ID Mapping

Interface to mapping between species IDs.

We constructed two classes for mappings ids. 1. GeneMapper 2. ChemicalMapper

Currently supported options

  1. Genes

    KEGG, HGNC, Uniprot, Entrez, ensembl_gene_id

  2. Metabolites/compounds

    kegg_id, name, accession, chebi_id, chemspider_id, biocyc_id, synonyms, pubchem_compound_id, protein_associations, inchikey, iupac_name, ontology, drugbank_id, chemical_formula, smiles, metlin_id, average_molecular_weight

class magine.mappings.ChemicalMapper(fresh_download=False)[source]

Bases: object

Convert chemical species across various ids.

Database was creating using HMDB

check_synonym_dict(term, format_name)[source]

checks hmdb database for synonyms and returns formatted name

Parameters
termstr
format_namestr
Returns
dict

Examples

>>> cm = ChemicalMapper()
>>> cm.check_synonym_dict(term='dodecene', format_name='main_accession')
['HMDB0000933', 'HMDB0059874']
property chem_name_to_hmdb
convert_kegg_nodes(network)[source]

Maps network from kegg to gene names

Parameters
networknx.DiGraph
Returns
dict
property drugbank_to_hmdb
property hmdb_accession_to_main
property hmdb_main_to_protein
property hmdb_to_kegg
property hmdb_to_protein
print_info()[source]

print information about the dataframe

valid_columns = ['kegg_id', 'name', 'accession', 'chebi_id', 'inchikey', 'chemspider_id', 'biocyc_id', 'synonyms', 'iupac_name', 'pubchem_compound_id', 'protein_associations', 'ontology', 'drugbank_id', 'chemical_formula', 'smiles', 'metlin_id', 'average_molecular_weight', 'secondary_accessions']
class magine.mappings.GeneMapper(species='hsa')[source]

Bases: object

Mapping class between common gene ids

Database was creating by pulling down from NCBI, UNIPROT, HGNC

check_synonym_dict(term, format_name)[source]

checks hmdb database for synonyms and returns formatted name

Parameters
termstr
format_namestr
Returns
dict
convert_kegg_nodes(network, species='hsa')[source]

Convert kegg ids to HGNC gene symbol.

Parameters
networknx.DiGraph
speciesstr {‘hsa’}

Main support for humans only.

Returns
kegg_to_gene_name, kegg_shortdict, dict
property gene_name_to_alias_name
property gene_name_to_ensembl
property gene_name_to_kegg
property gene_name_to_uniprot
property kegg_to_gene_name
kegg_to_hugo(genes, species='hsa')[source]

Converts all KEGG names to HGNC

Parameters
geneslist
speciesstr
Returns
dict
kegg_to_symbol_through_uniprot(unknown_genes)[source]
property kegg_to_uniprot
property ncbi_to_symbol
property uniprot_to_gene_name
property uniprot_to_kegg

Database Mapping

Interface to downloading ID mapping databases.

Databases supported

URL

https://www.uniprot.org/

URL

https://www.ncbi.nlm.nih.gov/

URL

http://www.hmdb.ca/

class magine.mappings.databases.HMDB[source]

Bases: object

Downloads and processes HMDB metabolites database

http://www.hmdb.ca/

download_db(fresh_download)[source]

parse HMDB to Pandas.DataFrame

load_db(fresh_download=False)[source]
magine.mappings.databases.load_hgnc()[source]
magine.mappings.databases.load_ncbi()[source]
magine.mappings.databases.load_uniprot()[source]