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An NWB Extension Catalog record for the extension ndx-odor-metadata.

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ndx-odor-metadata

pipeline status license

python version release pypi package conda package

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:

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.


This extension was created using ndx-template.

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