GitHub Contribution (obsolete)

This documentation should be condiered obsolete. Please register with the EukMap application at http://eukmap.unieuk.org, if you plan to contribue to the UniEuk taxonomy.

The UniEuk project encourages taxonomists to provide feedback regarding the UniEuk taxonomy requesting additions, updates, and correction of the current taxonomy. In the long term, these contributions will be accepted directly by the EukMap platform but for now this GitHub repository is used to collect such requests.

Users who want to contribute to the UniEuk taxonomy have to register with GitHub and link their GitHub account with the EukMap platform by selecting GitHub as identity provider on the EukMap login page (not the registration page). The EukMap account must have the same username as the GitHub account.

Step-by-step instructions including screenshots how to contribute using GitHub are provide on the GitHub-Contribution: Step by Step page.

Proposing Changes

Users have to ask for write permission on the GitHub contributions repository in order to propose changes. Changes then may be proposed by creating a pull request to create or upload files into the curated_subtrees directory. Pull requests will be reviewed and additional changes/fixes may be requested if necessary before the proposed changes are imported into the UniEuk taxonomy.

File Requirements

Files have to conform to the EukMap TSV format and, additionally, have to meet the following requirements:

• The first line of the created/uploaded file must specify the parent taxon of the subtree that is to be updated.
• All taxa specified in the file must be descendent of parent taxon, otherwise the subtree update will fail!
• Previous taxon data, that should be retained must be included in the file, missing data will otherwise be removed/blanked by the update!

The parent taxon does not necessarily need to be the root taxon of the taxonomy, for example Eukaryota, but can be any valid taxon currently existing in the taxonomy, for example Eukaryota;Discoba;Jakobida. All taxa must be descendent of the parent taxon, otherwise the import will fail. Considering the Jakobida parent taxon, specifying Eukaryota;Discoba;Euglenozoa; will cause the import to fail because Euglenozoa is not a descendent of Jakobida but a sibling.

The file may specify both new taxa as well as existing taxa. If taxa specified in the file exist in the taxonomy already, the existing taxon will be replaced by the taxon specified in the file. All data of the existing taxon will be replaced by this operation.

The file may contain any column supported by the EukMap TSV Format including custom columns not specified by the format. Columns not specified in the file will be treated as if the column was specified with an empty value, this will delete existing taxon data that is not specified in the file. For example, if a taxon is linked to as set of INSDC sequences entries via (INSDC) accessions and these accessions are not provided in the update file, the accessions currently linked to the taxon will be replaced by the accessions specified in the file or the set will be deleted if the accessions field is empty or not included in the file at all. To keep the current set of accessions, they would have to be included in the update file.

Correctly formatted file:

taxon       rank      accession   custom field
A;B;C       class                 some value
A;B;C;D     order
A;B;C;D;E   species   AB00001
A;B;C;F     order                 another value

Generally, columns in the file will not be aligned as only a single tab must be used to separate columns/value.

Incorrectly formatted file:

taxon
A;B;C
A;B;C;D
A;B;C;D;E;G   <-- The parent of G (taxon E) is missing in the file.
A;B;F         <-- taxon F is *not* a child of A;B;C

Committing Changes

To propose changes, new TSV files have to created, uploaded or existing files have to updated. Before requests can be reviewed, changes have to be committed which requires to provide a short descriptive summary and more extensive description. The summary should include the name of the parent taxon defining the updated subtree. The description should contain details why changes are proposed as well as reference (or DOI, PUBMEDID) to a publication describing the changes.

Reviewing Changes

Proposed changes will be reviewed by the taxonomic coordinator, who may invite more users to evaluate the changes. Reviewers may provide feedback on a specific line changing or adding a taxon or more general feedback as comment on the pull request.