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BioThings Resolver

Library to lookup BioThings API identifiers.

Installation

To install, clone the project and install it, or run the following command. It will be released as a package in the future when it is more mature.

pip install git+https://github.com/biothings/biothings_resolver.git

Example Usage

Using Predefined Resolvers

Predefined Resolvers can be imported from biothings_resolver.predefined_resolvers. Currently, the following are implemented:

  • ChemResolver which resolves drug identifiers available in MyChem.info
  • GeneResolver which resolves gene identifiers available in MyGene.info

Supported input and output identifier types

Check by running:

In [1]: import biothings_resolver 
   ...: resolver = biothings_resolver.predefined_resolvers.GeneResolver() 
   ...:  
   ...: print("Inputs:", ", ".join(resolver.agents.sources)) 
   ...: print("Outputs:", ", ".join(resolver.agents.targets))                   
Inputs: WormBase, ZFIN, FlyBase, NCBIGene, HGNC, MGI, ENSEMBL, UniProtKB, RGD
Outputs: WormBase, ZFIN, FlyBase, NCBIGene, HGNC, MGI, ENSEMBL, UniProtKB, RGD

Resolve identifiers

Takes in a sequence of dictionaries, returns a list of dictionaries in the same order, the items in the returned dictionary contains lists of new identifiers.

It can either return the most preferred available identifier type, or expand to have all available preferred types, as defined in Resolver.preferred.

In [1]: import biothings_resolver 
   ...:  
   ...: resolver = biothings_resolver.predefined_resolvers.ChemResolver() 
   ...: resolve_input = [{ 
   ...:     'INCHI': 'InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3', 
   ...:     'DRUGBANK': 'DB00201', 
   ...: }]                                                                      

In [2]: # don't expand 
   ...: output = list(resolver.resolve_identifier(resolve_input, expand=False)) 
   ...: for k, identifiers in output[0].items(): 
   ...:     print(f"{k}:", ", ".join(identifiers)) 
   ...:                                                                         
INCHIKEY: RYYVLZVUVIJVGH-UHFFFAOYSA-N

In [3]: # or expand 
   ...: output = list(resolver.resolve_identifier(resolve_input, expand=True)) 
   ...: for k, identifiers in output[0].items(): 
   ...:     print(f"{k}:", ", ".join(identifiers)) 
   ...:                                                                         
INCHIKEY: RYYVLZVUVIJVGH-UHFFFAOYSA-N
UNII: 3G6A5W338E
DRUGBANK: DB00201
CHEBI: CHEBI:27732
CHEMBL.COMPOUND: CHEMBL113
PUBCHEM.COMPOUND: 2519

Resolve CURIE style input, expanding to obtain all available fields

Using a shorter CURIE-like input, is more compact than having a dictionary input. This is shorter but one input can only have one identifier, where the previous method can support multiple inputs for a single query, providing the resolver with more information.

In [1]: import biothings_resolver 
   ...:  
   ...: resolver = biothings_resolver.predefined_resolvers.ChemResolver() 
   ...: resolve_input = [ 
   ...:     "InChIKey:GKKDCARASOJPNG-UHFFFAOYSA-N", 
   ...:     "[inchikey:DVARTQFDIMZBAA-UHFFFAOYSA-O]",  # safe_curie, not required 
   ...:     "CHEBI:32146", 
   ...: ] 
   ...: for orig, new in zip(resolve_input, resolver.resolve_curie(resolve_input, expand=True)): 
   ...:     print("Original:", orig) 
   ...:     for new_id in new: 
   ...:         print(new_id) 
   ...:     print() 
   ...:                                                                                                                                   
Original: InChIKey:GKKDCARASOJPNG-UHFFFAOYSA-N
INCHIKEY:GKKDCARASOJPNG-UHFFFAOYSA-N
CHEBI:81931
CHEMBL.COMPOUND:CHEMBL2251334
PUBCHEM.COMPOUND:61021

Original: [inchikey:DVARTQFDIMZBAA-UHFFFAOYSA-O]
INCHIKEY:DVARTQFDIMZBAA-UHFFFAOYSA-O
UNII:T8YA51M7Y6
CHEBI:63038
CHEMBL.COMPOUND:CHEMBL1500032
PUBCHEM.COMPOUND:22985

Original: CHEBI:32146
INCHIKEY:SUKJFIGYRHOWBL-UHFFFAOYSA-N
UNII:DY38VHM5OD
DRUGBANK:DBSALT001517
CHEBI:32146
CHEMBL.COMPOUND:CHEMBL1334078
PUBCHEM.COMPOUND:23665760

Use as a decorator

When using as a decorator, the decorated function/method must return/yield dictionaries, then resolver will update a specific field in the dictionary to contain an identifier in the order of preference.

The field key is specified in Resolver.document_resolve_id_field and by default it is set to _id.

import biothings_resolver

# For using as a decorator to update documents output from a function
resolver = biothings_resolver.predefined_resolvers.ChemResolver([
        ('INCHI', 'pharmgkb.inchi'),
        ('PUBCHEM.COMPOUND', 'pharmgkb.xrefs.pubchem.cid'),
        ('DRUGBANK', 'pharmgkb.xrefs.drugbank'),
        ('CHEBI', 'pharmgkb.xrefs.chebi'),
])
@resolver
def load_data():
     # a typical dataloader for PharmGKB
    ... 
    for doc in ...:
        yield doc

Change Pathfinding Options

Pathfinding behavior can be configured by altering attributes of the Resolver instance. Currently the following can be modified.

Maximum path length

The maximum number of agents that Resolver will use in one run. It can be set by changing the max_path_length attribute. Default is 3.

import biothings_resolver

resolver = biothings_resolver.predefined_resolvers.ChemResolver()
resolver.max_path_length = 5

Using customized Resolver instance

1. Initialize an empty Resolver

import biothings_resolver

# Using a pre-defined resolver
resolver = biothings_resolver.Resolver()

# Setting identifier type preference
resolver.preferred = ['INCHIKEY', 'UNII']

2. Add resolver agents to a resolver

import biothings_resolver

resolver = biothings_resolver.Resolver()
# Unfreeze the agents container to make updates
resolver.agents.frozen = False
resolver.agents.add(
    'CHEMBL.COMPOUND', 'INCHIKEY', biothings_resolver.BioThingsAPIAgent(
        'chem', 'chembl.molecule_chembl_id', 'chembl.inchi_key',
    ), cost=1.0             
)
# Re-freeze to update paths
resolver.agents.frozen = True

3. Use