Comments (3)
Mapper is now able to setup the 'root_map' table from UniProt (human is in default_dict). With mapping to 66 namespaces (5.140.771 columns). The mapping goes from UniProt_id to the required namespace. The approx. runtime with SQLite on Linux is ~2min. (including download and insert).
Next step is to create a dict with this table like:
map_dict[from][to][identifier]
from pybel.
The previous mapping_dict example was to slow. Following mapping_dict is created now by calling create_map()
:
map_dict[namespace][identifier]
results in a set of UniProtACC_ids.
map_dict['UniProt'][acc_id][namespace2]
can be used to map to another namespace.
I included also a method map(source_namespace, identifier, target_namespace, use_uniprot_api=False)
to map using the given database or (not yet implemented) using the UniProt-API for mapping.
from pybel.
Added the mappings from UniProt for Mouse and Rat.
The database contains a Gene_Name
Namespace, too. This seems similar to HGNC Symbols
but I did not check that yet.
from pybel.
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