GLiNKER - Entity Linking Framework

A modular, production-ready entity linking framework combining NER, multi-layer database search, and neural entity disambiguation.

Overview

GLiNKER is a modular entity linking pipeline that transforms raw text into structured, disambiguated entity mentions. It's designed for:

Production use: Multi-layer caching (Redis → Elasticsearch → PostgreSQL)
Research flexibility: Fully configurable YAML pipelines
Performance: Embedding precomputation for BiEncoder models
Scalability: DAG-based execution with batch processing

GLiNKER is built around GLiNER — a family of lightweight, generalist models for information extraction. It brings several key advantages to the entity linking pipeline:

Zero-shot recognition — Identify any entity type by simply providing label names. No fine-tuning or annotated data required. Switch from biomedical genes to legal entities by changing a list of strings.
Unified architecture — A single model handles both NER (L1) and entity disambiguation (L3/L4), reducing deployment complexity and keeping the inference stack consistent.
Efficient BiEncoder support — BiEncoder variants allow precomputing label embeddings once and reusing them across millions of documents, delivering 10–100× speedups for large-scale linking.
Compact and fast — Base models are small enough to run on CPU, while larger variants scale with GPU for production throughput.
Open and extensible — Apache 2.0 licensed models on Hugging Face, easy to swap for domain-specific fine-tunes when needed.

Models

NER (L1)

Model name	Params	Text Encoder	Label Encoder	Avg. CrossNER	Inference Speed (H100, ex/s)	Inference Speed (pre-computed)
gliner-bi-edge-v2.0	60 M	ettin-encoder-32m	all-MiniLM-L6-v2	54.0%	13.64	24.62
gliner-bi-small-v2.0	108 M	ettin-encoder-68m	all-MiniLM-L12-v2	57.2%	7.99	15.22
gliner-bi-base-v2.0	194 M	ettin-encoder-150m	bge-small-en-v1.5	60.3%	5.91	9.51
gliner-bi-large-v2.0	530 M	ettin-encoder-400m	bge-base-en-v1.5	61.5%	2.68	3.60

Linking (L3)

Model	Base Encoder	Use Case
gliner-linker-base-v1.0	deberta-base	Balanced performance
gliner-linker-large-v1.0	deberta-large	Maximum accuracy

Reranking (L4)

Model	Base Encoder	Use Case
gliner-linker-rerank-v1.0	ettin-encoder-68m	Reranking

Traditional vs GLiNKER Approach

# Traditional approach: Complex, coupled code
ner_results = spacy_model(text)
candidates = search_database(ner_results)
linked = gliner_model.disambiguate(candidates)
# Mix of models, databases, and business logic

# GLiNKER approach: Declarative configuration
from glinker import ConfigBuilder, DAGExecutor

builder = ConfigBuilder(name="biomedical_el")
builder.l1.gliner(model="knowledgator/gliner-bi-base-v2.0", labels=["gene", "protein", "disease"])
builder.l2.add("redis", priority=2).add("postgres", priority=0)
builder.l3.configure(model="knowledgator/gliner-linker-large-v1.0")

executor = DAGExecutor(builder.get_config())
result = executor.execute({"texts": ["CRISPR-Cas9 enables precise gene therapy"]})

Quick Start

Installation

Install easily using pip:

pip install git+https://github.com/Knowledgator/GLinker.git

Or install from source for development purposes:

git clone https://github.com/Knowledgator/GLinker.git
cd GLinker
pip install -e .

# With optional dependencies
pip install -e ".[dev,demo]"

30-Second Example

from glinker import ConfigBuilder, DAGExecutor

# 1. Build configuration
builder = ConfigBuilder(name="demo")
builder.l1.spacy(model="en_core_web_sm")
builder.l3.configure(model="knowledgator/gliner-linker-large-v1.0")

# 2. Create executor
executor = DAGExecutor(builder.get_config())

# 3. Load entities
executor.load_entities("data/entities.jsonl", target_layers=["dict"])

# 4. Process text
result = executor.execute({
    "texts": ["Farnese Palace is one of the most important palaces in the city of Rome."]
})

# 5. Get results
l0_result = result.get("l0_result")
for entity in l0_result.entities:
    if entity.linked_entity:
        print(f"{entity.mention_text} → {entity.linked_entity.label}")
        print(f"  Confidence: {entity.linked_entity.score:.3f}")

Output:

BRCA1 → BRCA1: Breast cancer type 1 susceptibility protein
  Confidence: 0.923
breast cancer → Breast Cancer: Malignant neoplasm of the breast
  Confidence: 0.887

Creating Pipelines

GLiNKER offers three ways to create a pipeline, from simplest to most configurable.

Option 1: `create_simple` (recommended start)

ProcessorFactory.create_simple builds a L2 → L3 → L0 pipeline in one call. No NER step — the model links entities directly from the input text against all loaded entities.

from glinker import ProcessorFactory

# Minimal — just a model name
executor = ProcessorFactory.create_simple(
    model_name="knowledgator/gliner-bi-base-v2.0",
    threshold=0.5,
)

# Load entities and run
executor.load_entities("data/entities.jsonl")
result = executor.execute({"texts": ["CRISPR-Cas9 enables precise gene therapy."]})

With inline entities (no file needed):

executor = ProcessorFactory.create_simple(
    model_name="knowledgator/gliner-bi-base-v2.0",
    threshold=0.5,
    entities=[
        {"entity_id": "Q101", "label": "insulin", "description": "Peptide hormone regulating blood glucose"},
        {"entity_id": "Q102", "label": "glucose", "description": "Primary blood sugar and key metabolic fuel"},
        {"entity_id": "Q103", "label": "GLUT4", "description": "Insulin-responsive glucose transporter in muscle and adipose tissue"},
        {"entity_id": "Q104", "label": "pancreatic beta cell", "description": "Endocrine cell type that secretes insulin"},
    ],
)

result = executor.execute({
    "texts": [
        "After a meal, pancreatic beta cells release insulin, which promotes GLUT4 translocation and increases glucose uptake in muscle."
    ]
})

With a reranker (L2 → L3 → L4 → L0):

executor = ProcessorFactory.create_simple(
    model_name="knowledgator/gliner-bi-base-v2.0",
    threshold=0.5,
    reranker_model="knowledgator/gliner-multitask-large-v0.5",
    reranker_max_labels=20,
    reranker_threshold=0.3,
    entities="data/entities.jsonl",
    precompute_embeddings=True,
)

With entity descriptions in the template:

executor = ProcessorFactory.create_simple(
    model_name="knowledgator/gliner-bi-base-v2.0",
    template="{label}: {description}",  # L3 sees "BRCA1: Breast cancer type 1 susceptibility protein"
    entities="data/entities.jsonl",
)

All create_simple parameters:

Parameter	Default	Description
`model_name`	(required)	HuggingFace model ID or local path
`device`	`"cpu"`	Torch device (`"cpu"`, `"cuda"`, `"cuda:0"`)
`threshold`	`0.5`	Minimum score for entity predictions
`template`	`"{label}"`	Format string for entity labels (e.g. `"{label}: {description}"`)
`max_length`	`512`	Max sequence length for tokenization
`token`	`None`	HuggingFace auth token for gated models
`entities`	`None`	Entity data to load immediately (file path, list of dicts, or dict of dicts)
`precompute_embeddings`	`False`	Pre-embed all entity labels after loading (BiEncoder only)
`verbose`	`False`	Enable verbose logging
`reranker_model`	`None`	GLiNER model for L4 reranking (adds L4 node when set)
`reranker_max_labels`	`20`	Max candidate labels per L4 inference call
`reranker_threshold`	`None`	Score threshold for L4 (defaults to `threshold`)

Option 2: From a YAML config file

For full control over every layer, define the pipeline in YAML and load it:

from glinker import ProcessorFactory

executor = ProcessorFactory.create_pipeline("configs/pipelines/dict/simple.yaml")
executor.load_entities("data/entities.jsonl")
result = executor.execute({"texts": ["TP53 mutations cause cancer"]})

See YAML Configuration Reference for full config examples.

Option 3: `ConfigBuilder` (programmatic)

Build configs in Python with full control over each layer:

from glinker import ConfigBuilder, DAGExecutor

builder = ConfigBuilder(name="my_pipeline")
builder.l1.gliner(model="knowledgator/gliner-bi-base-v2.0", labels=["gene", "disease"])
builder.l3.configure(model="knowledgator/gliner-linker-large-v1.0")

executor = DAGExecutor(builder.get_config())
executor.load_entities("data/entities.jsonl", target_layers=["dict"])

With multiple database layers:

builder = ConfigBuilder(name="production")
builder.l1.gliner(model="knowledgator/gliner-bi-base-v2.0", labels=["gene", "protein"])
builder.l2.add("redis", priority=2, ttl=3600)
builder.l2.add("elasticsearch", priority=1, ttl=86400)
builder.l2.add("postgres", priority=0)
builder.l3.configure(model="knowledgator/gliner-linker-large-v1.0", use_precomputed_embeddings=True)
builder.l0.configure(strict_matching=True, min_confidence=0.3)
builder.save("config.yaml")

With L4 reranker:

builder = ConfigBuilder(name="reranked")
builder.l1.gliner(model="knowledgator/gliner-bi-base-v2.0", labels=["gene", "disease"])
builder.l3.configure(model="knowledgator/gliner-linker-base-v1.0")
builder.l4.configure(
    model="knowledgator/gliner-linker-rerank-v1.0",
    threshold=0.3,
    max_labels=20,
)
builder.save("config.yaml")  # Generates L1 → L2 → L3 → L4 → L0

Loading Entities

Entities can be loaded after pipeline creation via executor.load_entities(), or passed directly to create_simple(entities=...). Three input formats are supported.

From a JSONL file

One JSON object per line:

executor.load_entities("data/entities.jsonl")

# Or target specific database layers
executor.load_entities("data/entities.jsonl", target_layers=["dict", "postgres"])

data/entities.jsonl:

{"entity_id": "Q123", "label": "Kyiv", "description": "Capital and largest city of Ukraine", "entity_type": "city", "popularity": 1000000, "aliases": ["Kiev"]}
{"entity_id": "Q456", "label": "Dnipro River", "description": "Major river flowing through Ukraine and Belarus", "entity_type": "river", "popularity": 950000, "aliases": ["Dnieper"]}
{"entity_id": "Q789", "label": "Carpathian Mountains", "description": "Mountain range in Central and Eastern Europe", "entity_type": "mountain_range", "popularity": 800000, "aliases": ["Carpathians"]}

From a Python list

entities = [
    {
        "entity_id": "Q123",
        "label": "Kyiv",
        "description": "Capital and largest city of Ukraine",
        "entity_type": "city",
        "aliases": ["Kiev"],
    },
    {
        "entity_id": "Q456",
        "label": "Dnipro River",
        "description": "Major river flowing through Ukraine and Belarus",
        "entity_type": "river",
        "aliases": ["Dnieper"],
    },
]

executor.load_entities(entities)

From a Python dict

Keys are entity IDs, values are entity data:

entities = {
    "Q123": {
        "label": "Kyiv",
        "description": "Capital and largest city of Ukraine",
        "entity_type": "city",
    },
    "Q456": {
        "label": "Dnipro River",
        "description": "Major river flowing through Ukraine and Belarus",
        "entity_type": "river",
    },
}

executor.load_entities(entities)

Entity format reference

Field	Type	Required	Default	Description
`entity_id`	str	yes	—	Unique identifier
`label`	str	yes	—	Primary name
`description`	str	no	`""`	Text description (used in templates like `"{label}: {description}"`)
`entity_type`	str	no	`""`	Category (e.g. `"gene"`, `"disease"`)
`aliases`	list[str]	no	`[]`	Alternative names for search matching
`popularity`	int	no	`0`	Ranking score for candidate ordering

Architecture

GLiNKER uses a layered pipeline with an optional reranking stage:

Layer	Purpose	Processor
L1	Mention extraction (spaCy or GLiNER NER)	`l1_spacy`, `l1_gliner`
L2	Candidate retrieval from database layers	`l2_chain`
L3	Entity disambiguation via GLiNER	`l3_batch`
L4	(Optional) GLiNER reranking with candidate chunking	`l4_reranker`
L0	Aggregation, filtering, and final output	`l0_aggregator`

Supported topologies:

Full pipeline:       L1 → L2 → L3 → L0
With reranking:      L1 → L2 → L3 → L4 → L0
Simple (no NER):          L2 → L3 → L0
Simple + reranker:        L2 → L4 → L0

Key Concepts:

DAG Execution: Layers execute in dependency order with automatic data flow
Component-Processor Pattern: Each layer has a Component (methods) and Processor (orchestration)
Schema Consistency: Single template (e.g., "{label}: {description}") across layers
Cache Hierarchy: Upper layers cache results from lower layers automatically

Features

Multiple NER Backends

spaCy — Fast, rule-based NER for standard use cases
GLiNER — Neural NER with custom labels (no training required)

Multi-Layer Database Support

Dict — In-memory (perfect for demos)
Redis — Fast cache (production)
Elasticsearch — Full-text search with fuzzy matching
PostgreSQL — Persistent storage with pg_trgm fuzzy search

Performance Optimization

Embedding Precomputation — Cache label embeddings for BiEncoder models
Cache Hierarchy — Automatic write-back: Redis → ES → PostgreSQL
Batch Processing — Efficient parallel processing

L4 Reranker (Optional)

When the candidate set from L2 is large (tens or hundreds of entities), a single GLiNER call may be impractical. The L4 reranker solves this by splitting candidates into chunks:

100 candidates, max_labels=20  →  5 GLiNER inference calls
Results merged, deduplicated, filtered by threshold

L4 uses a uni-encoder GLiNER model and can be placed after L3 (true reranking) or used directly after L2 (replacing L3):

# Via ConfigBuilder
builder.l4.configure(
    model="knowledgator/gliner-multitask-large-v0.5",
    threshold=0.3,
    max_labels=20   # candidates per inference call
)

# Via create_simple
executor = ProcessorFactory.create_simple(
    model_name="knowledgator/gliner-bi-base-v2.0",
    reranker_model="knowledgator/gliner-multitask-large-v0.5",
    reranker_max_labels=20,
)

YAML Configuration Reference

YAML configs give full control over every node in the pipeline. Load them with:

from glinker import ProcessorFactory

executor = ProcessorFactory.create_pipeline("path/to/config.yaml")

Simple pipeline (L2 → L3 → L0, no NER)

Equivalent to create_simple. No L1 node — texts are passed directly to L2/L3:

name: "simple"
description: "Simple pipeline - L3 only with entity database"

nodes:
  - id: "l2"
    processor: "l2_chain"
    inputs:
      texts:
        source: "$input"
        fields: "texts"
    output:
      key: "l2_result"
    schema:
      template: "{label}"
    config:
      max_candidates: 30
      min_popularity: 0
      layers:
        - type: "dict"
          priority: 0
          write: true
          search_mode: ["exact"]

  - id: "l3"
    processor: "l3_batch"
    requires: ["l2"]
    inputs:
      texts:
        source: "$input"
        fields: "texts"
      candidates:
        source: "l2_result"
        fields: "candidates"
    output:
      key: "l3_result"
    schema:
      template: "{label}"
    config:
      model_name: "knowledgator/gliner-bi-base-v2.0"
      device: "cpu"
      threshold: 0.5
      flat_ner: true
      multi_label: false
      use_precomputed_embeddings: true
      cache_embeddings: false
      max_length: 512

  - id: "l0"
    processor: "l0_aggregator"
    requires: ["l2", "l3"]
    inputs:
      l2_candidates:
        source: "l2_result"
        fields: "candidates"
      l3_entities:
        source: "l3_result"
        fields: "entities"
    output:
      key: "l0_result"
    config:
      strict_matching: false
      min_confidence: 0.0
      include_unlinked: true
      position_tolerance: 2

Full pipeline with spaCy NER (L1 → L2 → L3 → L0)

name: "dict_default"
description: "In-memory dict layer with spaCy NER"

nodes:
  - id: "l1"
    processor: "l1_spacy"
    inputs:
      texts:
        source: "$input"
        fields: "texts"
    output:
      key: "l1_result"
    config:
      model: "en_core_sci_sm"
      device: "cpu"
      batch_size: 1
      min_entity_length: 2
      include_noun_chunks: true

  - id: "l2"
    processor: "l2_chain"
    requires: ["l1"]
    inputs:
      mentions:
        source: "l1_result"
        fields: "entities"
    output:
      key: "l2_result"
    schema:
      template: "{label}: {description}"
    config:
      max_candidates: 5
      layers:
        - type: "dict"
          priority: 0
          write: true
          search_mode: ["exact", "fuzzy"]
          fuzzy:
            max_distance: 64
            min_similarity: 0.6

  - id: "l3"
    processor: "l3_batch"
    requires: ["l2"]
    inputs:
      texts:
        source: "$input"
        fields: "texts"
      candidates:
        source: "l2_result"
        fields: "candidates"
    output:
      key: "l3_result"
    schema:
      template: "{label}: {description}"
    config:
      model_name: "knowledgator/gliner-linker-large-v1.0"
      device: "cpu"
      threshold: 0.5
      flat_ner: true
      multi_label: false
      max_length: 512

  - id: "l0"
    processor: "l0_aggregator"
    requires: ["l1", "l2", "l3"]
    inputs:
      l1_entities:
        source: "l1_result"
        fields: "entities"
      l2_candidates:
        source: "l2_result"
        fields: "candidates"
      l3_entities:
        source: "l3_result"
        fields: "entities"
    output:
      key: "l0_result"
    config:
      strict_matching: true
      min_confidence: 0.0
      include_unlinked: true
      position_tolerance: 2

Pipeline with L4 reranker (L1 → L2 → L3 → L4 → L0)

Use when the candidate set is large. L4 splits candidates into chunks of max_labels and runs GLiNER inference on each chunk:

name: "dict_reranker"
description: "In-memory dict with L4 GLiNER reranking"

nodes:
  - id: "l1"
    processor: "l1_gliner"
    inputs:
      texts:
        source: "$input"
        fields: "texts"
    output:
      key: "l1_result"
    config:
      model: "knowledgator/gliner-bi-base-v2.0"
      labels: ["gene", "drug", "disease", "person", "organization"]
      device: "cpu"

  - id: "l2"
    processor: "l2_chain"
    requires: ["l1"]
    inputs:
      mentions:
        source: "l1_result"
        fields: "entities"
    output:
      key: "l2_result"
    schema:
      template: "{label}: {description}"
    config:
      max_candidates: 100
      layers:
        - type: "dict"
          priority: 0
          write: true
          search_mode: ["exact", "fuzzy"]

  - id: "l3"
    processor: "l3_batch"
    requires: ["l1", "l2"]
    inputs:
      texts:
        source: "$input"
        fields: "texts"
      candidates:
        source: "l2_result"
        fields: "candidates"
    output:
      key: "l3_result"
    schema:
      template: "{label}: {description}"
    config:
      model_name: "knowledgator/gliner-linker-base-v1.0"
      device: "cpu"
      threshold: 0.5
      use_precomputed_embeddings: true

  - id: "l4"
    processor: "l4_reranker"
    requires: ["l1", "l2", "l3"]
    inputs:
      texts:
        source: "$input"
        fields: "texts"
      candidates:
        source: "l2_result"
        fields: "candidates"
      l1_entities:
        source: "l1_result"
        fields: "entities"
    output:
      key: "l4_result"
    schema:
      template: "{label}: {description}"
    config:
      model_name: "knowledgator/gliner-multitask-large-v0.5"
      device: "cpu"
      threshold: 0.3
      max_labels: 20          # candidates per inference call

  - id: "l0"
    processor: "l0_aggregator"
    requires: ["l1", "l2", "l4"]
    inputs:
      l1_entities:
        source: "l1_result"
        fields: "entities"
      l2_candidates:
        source: "l2_result"
        fields: "candidates"
      l3_entities:
        source: "l4_result"   # L0 reads from L4 instead of L3
        fields: "entities"
    output:
      key: "l0_result"
    config:
      strict_matching: true
      min_confidence: 0.0
      include_unlinked: true

Simple pipeline with reranker only (L2 → L4 → L0, no L1/L3)

Skips both NER and L3 — L4 handles entity linking directly with chunked inference:

name: "simple_reranker"
description: "Simple pipeline with L4 reranker - no L1 or L3"

nodes:
  - id: "l2"
    processor: "l2_chain"
    inputs:
      texts:
        source: "$input"
        fields: "texts"
    output:
      key: "l2_result"
    schema:
      template: "{label}: {description}"
    config:
      max_candidates: 100
      layers:
        - type: "dict"
          priority: 0
          write: true
          search_mode: ["exact"]

  - id: "l4"
    processor: "l4_reranker"
    requires: ["l2"]
    inputs:
      texts:
        source: "$input"
        fields: "texts"
      candidates:
        source: "l2_result"
        fields: "candidates"
    output:
      key: "l4_result"
    schema:
      template: "{label}: {description}"
    config:
      model_name: "knowledgator/gliner-multitask-large-v0.5"
      device: "cpu"
      threshold: 0.5
      max_labels: 20

  - id: "l0"
    processor: "l0_aggregator"
    requires: ["l2", "l4"]
    inputs:
      l2_candidates:
        source: "l2_result"
        fields: "candidates"
      l3_entities:
        source: "l4_result"
        fields: "entities"
    output:
      key: "l0_result"
    config:
      strict_matching: false
      min_confidence: 0.0
      include_unlinked: true

Production config with multiple database layers

name: "production_pipeline"

nodes:
  - id: "l2"
    processor: "l2_chain"
    config:
      layers:
        - type: "redis"
          priority: 2
          ttl: 3600
        - type: "elasticsearch"
          priority: 1
          ttl: 86400
        - type: "postgres"
          priority: 0

Use Cases

Biomedical Text Mining

builder.l1.gliner(
    model="knowledgator/gliner-bi-base-v2.0",
    labels=["gene", "protein", "disease", "drug", "chemical"]
)

News Article Analysis

builder.l1.spacy(model="en_core_web_lg")
# Link to Wikidata/Wikipedia entities

Clinical NLP

builder.l1.gliner(
    model="knowledgator/gliner-bi-base-v2.0",
    labels=["symptom", "diagnosis", "medication", "procedure"]
)

Advanced Features

Precomputed Embeddings (BiEncoder)

For BiEncoder models, precomputing label embeddings gives 10–100× speedups:

# Load entities, then precompute
executor.load_entities("data/entities.jsonl")
executor.precompute_embeddings(batch_size=64)

# Or do both in create_simple
executor = ProcessorFactory.create_simple(
    model_name="knowledgator/gliner-bi-base-v2.0",
    entities="data/entities.jsonl",
    precompute_embeddings=True,
)

On-the-Fly Embedding Caching

Instead of precomputing all embeddings upfront, cache them as they are computed during inference:

builder.l3.configure(
    model="knowledgator/gliner-linker-large-v1.0",
    cache_embeddings=True,
)

Custom Pipelines

# Custom L1 processing pipeline
l1_processor = processor_registry.get("l1_spacy")(
    config_dict={"model": "en_core_sci_sm"},
    pipeline=[
        ("extract_entities", {}),
        ("filter_by_length", {"min_length": 3}),
        ("deduplicate", {}),
        ("sort_by_position", {})
    ]
)

Database Setup

Quick Start (Docker)

# Start all databases
cd scripts/database
docker-compose up -d

# Load entities
python scripts/database/setup_all.sh

Manual Setup

from glinker import DAGExecutor

executor = DAGExecutor(pipeline)
executor.load_entities(
    filepath="data/entities.jsonl",
    target_layers=["redis", "elasticsearch", "postgres"],
    batch_size=1000
)

Testing

# Run all tests
pytest

# Run specific layer tests
pytest tests/l1/
pytest tests/l2/

# Run with coverage
pytest --cov=glinker --cov-report=html

Citations

If you find GLiNKER useful in your research, please consider citing our papers:

@misc{stepanov2024glinermultitaskgeneralistlightweight,
      title={GLiNER multi-task: Generalist Lightweight Model for Various Information Extraction Tasks},
      author={Ihor Stepanov and Mykhailo Shtopko},
      year={2024},
      eprint={2406.12925},
      archivePrefix={arXiv},
      primaryClass={cs.LG},
      url={https://arxiv.org/abs/2406.12925},
}

Contributing

We welcome contributions! Areas of interest:

Database layers (MongoDB, Neo4j, vector databases)
Performance optimizations
Documentation improvements

License

Apache 2.0 License — see LICENSE file for details.

Acknowledgments

GLiNER — Zero-shot NER and entity linking (urchade/GLiNER)
spaCy — Industrial-strength NLP (explosion/spaCy)

Contact

GitHub: Knowledgator/GLinker
Email: info@knowledgator.com

Developed by Knowledgator

Name		Name	Last commit message	Last commit date
Latest commit History 64 Commits
configs/pipelines		configs/pipelines
data		data
docs		docs
example		example
logo		logo
papers		papers
scripts/database		scripts/database
src/glinker		src/glinker
tests		tests
.gitignore		.gitignore
LICENSE		LICENSE
MANIFEST.in		MANIFEST.in
README.md		README.md
demo.py		demo.py
pyproject.toml		pyproject.toml
pytest.ini		pytest.ini
requirements.txt		requirements.txt
setup.py		setup.py

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GLiNKER - Entity Linking Framework

Overview

Models

NER (L1)

Linking (L3)

Reranking (L4)

Traditional vs GLiNKER Approach

Table of Contents

Quick Start

Installation

30-Second Example

Creating Pipelines

Option 1: create_simple (recommended start)

Option 2: From a YAML config file

Option 3: ConfigBuilder (programmatic)

Loading Entities

From a JSONL file

From a Python list

From a Python dict

Entity format reference

Architecture

Features

Multiple NER Backends

Multi-Layer Database Support

Performance Optimization

L4 Reranker (Optional)

YAML Configuration Reference

Simple pipeline (L2 → L3 → L0, no NER)

Full pipeline with spaCy NER (L1 → L2 → L3 → L0)

Pipeline with L4 reranker (L1 → L2 → L3 → L4 → L0)

Simple pipeline with reranker only (L2 → L4 → L0, no L1/L3)

Production config with multiple database layers

Use Cases

Biomedical Text Mining

News Article Analysis

Clinical NLP

Advanced Features

Precomputed Embeddings (BiEncoder)

On-the-Fly Embedding Caching

Custom Pipelines

Database Setup

Quick Start (Docker)

Manual Setup

Testing

Citations

Contributing

License

Acknowledgments

Contact

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Option 1: `create_simple` (recommended start)

Option 3: `ConfigBuilder` (programmatic)

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