In-depth architectural comparison of the Plant Genomics MCP and Opdstar Nhi MCP MCP servers. Compare execution transports, security boundaries, tool capabilities, quality scores, and ready-to-paste client installation snippets for Claude, Cursor, Windsurf, and VS Code.
At a Glance & Executive Verdict
Plant Genomics MCP
Biology, Medicine and Bioinformatics · Local stdio
Quality: 60/100 (Good) | Auth: No auth required
Opdstar Nhi MCP
Biology, Medicine and Bioinformatics · Local stdio
Quality: 61/100 (Good) | Auth: No auth required
Verdict Summary: Choose Plant Genomics MCP if you need specialized Biology, Medicine and Bioinformatics tools running via a local process. Choose Opdstar Nhi MCP if your workspace requires Biology, Medicine and Bioinformatics integration with local subprocess execution. Both servers can be configured concurrently in your client's mcpServers manifest.
Which MCP Server Should You Choose?
Choose Plant Genomics MCP when:
You need dedicated capabilities in the Biology, Medicine and Bioinformatics domain.
You prefer local stdio subprocess transport architecture.
Your security boundary fits: No auth required (Free / Open Source).
Fetch metadata for a plant locus identifier from Ensembl Plants. Defaults to arabidopsis_thaliana; pass organism= for other plant species (oryza_sativa, zea_mays, ...). Locus is the TAIR-style identifier (e.g. AT1G01010 for Arabidopsis NAC001).
get_gene_xrefs
Fetch cross-database references (UniProt, NCBI Gene, TAIR, ArrayExpress, …) for a plant locus from Ensembl Plants. Defaults to arabidopsis_thaliana; pass organism= for other Ensembl Plants species. Returns count + raw xref list + a by_db rollup keyed on Ensembl's dbname (e.g. 'Uniprot_gn', 'EntrezGene') for fast lookup of a single foreign identifier.
get_sequence
Fetch a locus's sequence from Ensembl Plants. seq_type is one of genomic / cds / cdna / protein (default protein — the canonical-transcript product). Closes the lookup → fetch → BLAST loop: feed the returned `sequence` straight to blast_sequence (protein for blastp, cds/cdna for blastn). Defaults to arabidopsis_thaliana; pass organism= for other plant species.
ensembl_region_query
List features overlapping a genomic interval via Ensembl Plants /overlap/region. region is the seq-region name (chromosome / contig, e.g. '1'); start and end are 1-based inclusive. feature is one of gene / transcript / cds / exon (default gene). Answers 'what genes are in this QTL interval / assembly window' without a per-locus lookup. Ensembl caps the span — oversized regions error. Defaults to arabidopsis_thaliana; pass organism= for other species.
Ready-to-Paste Client Configurations
Paste either (or both) of these JSON server blocks into your client config file (e.g. claude_desktop_config.json or ~/.cursor/mcp.json).
Plant Genomics MCP is categorized under Biology, Medicine and Bioinformatics and uses a local stdio subprocess. In contrast, Opdstar Nhi MCP belongs to Biology, Medicine and Bioinformatics using local stdio subprocess. Select Plant Genomics MCP when you need capabilities focused on biology, medicine and bioinformatics and Opdstar Nhi MCP when you require tools for biology, medicine and bioinformatics.
Fetch a gene record from Phytozome BioMart (phytozome-next.jgi.doe.gov). Defaults to arabidopsis_thaliana; pass organism= for other Phytozome proteomes (slug, scientific/common name, or NCBI taxid — e.g. glycine_max, sorghum_bicolor). Locus is the source-genome gene name (e.g. AT1G01010, Glyma.01G000100). Returns organism_name, gene_name, chromosome, gene_start, gene_end, strand, description.
resolve_locus_to_uniprot
Resolve a plant locus to its canonical UniProtKB record. Prefers reviewed (Swiss-Prot) entries; falls back to unreviewed (TrEMBL) when no curated record exists (common for non-Arabidopsis plants). organism accepts a canonical slug, scientific/common name, or NCBI taxid (default arabidopsis_thaliana; e.g. oryza_sativa, zea_mays). Returns primaryAccession, uniProtkbId, entryType, recommendedName, geneNames, organism, taxonId, sequenceLength, web_url. This is the protein-side entry point — pair with InterPro / AlphaFold / Reactome / structural-bio tools.
locus_literature
Search Europe PMC for literature mentioning a plant locus. Free, no API key. Returns up to `size` results (default 10, capped at 25) with title, authors, journal, year, DOI, PMID, open-access status, citation count, and abstract. For non-Arabidopsis species the species common name is appended to the query to disambiguate locus IDs (rice, maize, ...). Pair with resolve_locus_to_uniprot or ensembl_plants_lookup_locus to ground the locus before fanning out to the literature.
locus_go_annotations
Fetch Gene Ontology annotations for a plant locus from QuickGO (EBI). Free, no API key. The locus is first resolved to a UniProt accession via the same logic as resolve_locus_to_uniprot, then QuickGO is queried by geneProductId. Returns annotations[] with goId/goName/goAspect/qualifier/evidence + a by_aspect rollup ({molecular_function: [{goId, goName}, ...], biological_process: [...], cellular_component: [...]}) deduped on goId so the high-level term set is one read away.
locus_plant_ontology
Fetch Plant Ontology (PO) + Trait Ontology (TO) + experimental-condition (PECO) annotations for a plant locus from Planteome (browser.planteome.org, AmiGO2/GOlr; free, no API key). Complements locus_go_annotations: QuickGO serves GO (species-agnostic), Planteome serves the plant-specific ontologies — PO (anatomy + developmental stage), TO (traits). The locus is matched across Planteome's searchable bioentity fields and filtered by the organism's NCBI taxon. Returns annotations[] (term_id / term_name / ontology / aspect / evidence / reference) + a by_ontology rollup ({PO: [{term_id, term_name}, ...], TO: [...], PECO: [...]}) deduped on term_id. Coverage is strong for arabidopsis, rice, maize, grape, soybean, tomato; other organisms return an empty list, not an error. Defaults to arabidopsis_thaliana; pass organism= for other species.
go_enrichment
GO + KEGG over-representation analysis for a gene LIST via g:Profiler g:GOSt (biit.cs.ut.ee/gprofiler; free, no API key). Unlike locus_go_annotations (one locus → its terms), this answers 'what is my gene SET enriched for?' — the dominant question for a differential-expression or co-expression cluster. loci is the query gene list (e.g. AT-codes for Arabidopsis, RAP-DB IDs for rice). sources defaults to GO:BP/GO:MF/GO:CC + KEGG; user_threshold is the g:SCS-corrected significance cutoff (default 0.05). Optional background sets a custom statistical domain (default: all annotated genes). Returns enriched[] (term_id/name/p_value/intersection_size/…, capped at top_n by p-value) plus unmapped[] — query loci g:Profiler could not recognize, surfaced so a locus-namespace mismatch is visible. Defaults to arabidopsis_thaliana; pass organism= for any of the 12 species.
gramene_homologs
Fetch orthologs and paralogs for a plant locus from Gramene compara (data.gramene.org v69). Default homology_type='ortholog'; pass 'paralog' for in-species duplicates or 'all' for everything. Returns target_locus + homology category (type) + shared gene_tree_id per hit. The fl=homology projection does not carry per-row taxon, identity, or protein ID; pair with resolve_locus_to_uniprot for protein-level enrichment and with blast_sequence for sequence similarity discovery.
kegg_pathways
Fetch KEGG pathway memberships for an Arabidopsis locus from rest.kegg.jp. Returns a list of pathway IDs + names + KEGG category classes the locus participates in. Pairs with locus_go_annotations for the GO-level functional view. Multi-organism caveat (v1.1.0): the organism= field accepts any plant in the matrix for symmetry with the other backends, but only arabidopsis_thaliana resolves — KEGG uses NCBI Entrez Gene IDs for rice/maize/etc. and our cross-backend locus contract can't produce those yet, so any other organism raises OrganismNotSupported before any HTTP call. KEGG v118+ is case-sensitive on the locus: pass AGI loci as uppercase.
+38 more tools listed on main page
Opdstar Nhi MCP Tools (24)
lookup_rejection_code
Look up a single Taiwan NHI rejection code (5-character format `NNNNL` — 4 digits + 1 uppercase letter A/B/C/..., e.g. '0317A', '0338A', '0114A'). Returns severity (low / medium / high), category (00 診療品質 · 01 病歷紀錄 · 02 基本診療 · 03 藥品特材 · 04 手術處置 · 05 檢查檢驗 · 06 論病例計酬 · 07 復健精神 · 08 其他 · 09 法令 — first two digits encode the category), and the official Chinese description from 健保署 專業審查不予支付理由代碼. Returns a not-found message (not an error) if the code does not exist. **Use when** an agent encounters a known rejection code in a notice or claim response and needs the human-readable explanation, or when triaging which category a code belongs to. **Typical follow-up**: call `get_drug_rules({rejection_code})` if the code is in category 03 (藥品特材) to surface the drug rule behind the rejection; call `search_audit_guidelines({query: <code>})` for codes in 04 / 05 to read the underlying audit-clause text; call `count_appeal_precedents_for_rejection_code({rejection_code})` to gauge whether disputes for this code are commonly successful. **Don't use** to enumerate codes by category — call `get_rejection_code_category({category})` instead. **Reference only** — the official 健保署 code list is authoritative. Curated by OPDSTAR (https://opdstar.com).
get_procedures_for_icd
Given a Taiwan ICD-10 code and a medical specialty, return the NHI procedure codes plausibly applicable to that diagnosis within that specialty. Each result includes the procedure code, Chinese name, English name, nhi_points (payment points), and audit_notes (specialty-specific review caveats and risk hints). Results are ordered by curated relevance (most commonly applied codes first), capped at `limit` (default 10, max 20). Returns an empty list (not an error) when no curated mapping exists for the given (icd10, specialty) pair — this is common because the mapping is intentionally conservative. **Use when** an agent is drafting SOAP and needs a starting set of procedure codes for the diagnosis within the clinician's specialty context — e.g. dermatologist with `L30.9` (chronic eczema) needs candidate procedure codes. **Typical follow-up**: for each candidate code, call `lookup_fee_code({q: <code>})` to confirm current points and effective dates, and `lookup_audit_clauses_for_procedure({procedure_code})` to surface any audit-clause caveats. **Don't use** as a billing source of truth — the original NHI fee schedule has no ICD field, this is a curated, intentionally conservative mapping that prefers false negatives over false positives; for the canonical fee-schedule entry of a known code, call `lookup_fee_code`. **Reference only** — final code selection remains the clinician's responsibility. Curated by OPDSTAR (https://opdstar.com).
get_indicator
Look up a single Taiwan NHI prescribing-pattern indicator. These are short codes (numeric, or 'P'-prefixed) that encode common over-prescribing patterns such as antibiotic-on-URI, multi-drug co-prescribing, or duration limits. Returns the indicator name, the threshold (e.g. '7-day URI episode'), applicable drugs / diagnoses, and the compliance meaning. Returns a not-found message (not an error) if the code does not exist. **Use when** an agent needs the human-readable explanation for a specific indicator code referenced during a SOAP review or audit response — e.g. an audit notice cites an indicator and the agent needs to surface what it monitors and why a prescription tripped it. **Typical follow-up**: call `get_drug_rules({rejection_code})` with the indicator's downstream rejection code to read the formal payment rule, or `search_audit_guidelines({query})` to read related audit-clause text. **Don't use** for the official 分析審查不予支付指標 (percentage-cap audit) list — that's a different system — call `lookup_audit_indicator` instead. **Reference only** — thresholds and applicable lists reflect published guidance and may change with each NHI release; agents should re-read the indicator each session rather than caching values across sessions. Curated by OPDSTAR (https://opdstar.com).
search_nhi_wiki
Search across Taiwan's official NHI knowledge base (健保署全球資訊網) for natural-language background questions. Covers 9 categories: audit (審查 — review rules / rejection grounds), drugs (藥品特材 — formulary, payment limits), fees (費用 — copay, premiums, contribution), plans (醫療計畫 — disease-management programs), services (醫療服務 — covered benefits), insurance (投保 — enrollment), forms (表單 — applications), records (紀錄 — documentation rules), admin (行政 — contracting, accreditation). Returns up to 10 ranked excerpts (most relevant first); each result includes title, content snippet, source URL, and category tag. Returns an empty list (not an error) when the query has no matches. **Use when** an agent needs broad NHI policy background not tied to a specific code — e.g. '慢性病連續處方箋天數上限' / 'how does balance billing work for orthodontics' / 'what are the rules for telemedicine reimbursement'. **Typical follow-up**: when an excerpt mentions a specific code (e.g. '0317A', '00101B'), call the appropriate code-specific tool (`lookup_rejection_code`, `lookup_fee_code`) for the canonical entry. **Don't use** when you already know a specific rejection code, procedure code, drug name, or audit-clause topic — those have dedicated tools that return structured fields rather than excerpts. **Reference only** — official 健保署 publications are authoritative; ranked excerpts may lag the latest revision and the snippet is not the full document. Curated by OPDSTAR (https://opdstar.com).
search_nhi_interpretations
Search Taiwan's official NHI administrative interpretations (健保署行政函釋 / 函令) — the binding 公告 and 解釋函 issued by the National Health Insurance Administration that clarify how payment rules, drug-formulary provisions, special-material coverage, and review policy apply in practice. Each result returns the official document number (字號), issue date, 主旨 (subject), a content excerpt, and the source URL on the government law portal. Returns up to 10 ranked excerpts (most relevant first); returns an empty list (not an error) when nothing matches. **Use when** a question turns on an official ruling rather than a code definition — e.g. '函釋怎麼說人工水晶體的給付規定' / 'is there an interpretation on continuous-prescription day limits' — or when the user cites a 函釋 文號 directly (e.g. 健保審字第 1090017813 號). **Don't use** when you already have a specific rejection code, fee code, or drug name — those have dedicated lookup tools (`lookup_rejection_code`, `lookup_fee_code`, `lookup_drug`). **Reference only** — the official 健保署 / 衛福部 publication is authoritative; an excerpt may lag the latest revision and is not the full document, so open the source URL for the binding text. Curated by OPDSTAR (https://opdstar.com).
get_drug_rules
Look up Taiwan NHI drug payment rules (藥品給付規定) — when a drug class is / isn't reimbursable, with severity and source citation. Filter by `specialty`, `rejection_code`, or `drug_category_query` (at least one required). **Use when** an agent is checking whether a drug choice will trigger a rejection before submission, or wants to read the rule behind a known rejection code. **Don't use** to identify a specific drug (brand / generic / strength) — call `lookup_drug` instead; for the underlying audit clauses, use `lookup_audit_clauses_for_procedure` or `lookup_audit_clauses_for_specialty`. **Reference only** — official 健保藥品給付規定 is authoritative; curated subset, not exhaustive. Curated by OPDSTAR (https://opdstar.com).
get_safe_phrases
Preview which documentation scenarios have OPDSTAR-curated NHI-safe phrasing patterns for a given specialty (e.g. dermatology + 抗生素) — returns scenario name, high-risk wording to avoid, the key difference, and the first sentence of the safe-phrasing example. Up to 5 scenarios per call. **Use when** an agent is helping draft SOAP wording and needs to flag risky phrasing before submission. **Don't use** to retrieve full ready-to-copy templates (full library is part of the paid OPDSTAR product — link the user to opdstar.com); for the underlying audit rule that motivates a safe phrase, call `search_audit_guidelines`. **Reference only** — phrasing patterns reflect curated review experience, not formal NHI directives. Curated by OPDSTAR (https://opdstar.com).
search_audit_guidelines
Free-text search over Taiwan NHI 審查注意事項 rules — returns reason + suggestion summaries (first sentence only) for up to 10 rules matching a keyword (Traditional Chinese or English). **Use when** an agent is exploring whether any audit rule covers a topic (e.g. '抗生素', '檢查頻率', '慢性病處方') without knowing a specific code. **Don't use** for clauses tied to a known procedure code — call `lookup_audit_clauses_for_procedure` instead. Full SOAP example templates and detailed reasoning are part of the paid OPDSTAR product. **Reference only** — official 健保署 審查注意事項 is authoritative; results are previews. Curated by OPDSTAR (https://opdstar.com).
get_rejection_code_category
Browse Taiwan NHI rejection codes by category (00-09) for discovery — returns code, severity, and short description, up to 50 per call. Categories: 00 診療品質 · 01 病歷紀錄 · 02 基本診療 · 03 藥品特材 · 04 手術處置 · 05 檢查檢驗 · 06 論病例計酬 · 07 復健精神 · 08 其他 · 09 法令. **Use when** an agent needs to enumerate all rejection codes within a workflow domain (e.g. all surgery-handling codes). **Don't use** to look up a known specific code — call `lookup_rejection_code` instead. **Reference only** — official 健保署 不予支付理由代碼 is authoritative. Curated by OPDSTAR (https://opdstar.com).
lookup_drug
Look up the active Taiwan NHI drug catalog by generic name, brand name, NHI drug code, or alias — returns up to 10 matches with strength, dosage form, route, ATC code, therapeutic class, and brand list. **Use when** an agent needs to identify or disambiguate a drug before recommending dosage / formulation in a SOAP draft. **Don't use** to look up payment / reimbursement rules for the drug — call `get_drug_rules` instead; for an audit clause referencing the drug, call `search_audit_guidelines`. **Reference only** — official 健保署 藥品給付項目及支付標準 is authoritative; the catalog is a working snapshot. Curated by OPDSTAR (https://opdstar.com).
lookup_fee_code
Look up the Taiwan NHI fee schedule (全民健康保險醫療服務給付項目及支付標準, current effective edition). Search by exact code (e.g. '00101B', 'P15001') or by Chinese / English name (e.g. '門診診察', 'ICU') — returns code, points, effective dates, and audit notes (truncated to 600 chars). Use `category` prefix to scope ('00' 基本診療, '06' 手術, 'P1' 病例計酬, 'N2' 護理). **Use when** an agent needs the canonical fee entry for a known procedure code, or wants to discover codes by name. **Don't use** for drugs (call `lookup_drug`) or for ICD-10 → procedure suggestions (call `get_procedures_for_icd`). The optional `icd` filter applies an OPDSTAR-curated mapping that is intentionally sparse (the original NHI data has no ICD field) — most codes will return no result with `icd` active. **Reference only** — official 健保署 支付標準 is authoritative. Curated by OPDSTAR (https://opdstar.com).
lookup_audit_clauses_for_procedure
Find Taiwan NHI 審查注意事項 clauses that reference a specific procedure code (e.g. '00101B', '51017C') — each result indicates whether the clause carries an amount limit, frequency rule, or indication restriction (critical signals for rejection-risk assessment). Returns clause summary, specialty, and risk flags. **Use when** an agent has a candidate procedure code and needs to surface the audit context attached to it. **Don't use** for the procedure's fee-schedule entry (points / effective dates) — call `lookup_fee_code`; for browsing all clauses within a specialty, call `lookup_audit_clauses_for_specialty`. **Reference only** — clause summaries are first-sentence previews; official 健保署 審查注意事項 is the source of truth. Curated by OPDSTAR (https://opdstar.com).
32 tools for plant-genomics locus lookup across 11 public backends (Ensembl Plants, Phytozome, UniProtKB, KEGG, STRING-DB, Gramene, Europe PMC, QuickGO, NCBI BLAST, ATTED-II, BAR). Single-locus, parallel-batch, and cross-source synthesis variants; JSON output schemas and EDAM ontology tags on every tool. pipx install plant-genomics-mcp.
Taiwan's first public MCP server for National Health Insurance (NHI) data — 234 rejection codes, 1,497 ICD-10→procedure mappings across 20 specialties, audit indicators (008/014/027/P043), and semantic wiki search over 8,232 chunks of official NHI documentation. Powered by OPDSTAR. Install: npx @opdstar/nhi-mcp.