Our RAG development methodology for Boston institutions prioritizes retrieval accuracy, source attribution, and domain-specific optimization. Phase 1 — Knowledge Base Design: the foundation of any RAG system is the quality of its document corpus: document inventory and prioritization (cataloging all available document sources: clinical guidelines, case law databases, financial filings, institutional documents — prioritizing by: authority, currency, usage frequency, and user need), document processing pipeline (building the ingestion pipeline: document parsing (extracting text from PDFs, HTML, DOCX — handling: multi-column layouts, tables, figures, headers/footers, and footnotes), chunking strategy (splitting documents into retrieval units — the critical design decision that determines RAG quality. Too large: the retrieved chunk contains irrelevant information that dilutes the LLM's context. Too small: the retrieved chunk lacks the context needed for the LLM to understand the information. We use: semantic chunking (splitting at paragraph or section boundaries that preserve meaning), overlapping chunks (each chunk includes context from adjacent sections), and hierarchical chunking (parent-child relationships between summary chunks and detail chunks)), and metadata extraction (extracting: document type, publication date, author/authority, section headings, and domain-specific metadata — enabling filtered retrieval that narrows search to the most relevant document subset)). Phase 2 — Embedding and Indexing: converting documents into searchable vector representations: embedding model selection (evaluating domain-specific embedding models: for clinical RAG: PubMedBERT embeddings, BioLORD, or general-purpose models fine-tuned on medical text, for legal RAG: Legal-BERT embeddings or general-purpose models fine-tuned on legal text, for financial RAG: FinBERT embeddings or general-purpose models fine-tuned on financial text — domain-specific embeddings typically outperform general-purpose embeddings by 15-25% on domain-specific retrieval tasks), vector database selection (choosing the vector store: Pinecone (managed, scalable, production-ready), Weaviate (open-source, hybrid search, flexible schema), pgvector (PostgreSQL extension — good for teams already using PostgreSQL), or Qdrant (high-performance, efficient filtering) — selection depends on: scale, filtering requirements, infrastructure preferences, and budget), hybrid search implementation (combining vector (semantic) search with keyword (BM25) search — because: semantic search excels at finding conceptually related content even when the exact terms differ, keyword search excels at finding exact matches for specific terms, medical codes, case citations, and financial identifiers — and the combination outperforms either approach alone by 10-20% on most retrieval benchmarks), and re-ranking (applying a cross-encoder re-ranker to the top candidates from initial retrieval — re-ranking with a model like Cohere Rerank or a cross-encoder BERT produces significantly better relevance ordering than vector similarity alone). Phase 3 — Generation Pipeline: building the query-to-answer pipeline: query understanding (analyzing the user's question to determine: the information need, relevant filters (date range, document type, jurisdiction, specialty), and the expected answer format (factual answer, summary, comparison, citation list)), retrieval orchestration (executing the search: initial retrieval (hybrid search across the vector database), filtering (applying metadata filters based on query analysis), re-ranking (cross-encoder scoring of top candidates), and context assembly (selecting the optimal set of passages to include in the LLM prompt — balancing: relevance, diversity, and context window constraints)), prompt engineering (designing the system prompt and retrieval-augmented prompt: instructing the LLM to: answer based only on the provided context, cite specific sources for each claim, indicate when the provided context is insufficient to answer the question, and distinguish between what the sources say and what can be inferred), and citation generation (mapping the LLM's response back to source documents: inline citations (linking each claim to the specific passage that supports it), source cards (displaying the retrieved documents with highlighted relevant passages), and confidence scoring (indicating the strength of evidence for each part of the answer)). Phase 4 — Evaluation and Optimization: systematic measurement and improvement: retrieval evaluation (measuring: precision at k (are the top-k results relevant?), recall (are all relevant documents being found?), and mean reciprocal rank (how high does the first relevant result appear?) — using domain expert-created evaluation sets), generation evaluation (measuring: faithfulness (does the response accurately represent the source material?), relevance (does the response answer the user's question?), and completeness (does the response include all important information from the retrieved sources?)), end-to-end evaluation (measuring: answer accuracy against expert-verified ground truth, citation accuracy (do the citations actually support the claims?), and user satisfaction (do domain experts find the answers useful and trustworthy?)), and continuous improvement (analyzing: queries where retrieval failed (relevant documents not surfaced), queries where generation failed (correct documents retrieved but answer was wrong), and new documents that need to be ingested (keeping the knowledge base current)).