Documentation PlantQTLdb Assistant External Biological Evidence Sources
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Getting Started with Assistant Gene Structure and Sequence Extraction Variant Annotation and Local QTL Evidence Functional Enrichment with g:Profiler Network Analysis with STRING Finding Sequencing Data with ENA Sequence Similarity Search with BLAST Plant Motif Analysis with JASPAR and FIMO DNA Analysis with Evo2 External Biological Evidence Sources Troubleshooting and Limitations

PlantQTLdb Assistant

External Biological Evidence Sources

understand the protein, ontology, pathway, expression and literature sources used during evidence investigation

Requires Research mode

Open PlantQTLdb Assistant

How these sources are used

Research can select external evidence tools according to the question, supported identifiers and remaining investigation budget. These sources are not six additional sequence-analysis jobs; a question may use only the relevant subset. Inspect the named source in the answer rather than assuming every source was queried.

Sources and their roles

UniProtKB
Protein function, accession, sequence and annotation context. Review curation and evidence labels.
QuickGO
GO annotations and their evidence codes. Annotation lookup is different from gene-set enrichment.
Gramene
Plant gene identifiers and comparative or annotation context; check species and reference version.
Plant Reactome
Plant pathway context. Species coverage and projected annotations affect interpretation.
Expression Atlas
Public baseline or differential expression context. Compare tissue, condition and experimental design.
PubTator
Literature entities and supporting text. An entity mention is not proof of a mechanistic relationship.

How to ask and what you receive

Investigate a candidate gene

ask
Summarize functional evidence for rice LOC_Os01g25484, separating database annotations, expression evidence and findings from the literature

what you receive

A source-labelled evidence summary and references when available, with unresolved gaps. Source selection depends on the actual retrieval; this request does not guarantee a query to every external database.

Ask about the strength of support

ask
What evidence links rice LOC_Os01g25484 to traits? Distinguish association results from direct experimental support

what you receive

An evidence investigation separating indexed associations from cited experimental claims, with source links and limitations where available. Missing retrieved evidence does not establish biological absence.

Verify before citing

  • Follow original source records and publications, checking organism, identifier mapping, assay and evidence code.
  • Keep reported observations separate from model interpretation. Database absence, failed retrieval and a contradictory experimental result are different situations.
  • Some requests return an evidence summary and citations rather than an analysis result card. Only explicit supported analysis operations should be expected to produce their dedicated charts.