Document complete CultureBotAI project ecosystem with tool interconnections

Add comprehensive project ecosystem section showing how all 12 repositories work together, enabling users to understand tool relationships and workflows. Add 5 missing repositories (PFASCommunityAgents, CultureMech, eggnog_runner, eggnogtable, MATE-LLM, MicroGrowLinkService) with detailed descriptions and relationship mappings.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: realmarcin

index.md

@@ -36,6 +36,17 @@ Read our bioRxiv preprint by Dr. Marcin P. Joachimiak detailing the development
 ### 📊 [METPO Ontology](https://github.com/Knowledge-Graph-Hub/kg-microbe/tree/main/src/kg_microbe/transform/metpo)
 Microbial experimental and theoretical preference ontology for standardizing growth preference data.
 
+## How Our Tools Work Together
+
+CultureBotAI's projects form an integrated ecosystem built on the [kg-microbe knowledge graph](https://github.com/Knowledge-Graph-Hub/kg-microbe):
+
+- **Data processing pipelines** prepare chemical, genomic, and literature data
+- **AI agent systems** combine multiple data sources for intelligent predictions
+- **Specialized applications** target specific research domains (PFAS, lanthanide)
+- **Web services** provide API access to prediction models
+
+[Explore the complete project ecosystem →](/resources/#project-ecosystem--workflows)
+
 ---
 
 ## Frequently Asked Questions

kg-microbe.md

@@ -60,6 +60,27 @@ The **Microbial Experimental and Theoretical Preference Ontology (METPO)** provi
 - **Knowledge Discovery**: Identify novel microbial relationships
 - **Data Mining**: Extract patterns from large-scale microbial datasets
 
+## Projects Built on KG-Microbe
+
+The kg-microbe knowledge graph serves as the foundation for numerous CultureBotAI projects:
+
+### Data Integration Projects
+- **CultureMech & MicroMediaParam** - Integrate chemical compound data with standardized identifiers
+- **assay-metadata** - Add phenotypic assay results from 99K+ BacDive strains
+- **MATE-LLM** - Extract and integrate literature-derived cultivation data
+- **eggnogtable** - Map genome functional annotations to ontology terms
+
+### Prediction & Analysis Tools
+- **MicroGrowAgents** - Multi-agent system using kg-microbe for evidence-based media design
+- **MicroGrowLink** - Graph transformer models trained on kg-microbe structure
+- **PFAS-AI & PFASCommunityAgents** - PFAS biodegradation using microbial relationships
+- **CMM-AI** - Lanthanide bioprocessing research leveraging metabolic data
+
+### Web Services
+- **MicroGrowLinkService** - RESTful API providing programmatic access to predictions
+
+[Explore all projects and their relationships →](/resources/#project-ecosystem--workflows)
+
 ## Access and Usage
 
 ### Repository

research.md

@@ -97,26 +97,35 @@ Expanding kg-microbe capabilities for:
 - Novel organism property inference
 - Integration with laboratory information systems
 
+## Tools Supporting Our Research
+
+Our research goals are enabled by a suite of interconnected software tools:
+
+### For Cultivation of Novel Organisms
+- [MicroGrowAgents](/resources/#microgrowagents) - AI-driven media design with multi-agent reasoning
+- [MicroGrowLink](/resources/#microgrowlink) - Graph-based growth prediction using transformers
+- [MATE-LLM](/resources/#mate-llm) - Literature protocol extraction with LLMs
+
+### For Culture Optimization
+- [CultureMech](/resources/#culturemech) - Chemical compound processing pipeline
+- [MicroMediaParam](/resources/#micromediaparam) - Media composition analysis and mapping
+- [microbe-rules](/resources/#microbe-rules) - ML model optimization and comparison
+
+### For Growth Preference Prediction
+- [kg-microbe](/kg-microbe/) - Knowledge graph foundation with 864K+ validated species
+- [assay-metadata](/resources/#assay-metadata-bacdive-api-assay-metadata-extractor) - Phenotypic assay data from BacDive
+- [eggnog_runner & eggnogtable](/resources/#eggnog_runner) - Genome functional annotation
+
+[See all tools and workflows →](/resources/)
+
 ## Collaborative Research
 
 We actively collaborate with:
 - **Academic institutions** developing novel cultivation techniques
-- **Industry partners** scaling up microbial production processes  
+- **Industry partners** scaling up microbial production processes
 - **Government laboratories** studying environmental microorganisms
 - **Open source communities** building computational biology tools
 
-## Future Directions
-
-### Short-term Goals (1-2 years)
-- Release production version of kg-microbe knowledge graph
-- Deploy automated culture monitoring in partner laboratories
-- Publish comprehensive growth prediction models
-
-### Long-term Vision (3-5 years)  
-- Achieve high success rate in novel organism cultivation
-- Enable fully automated microbial cultivation pipelines
-- Integrate CultureBotAI tools into standard laboratory workflows
-
 ---
 
 ## Publications & Preprints