ndx-odor-metadata 0.1.1

NWB Extension for documenting odor stimulus metadata

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 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:

pip install ndx-odor-metadata

Or conda:

conda install -c fleischmannlab ndx-odor-metadata

Or directly from the git repository:

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

Usage

Main usage

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 folder.

TODOs

• Create test
• Update documentation for sphinx (also update style)
• Publish on conda
• Publish on pypi
• Fetch pubchem data using pubchempy
• Use pyproject.toml instead of setup.py

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This extension was created using ndx-template.