--- name: curate-genome-assembly description: Process genome assembly datasets for VEuPathDB resources --- # Genome Assembly Dataset Curation This skill guides processing of genome assembly datasets for VEuPathDB resources. ## Prerequisites Check This workflow requires the following repositories in `veupathdb-repos\/`: - ApiCommonPresenters - EbrcModelCommon **First, run the repository status check** to verify repositories are present: _Note: this script is located in the skill directory_ ```bash bash scripts\/check-repos.sh ApiCommonPresenters EbrcModelCommon ``` If repositories are missing, the script will provide clone instructions. **Branch Confirmation:** After verifying repositories exist, check their current branches and status using `git -C `, then confirm with the user before proceeding. Users typically create dataset-specific branches (see [curator branching guidelines](resources\/curator-branching.md)). Example: ```bash git -C veupathdb-repos\/ApiCommonPresenters branch --show-current git -C veupathdb-repos\/ApiCommonPresenters status -sb ``` ## Working Directory (Curation Workspace Directory) **IMPORTANT**: All commands in this workflow must be run from your curation workspace directory (the directory that contains `veupathdb-repos\/` as a subdirectory). **For Claude Code**: - DO NOT use `cd` commands to change into `veupathdb-repos\/` subdirectories - Use `git -C ` for git operations in subdirectories - Use absolute paths or relative paths from the curation workspace directory - Example: `git -C veupathdb-repos\/ApiCommonPresenters status` instead of `cd veupathdb-repos\/ApiCommonPresenters && git status` The workflow will create a `tmp\/` subdirectory in the curation workspace directory for intermediate files. ## Required Information Gather the following before starting: - **VEuPathDB project** - Valid projects listed in [resources\/valid-projects.json](resources\/valid-projects.json) - **Assembly GenBank accession** (e.g., `GCA_000988875.2` including version) ## Workflow Overview ### Step 1: Fetch Assembly Metadata from NCBI Fetch assembly metadata from NCBI using the GenBank accession. **Command:** ```bash curl -X GET "https:\/\/api.ncbi.nlm.nih.gov\/datasets\/v2\/genome\/accession\/\/dataset_report" \ -H "Accept: application\/json" > tmp\/_dataset_report.json ``` **Detailed instructions:** [Step 1 - Fetch NCBI Metadata](resources\/step-1-fetch-ncbi.md) ### Step 2: Fetch BioProject Metadata Extract the BioProject accession from the assembly report and fetch additional details. **Command:** ```bash node scripts\/fetch-bioproject.js ``` This retrieves the BioProject title and description, saved to `tmp\/_bioproject.json`. **Detailed instructions:** [Step 2 - Fetch BioProject](resources\/step-2-fetch-bioproject.md) ### Step 3: Fetch PubMed Data Find and fetch publications for the genome assembly. **Command:** ```bash node scripts\/fetch-pubmed.js ``` Results saved to `tmp\/_pubmed.json`. **Detailed instructions:** [Step 3 - Fetch PubMed](resources\/step-3-fetch-pubmed.md) ### Step 4: Curate Contacts Identify and curate contact entries for the genome submission. **Contact identification priority:** 1. Named submitter from assembly metadata 2. Senior\/last author from PubMed publications (if available) 3. Curator judgment for additional contacts **Actions:** - Search existing contacts in `veupathdb-repos\/EbrcModelCommon\/Model\/lib\/xml\/datasetPresenters\/contacts\/allContacts.xml` - Create new contact entries if needed - Present choices to curator for review **Detailed instructions:** [Step 4 - Curate Contacts](resources\/step-4-curate-contacts.md) ### Step 5: Generate and Insert Presenter XML Generate the datasetPresenter XML and insert it into the appropriate presenter file. **Command:** ```bash node scripts\/generate-presenter-xml.js [ADDITIONAL_CONTACT_IDS...] ``` **Target file:** `veupathdb-repos\/ApiCommonPresenters\/Model\/lib\/xml\/datasetPresenters\/.xml` **Detailed instructions:** [Step 5 - Update Presenter Files](resources\/step-5-update-presenter.md) ## Next Steps After completing this workflow: 1. Review generated XML for TODO fields that require curator input 2. Commit changes to dataset branch (curator handles git operations) 3. Create pull request for review (curator handles PR creation) ## Resources - [Step 1 - Fetch NCBI Metadata](resources\/step-1-fetch-ncbi.md) - [Step 2 - Fetch BioProject](resources\/step-2-fetch-bioproject.md) - [Step 3 - Fetch PubMed](resources\/step-3-fetch-pubmed.md) - [Step 4 - Curate Contacts](resources\/step-4-curate-contacts.md) - [Step 5 - Update Presenter Files](resources\/step-5-update-presenter.md) - [Curator Branching Guidelines](resources\/curator-branching.md) - [Valid VEuPathDB Projects](resources\/valid-projects.json) ## Scripts - `scripts\/fetch-bioproject.js` - Fetches BioProject metadata from NCBI (esearch + esummary) - `scripts\/fetch-pubmed.js` - Fetches PubMed records linked to a BioProject (elink + esummary) - `scripts\/generate-presenter-xml.js` - Generates datasetPresenter XML from fetched metadata - `scripts\/check-repos.sh` - Validates veupathdb-repos\/ repository setup (synced from shared\/)