Curation

There are several curation workflows implemented in bioregistry.curation.

Bulk Import

A script for doing bulk import.

If you have a local file or remote file accessible by HTTP/HTTPS/FTP, you can use the –path option like in:

$ python -m bioregistry.curation.bulk_google_import --path <your file path>

If you are doing curation on Google Sheets, you can copy the sheet identifier and use the –google-sheet option like in:

$ python -m bioregistry.curation.bulk_google_import --google-sheet 10MPt-H6My33mOa1V_VkLh4YG8609N7B_Dey0CBnfTL4

Semi-automated Literature Curation

Utilities for working with the data produced by the semi-automated curation workflow.

Classes

CurationRelevance(*values)

An enumeration for curation relevance.

Class Inheritance Diagram

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Adding LinkML

Import a resource from a LinkML configuration.

This curation workflow can be called from the command line by passing a URL to a LinkML YAML configuration file like in the following:

$ python -m bioregistry.curation.add_linkml https://github.com/HendrikBorgelt/CatCore/blob/main/src/catcore/schema/catcore.yaml

Here are some more example LinkML YAML configuration files:

Warning

This workflow doesn’t produce complete Bioregistry records! You still must add:

  1. homepage

  2. contributor

Given most LinkML configurations are on GitHub, you can probably figure out:

  • repository

  • contact

Functions

get_resource_from_linkml(url)

Get a resource from a LinkML configuration.

import_from_linkml(url)

Get a resource from a LinkML configuration and write it to the registry.