Add TYQ1 nematode biocontrol SynCom (closes #25)

[cmungall]

Summary

• Add new community YAML: kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml
• 8-member SynCom centered on keystone species Rhizobium pusense TYQ1, which is enriched during root-knot nematode (Meloidogyne incognita) infection of cucumber
• TYQ1 recruits 7 biomarker species (Sphingomonas panni, Sphingomonas sp., Acidovorax soli, Acidovorax facilis, Novosphingobium subterraneum, Xenophilus aerolatus, Microbacterium arborescens) that enhance biofilm formation and metabolic cross-feeding for synergistic nematode suppression
• Based on PMID:41660888 (Liu et al., ISME J. 2025, doi:10.1093/ismejo/wrag022)
• Validated across 12 soil types; 3 associated BioProject datasets (PRJNA1313845, PRJNA1313795, PRJNA1314495)
• Passes just validate against the LinkML schema

Closes #25

Test plan

• just validate kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml passes with no issues

🤖 Generated with Claude Code

[Copilot]

Pull request overview

Adds a new curated microbial community entry to the knowledge base for the TYQ1-centered nematode biocontrol SynCom described in PMID:41660888, expanding the set of engineered rhizosphere communities represented in kb/communities/.

Changes:

• Introduces a new community YAML for the TYQ1 Nematode Biocontrol SynCom (engineered rhizosphere SynCom).
• Captures member taxonomy (8 taxa), interaction summaries, and linked BioProject datasets with evidence snippets.

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[Copilot]

The Sphingomonas xanthus SX entry uses a genus-level NCBITaxon ID (NCBITaxon:13687, label Sphingomonas) while the preferred_term claims a species-level identification (Sphingomonas xanthus). This is internally inconsistent and can mislead downstream consumers (e.g., taxonomy summaries). Either update the taxon name to genus-level (e.g., Sphingomonas sp./Sphingomonas sp. SX) to match the ID+label, or switch to a species-level NCBITaxon ID if available.