Plant Genomics

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 even when the row list is page-capped. Works for all 12 organisms (UniProt-keyed). Defaults to arabidopsis_thaliana; pass organism= for other species.

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.

Fetch KEGG pathway memberships for a plant 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. Covers: arabidopsis_thaliana, brachypodium_distachyon, glycine_max, hordeum_vulgare, oryza_sativa, populus_trichocarpa, zea_mays. Any other organism raises OrganismNotSupported before any request (both the single and batch forms). Non-Arabidopsis loci are bridged to the NCBI Entrez Gene ID KEGG indexes (returned as entrez_gene_id). A gene KEGG knows with no pathway memberships is an ok answer with pathways=[]; a gene KEGG has no record of raises NotFoundError. KEGG v118+ is case-sensitive on the locus: pass AGI loci as uppercase.

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. found=false means the gene exists but has no GeneRIF; an unknown locus raises a typed NotFoundError. Arabidopsis only.

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 (max 100).

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}, ...], TO: [...], PECO: [...]}) deduped on term_id. Planteome names genes by these locus ids for arabidopsis, rice, wheat and tomato only; other organisms are refused, and a gene Planteome has no record of is not found. Defaults to arabidopsis_thaliana; pass organism= for other species.

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.

Translate maize B73 gene-model IDs between RefGen_v4 (Zm00001d) and RefGen_v5 (Zm00001eb) with MaizeGDB's published translation table. UniProt and Ensembl Plants know only v5 IDs, so a v4 ID answers nothing there until it is translated. direction v4_to_v5 (default) or v5_to_v4. Each ID comes back mapped (targets: one, or several when the model split or merged), no_counterpart (MaizeGDB lists it with no model in the other assembly: report it as unmappable), or not_in_table (MaizeGDB does not list it, so this source says nothing about it). Gene-model IDs only, no transcript suffix; up to 1000 per call. source gives the table's URL (a link for the client to open; no tool on this server retrieves it), its Last-Modified date and sha256, so an answer can be tied to one release of the table.

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, and organism is only validated and echoed back. Passing a mismatched organism therefore still returns the locus's real group. target_organism= DOES filter: it keeps only that organism's members, before the cap, so a 2,000-member group cannot hide rice or wheat behind 'limit'.

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_thaliana; pass organism= for other species.

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 than are walked for pathways. 11 organisms have a PGDB (arabidopsis, rice, maize, soybean, grape, poplar, tomato, barley, sorghum, medicago, brachypodium); wheat is not yet mapped. Defaults to arabidopsis_thaliana (AraCyc, the best-curated); pass organism= for other species.

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 to open; no tool on this server retrieves it). This is the protein-side entry point — pair with InterPro / AlphaFold / Reactome / structural-bio tools.

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 name is still accepted, deprecated.

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 JASPAR web_url — links for the client to fetch; no tool on this server retrieves them. IMPORTANT: JASPAR's name search is fuzzy, so name-similarity hits belonging to a DIFFERENT gene are returned separately in name_only_matches and must NOT be attributed to this locus; only `motifs` is UniProt-confirmed. found=false means the gene has no curated profile (not a TF, or its family is unprofiled for that species) — a normal outcome, not an error. Use jaspar_motif to retrieve the raw matrix for any matrix_id. Coverage is Arabidopsis-heavy (1236 profiles) and thin elsewhere (maize 131, soybean 91, wheat 58, tomato 51, rice 10; Brachypodium and sorghum have none). Defaults to arabidopsis_thaliana; pass organism= for other species.

Map a batch of gene, transcript or protein IDs to EVERY UniProtKB entry UniProt's own ID mapping service returns, one job for the whole batch. Use it when a question asks for all accessions, or for many IDs at once: resolve_locus_to_uniprot returns one entry per locus (its best search hit), so a gene with several entries loses the rest. from_db names the IDs' source as UniProt does: Ensembl_Genomes for plant gene IDs such as maize Zm00001eb, rice Os01g, wheat TraesCS (the default), Ensembl_Genomes_Transcript, Ensembl_Genomes_Protein, or Araport for Arabidopsis AGIs. Each ID comes back mapped (accessions, each with entry_type and reviewed) or unmapped (UniProt lists it as failed: it maps to no entry). Up to 500 IDs per call; duplicates are collapsed. upstream_version is the UniProt release. Maize RefGen_v4 IDs (Zm00001d) are not in UniProt: translate them first with maize_gene_model_translation.

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 pathway and genes last-update dates (KEGG has no release number). pdbe, aragwas and europe_pmc publish no data release: release is null and reason says why. Backends whose answers state or pin their release (UniProt, InterPro, PANTHER, AlphaFold, Gramene, ATTED-II, OrthoDB) are not listed: read upstream_version on their answers instead.

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 other species.