Entity spans, relation triples with evidence sentences, and QA answers with confidence scores. BioBERT is deprecated and chat cannot call it.

BioBERT returns extracted entities, relationship triples, or answers — each with a type and a confidence score, exportable as annotated text, CSV, or JSON. Use these to feed knowledge graphs, prioritize targets, or support literature-review workflows.

Not available in chat

BioBERT is deprecated on the platform and not registered with the orchestrator, so chat cannot call it. A current LLM performs BioBERT's entity extraction and relevance ranking natively over text retrieved with PubMed; for curated identifiers an LLM must not invent (NCBI Gene IDs, MeSH terms), use PubTator3. Existing BioBERT job results remain viewable.

Output formats

Named Entity Recognition (NER)

Annotated text:

Entity spans with start/end positions
Entity type classifications
Confidence scores per entity

CSV export:

text,entity,type,start,end,confidence
"BRCA1 mutation...",BRCA1,GENE,0,5,0.98

Relation Extraction (RE)

Relationship triples:

Subject entity (with type)
Relationship type
Object entity (with type)
Evidence sentence
Confidence score

CSV export:

subject,subject_type,relation,object,object_type,evidence,confidence
Aspirin,DRUG,inhibits,COX-2,PROTEIN,"Aspirin inhibits...",0.94

Question Answering (QA)

Answer extraction:

Extracted answer text
Answer span in source
Supporting context
Confidence score

Entity types

Type	Description	Examples
GENE	Genes and proteins	BRCA1, p53, insulin
DISEASE	Diseases and conditions	cancer, diabetes
CHEMICAL	Chemicals and drugs	aspirin, glucose
SPECIES	Organisms	human, mouse, E. coli
MUTATION	Genetic variants	V600E, c.248T>C
CELL	Cell types	T cells, neurons

Confidence interpretation

High (>0.9): Very confident prediction
Medium (0.7-0.9): Confident, suitable for most uses
Low (0.5-0.7): Less certain, review recommended
Very low (<0.5): Not output by default

Canvas Visualization

When a BioBERT job completes, a result card appears on the canvas.

Card size: 400x300px
Border color: Brown (#795548)
Visualization: Entity network showing extracted entities and relationships

Tier 2 Metrics

Entity count by type (genes, proteins, diseases, compounds)
Relation count
Entity types extracted
Confidence scores per entity

BioBERT outputs & interpretation