WikiPathways Test: Metabolites and Metabolic Interactions (Homo sapiens)

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1-5Metabolite Mapping FilesR03571 (Kegg Reaction)[Should link out to Rhea]Note: Doesn't take directionality into account in pathways.H+C00019VALID IDENTIFIERSMetabolites with identifiers in properly annotated datasources and valid values.Expected output in backpage:- Full list of identifiers- Links out all working- Correct linkouts between old and new ID structure (for HMDB)- Correct names for compoundsSTEP1Version 10 (2019-05-09)Acetic acidOld PubChem DB id1. Double click this Metabolite DataNode and verifythat "Glucose" gives search results.Aspirin (HMDB new IDs)DEPRECATED and/or SECONDARY DATA SOURCESMetabolites with identifiers with deprecated datasource strings.Optional output in the Backpage:- full list of identifiers- links out all workingMetabolites with identifiers with secondary datasource strings.Optional output in the Backpage:- Mapping to primary ID from same datasource- Some mapping to other identifiers - links out all workingSPECIAL METABOLITESThese metabolites are special in some way, for example,because they constitute a metabolite class.Expected output:- 1:n (directed) mappings to HMDB, ChemSpider, etcAspirin (KEGG)Aspirin (ChEBI, number only)Aspirin (CAS)Aspirin (PubChem)Aspirin (ChemSpider)long chain fatty acids (ChEBI)Enterobactin (not in HMDB, no mapping to Wikidata due to secondary ChEBI)Aspirin (ChEBI, with prefix)Old KEGG DB idAspirin (Wikidata)Aspirin (InChIKey)Gibberellin A1 (KNApSAcK)ACE Inhibitor (ChEBI)AcetateAspirin (EPA CompTox)Aspirin (HMDB old IDs)TG(15:0/i-15:0/i-21:0)(HMDB new IDs, no sec.)Armillaramide(HMDB new IDs, one sec.)Aspirin (KEGG-DRUG)Enterobactin (part of HMDB, has mapping to Wikidata due to primary ChEBI)STEP2STEP3STEP4Aspirin (ChEMBL)Aspirin (DrugBank)Aspirin (IUPHAR)Metabolic Interactions Mapping FilesSTEP1C01477C00021C01470VALID IDENTIFIERSReactions with identifiers in properly annotated datasources and valid values (check red coloured interactions).Expected output in backpage:- Original identifiers working- Links out (if available) all workingRXN-14819 (MetaCyc shorthand)[Should link out to Rhea and KEGG]Note: can linkout to multiple IDs for the same database, check directionality!NADP+D-glucopyranose-6-PNADPH6-P D-glucono-1,5-lactoneH+NADP+D-glucopyranose-6-PNADPH6-P D-glucono-1,5-lactoneGLU6PDEHYDROG-RXN (MetaCyc longhand/EcoCyc)[Should link out to Rhea and EcoCyc]Note: Does take directionality into account


Description

This is a test pathway, to be used to test mappings to other databases, old system codes, etc. Each time a new metabolite mapping database is loaded onto the BridgeDb webservice that supports the linking on WikiPathways, this pathway should be opened and tested. The pathway has notes of the expected outcome.

Quality Tags

Ontology Terms

 

Bibliography

  1. Slenter DN, Kutmon M, Hanspers K, Riutta A, Windsor J, Nunes N, Mélius J, Cirillo E, Coort SL, Digles D, Ehrhart F, Giesbertz P, Kalafati M, Martens M, Miller R, Nishida K, Rieswijk L, Waagmeester A, Eijssen LMT, Evelo CT, Pico AR, Willighagen EL; ''WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.''; Nucleic Acids Res, 2018 PubMed Europe PMC
  2. van Iersel MP, Pico AR, Kelder T, Gao J, Ho I, Hanspers K, Conklin BR, Evelo CT; ''The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services.''; BMC Bioinformatics, 2010 PubMed Europe PMC
  3. Kell DB, Goodacre R; ''Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery.''; Drug Discov Today, 2014 PubMed Europe PMC
  4. Wishart DS; ''Emerging applications of metabolomics in drug discovery and precision medicine.''; Nat Rev Drug Discov, 2016 PubMed Europe PMC
  5. Gao J, Zhang C, van Iersel M, Zhang L, Xu D, Schultz N, R Pico A; ''BridgeDb app: unifying identifier mapping services for Cytoscape.''; F1000Res, 2014 PubMed Europe PMC

History

View all...
CompareRevisionActionTimeUserComment
104196view14:07, 9 May 2019DeSlUpdated character in lit refs.
104195view14:02, 9 May 2019DeSlUpdated DrugBank identifier.
103428view12:29, 28 February 2019DeSlUpdated layout
103426view12:26, 28 February 2019DeSlAdded new test for metabolic interaction mapping files.
103058view11:53, 7 February 2019DeSlEnterobacterin is part of HMDB now, changed note in DataNode on this.
103050view10:52, 7 February 2019DeSlAdded name for IUPHAR database manually (waiting for new release of bridgeDb).
103049view10:51, 7 February 2019DeSlAdded checks for ChEMBL, Drugbank and IUPHAR.
102473view09:21, 24 December 2018DeSlAdded latest WPs paper as reference
102472view09:17, 24 December 2018DeSlAdded 2 new tests, changed layout
98035view10:57, 5 July 2018DeSlAdded new testcase for recently added LIPID Maps IDs to wikidata
98034view09:54, 5 July 2018DeSlAdded correct ID for latest testcase.
98033view09:46, 5 July 2018DeSlAdded lit. ref to BridgeDb paper and BridgeDb Cytoscape app paper.
98032view09:43, 5 July 2018DeSlChanged version number.
98031view09:41, 5 July 2018DeSlAdded more testcases
95851view14:52, 26 January 2018DeSlAdded node to check mapping to old and new HMDB IDs.
92873view08:07, 12 July 2017EgonwAdded an EPA CompTox test case.
90665view19:33, 4 December 2016AlexanderPicoModified title
85438view09:46, 15 May 2016EgonwAdded two review papers about metabolomics.
85430view09:30, 15 May 2016EgonwAdded quotes around "Glucose".
85429view09:27, 15 May 2016EgonwSome tweaks, and "released" as version 4.
85428view09:27, 15 May 2016EgonwRemoved redundant new lines.
85427view09:21, 15 May 2016EgonwAdded MOM test cases.
85076view06:33, 12 April 2016EgonwAdded a KNApSAcK test.
84782view10:07, 20 March 2016EgonwReverted to version '20:28, 17 July 2015' by Egonw
84480view20:41, 25 February 2016AlexanderPicoReverted to version '13:36, 25 February 2016' by AlexanderPico
84479view20:41, 25 February 2016AlexanderPico
84478view20:36, 25 February 2016AlexanderPicoQuick edit to datanode annotation or property
81054view20:28, 17 July 2015EgonwHacked in the InChIKey DataSource via the GPML.
81053view20:27, 17 July 2015EgonwAn InChIKey node.
81052view20:14, 17 July 2015EgonwHacked in the Wikidata DataSource via the GPML.
81051view20:12, 17 July 2015EgonwAdded a Wikidata node (for future testing).
80972view13:53, 6 July 2015EgonwModified description
72071view18:10, 24 October 2013EgonwModified description
72070view18:09, 24 October 2013EgonwNew pathway

External references

DataNodes

View all...
NameTypeDatabase referenceComment
1. Double click this Metabolite DataNode and verify that "Glucose" gives search results.Metabolite
6-P D-glucono- 1,5-lactoneMetaboliteCHEBI:57955 (ChEBI)
ACE Inhibitor (ChEBI)MetaboliteCHEBI:35457 (ChEBI)
AcetateMetaboliteCHEBI:30089 (ChEBI)
Acetic acidMetaboliteCHEBI:15366 (ChEBI)
Armillaramide (HMDB new IDs, one sec.)MetaboliteHMDB0037105 (HMDB)
Aspirin (CAS)Metabolite50-78-2 (CAS)
Aspirin (ChEBI, number only)Metabolite15365 (ChEBI)
Aspirin (ChEBI, with prefix)MetaboliteCHEBI:15365 (ChEBI)
Aspirin (ChEMBL)MetaboliteCHEMBL25 (ChEMBL compound)
Aspirin (ChemSpider)Metabolite2157 (Chemspider)
Aspirin (DrugBank)MetaboliteDB00945 (DrugBank)
Aspirin (EPA CompTox)MetaboliteDTXSID5020108 (EPA CompTox)
Aspirin (HMDB new IDs)MetaboliteHMDB0001879 (HMDB)
Aspirin (HMDB old IDs)MetaboliteHMDB01879 (HMDB)
Aspirin (IUPHAR)Metabolite4139 (Guide to Pharmacology)
Aspirin (InChIKey)MetaboliteBSYNRYMUTXBXSQ-UHFFFAOYSA-N (InChIKey)
Aspirin (KEGG)MetaboliteC01405 (KEGG Compound)
Aspirin (KEGG-DRUG)MetaboliteD00109 (KEGG Drug)
Aspirin (PubChem)Metabolite2244 (PubChem-compound)
Aspirin (Wikidata)MetaboliteQ18216 (Wikidata)
C00019MetaboliteC00019 (KEGG Compound)
C00021MetaboliteC00021 (KEGG Compound)
C01470MetaboliteC01470 (KEGG Compound)
C01477MetaboliteC01477 (KEGG Compound)
D-gluco pyranose-6-PMetaboliteCHEBI:61548 (ChEBI)
Enterobactin (not in HMDB, no mapping to Wikidata due to secondary ChEBI)MetaboliteCHEBI:4799 (ChEBI)
Enterobactin (part of HMDB, has mapping to Wikidata due to primary ChEBI)MetaboliteCHEBI:28855 (ChEBI)
Gibberellin A1 (KNApSAcK)MetaboliteC00000001 (KNApSAcK)
H+MetaboliteCHEBI:15378 (ChEBI)
NADP+MetaboliteCHEBI:58349 (ChEBI)
NADPHMetaboliteCHEBI:57783 (ChEBI)
Old KEGG DB idMetabolite2244 (Kegg Compound)
Old PubChem DB idMetabolite2244 (PubChem)
TG(15:0/i-15:0/i-21:0) (HMDB new IDs, no sec.)MetaboliteHMDB0101879 (HMDB)
long chain fatty acids (ChEBI)MetaboliteCHEBI:15904 (ChEBI)

Annotated Interactions

SourceTargetTypeDatabase referenceComment
C01477C01470mim-conversionR03571 (KEGG Reaction)
D-gluco pyranose-6-P6-P D-glucono- 1,5-lactonemim-conversionGLU6PDEHYDROG-RXN (MetaCyc)
D-gluco pyranose-6-P6-P D-glucono- 1,5-lactonemim-conversionRXN-14819 (MetaCyc)
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