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documentation for extra_attributes
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cgirardot committed Jan 6, 2025

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10 changes: 10 additions & 0 deletions README.md
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@@ -108,6 +108,14 @@ The command line tool will automatically fetch the correct scientific name based
| sample_alias_4 | sample_title_2 | 2697049 | Severe acute respiratory syndrome coronavirus 2 | covid-19 | sample_description_1 | 2020-10-11 | Argentina |
| sample_alias_5 | sample_title_3 | 2697049 | Severe acute respiratory syndrome coronavirus 2 | covid-19 | sample_description_2 | 2008-01-24 | Belgium |

#### Custom attributes
Additional custom attributes (i.e. attributes not specified in the ERC checklist) can be added to the sample table by adding columns which headers are named like `sample_attribute[attribute_name]`; for example `sample_attribute[treatment]`, `sample_attribute[age]`...

| alias | ... | sample_attribute[treatment] | sample_attribute[age]
|----------------|----------------|---------------------|------------------------|
| sample_alias_4 | ... | treated | 2 days
| sample_alias_5 | ... | untreated | 2 days

#### Viral submissions

If you want to submit viral samples you can use the [ENA virus pathogen](https://www.ebi.ac.uk/ena/browser/view/ERC000033) checklist by adding `ERC000033` to the checklist parameter. Check out our [viral example command](#test-the-tool) as demonstration. Please use the [ENA virus pathogen](https://github.com/ELIXIR-Belgium/ENA-metadata-templates/tree/main/templates/ERC000033) checklist in our template repo to know what is allowed/possible in the `Controlled vocabulary`fields.
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Please check out the [template](https://github.com/ELIXIR-Belgium/ENA-metadata-templates) of your checklist to discover which attributes are mandatory for the study, experiment and run ENA object.

#### Study and Experiment custom attributes
Similarly to samples, additional custom attributes can be added to the experiment and study tables by adding columns which headers are named like `experiment_attribute[attribute_name]` and `study_attribute[attribute_name]` in the experiment and study tables, respectively.

### Dev instance

3 changes: 3 additions & 0 deletions example_tables/ENA_template_samples_xtra_attrs.tsv
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alias title scientific_name sample_description collection date geographic location (country and/or sea) sample_attribute[age] sample_attribute[treatment]
sample_alias_4 sample_title_1 homo sapiens sample_description_1 2020-10-11 Argentina 2 days treated
sample_alias_5 sample_title_2 human metagenome sample_description_2 2008-01-24 Belgium 2 days untreated

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