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

text2term supports mapping strings specified in different input formats:

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

To show a help message describing all arguments type into a terminal:
```shell
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The function returns a pandas `DataFrame` containing the generated ontology mappings.

<details>
<summary><b><font size="+1">Argument Details</font></b></summary>
<summary><h4><b>Argument Details</b></h4></summary>

`source_terms`&mdash;Strings to be mapped to an ontology, which can be specified as a:
1. list of strings
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</details>

<details>
<summary><b><font size="+1">Ontology Caching</font></b></summary>
<summary><h4><b>Ontology Caching</b></h4></summary>

text2term supports caching ontologies for faster or repeated mapping to the same ontology. An ontology can be cached using the function:

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</details>

<details>
<summary><h3>Input Preprocessing</h3></summary>
<summary><h4>Input Preprocessing</h4></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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`-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 style="font-size: large"><b>Optional arguments</b></summary>
<summary style="font-size: larger"><b>Optional arguments</b></summary>

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

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