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Introduce KEGG ID conversions to BridgeDB service #104

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merged 2 commits into from
May 12, 2022
Merged

Introduce KEGG ID conversions to BridgeDB service #104

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a516dbb
Introduced KEGG ID conversions to BridgeDB service
xtrojak May 12, 2022
26d3bd5
Update changelog
xtrojak May 12, 2022
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6 changes: 6 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -4,6 +4,12 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [dev] - unreleased
### Added
* KEGG ID conversions support to BridgeDB service [#101](https://github.com/RECETOX/MSMetaEnhancer/issues/101)
### Changed
### Removed

## [0.2.2] - 2022-04-27
### Added
* introduced `error` level into logging [#95](https://github.com/RECETOX/MSMetaEnhancer/issues/95)
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27 changes: 24 additions & 3 deletions MSMetaEnhancer/libs/converters/web/BridgeDB.py
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Expand Up @@ -13,31 +13,42 @@ def __init__(self, session):
# service URLs
self.endpoints = {'BridgeDB': 'https://webservice.bridgedb.org/Human/xrefs/'}

self.codes = {'hmdbid': 'Ch', 'pubchemid': 'Cpc', 'chemspiderid': 'Cs', 'wikidataid': 'Wd', 'chebiid': 'Ce'}
self.codes = {'hmdbid': 'Ch', 'pubchemid': 'Cpc', 'chemspiderid': 'Cs', 'wikidataid': 'Wd', 'chebiid': 'Ce',
'keggid': 'Ck'}
self.identifiers = {'PubChem-compound': 'pubchemid', 'Chemspider': 'chemspiderid', 'ChEBI': 'chebiid',
'HMDB': 'hmdbid', 'Wikidata': 'wikidataid'}
'HMDB': 'hmdbid', 'Wikidata': 'wikidataid', 'KEGG Compound': 'keggid'}

# generate top level methods defining allowed conversions
conversions = [('hmdbid', 'pubchemid', 'from_hmdbid'),
('hmdbid', 'chemspiderid', 'from_hmdbid'),
('hmdbid', 'wikidataid', 'from_hmdbid'),
('hmdbid', 'chebiid', 'from_hmdbid'),
('hmdbid', 'keggid', 'from_hmdbid'),
('pubchemid', 'hmdbid', 'from_pubchemid'),
('pubchemid', 'chemspiderid', 'from_pubchemid'),
('pubchemid', 'wikidataid', 'from_pubchemid'),
('pubchemid', 'chebiid', 'from_pubchemid'),
('pubchemid', 'keggid', 'from_pubchemid'),
('chemspiderid', 'hmdbid', 'from_chemspiderid'),
('chemspiderid', 'pubchemid', 'from_chemspiderid'),
('chemspiderid', 'wikidataid', 'from_chemspiderid'),
('chemspiderid', 'chebiid', 'from_chemspiderid'),
('chemspiderid', 'keggid', 'from_chemspiderid'),
('wikidataid', 'hmdbid', 'from_wikidataid'),
('wikidataid', 'pubchemid', 'from_wikidataid'),
('wikidataid', 'chemspiderid', 'from_wikidataid'),
('wikidataid', 'chebiid', 'from_wikidataid'),
('wikidataid', 'keggid', 'from_wikidataid'),
('chebiid', 'hmdbid', 'from_chebiid'),
('chebiid', 'pubchemid', 'from_chebiid'),
('chebiid', 'chemspiderid', 'from_chebiid'),
('chebiid', 'wikidataid', 'from_chebiid')
('chebiid', 'wikidataid', 'from_chebiid'),
('chebiid', 'keggid', 'from_chebiid'),
('keggid', 'hmdbid', 'from_keggid'),
('keggid', 'pubchemid', 'from_keggid'),
('keggid', 'chemspiderid', 'from_keggid'),
('keggid', 'wikidataid', 'from_keggid'),
('keggid', 'chebiid', 'from_keggid'),
]
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I think this could be also at some point made as all possible combinations between the 4 initial identifiers - otherwise all good!

self.create_top_level_conversion_methods(conversions)

Expand Down Expand Up @@ -91,6 +102,16 @@ async def from_chebiid(self, chebiid):
args = f'{self.codes["chebiid"]}/{chebiid}'
return await self.call_service(args)

async def from_keggid(self, keggid):
"""
Convert KEGG ID to all possible IDs using BridgeDB web service

:param keggid: given KEGG ID number
:return: obtained IDs
"""
args = f'{self.codes["keggid"]}/{keggid}'
return await self.call_service(args)

async def call_service(self, args):
response = await self.query_the_service('BridgeDB', args)
if response:
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