SckanCompare Class

A package for retrieving and visualizing data contained in SCKAN (e.g., across species, relationship to spinal segments) to highlight similarities and differences in neuronal pathways

License: Apache License 2.0

class sckan_compare.SckanCompare(endpoint='https://blazegraph.scicrunch.io/blazegraph/sparql', max_cache_days=7)

Bases: object

Base class for accessing functionality

execute_query(query_string, species=None, cached=True)

Execute a SPARQL query and return the result.

Parameters:

query_string (str) – The SPARQL query string to execute.
species (str, optional) – The species to consider in the query, if applicable.
cached (bool, optional) – Whether to use cached data if available. Defaults to False.

Returns:

The query result.

Return type:

list

get_filtered_dataframe(result, species=None, filter_column=None, filter_value=None)

Create a filtered DataFrame from a query result. Replaces all synonyms for species and regions with unique labels, followed by the deletion of duplicate rows.

Parameters:

data (list) – The query result.
species (str) – The species for which the data is provided.
filter_column (str, optional) – The column to be filtered.
filter_value (str, optional) – The value to be used for filtering column.

Returns:

The filtered DataFrame.

Return type:

pandas.DataFrame

get_valid_phenotypes()

Retrieve a list of valid phenotypes from the data source.

Returns:: Dict with valid phenotypes URIs as keys and corresponding labels as values.
Return type:: dict

get_valid_phenotypes_circuit_role()

Retrieve a list of valid phenotypes with circuit role from the data source.

Returns:: Dict with valid phenotypes URIs as keys and corresponding labels as values.
Return type:: dict

get_valid_regions_specify_species(species, region=None)

Retrieve a list of valid regions for a specific species from the data source.

Parameters:

species (str) – The species for which to retrieve valid regions.
region (str, optional) – The region for which to retrieve valid regions. Valid values are: A, B, C or None. Defaults to None and returns all regions.

Returns:

Dict of valid region URIs as keys and corresponding labels as values

Return type:

dict

get_valid_species()

Retrieve a list of valid species from the data source.

Returns:: Dict with valid species URIs as keys and corresponding labels as values.
Return type:: dict

plot_dataframe_anatomy_vis(df, species=None, region_A=None, region_B=None, region_C=None)

Plot anatomical connectivity map based on a DataFrame.

Parameters:

df (pandas.DataFrame) – The DataFrame containing connectivity information.
species (str, optional) – The species for visualization.
region_A (str, optional) – The source region for filtering.
region_B (str, optional) – The target region for filtering.
region_C (str, optional) – The intermediate region for filtering.

Returns:

The Plotly figure widget.

Return type:

go.FigureWidget

plot_dataframe_block_vis(df, region_A=None, region_B=None)

Plot anatomical connectivity map based on a DataFrame.

Parameters:

df (pandas.DataFrame) – The DataFrame containing connectivity information.
species (str, optional) – The species for visualization.
region_A (str, optional) – The source region for filtering.
region_B (str, optional) – The target region for filtering.

Returns:

The Plotly figure widget.

Return type:

go.FigureWidget

replace_region_synonyms_dataframe(df, species)

Replace region synonyms in a DataFrame with unique labels.

e.g. ‘ovary’ : http://purl.obolibrary.org/obo/UBERON_0000992 has several synonyms, such as ‘animal ovary’, ‘female gonad’, etc. This method is used to map these synonyms to the parent label.

Parameters:: df (pandas.DataFrame) – The DataFrame containing region information.
Returns:: The DataFrame with replaced region synonyms.
Return type:: pandas.DataFrame

replace_species_synonyms_dataframe(df)

Replace species synonyms in a DataFrame with unique labels.

e.g. ‘Rattus norvegicus’ : http://purl.obolibrary.org/obo/NCBITaxon_10116 has several synonyms, such as ‘brown rat’, ‘Norway rat’, ‘rats’, ‘rat’. This method is used to map these synonyms to the parent label.

Parameters:: df (pandas.DataFrame) – The DataFrame containing species information.
Returns:: The DataFrame with replaced species synonyms.
Return type:: pandas.DataFrame