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Update formatting of collapsible headers in README
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rsgoncalves committed Jun 5, 2024
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Expand Up @@ -10,7 +10,7 @@ pip install text2term
## Basic Examples

<details>
<summary><b><font size="+1">Examples of Programmatic Use</font></b></summary>
<summary style="font-size: large"><u>Examples of Programmatic Use</u></summary>

text2term supports mapping strings specified in different input formats:

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<details>
<summary><b><font size="+1">Examples of Command Line Interface Use</font></b></summary>
<summary style="font-size: large"><b>Examples of Command Line Interface Use</b></summary>

To show a help message describing all arguments type into a terminal:
```shell
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</details>

<details>
<summary><b><font size="+1">Input Preprocessing</font></b></summary>
<summary><h3>Input Preprocessing</h3></summary>

text2term includes regular expression-based preprocessing functionality for input terms. There are functions that take the input terms and a collection of (user-defined) regular expressions, then match each term to each regular expression to simplify the input term.

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</details>

## Command Line Usage
## Command Line Interface Usage

After installing, execute the tool from a command line as follows:

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`-t TARGET` Path or URL of 'target' ontology to map source terms to. When the chosen mapper is BioPortal or Zooma, provide a comma-separated list of acronyms (eg 'EFO,HPO') or write `'all'` to search all ontologies.

<details>
<summary><b><font size="+1">Optional arguments</font></b></summary>
<summary style="font-size: large"><b>Optional arguments</b></summary>

`-o OUTPUT` Path to desired output file for the mappings.

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