Plant Genomics

Run one locus-keyed tool over up to 50 loci in one call (#131). 'tool' names any tool whose only required argument is 'locus' (interpro_domains, alphafold_structure, panther_family, orthodb_orthologs, gene_report, ...); 'args' holds that tool's other arguments, shared by every locus and checked against its schema once before any call. Returns the standard batch envelope: results keyed by locus, each exactly what the single tool returns, and per-locus errors. The dedicated batch_* tools remain.

Description is built at runtime.

Description is built at runtime.

Description is built at runtime.

Description is built at runtime.

Batch version of string_interactions. Up to 50 inputs per call. The argument was called loci_or_accessions before #129; that name is still accepted, deprecated.

Synthesis: one-call equivalent of the biological_context prompt. Resolves UniProt accession, then fans out to Gramene homologs, KEGG pathways, STRING-DB partners, and ATTED-II coexpression in parallel. Adds a consensus_partners ranking that merges STRING + ATTED scores.

Run a BLAST sequence-similarity search against NCBI BLAST URLAPI. Async Put/Get under the hood — submits the query, polls the RID (honoring NCBI's per-RID 60s floor), and returns the parsed top hits + raw text report excerpt. Programs: blastn / blastp / blastx / tblastn / tblastx. Database defaults to swissprot for protein programs, core_nt for nucleotide. Emits notifications/progress on each poll. Long searches (>10 min) raise [UpstreamUnavailableError] with the RID preserved so the client can re-poll. Set PLANT_GENOMICS_MCP_NCBI_EMAIL to identify the request per NCBI etiquette.

Synthesis: cross-source homology consensus. Resolves UniProt + FASTA sequence, then runs Gramene homology calls and NCBI BLAST in parallel. Dedupes hits by normalized locus token and scores by n_sources * mean_identity — Gramene contributes identity=1.0, BLAST contributes pident/100.

Describe an organism's Ensembl assembly (rest.ensembl.org /info/assembly; free, no key): assembly name, GCA accession and date, the karyotype, and every top-level seq-region with its length. The names are the region values ensembl_region_query takes, and a start past a region's length is refused there, so a region walk can be planned before the first call. Karyotype regions come first, in karyotype order, then unplaced scaffolds and contigs, longest first. Names are Ensembl's: tomato's chromosomes are CM001064.4 and so on, not '1'. coord_system labels differ between assemblies (chromosome, sca…

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).

List the paralogues Ensembl Compara (plants) records for a plant locus (rest.ensembl.org /homology, type=paralogues; free, no key). Each row gives the paralogue's locus, its type — within_species_paralog, or other_paralog: Ensembl's 'ancient paralogues', inferred across a super tree, so the two genes can sit in different gene trees — the taxonomy_level of the duplication, perc_id/perc_pos and protein_id, closest first. gramene_homologs carries only within_species_paralog, so a gene can have paralogues here and none there. A paralogue list is not a family list: other_paralog can name a gene out…

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. ensembl_plants_assembly lists an organism's region names and their lengths; a region outside that list, or a start past its length, is an error here. Defaults to arabidopsis_thaliana; pass organism= for other spec…

List every protein in one organism that carries an InterPro, Pfam or PANTHER entry, with the gene locus each maps to — the reverse of interpro_domains / panther_family (entry -> genes, not gene -> entries). One UniProt query (rest.uniprot.org; free, no key). Each member gives accession, symbol and locus; locus is the id the locus-keyed tools accept, or null when UniProt links the protein to no gene (e.g. an old cDNA submission). reviewed_only=true (default) keeps Swiss-Prot entries: complete for Arabidopsis and rice, empty for most other crops, so pass reviewed_only=false there. total is UniPr…

Fetch CURATED EXPERIMENTAL protein/genetic interaction partners for an Arabidopsis locus from ThaleMine (BAR's InterMine instance; free, no key), sourced from BioGRID, IntAct and PSI-MI. Unlike string_interactions (predicted / text-mined, scored) and bar_aiv_interactions (which returns GRN *paper references* for Arabidopsis, not partner pairs), every partner here carries the actual experimental provenance: detection method (two hybrid, pull down, genetic interference, ...), PSI-MI relationship type, physical vs genetic class, source database, and the PubMed IDs that reported it. ThaleMine emit…

Fetch experimentally-solved (X-ray / cryo-EM / NMR) protein structures for a locus from PDBe (www.ebi.ac.uk/pdbe; free, no key). Resolves the locus → UniProt accession, then returns PDBe's best_structures mapping ranked best-first: per entry the PDB id, chain, experimental method, resolution, coverage, and modelled residue span. Most plant proteins have NO deposited structure — that returns found=false (a normal outcome, not an error); a locus with no UniProt entry raises a typed NotFoundError. structure_count is the true total even when the list is capped. Complements alphafold_structure (the…

Synthesis: one-call equivalent of the find_homologs prompt. Runs BLAST then resolves UniProt-shaped subject accessions via the batch UniProt helper. Returns ranked hits each annotated with their UniProt record (or null if subject_id is not a UniProt accession).

Synthesis: one-shot 'tell me about this gene' dossier. Resolves a locus through Ensembl Plants + UniProt, then fans out to cross-references, KEGG pathways, STRING interactors, Europe PMC literature, and QuickGO GO terms. Returns a SynthesisEnvelope whose result.markdown is a rendered Markdown gene dossier (the headline output) alongside a structured result.sections mirror; each backend payload appears once, under sections, while steps[] carries status and per-step timing only. The literature section carries no abstracts (abstracts_included: false) and the GO section no withFrom (with_from_incl…

List the member genes of an Ensembl Compara (plants) gene tree (rest.ensembl.org /genetree; free, no key). Name the tree by locus= (any member gene, with organism=) and Ensembl finds the tree that gene is in now, or by gene_tree_id=; exactly one. A gramene_homologs gene_tree_id comes from an older Compara release and may not exist here, so prefer locus=. Each member gives the locus (the id the locus-keyed tools accept), protein_id, species and taxid, and organism (the canonical slug, or null for a species outside this server's 12). target_organism= keeps one organism's members; omit it for eve…

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.

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.

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 e…

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. 'ortholog' includes syntenic_ortholog_* rows; homoeologs (polyploid subgenome copies) come back only under 'all', and excluded_categories counts every category the filter left out. Returns target_locus + homology category (type) + shared gene_tree_id per hit (Gramene's tree id; for the tree's members pass the locus to gene_tree_members). Rows carry no taxon unless with_organism=true (adds 'organism' per r…

Fetch the InterPro domain / family architecture for a locus (www.ebi.ac.uk/interpro; free, no key). Resolves the locus → UniProt accession, then returns the protein's InterPro entries — each with accession, name, type (domain / family / homologous_superfamily / …), source_database (Pfam appears here as source_database='pfam', not a separate tool), the integrated InterPro accession, and residue spans — plus a count_by_type rollup. A protein with no annotated domains returns found=true with an empty list; a locus with no UniProt entry raises a typed NotFoundError. domain_count is the true total …

Fetch one JASPAR binding profile by matrix id, including its raw position-frequency matrix (PFM: per-base count vectors keyed A/C/G/T) plus TF class/family, assay type, source species, UniProt accessions, PubMed refs, IUPAC consensus, and the sequence-logo URL (a link for the client to fetch; no tool on this server retrieves it). The drill-down companion to tf_binding_motifs, which returns the derived consensus but not the matrix. Accepts a versioned id (MA0570.1) or a bare base id (MA0570, which resolves to the newest version). Unknown ids raise a typed NotFoundError.

Description is built at runtime.

Fetch curated GeneRIF functional statements for an Arabidopsis locus from ThaleMine (free, no key). A GeneRIF is a one-sentence, manually curated statement of what the gene does, each anchored to the PubMed ID of the publication that demonstrated it — dense, directly citable functional context that GO terms (locus_go_annotations) and raw abstracts (locus_literature) do not provide. Well-studied genes have many: HY5 (AT5G11260) has 114. Upstream order is preserved because ThaleMine supplies no meaningful ranking, so `truncated` means later statements were cut, not that they were less relevant. …

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; by_aspect_deduped_on names that key in the payload. truncated is true when numberOfHits exceeds returned — raise limit (ma…

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, abstract, and the article's web_url (a link for the client to open; no tool on this server retrieves it). 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.

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},…

List natural (germline) variants overlapping a locus's genomic span via Ensembl (rest.ensembl.org; free, no key). Resolves the locus → gene coordinates, then returns EVA/dbSNP-sourced SNPs and indels with id, source, consequence class, alleles, and clinical significance. variant_count is the true overlap total; the variant list is capped for payload size with truncated flagged. Opens the variation axis (distinct from get_sequence / ensembl_region_query). Works for all 12 organisms. Defaults to arabidopsis_thaliana; pass organism= for other species.

Resolve a locus to its OrthoDB ortholog group and cross-species member genes (data.orthodb.org; free, no key). Searches at the Viridiplantae level, then returns the group metadata (name, evolutionary rate) and member genes grouped by organism (organism, gene id, description). organism_count is the true cluster total; the member list is capped with truncated flagged. found=false when the locus maps to no ortholog group. Works for all 12 organisms. NOTE: unlike the other locus tools, organism= does NOT scope the search — the group is resolved from the locus id alone at the Viridiplantae level, a…

Fetch the PANTHER protein-family classification for a locus (pantherdb.org; free, no key). Returns the PANTHER family and subfamily (id + name) plus curated GO terms grouped by aspect (molecular_function / biological_process / cellular_component), the PANTHER protein class, and pathways. found=false when PANTHER cannot map the locus; a mapped locus can still have a null family or subfamily, which means PANTHER assigns it none. Complements the sequence-homology tools (gramene_homologs / consensus_homologs) with an evolutionary-family view. Works for all 12 organisms. Defaults to arabidopsis_tha…

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.

Fetch metabolic annotation for a locus from PlantCyc / the Plant Metabolic Network (pmn.plantcyc.org; free BioCyc web-services API, no key). Walks gene → enzyme → catalyzed reactions → PlantCyc pathways in the organism's PGDB, returning enzymes[] + reactions[] (id/name) + pathways[] (id/name) — the metabolic-pathway view KEGG and GO don't provide. A non-enzymatic gene (e.g. a transcription factor) returns found=false with empty lists, not an error. reaction_count is the true total even when the lists are capped; pathway_count is too, or null (unknown) when the gene catalyzes more reactions tha…

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). A gene symbol answers only when it names one locus; a symbol shared by several loci (ARF1) is InvalidArguments listing them. Returns primaryAccession, uniProtkbId, entryType, recommendedName, geneNames, organism, taxonId, sequenceLength, web_url (a link for the client …

Fetch protein-protein interaction partners from STRING-DB (string-db.org). Accepts either a UniProt accession or a locus identifier. A locus goes to STRING's own resolver, except for wheat, whose STRING proteins carry no locus alias: a wheat locus is resolved via UniProt first. Defaults to arabidopsis_thaliana; pass organism= for other plant species (slug, scientific/common name, or NCBI taxid). Returns first-neighbor partners with the combined STRING score plus per-channel sub-scores (experimental, database, textmining, predicted). The argument was called locus_or_accession before #129; that …

Fetch the TAIR curator-vetted Arabidopsis locus summary. Served via BAR/ThaleMine (U Toronto, Global Core Biodata Resource 2023) since TAIR's free per-locus REST API is gated behind a paid Phoenix Bioinformatics subscription. Returns TAIR curator summary + Araport11 computational description + NCBI Gene ID + cross-DB aliases (RefSeq, UniProt, TIGR locus-model IDs). Arabidopsis only. Alias of bar_gene_summary.

Fetch curated transcription-factor DNA binding motifs for a locus from JASPAR (jaspar.elixir.no; free, no key) — the cis-regulatory view. Resolves the locus → UniProt accession + gene symbol, searches JASPAR by symbol scoped to the organism's taxid, then CONFIRMS each candidate by matching the accession against the profile's uniprot_ids. Returns per motif the JASPAR matrix id, TF class/family, assay type (SELEX / ChIP-seq / PBM / DAP-seq), an IUPAC consensus derived from the position-frequency matrix (e.g. CACGTG, the G-box/ABRE core), motif length, PubMed refs, and the SVG sequence_logo and J…

Report the release a backend's own release endpoint calls current, for the backends whose answers state none (their tools' upstream_version is always null). It is read by a SEPARATE request at query time, so it is not proof of the release that answered any one call: read it before and after a run, and equal values mean no release changed in between. Never cached. ensembl_plants: the Ensembl Genomes release (e.g. '63'); string: the STRING release ('12.0'); quickgo: the GO annotation load date and the GO ontology date; jaspar: the newest ACTIVE release (several are active at once); kegg: the pat…

Predict a variant's molecular consequences with Ensembl VEP (rest.ensembl.org; free, no key). Variant-first (not locus-first): supply an Ensembl region (chr:start-end:strand, e.g. '1:10000-10000:1') and an alternate allele (e.g. 'C'); returns the most-severe consequence plus one row per overlapping transcript (consequence terms, IMPACT, and SIFT when the variant is coding-missense; the polyphen fields stay null, as Ensembl runs PolyPhen for human only). found=false when Ensembl reports no overlapping feature. Works for all 12 organisms. Defaults to arabidopsis_thaliana; pass organism= for othe…