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Add ndx-odor-metadata (#40)
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Co-authored-by: Ryan Ly <[email protected]>
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@tuanpham96 @rly
tuanpham96 and rly authored Jul 24, 2023
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97 changes: 97 additions & 0 deletions ndx-odor-metadata/README.md
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# `ndx-odor-metadata`

[![pipeline status](https://img.shields.io/gitlab/pipeline-status/fleischmann-lab/ndx/ndx-odor-metadata?branch=main&label=pipeline&style=flat-square)](https://gitlab.com/fleischmann-lab/ndx/ndx-odor-metadata/-/commits/main)
[![license](https://img.shields.io/gitlab/license/fleischmann-lab/ndx/ndx-odor-metadata?color=yellow&label=license&style=flat-square)](LICENSE.txt)

![python version](https://img.shields.io/pypi/pyversions/ndx-odor-metadata?style=flat-square)
[![release](https://img.shields.io/gitlab/v/release/fleischmann-lab/ndx/ndx-odor-metadata?label=release&sort=date&style=flat-square)](https://gitlab.com/fleischmann-lab/ndx/ndx-odor-metadata/-/releases)
[![pypi package](https://img.shields.io/pypi/v/ndx-odor-metadata?label=pypi%20package&style=flat-square&color=blue)](https://pypi.org/pypi/ndx-odor-metadata)
[![conda package](https://img.shields.io/conda/v/fleischmannlab/ndx-odor-metadata?color=green&style=flat-square)](https://anaconda.org/FleischmannLab/ndx-odor-metadata)

NWB extension to store odor stimulus metadata with `DynamicTable` format. Entries that have a PubChem and `stim_types` indicate odor/chemical will also be queried with `pubchempy` for more information.

This is in alpha development stages **WITHOUT** any appropriate tests yet. Please use with discretion.


## Installation

You can install via `pip`:

```bash
pip install ndx-odor-metadata
```

Or `conda`:

```bash
conda install -c fleischmannlab ndx-odor-metadata
```

Or directly from the `git` repository:

```bash
pip install git+https://gitlab.com/fleischmann-lab/ndx/ndx-odor-metadata
```

## Usage

### Main usage

```python
from ndx_odor_metadata import OdorMetaData

odor_table = OdorMetaData(name='odor_table', description='an odor table')

odor_table.add_stimulus(
pubchem_id = 7662.0,
stim_name = "3-Phenylpropyl isobutyrate",
raw_id = 3,
stim_id = 1,
stim_types = "odor",
chemical_dilution_type='vaporized',
chemical_concentration = 0.01,
chemical_concentration_unit='%',
chemical_solvent = "Mineral Oil",
chemical_provider = "Sigma",
stim_description = "Legit odor stimulus #1",
)

nwbfile.add_acquisition(odor_table)
```

### Details on arguments

| | name | dtype | doc | default_value | quantity |
|---:|:----------------------------|:--------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------|:-----------|
| 0 | stim_name | text | Stimulus name, e.g. "hexanal" or "sound" | nan | nan |
| 1 | pubchem_id | float | PubChem ID, `NaN` indicates non-(standard)-odor stimulus | nan | ? |
| 2 | raw_id | text | Raw acquisition stimulus ID. Will be converted to `str`. | nan | nan |
| 3 | raw_id_dtype | text | The actual dtype of `raw_id` value. Useful for (re)casting. | N/A | ? |
| 4 | stim_id | text | Preferred stimulus ID, which can be used to remap acquisition stimulus id `raw_id`. Will be converted to `str`. If not explicitly given, will copy from `raw_id` | nan | ? |
| 5 | stim_id_dtype | text | The actual dtype of `stim_id` value. Useful for (re)casting. | N/A | ? |
| 6 | stim_types | text | Type(s) of stimulus, e.g. 'odor', 'sound', 'control', 'CS', 'US', ... | nan | nan |
| 7 | stim_types_index | nan | Index for `stim_types` | nan | nan |
| 8 | stim_description | text | Human-readable description, notes, comments of each stimulus | N/A | ? |
| 9 | chemical_dilution_type | text | Type of dilution, e.g. 'volume/volume', 'vaporized' | N/A | ? |
| 10 | chemical_concentration | float | Concentration of chemical | nan | ? |
| 11 | chemical_concentration_unit | text | Unit of concentration, e.g. "%" or "M" | N/A | ? |
| 12 | chemical_solvent | text | Solvent to dilute the chemicals in, e.g. 'mineral oil' | N/A | ? |
| 13 | chemical_provider | text | Provider of the chemicals, e.g. 'Sigma' | N/A | ? |
| 14 | nonchemical_details | text | Information about non-chemical/odor stimulus, e.g. 'sound' frequencies | N/A | ? |
| 15 | is_validated | bool | Whether the stimulus, if chemical/odor, is validated against PubChem (or other sources listed in `validation_info`.If does not have a valid PubChem ID, this assumes to default `False` value | False | ? |
| 16 | validation_details | text | Additional information/details/notes about stimulus validation, e.g. source, software used & version, validation date, ... | N/A | ? |
| 17 | pubchem_cid | float | PubChem CID, `NaN` indicates non-(standard)-odor stimulus | nan | ? |
| 18 | chemical_IUPAC | text | Official chemical IUPAC name | N/A | ? |
| 19 | chemical_SMILES | text | Canonical SMILES | N/A | ? |
| 20 | chemical_synonyms | text | List of chemical synonyms | | ? |
| 21 | chemical_synonyms_index | nan | Index for `chemical_synonyms` | nan | ? |
| 22 | chemical_molecular_formula | text | Molecular formula of chemical used | N/A | ? |
| 23 | chemical_molecular_weight | float | Molecular weight of chemical used | nan | ? |

### Demonstration

For more detailed demonstration, please visit the [`demo`](https://gitlab.com/fleischmann-lab/ndx/ndx-odor-metadata/-/tree/main/demo) folder.


---
This extension was created using [ndx-template](https://github.com/nwb-extensions/ndx-template).
8 changes: 8 additions & 0 deletions ndx-odor-metadata/ndx-meta.yaml
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name: ndx-odor-metadata
version: 0.1.1
src: https://gitlab.com/fleischmann-lab/ndx/ndx-odor-metadata
pip: https://pypi.org/project/ndx-odor-metadata/
license: BSD-3
maintainers:
- tuanpham96 # github
# - tuanhpham # gitlab

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