napistu.ontologies.dogma

Functions

create_dogmatic_sbml_dfs(organismal_species)

Create Dogmatic SMBL_DFs

napistu.ontologies.dogma._connect_dogmatic_mappings(organismal_species: str, preferred_method: str = 'bioconductor', allow_fallback: bool = True, r_paths: str | None = None) → dict

Connect Dogmatic Mappings

Merge all ontologies into greedy clusters based on shared associations to entrez ids

Parameters:

• organismal_species (str) – An organismal species (e.g., Homo sapiens)

• r_paths (str or None) – Optional, p]ath to an R packages directory

• Returns – dict with: - s_name_series: a series where the index is distinct molecular species and the values are names. - cluster_consensus_identifiers_df: a pd.DataFrame where the index is distinct molecular species and values are identifiers objects.

napistu.ontologies.dogma.create_dogmatic_sbml_dfs(organismal_species: str | OrganismalSpeciesValidator, preferred_method: str = 'bioconductor', allow_fallback: bool = True, r_paths: str | None = None) → SBML_dfs

Create Dogmatic SMBL_DFs

Create an SBML_dfs model which is pretty much just proteins and no reactions, as well as annotations linking proteins to genes, and creating nice labels for genes/proteins.

Parameters:

• organismal_species (str | OrganismalSpeciesValidator) – An organismal species (e.g., Homo sapiens)

• r_paths (str or None) – Optional, p]ath to an R packages directory

• Returns –

  dogmatic_sbml_dfs (sbml.SBML_dfs)

  A pathway model which (pretty much) just contains proteins and diverse identifiers