal-environment association synthesis while adding confounds around co-contamination, conditional R2, and proximity joins.
• harvard_forest_warming: strengthens the field-validation topic by showing how DNA and RNA functional pools can converge after long-term warming and how design confounds can reverse apparent omics-layer conclusions.
• t4ss_cazy_environmental_hgt: strengthens the mobile-element topic by connecting T4SS, CAZy HGT, and metal-resistance enrichment.
• soil_frontier_genomics: contributes mainly as a data-gap and validation-method signal, not as a settled biological claim.

Exit Criteria

An integration pass is complete when Atlas lint passes, inventory shows no new orphaned pages, every new claim has evidence metadata, and every touched topic has a clear "what changed" statement rather than a project list.

How Agents Should Use This Page

Use this method after any merged project batch. Treat it as a checklist for deciding whether the Atlas needs a topic edit, a claim, a conflict, an opportunity, or no change.