Do I need specific genome information to use this skill?

Yes, the skill validates organism names against canonical taxids and assembly accessions to ensure the resulting knowledge graph is biologically accurate.

How does it handle environmental conditions?

It allows users to define conditions like light intensity or salinity as specific nodes in the knowledge graph, linking them to observed expression changes.

Can it handle multiple analyses from one supplementary file?

Yes, the configuration structure allows multiple statistical analyses to reference different columns or comparisons within the same supplementary CSV file.

Which omics data types does this skill support?

It supports RNA-seq, Proteomics, Metabolomics, and Microarray data integration.

What is the main purpose of the paperconfig skill?

It helps researchers create standardized YAML configuration files to ingest omics data from publications into a BioCypher-based knowledge graph.

Multi-Omics Paper Configurator

Name: Multi-Omics Paper Configurator
Author: wosnat

bywosnat

0•

数据科学与机器学习

Generates and validates YAML configurations to ingest differential expression and omics publication data into BioCypher knowledge graphs.

The paperconfig skill streamlines the complex process of integrating biological datasets from scientific publications into a structured multi-omics knowledge graph. It provides a standardized framework for defining publication metadata, environmental conditions, and statistical analyses (including RNA-seq, proteomics, and metabolomics) within paperconfig.yaml files. By automating the mapping of supplementary CSV data to specific organisms and experimental treatments, it ensures data consistency and accelerates the creation of queryable knowledge bases for bioinformaticians and researchers.

主要功能

01Automated mapping for RNA-seq, proteomics, and metabolomics data

02Standardized paperconfig.yaml generation for omics data integration

03Support for defining environmental stress factors as graph nodes

040 GitHub stars

05Flexible parsing of supplementary CSV tables and statistical fields

06Validation of organism metadata against canonical taxon and assembly IDs

使用场景

01Integrating new RNA-seq differential expression data from Prochlorococcus studies

02Mapping proteomics results to specific NCBI assembly accessions for genomic context

03Standardizing metadata for cross-study comparisons of environmental stress responses

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add wosnat/multiomics_biocypher_kg paperconfig

For use in Claude.ai and ChatGPT

Download Skill