Can I use this for any NCBI assembly?

Yes, as long as you have a valid GenBank accession (e.g., GCA_...) and the target organism belongs to a supported VEuPathDB project.

What repositories are required to use this skill?

This skill requires ApiCommonPresenters and EbrcModelCommon repositories to be present within a 'veupathdb-repos' subdirectory in your curation workspace.

How does it handle existing contacts in the database?

The skill searches the existing allContacts.xml file to prevent duplicates and allows curators to select existing IDs or create new entries based on PubMed data.

Does this skill automatically commit changes to Git?

No, the skill generates and modifies the necessary files, but curators are responsible for reviewing the changes and performing Git operations like committing and creating pull requests.

Genome Assembly Dataset Curator

Name: Genome Assembly Dataset Curator
Author: VEuPathDB

byVEuPathDB

Web Scraping & Data Collection

Automates the end-to-end processing and metadata curation of genome assembly datasets for VEuPathDB resources.

About

This skill streamlines the complex workflow of integrating new genome assemblies into VEuPathDB databases. It automates the retrieval of critical metadata from NCBI services—including GenBank reports, BioProject details, and PubMed publications—to ensure data accuracy and consistency. By guiding the curator through contact identification and automated XML generation, it reduces manual errors and ensures that all datasets follow standardized operating procedures within the VEuPathDB ecosystem.

Key Features

Automated metadata fetching from NCBI GenBank, BioProject, and PubMed APIs
Automated datasetPresenter XML generation and file insertion
Workspace-aware command execution following VEuPathDB directory structures
0 GitHub stars
Streamlined contact curation and identification from publication records
Dependency validation for ApiCommonPresenters and EbrcModelCommon repositories

Use Cases

Updating metadata and contact information for existing genomic datasets
Integrating a new organism's genome assembly into a VEuPathDB project
Automating the creation of presenter XML files to ensure schema compliance

About

Key Features

Automated metadata fetching from NCBI GenBank, BioProject, and PubMed APIs
Automated datasetPresenter XML generation and file insertion
Workspace-aware command execution following VEuPathDB directory structures
0 GitHub stars
Streamlined contact curation and identification from publication records
Dependency validation for ApiCommonPresenters and EbrcModelCommon repositories

Use Cases

Updating metadata and contact information for existing genomic datasets
Integrating a new organism's genome assembly into a VEuPathDB project
Automating the creation of presenter XML files to ensure schema compliance