Connect2resources

VMH2Metabolon(metabolite_structure)[source]

Read a manually curated Metabolon-to-VMH mapping and add the matched Metabolon, HMDB, InChIKey, InChIString, CAS registry, KEGG, ChemSpider and PubChem identifiers to the metabolite structure. The mapping was done in parts manually and cross checked from two sides independently. Existing annotation entries may be overwritten.

USAGE:

[metabolite_structure] = VMH2Metabolon (metabolite_structure)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding annotation fields

OUTPUT:

metabolite_structure – metabolite structure updated with the Metabolon cross-matched identifiers

VMH2Seed(metabolite_structure)[source]

Read a VMH-to-SEED metabolite translation table and add the matched SEED identifiers to the metabolite structure. Existing SEED entries may be overwritten.

USAGE:

[metabolite_structure] = VMH2Seed (metabolite_structure)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding annotation fields

OUTPUT:

metabolite_structure – metabolite structure updated with the matched SEED identifiers

assignAGORAReconPresence(metabolite_structure, reaction)[source]

Assign whether each metabolite (or reaction) occurs in AGORA2 and in Recon3D by flagging the matched entries with .Agora2 and .Recon3D fields.

USAGE:

[metabolite_structure] = assignAGORAReconPresence (metabolite_structure, reaction)

INPUTS:

metabolite_structure – metabolite structure whose fields are VMH metabolite (or reaction) IDs

OPTIONAL INPUT:

reaction – default: false (0). Set to true (1) if the input is a reaction structure

OUTPUT:

metabolite_structure – metabolite structure updated with the AGORA2 and Recon3D presence flags

assignClassyFire(metabolite_structure, startSearch, endSearch)[source]

Get the metabolite taxonomic classification from ClassyFire (online), based on each metabolite InChIKey, and store the Kingdom, Superclass, Class, Subclass and Level 5 assignments as classyFire_* fields.

USAGE:

[metabolite_structure] = assignClassyFire (metabolite_structure, startSearch, endSearch)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs

OPTIONAL INPUTS:

  • startSearch – numeric index of where the search should start in the metabolite structure (default: 1)

  • endSearch – numeric index of where the search should end in the metabolite structure (default: last metabolite)

OUTPUT:

metabolite_structure – metabolite structure updated with the ClassyFire classification fields

convertOld2NewHMDB(HMDBId)[source]

Convert an old style HMDB id to the new style by zero padding the numeric part to 7 digits (old style ‘HMDB06525’, new style ‘HMDB0006525’). Ids that are already in the new style are returned as an empty char.

USAGE:

[HMDBId_new] = convertOld2NewHMDB (HMDBId)

INPUT:

HMDBId – old style HMDB id

OUTPUT:

HMDBId_new – new style HMDB id (7 digit numeric part)

getAnnoFromHMDB[source]

Annotate the metabolite structure with identifiers parsed from HMDB. HMDB IDs already present are written to a file, parsed offline, and the returned cross-references (SMILES, InChIString, InChIKey, KEGG, BioCyc, ChEBI, FooDB, DrugBank, ChemSpider, PubChem) are added; missing HMDB IDs are then inferred from the other identifiers.

getCas2CTD(metabolite_structure)[source]

Add CTD (Comparative Toxicogenomics Database) identifiers to the metabolite structure by matching on the CAS registry number. The input file was obtained from http://ctdbase.org/reports/CTD_chemicals.csv.gz (1st column: ctd id, 3rd column: cas).

USAGE:

[metabolite_structure, IDsAdded] = getCas2CTD (metabolite_structure)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding a casRegistry field

OUTPUTS:

  • metabolite_structure – metabolite structure updated with the matched CTD identifiers

  • IDsAdded – cell array logging the added identifiers, with the metabolite field name, the annotation type (ctd), and the assigned identifier per row

getCas2Echa(metabolite_structure)[source]

Add ECHA (European Chemicals Agency) identifiers to the metabolite structure by matching on the CAS registry number. The input file was downloaded from https://echa.europa.eu/documents/10162/13629/ec_inventory_en.xlsx (first column: echa_id, 4th column: cas registry).

USAGE:

[metabolite_structure, IDsAdded] = getCas2Echa (metabolite_structure)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding a casRegistry field

OUTPUTS:

  • metabolite_structure – metabolite structure updated with the matched ECHA identifiers

  • IDsAdded – cell array logging the added identifiers, with the metabolite field name, the annotation type (echa_id), and the assigned identifier per row

getIDsFromBIGG[source]

This m file annotates the metabolite studeture with IDs from BiGG using an offline file. Ines Thiele 2020/2021

getIDsfromFiehnLab(metabolite_structure, sourceId, targetId, startSearch, endSearch)[source]

Use the Fiehn lab Chemical Translation Service (online) to convert a source identifier into a target identifier for each metabolite and store the result (associated paper https://academic.oup.com/bioinformatics/article/26/20/2647/194184; query pattern http://cts.fiehnlab.ucdavis.edu/service/convert/from/to/term).

USAGE:

[metabolite_structure, IDsAdded] = getIDsfromFiehnLab (metabolite_structure, sourceId, targetId, startSearch, endSearch)

INPUTS:

  • metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding identifier fields

  • sourceId – metabolite field name of the identifier to translate from (e.g. keggId, inchiKey)

  • targetId – metabolite field name of the identifier to translate to (e.g. hmdb, cheBIId)

OPTIONAL INPUTS:

  • startSearch – numeric index of where the search should start in the metabolite structure (default: 1)

  • endSearch – numeric index of where the search should end in the metabolite structure (default: last metabolite)

OUTPUTS:

  • metabolite_structure – metabolite structure updated with the translated target identifiers

  • IDsAdded – cell array logging the added identifiers, with the metabolite field name, the target identifier type, and the assigned identifier per row

getIds2VMH(metabolite_structure)[source]

Map SEED, KEGG, BioCyc and BiGG metabolite identifiers onto the metabolite structure using the published cross-reference table for PMID 24927599 (file obtained from https://www.pnas.org/highwire/filestream/616377/field_highwire_adjunct_files/0/pnas.1401329111.sd01.xlsx). When adding BiGG identifiers, the script checks that the id is still valid by testing its web link; only valid BiGG ids are added.

USAGE:

[metabolite_structure, IDsAdded] = getIds2VMH (metabolite_structure)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding identifier fields

OUTPUTS:

  • metabolite_structure – metabolite structure updated with the mapped identifiers

  • IDsAdded – cell array logging the added identifiers, with the metabolite field name, the identifier type, and the assigned identifier per row

getInchiStringFromHMDB(HMDBID)[source]

Retrieve the InChIString from HMDB (online) for a given HMDB ID. Returns an empty array if the retrieval fails.

USAGE:

[inchiString] = getInchiStringFromHMDB (HMDBID)

INPUT:

HMDBID – Human metabolome database (HMDB) ID

OUTPUT:

inchiString – retrieved InChIString

getInchisFromDatabases(model)[source]

Collect InChIStrings and InChIKeys for the metabolites of a COBRA model from multiple sources (the model itself, HMDB, ChEBI and KEGG) and assemble them into comparison tables, one row per metabolite and one column per source.

USAGE:

[TableInchiStrings, TableInchiKeys] = getInchisFromDatabases (model)

INPUT:

model – COBRA model structure. Only the following field is used:

  • .modelID - identifier used to name the KEGG mol-file folder

OUTPUTS:

  • TableInchiStrings – cell array of InChIStrings per metabolite (rows) and source (columns)

  • TableInchiKeys – cell array of InChIKeys per metabolite (rows) and source (columns)

getMetIdsFromInchiKeys(metabolite_structure, inchiKeyCheck, inchiStringCheck, inchiKeyAltCheck, metList)[source]

Connect to UniChem and grab available identifiers (ChEBI, PubChem, MetaboLights, Rhea, SwissLipids, BindingDB, DrugBank, KEGG, HMDB, EPA and LipidMaps) for metabolites that have InChIKeys or InChIStrings.

USAGE:

[metabolite_structure, IDsAdded] = getMetIdsFromInchiKeys (metabolite_structure, inchiKeyCheck, inchiStringCheck, inchiKeyAltCheck, metList)

INPUTS:

  • metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding InChIKey/InChIString fields

  • inchiKeyCheck – if true, query UniChem using the InChIKey

  • inchiStringCheck – if true, query UniChem using the InChIString

  • inchiKeyAltCheck – if true, query UniChem using the neutral form of the InChIKey

OPTIONAL INPUT:

metList – list of metabolite field names to process (default: all fields of metabolite_structure)

OUTPUTS:

  • metabolite_structure – metabolite structure updated with the retrieved identifiers

  • IDsAdded – cell array logging the added identifiers, with the metabolite field name, the identifier type, and the assigned identifier per row

getMetIdsFromUniChem(metabolite_structure, startSearch, endSearch, vmhIdCheck, cheBIIdCheck, drugBankCheck, pubChemIdCheck, keggIdCheck, hmdbCheck, inchiKeyCheck, inchiStringCheck, inchiKeyAltCheck)[source]

Connect to UniChem and grab available identifiers (ChEBI, PubChem, MetaboLights, Rhea, SwissLipids, BindingDB, DrugBank, KEGG, HMDB, EPA and LipidMaps) for the metabolites in the structure. The query identifier is selected by the corresponding check flag.

USAGE:

[metabolite_structure, IDsAdded] = getMetIdsFromUniChem (metabolite_structure, startSearch, endSearch, vmhIdCheck, cheBIIdCheck, drugBankCheck, pubChemIdCheck, keggIdCheck, hmdbCheck, inchiKeyCheck, inchiStringCheck, inchiKeyAltCheck)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding identifier fields

OPTIONAL INPUTS:

  • startSearch – numeric index of where the search should start in the metabolite structure (default: 1)

  • endSearch – numeric index of where the search should end in the metabolite structure (default: last metabolite)

  • vmhIdCheck – if true, query UniChem using the VMH id (default: 0)

  • cheBIIdCheck – if true, query UniChem using the ChEBI id (default: 0)

  • drugBankCheck – if true, query UniChem using the DrugBank id (default: 0)

  • pubChemIdCheck – if true, query UniChem using the PubChem id (default: 0)

  • keggIdCheck – if true, query UniChem using the KEGG id (default: 0)

  • hmdbCheck – if true, query UniChem using the HMDB id (default: 0)

  • inchiKeyCheck – if true, query UniChem using the InChIKey (default: 0)

  • inchiStringCheck – if true, query UniChem using the InChIString (default: 0)

  • inchiKeyAltCheck – if true, query UniChem using the neutral form of the InChIKey (default: 0)

OUTPUTS:

  • metabolite_structure – metabolite structure updated with the retrieved identifiers

  • IDsAdded – cell array logging the added identifiers, with the metabolite field name, the identifier type, and the assigned identifier per row

getRxnFromKegg(metabolite_structure, metabolite_structure_rBioNet, metsField)[source]

Retrieve, for the KEGG-annotated metabolites in the structure, the associated KEGG reactions from the KEGG website and collect for each reaction its KEGG ID, name, definition, equation, VMH abbreviation and name, EC number and the associated human gene and KEGG ontology term.

USAGE:

[keggkeggRxn] = getkeggRxnFromKegg (metabolite_structure, metabolite_structure_rBioNet, metsField)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding a keggId field

OPTIONAL INPUTS:

  • metabolite_structure_rBioNet – rBioNet-derived metabolite structure used to map KEGG ids back to VMH ids (default: loaded from met_strc_rBioNet)

  • metsField – list of metabolite field names to process (default: all fields of metabolite_structure)

OUTPUT:

keggkeggRxn – cell array of the KEGG reactions retrieved for the input metabolites

getSeed2Kegg(metabolite_structure)[source]

Add KEGG identifiers to the metabolite structure by mapping from the SEED id. The mapping parses the KBase file ftp://ftp.kbase.us/assets/KBase_Reference_Data/Biochemistry/compounds.xls (first column: seed ID, 5th column: KEGG ID), provided in /data/ as ‘compounds.xlsx’.

USAGE:

[metabolite_structure, IDsAdded] = getSeed2Kegg (metabolite_structure)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding a seed field

OUTPUTS:

  • metabolite_structure – metabolite structure updated with the matched KEGG identifiers

  • IDsAdded – cell array logging the added identifiers, with the metabolite field name, the annotation type (keggId), and the assigned identifier per row

parseBiggID4VMH(metabolite_structure, startSearch, endSearch, grebMoreIDs)[source]

Guess the BiGG identifier of each metabolite from its VMH id by testing the BiGG website, and add it when a valid page exists. Note that a BiGG and a VMH id may coincide by chance for different metabolites; no further check is done, so additional ids are not retrieved by default.

USAGE:

[metabolite_structure, IDsAdded] = parseBiggID4VMH (metabolite_structure, startSearch, endSearch, grebMoreIDs)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding a VMHId field

OPTIONAL INPUTS:

  • startSearch – numeric index of where the search should start in the metabolite structure (default: 1)

  • endSearch – numeric index of where the search should end in the metabolite structure (default: last metabolite)

  • grebMoreIDs – if true (1), also retrieve additional identifiers (InChIKey, HMDB, MetaNetX, KEGG, BioCyc, Reactome, ChEBI) from the BiGG page (default: 0)

OUTPUTS:

  • metabolite_structure – metabolite structure updated with the matched BiGG identifier and any additional identifiers

  • IDsAdded – cell array logging the added identifiers, with the metabolite field name, the identifier type, and the assigned identifier per row

parseBridgeDb(metabolite_structure, startSearch, endSearch)[source]

Take the existing database-dependent identifiers and search BridgeDB (https://bridgedb.github.io/) via their web service for other database identifiers, adding them to the metabolite structure when the metabolite does not already have the respective identifier. When the metabolite already has such an identifier but it mismatches, the discrepancy is listed in IdsMismatch.

USAGE:

[metabolite_structure, IDsAdded, IdsMismatch] = parseBridgeDb (metabolite_structure, startSearch, endSearch)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding identifier fields

OPTIONAL INPUTS:

  • startSearch – numeric index of where the search should start in the metabolite structure (default: 1)

  • endSearch – numeric index of where the search should end in the metabolite structure (default: last metabolite)

OUTPUTS:

  • metabolite_structure – updated metabolite structure

  • IDsAdded – list of added IDs from BridgeDB

  • IdsMismatch – list of mismatching IDs between VMH and BridgeDB

parseCHOmineWebpage(metabolite_structure, startSearch, endSearch)[source]

Guess the CHOmine abbreviation of each metabolite from its VMH id by testing the CHOmine website (https://chomine.boku.ac.at/) and add the chodb_id when a matching entry exists.

USAGE:

[metabolite_structure, IDsAdded] = parseCHOmineWebpage (metabolite_structure, startSearch, endSearch)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding a VMHId field

OPTIONAL INPUTS:

  • startSearch – numeric index of where the search should start in the metabolite structure (default: 1)

  • endSearch – numeric index of where the search should end in the metabolite structure (default: last metabolite)

OUTPUTS:

  • metabolite_structure – metabolite structure updated with the matched CHOmine identifier

  • IDsAdded – cell array logging the added identifiers, with the metabolite field name, the annotation type (chodb_id), and the assigned identifier per row

parseChebiIdWebPage(metabolite_structure, startSearch, endSearch, printInchis)[source]

Parse the ChEBI website for each metabolite that has a ChEBI id and retrieve its SMILES, InChIKey and InChIString, adding them to the metabolite structure.

USAGE:

[metabolite_structure, IDsAdded, InchiKeyList, InchiStringList] = parseChebiIdWebPage (metabolite_structure, startSearch, endSearch, printInchis)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding a cheBIId field

OPTIONAL INPUTS:

  • startSearch – numeric index of where the search should start in the metabolite structure (default: 1)

  • endSearch – numeric index of where the search should end in the metabolite structure (default: last metabolite)

  • printInchis – if true, return the InChIKey and InChIString lists (default: 0)

OUTPUTS:

  • metabolite_structure – metabolite structure updated with the retrieved SMILES, InChIKey and InChIString

  • IDsAdded – cell array logging the added identifiers, with the metabolite field name, the identifier type, and the assigned identifier per row

  • InchiKeyList – list of the retrieved InChIKeys

  • InchiStringList – list of the retrieved InChIStrings

parseChemIDPlusWebpage(metabolite_structure, startSearch, endSearch)[source]

Retrieve identifiers from the ChemIDPlus website for each metabolite. UNII ids are looked up from the metabolite InChIKey and added to the structure.

USAGE:

[metabolite_structure, IDsAdded] = parseChemIDPlusWebpage (metabolite_structure, startSearch, endSearch)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding a inchiKey field

OPTIONAL INPUTS:

  • startSearch – numeric index of where the search should start in the metabolite structure (default: 1)

  • endSearch – numeric index of where the search should end in the metabolite structure (default: last metabolite)

OUTPUTS:

  • metabolite_structure – metabolite structure updated with the retrieved identifiers

  • IDsAdded – cell array logging the added identifiers, with the metabolite field name, the identifier type, and the assigned identifier per row

parseDBCollection(metabolite_structure, startSearch, endSearch)[source]

Collect metabolite identifiers from a series of online resources (BridgeDB, HMDB, Wikipedia, KEGG, ChEBI, DrugBank, UniChem, MetaNetX, Fiehn lab, BiGG, CHOmine, EPA, FDAsis and ChemIDPlus) and add them to the metabolite structure. This function takes substantial time; note that order matters, so some resources are parsed twice.

USAGE:

[metabolite_structure] = parseDBCollection (metabolite_structure, startSearch, endSearch)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs

OPTIONAL INPUTS:

  • startSearch – numeric index of where the search should start in the metabolite structure (default: 1)

  • endSearch – numeric index of where the search should end in the metabolite structure (default: last metabolite)

OUTPUT:

metabolite_structure – updated metabolite structure

parseDrugBankWebpage(metabolite_structure, startSearch, endSearch)[source]

Parse the DrugBank website for each metabolite that has a DrugBank id and retrieve the cross-referenced identifiers and properties (e.g. ChemSpider, FooDB, Wikipedia, PubChem, ChEBI, KEGG, InChIKey, InChIString, molecular weights, IUPAC name, description, BioCyc, CAS registry and more), adding them to the metabolite structure.

USAGE:

[metabolite_structure, IDsAdded] = parseDrugBankWebpage (metabolite_structure, startSearch, endSearch)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding a drugbank field

OPTIONAL INPUTS:

  • startSearch – numeric index of where the search should start in the metabolite structure (default: 1)

  • endSearch – numeric index of where the search should end in the metabolite structure (default: last metabolite)

OUTPUTS:

  • metabolite_structure – metabolite structure updated with the retrieved identifiers

  • IDsAdded – cell array logging the added identifiers, with the metabolite field name, the identifier type, and the assigned identifier per row

parseEPA4VMH(metabolite_structure, startSearch, endSearch)[source]

Search the EPA CompTox dashboard for each metabolite (using the CAS registry number or, failing that, the InChIKey) and add the matched EPA identifier (epa_id) to the metabolite structure.

USAGE:

[metabolite_structure, IDsAdded] = parseEPA4VMH (metabolite_structure, startSearch, endSearch)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding casRegistry and inchiKey fields

OPTIONAL INPUTS:

  • startSearch – numeric index of where the search should start in the metabolite structure (default: 1)

  • endSearch – numeric index of where the search should end in the metabolite structure (default: last metabolite)

OUTPUTS:

  • metabolite_structure – metabolite structure updated with the matched EPA identifier

  • IDsAdded – cell array logging the added identifiers, with the metabolite field name, the annotation type (epa_id), and the assigned identifier per row

parseFDAsisWebpage(metabolite_structure, startSearch, endSearch)[source]

Parse the FDA Substance Registration System (FDAsis) website for each metabolite that has a UNII id and retrieve cross-referenced identifiers (e.g. the PubChem id), adding them to the metabolite structure.

USAGE:

[metabolite_structure, IDsAdded] = parseFDAsisWebpage (metabolite_structure, startSearch, endSearch)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding VMHId and unii fields

OPTIONAL INPUTS:

  • startSearch – numeric index of where the search should start in the metabolite structure (default: 1)

  • endSearch – numeric index of where the search should end in the metabolite structure (default: last metabolite)

OUTPUTS:

  • metabolite_structure – metabolite structure updated with the retrieved identifiers

  • IDsAdded – cell array logging the added identifiers, with the metabolite field name, the identifier type, and the assigned identifier per row

parseHmdbWebPage(metabolite_structure, startSearch, endSearch, printInchis)[source]

Parse the HMDB website for each metabolite that has an HMDB id and retrieve the cross-referenced identifiers and properties (e.g. ChemSpider, FooDB, Wikipedia, PubChem, ChEBI, KEGG, InChIKey, InChIString, molecular weights, IUPAC name, description, BioCyc, CAS registry and more), adding them to the metabolite structure. Mismatches with existing ids are reported in IDsMismatch.

USAGE:

[metabolite_structure, IDsAdded, IDsMismatch, InchiKeyList, InchiStringList] = parseHmdbWebPage (metabolite_structure, startSearch, endSearch, printInchis)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding a hmdb field

OPTIONAL INPUTS:

  • startSearch – numeric index of where the search should start in the metabolite structure (default: 1)

  • endSearch – numeric index of where the search should end in the metabolite structure (default: last metabolite)

  • printInchis – if true, return the InChIKey and InChIString lists (default: 0)

OUTPUTS:

  • metabolite_structure – metabolite structure updated with the retrieved identifiers

  • IDsAdded – cell array logging the added identifiers, with the metabolite field name, the identifier type, and the assigned identifier per row

  • IDsMismatch – list of mismatching IDs between the structure and HMDB

  • InchiKeyList – list of the retrieved InChIKeys

  • InchiStringList – list of the retrieved InChIStrings

parseKeggWebpage(metabolite_structure, startSearch, endSearch)[source]

Search KEGG for identifiers, using the KEGG ids provided by the metabolite structure, and add the cross-referenced identifiers (CAS registry, ChEBI, ChEMBL and KNApSAcK) to the metabolite structure.

USAGE:

[metabolite_structure, IDsAdded] = parseKeggWebpage (metabolite_structure, startSearch, endSearch)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding a keggId field

OPTIONAL INPUTS:

  • startSearch – numeric index of where the search should start in the metabolite structure (default: 1)

  • endSearch – numeric index of where the search should end in the metabolite structure (default: last metabolite)

OUTPUTS:

  • metabolite_structure – updated metabolite structure

  • IDsAdded – cell array logging the added identifiers, with the metabolite field name, the identifier type, and the assigned identifier per row

parseMetaNetXWebpage(metabolite_structure, startSearch, endSearch)[source]

Retrieve MetaNetX identifiers based on the existing identifiers in the metabolite structure. A MetaNetX id is added only if its InChIKey agrees with the metabolite structure InChIKey (otherwise it is added to IDsSuggested). Verified MetaNetX ids are then used to retrieve further identifiers; a MetaNetX id that cannot be verified by InChIKey comparison is removed and listed in IDsSuggested.

USAGE:

[metabolite_structure, IDsAdded, IDsSuggested] = parseMetaNetXWebpage (metabolite_structure, startSearch, endSearch)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding identifier fields

OPTIONAL INPUTS:

  • startSearch – numeric index of where the search should start in the metabolite structure (default: 1)

  • endSearch – numeric index of where the search should end in the metabolite structure (default: last metabolite)

OUTPUTS:

  • metabolite_structure – updated metabolite structure

  • IDsAdded – list of added IDs

  • IDsSuggested – list of suggested IDs

parseVMH4IDs(metabolite_structure, startSearch, endSearch)[source]

Query the VMH API for each metabolite (by its VMH id) and fill empty fields of the metabolite structure with the returned identifiers and properties (e.g. formula, charge, BiGG, LipidMaps, KEGG, PubChem, ChEBI, InChIString/InChIKey, SMILES, HMDB, MetaNetX, SEED, CAS registry and further cross-references).

USAGE:

[metabolite_structure] = parseVMH4IDs (metabolite_structure, startSearch, endSearch)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding a VMHId field

OPTIONAL INPUTS:

  • startSearch – numeric index of where the search should start in the metabolite structure (default: 1)

  • endSearch – numeric index of where the search should end in the metabolite structure (default: last metabolite)

OUTPUT:

metabolite_structure – updated metabolite structure

parseWikipediaWebpage(metabolite_structure, startSearch, endSearch)[source]

Search Wikipedia for identifiers, using the Wikipedia id provided by the metabolite structure or a perfect hit from a metabolite name search, and add the cross-referenced identifiers (e.g. IUPHAR, ChemSpider, ECHA, ChEMBL, CAS registry, PubChem, UNII, EPA) to the metabolite structure.

USAGE:

[metabolite_structure, IDsAdded] = parseWikipediaWebpage (metabolite_structure, startSearch, endSearch)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs

OPTIONAL INPUTS:

  • startSearch – numeric index of where the search should start in the metabolite structure (default: 1)

  • endSearch – numeric index of where the search should end in the metabolite structure (default: last metabolite)

OUTPUTS:

  • metabolite_structure – updated metabolite structure

  • IDsAdded – cell array logging the added identifiers, with the metabolite field name, the identifier type, and the assigned identifier per row

queryExposomeExplorer(metabolite_structure)[source]

Search the Exposome Explorer website (http://exposome-explorer.iarc.fr) by metabolite name and add the matched Exposome Explorer identifier to the metabolite structure for metabolites that lack a LipidMaps id.

USAGE:

[metabolite_structure] = queryExposomeExplorer (metabolite_structure)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding metNames and lipidmaps fields

OUTPUT:

metabolite_structure – updated metabolite structure

queryLipidMaps(metabolite_structure, startSearch, endSearch)[source]

Search the LipidMaps website (https://www.lipidmaps.org) by metabolite name and add the matched LipidMaps identifier to the metabolite structure for metabolites that lack a LipidMaps id.

USAGE:

[metabolite_structure] = queryLipidMaps (metabolite_structure, startSearch, endSearch)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding metNames and lipidmaps fields

OPTIONAL INPUTS:

  • startSearch – numeric index of where the search should start in the metabolite structure (default: 1)

  • endSearch – numeric index of where the search should end in the metabolite structure (default: last metabolite)

OUTPUT:

metabolite_structure – updated metabolite structure

retrievePotHitsHMDB(met)[source]

Connect to HMDB and search for the metabolite name. The first 10 hits are examined and the metabolite name is searched for in the traditional name, IUPAC name, synonyms and common name. If one or more hits are found, the HMDB ids are returned.

USAGE:

[hmdb, multipleHits] = retrievePotHitsHMDB (met)

INPUT:

met – metabolite name

OUTPUTS:

  • hmdb – one or more HMDB ids; empty if no HMDB id could be found

  • multipleHits – indicates whether there are multiple hits

searchMultipleUnknownMetOnline(metabolite_structure, metabolite_structure_rBioNet, metab_rBioNet_online, rxn_rBioNet_online, startSearch, endSearch)[source]

Search HMDB online by metabolite name for each metabolite in the structure (via searchUnknownMetOnline) and merge the newly created metabolite entries back into the metabolite structure.

USAGE:

[metabolite_structure, hit] = searchMultipleUnknownMetOnline (metabolite_structure, metabolite_structure_rBioNet, metab_rBioNet_online, rxn_rBioNet_online, startSearch, endSearch)

INPUT:

metabolite_structure – metabolite structure whose fields are VMH metabolite IDs, each holding metNames and VMHId fields

OPTIONAL INPUTS:

  • metabolite_structure_rBioNet – rBioNet-derived metabolite structure (default: loaded from met_strc_rBioNet)

  • metab_rBioNet_online – rBioNet metabolite database (default: loaded from data/metab.mat)

  • rxn_rBioNet_online – rBioNet reaction database (default: loaded from data/rxn.mat)

  • startSearch – numeric index of where the search should start in the metabolite structure (default: 1)

  • endSearch – numeric index of where the search should end in the metabolite structure (default: last metabolite)

OUTPUTS:

  • metabolite_structure – updated metabolite structure

  • hit – cell array logging the matched metabolites, with the metabolite name, the new field name, and the HMDB id per row

searchUnknownMetOnline(met, VMHId, metabolite_structure_rBioNet, metab_rBioNet_online, rxn_rBioNet_online)[source]

Search HMDB by name and return a metabolite structure with the HMDB id when the name appears in the common name, IUPAC name, synonyms or traditional name. A new metabolite entry (with InChIString, mol file and charged formula) is created for the matched metabolite.

USAGE:

[metabolite_structure] = searchUnknownMetOnline (met, VMHId, metabolite_structure_rBioNet, metab_rBioNet_online, rxn_rBioNet_online)

INPUT:

met – metabolite name (try to spell it correctly)

OPTIONAL INPUTS:

  • VMHId – VMH id for the new metabolite (default: generated de novo with generateVMHMetAbbr)

  • metabolite_structure_rBioNet – rBioNet-derived metabolite structure (default: loaded from met_strc_rBioNet)

  • metab_rBioNet_online – rBioNet metabolite database (default: loaded from data/metab.mat)

  • rxn_rBioNet_online – rBioNet reaction database (default: loaded from data/rxn.mat)

OUTPUT:

metabolite_structure – metabolite structure for the matched metabolite