There are many ways to contribute to this project and so here are a couple of ways to contribute. Contributions will almost always result in a pull request. Contributions must pass the automated testing.
To add a taxon, add it to src/nodes.dmp and src/names.dmp. If it is present in the NCBI taxonomy, please use that identifier. Please adhere to the NCBI taxonomy format specification. For names.dmp, the scientific name field is required.
Step 2 for adding a taxon is also adding representative chromosome(s). See the section below for details. You cannot add a taxon to this project without a representative chromosome.
Add an entry to either src/chromosomes.tsv or src/plasmids.tsv. The format is four columns, separated by tab:
- scientific name or similar
- NCBI nucleotide accession
- taxonomy ID
- parent taxonomy ID
The taxonomy IDs in each line must be represented in names.dmp and nodes.dmp in the folder src/taxonomy.
New nucleotide entries must be
- Trusted - subject matter experts must agree that this is a representative genome for the taxon
- Completed - no gaps
- Nonredundant - for the most part, most taxa are not represented by multiple assemblies
Note: some species such as Vibrio cholerae have multiple chromosomes. These can be denoted with multiple lines, one per nucleotide accession.
Please make a new issues ticket on GitHub and describe the potential contribution.