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Graph Configuration Reference

Graph configurations orchestrate one or more table configurations into a single knowledge-graph build — author one to produce KGX output with tablassert build-kg (see the CLI reference). To check a single table config on its own, use tablassert validate <table.yaml> --schema table.

Purpose

A graph configuration file specifies: - Output knowledge graph name, version, and description - List of table configurations to process - Database location for entity resolution - Resource Ingest Guide (RIG) metadata (contributions and UI explanation)

QC auditing and verbose logging are controlled at build time via the build-kg --qc and build-kg --log flags — they are not graph-config fields.

Schema

Required Fields

Field Type Description
name String Knowledge graph name (used in output filenames and the RIG)
version String Knowledge graph version (used in output filenames)
description String Source-scope description written into the generated RIG
tables List[Path] Paths to table configuration YAML files
fullmap Path Path to the fullmap redb file, or a base directory containing it

Optional Fields

Field Type Description
contributions List[String] RIG contribution statements for graph provenance. Defaults to ["Tablassert: KGX and RIG generation"]
ui_explanation String RIG explanation applied to generated edge-type metadata. Defaults to a built-in description of how Tablassert transforms source records into Biolink associations
infores String Graph-level infores: CURIE emitted as the default Biolink primary_knowledge_source and RIG source_info.infores_id. Defaults to infores:<kebab-name> derived from name

Field Details

Notes beyond the tables above:

  • version — common values: "1.0.0", "UNSTABLE", "BETA".
  • infores — must start with infores:; a name like MULTIOMICS_KG derives infores:multiomics-kg. Set it when the graph's Translator information resource differs from the output name, or a non-PMC/PMID source KG needs a stable manually-curated infores.
  • tables — paths are absolute or relative to the process CWD (not the graph-config file location; there is no config-relative resolver). See Table Configuration.
  • fullmap — a redb file or a base directory containing it, resolved via fullmap_db_path(). See Fullmap for build commands and schema.

Minimal Example

name: MY_GRAPH
version: 1.0.0
description: Knowledge graph built from configured tabular source data.
infores: infores:my-graph
tables:
  - ./my-table.yaml
fullmap: /data/fullmap

Multi-Table Example

name: MULTIOMICS_KG
version: UNSTABLE
description: Multi-omics knowledge graph integrating gene-disease, drug-target, and protein-interaction tables.
tables:
  - /configs/gene-disease-associations.yaml
  - /configs/drug-targets.yaml
  - /configs/protein-interactions.yaml
fullmap: /databases/fullmap

Processing Flow

When you run tablassert build-kg graph.yaml:

  1. Load graph configuration - Parse YAML, validate schema
  2. Load table configurations - Parse each YAML in tables
  3. Extract sections - Expand templates into per-section Tcode instances
  4. Collect instructions (per section):
  5. Read the source file from disk (source.local)
  6. Apply transformations and resolve entities using fullmap
  7. Validate with the QC audit when build-kg --qc is passed
  8. Build subgraphs - Compile each section's resolved data into a parquet file
  9. Compile graph - Aggregate all subgraph parquets and export {name}_{version}.nodes.ndjson / .edges.ndjson / .RIG.yaml

Output Files

Given this configuration: 

name: EXAMPLE_KG
version: 2.0.0

Produces: - EXAMPLE_KG_2.0.0.nodes.ndjson - EXAMPLE_KG_2.0.0.edges.ndjson - EXAMPLE_KG_2.0.0.RIG.yaml

Real-World Example

From MOKGV6.yaml:

name: MULTIOMICS_KG
version: UNSTABLE
description: Multi-omics knowledge graph derived from the ALAMV6 tabular source.
tables:
  - /local_raid1/sgoetz/STORE/CONFIG/TABLASSERT/TABLE/V6/ALAMV6.yaml
fullmap: /local_raid1/sgoetz/CODE/FULLMAP/fullmap

This processes a single table configuration (ALAMV6.yaml) into a knowledge graph named MULTIOMICS_KG_UNSTABLE.

Next Steps