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Remove collapsible headers from README #53

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Remove collapsible headers from README #53

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35 changes: 4 additions & 31 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +9,6 @@ pip install text2term
```
## Basic Examples

<details>
<summary><b>Examples of Programmatic Mapping</b></summary>

### Examples of Programmatic Mapping
text2term supports mapping strings specified in multiple input formats. In the first example, we map strings in a list to an ontology specified by its URL:

Expand Down Expand Up @@ -40,10 +37,6 @@ dfd = text2term.map_terms(source_terms={"asthma":"disease", "acute bronchitis":[
target_ontology="http://purl.obolibrary.org/obo/mondo.owl")
```

</details>

<details>
<summary><b>Examples of Programmatic Caching</b></summary>

### Examples of Programmatic Caching
text2term supports caching an ontology for repeated use. Here we cache an ontology and give it a name:
Expand All @@ -63,12 +56,8 @@ More succinctly, we can use the returned `OntologyCache` object `mondo` as such:
```python
dfo = mondo.map_terms(source_terms=["asthma", "acute bronchitis"])
```
</details>


<details>
<summary><b>Examples of Command Line Interface Use</b></summary>

### Examples of Command Line Interface Use
To show a help message describing all arguments type into a terminal:
```shell
Expand Down Expand Up @@ -117,8 +106,6 @@ Now the ontology is cached and we can refer to it as the target ontology using t
python text2term -s test/unstruct_terms.txt -t MONDO
```

</details>


## Programmatic Usage
After installing and importing to a Python environment, the main function is `map_terms`:
Expand All @@ -142,9 +129,6 @@ text2term.map_terms(source_terms,
```
The function returns a pandas `DataFrame` containing the generated ontology mappings.

<details>
<summary><b>Argument Details</b></summary>

### Argument Details

`source_terms`&mdash;Strings to be mapped to an ontology, which can be specified as a:
Expand Down Expand Up @@ -188,10 +172,6 @@ When using the BioPortal or Zooma interfaces, the value for `target_ontology` sh

`incl_unmapped`&mdash;Include unmapped terms in the output. If a term has been tagged 'Ignore' or has less than the `min_score`, it is included in the output data frame

</details>

<details>
<summary><b>Ontology Caching</b></summary>

### Ontology Caching
text2term supports caching ontologies for faster or repeated mapping to the same ontology. An ontology can be cached using the function:
Expand All @@ -217,14 +197,12 @@ text2term.clear_cache(ontology_acronym='')
If no arguments are specified, the entire cache will be cleared. Otherwise, only the ontology with the given acronym will be cleared.
Finally, `cache_exists(ontology_acronym='')` is a simple function that returns `True` if the given acronym exists in the cache, and `False` otherwise.

**_Notes:_**
- The `cache_ontology` function returns an object that can be used to directly call the `map_terms` function, as well as `clear_cache` and `cache_exists`. These have the same arguments, except `ontology_target` is no longer specified and there is no `use_cache` option, since it is always True.
- While ontology URLs can be repeatedly used, acronyms must be distinct in a given environment.
> [!NOTE]
> The `cache_ontology` function returns an object that can be used to directly call the `map_terms` function, as well as `clear_cache` and `cache_exists`. These have the same arguments, except `ontology_target` is no longer specified and there is no `use_cache` option, since it is always True.

</details>
> [!CAUTION]
> While ontology URLs can be repeatedly used, acronyms must be distinct in a given environment.

<details>
<summary><b>Input Preprocessing</b></summary>

### Input Preprocessing
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.
Expand Down Expand Up @@ -252,7 +230,6 @@ When the input to text2term is a table, any rows that contain `NA` values in the

If an ignore tag `"ignore"` or `"Ignore"` is added to a term, that term will not be mapped to any terms in the ontology. It will only be included in the output if the `incl_unmapped` argument is True. The following values are regarded as ignore tags: `"ignore", "Ignore".

</details>

## Command Line Interface Usage

Expand All @@ -269,8 +246,6 @@ To display a help message with descriptions of tool arguments do:

`-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>Optional Arguments</b></summary>

### Optional Arguments

Expand Down Expand Up @@ -298,8 +273,6 @@ To display a help message with descriptions of tool arguments do:

`-u` Include all unmapped terms in the output

</details>


## Supported Mappers

Expand Down
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