tablassert

Tablassert turns biomedical spreadsheets (Excel, CSV, TSV) into knowledge graphs ready for NCATS Translator. Declare how your columns map to subject–predicate–object statements in YAML; Tablassert resolves free text to standard CURIEs, attaches provenance and statistical annotations, and emits KGX-compliant nodes and edges.

A Configurable Agentic Platform (With Hugging Face Transformers And Langchain) To Draft Semantically Tablassert TableConfigs From Natural Language Inputs.

A Clojure utility for analyzing and resolving duplicate nodes in knowledge graph exchange (KGX) formatted knowledge graphs, with Tablassert integration and Biolink Model compliance. It rewrites Tablassert-integrated "table_configs" through a CLI.

QualifiersMCP is an MCP server for authoring and validating Tablassert table configuration files with Biolink qualifiers. It provides tools to fetch qualifier documentation, convert YAML/JSON table configurations, validate configuration syntax against Tablassert models, and call local helper services for PMC extraction and CURIE lookup workflows.

Migrate Tablassert configuration YAML files from v4.4.0 schema to TC3 schema.

MicrobiomeKG Visualization Tool. MBKGVisual reads compressed graph data (NODES and EDGES TSV files), builds a NetworkX graph, samples it using degree-based neighbor expansion (0.1% of nodes), and generates an interactive HTML visualization using Pyvis.

The up-to-date open-source configuration for MicrobiomeKG and MultiomicsKG builds. The current builds use the Tablassert knowledge extractor and are deployed to the NCATS Translator ecosystem via PloverDB.

Simple Elixir web API for extracting files from tar archives. Built with Ace and Raxx, provides a gzip-compressed extraction endpoint via HTTP.

A ConfigMigration microservice for the new cloud native Tablassert ecosystem. Update knowlegde graph configuration to the latest syntax with these APIs.

Simple Python FastAPI service for querying CURIE metadata from a Dbssert DuckDB file.

Improved DuckDB Export Of The NCATS Translator BABEL Project With Enhanced Indexing and NLP Capabilities. Dbssert Is Intended To Be Used With The Tablassert Knowledge Graph Backend's Fullmap Feature.

The TableConfig microservice for the new distributed, cloud-native Tablassert knowledge extractor. TableConfigs declare instructions that Tablassert uses to extract knowledge assertions from tabular data.

Here are the configs for MultiomicsKG. Feel free to add or edit any of these as you see fit. There's a config checker and guidelines here too.