# `ndx-odor-metadata`
[](https://gitlab.com/fleischmann-lab/ndx/ndx-odor-metadata/-/commits/main)
[](LICENSE.txt)
[](https://gitlab.com/fleischmann-lab/ndx/ndx-odor-metadata/-/releases)
[](https://pypi.org/pypi/ndx-odor-metadata)
[](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.
## Requirement
The requirements and additional development requirements can be seen in [`pyproject.toml`](pyproject.toml) file.
Here are the minimum requirements:
- `python >=3.8`
- `pynwb>=1.5.0,<3`
- `hdmf>=3.4.7,<4`
- `pubchempy>=1.0.4`
- `pyyaml>=5.0`
## 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`](demo/demo.ipynb) folder.
## TODOs
- [ ] Create test
- [ ] Update documentation for `sphinx` (also update style)
- [x] Publish on `conda`
- [x] Publish on `pypi`
- [x] Fetch pubchem data using `pubchempy`
- [x] Use `pyproject.toml` instead of `setup.py`
---
This extension was created using [ndx-template](https://github.com/nwb-extensions/ndx-template).
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"description": "# `ndx-odor-metadata`\n\n[](https://gitlab.com/fleischmann-lab/ndx/ndx-odor-metadata/-/commits/main)\n[](LICENSE.txt)\n\n\n\n[](https://gitlab.com/fleischmann-lab/ndx/ndx-odor-metadata/-/releases)\n[](https://pypi.org/pypi/ndx-odor-metadata)\n[](https://anaconda.org/FleischmannLab/ndx-odor-metadata)\n\nNWB 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.\n\nThis is in alpha development stages **WITHOUT** any appropriate tests yet. Please use with discretion.\n\n## Requirement\n\nThe requirements and additional development requirements can be seen in [`pyproject.toml`](pyproject.toml) file.\n\nHere are the minimum requirements:\n\n- `python >=3.8`\n- `pynwb>=1.5.0,<3`\n- `hdmf>=3.4.7,<4`\n- `pubchempy>=1.0.4`\n- `pyyaml>=5.0`\n\n## Installation\n\nYou can install via `pip`:\n\n```bash\npip install ndx-odor-metadata\n```\n\nOr `conda`:\n\n```bash\nconda install -c fleischmannlab ndx-odor-metadata\n```\n\nOr directly from the `git` repository:\n\n```bash\npip install git+https://gitlab.com/fleischmann-lab/ndx/ndx-odor-metadata\n```\n\n## Usage\n\n### Main usage\n\n```python\nfrom ndx_odor_metadata import OdorMetaData\n\nodor_table = OdorMetaData(name='odor_table', description='an odor table')\n\nodor_table.add_stimulus(\n pubchem_id = 7662.0,\n stim_name = \"3-Phenylpropyl isobutyrate\",\n raw_id = 3,\n stim_id = 1,\n stim_types = \"odor\",\n chemical_dilution_type='vaporized',\n chemical_concentration = 0.01,\n chemical_concentration_unit='%',\n chemical_solvent = \"Mineral Oil\",\n chemical_provider = \"Sigma\",\n stim_description = \"Legit odor stimulus #1\",\n)\n\nnwbfile.add_acquisition(odor_table)\n```\n### Details on arguments\n\n| | name | dtype | doc | default_value | quantity |\n|---:|:----------------------------|:--------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------|:-----------|\n| 0 | stim_name | text | Stimulus name, e.g. \"hexanal\" or \"sound\" | nan | nan |\n| 1 | pubchem_id | float | PubChem ID, `NaN` indicates non-(standard)-odor stimulus | nan | ? |\n| 2 | raw_id | text | Raw acquisition stimulus ID. 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