BioBERT inputs & parameters
Research query, max results, similarity threshold and entity-type options, with 512-token segments. BioBERT is deprecated and chat cannot call it.
You provide a research query or biomedical text — typed, uploaded, or fetched from PubMed — along with the task and entity types to extract. The similarity threshold most shapes what comes back: it sets the relevance cutoff that decides which papers and entities are kept.
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.
Webapp input methods
The .bloom* webapp provides a streamlined interface for BioBERT literature search.
Query input
- Label: "Research Query"
- Placeholder: "Enter your research question or keywords..."
- Character limit: Displayed as
{current}/{max}counter - Example queries (click to use):
- "CRISPR gene editing COVID-19 treatment"
- "Alzheimer's disease tau protein aggregation"
- "mRNA vaccine immunogenicity mechanisms"
- "CAR-T cell therapy cancer treatment"
- "Machine learning drug discovery"
Webapp parameters
Basic settings
| Parameter | Range | Default | Description |
|---|---|---|---|
| Max Results | 1-500 | 100 | Papers to retrieve |
| Similarity Threshold | 0-1 | 0.7 | Relevance cutoff (slider with 0.5/0.7/0.9 marks) |
Analysis options (checkboxes)
| Option | Default | Description |
|---|---|---|
| Semantic Analysis | Enabled | AI-powered content understanding |
| Extract Biomedical Entities | Enabled | Genes, proteins, diseases, chemicals |
| Generate AI Summaries | Enabled | Automated abstract summarization |
| Citation Analysis | Disabled | Analyze citation networks |
Advanced filters (accordion panel)
| Parameter | Description |
|---|---|
| Date From | Filter papers published on or after date |
| Date To | Filter papers published on or before date |
| Include Full Abstracts | Include complete abstract text (checkbox, default: enabled) |
Submit button
- Label: "Start Literature Search"
- Disabled when: Query is empty
- Icon: Search icon
Job progress
- EstimatedTimeWidget: Shows expected processing time
- Live ETA: Real-time completion estimate during processing
- Phase tracking: Progress through analysis phases
Accepted inputs
Text formats:
- Plain text (.txt)
- PDF documents (text extraction)
- CSV with text column
- JSON with text field
PubMed integration:
- PubMed IDs (PMIDs) for automatic fetch
- PubMed search queries
- PMC article IDs
Text preprocessing
- Automatic sentence segmentation
- Tokenization with biomedical vocabulary
- Special character handling
- Unicode normalization
Model configuration
Task selection:
- Named Entity Recognition (NER)
- Relation Extraction (RE)
- Question Answering (QA)
Entity type filtering:
- Genes/Proteins
- Diseases
- Chemicals/Drugs
- Species
- Cell types
- Mutations
Confidence thresholds:
- Minimum confidence for entity output
- Default: 0.5 (adjustable 0.1-0.9)
Input limits
- Text length: Up to 512 tokens per segment
- Batch size: Up to 1000 documents per job
- File size: Maximum 50MB per upload
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BioBERT API & automation
BioBERT job payloads for the ner, re and qa tasks and the entity-span JSON they return. BioBERT is deprecated and chat cannot call it.
BioBERT limits & performance
512-token segments with 64-token overlap, 1,000-document batches and 50MB uploads. BioBERT is deprecated and chat cannot call it.