Mapping compund name to SabioCompoundID

[Deepa]

Hello Everyone,

I'm trying to map compound name to SabioCompoundID.

I tried the example script provided here .

The following example returns ["Name","ChebiID","PubChemID","InChI","SabioCompoundID","KeggCompoundID"]  using SabioCompoundID":"36" as input.

# Example SABIO-RK script 3 - returns compound details

# ------------------------------------------------------------------------------

import requests

QUERY_URL = 'http://sabiork.h-its.org/sabioRestWebServices/searchCompoundDetails'


# input: SabioCompoundID
# valid output fields: "fields[]":["Name","ChebiID","PubChemID","InChI","SabioCompoundID","KeggCompoundID"]

# example
query = {"SabioCompoundID":"36", "fields[]":["Name","ChebiID","PubChemID"]}

request = requests.post(QUERY_URL, params = query)
request.raise_for_status()


# results

print(request.text) 

Outtput:

Name    ChebiID    PubChemID
Phosphate    35780 26078 18367    3311

I'd like to modify the script to query information using the field "Name" (name of the compound). I made the following change to the variable "query",

query = {"Name":"Phosphate", "fields[]":["SabioCOmpoundID","ChebiID","PubChemID"]}

Output:

SabioCompoundID    ChebiID    PubChemID
null    null    null

I'm not sure what's the right way to map compound name to sabio compound id.

Could someone help me with this?

Many thanks,

Deepa

[Ulrike Wittig]

Hi Deepa,

maybe you could use the MetaNetX mapping which includes compounds from SABIO-RK, KEGG, and ChEBI beside others.

The details you can find here https://www.metanetx.org/mnxdoc/mnxref.html

in the file: chem_xref.tsv

Best regards,

Ulrike

[Deepa]

Hi Ulrike,

Thanks a lot for the response. That helps.

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[Deepa]

Hi Ulrike,

Using the compound name I could map all the compounds names to MetaNetX id . Is there a way to map the MetaNetX id or bigg id obtained from "chem_xref.tsv" to SabioCompoundID  ?

Thank you very much,

Deepa

[Ulrike Wittig]

Hi Deepa,

the same file also contains the mapping from SABIO-RK compound ID to MetaNetX ID.

Best,

Ulrike

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[Deepa]

Hi Ulrike,

 I could find the following mappings listed for Phosphate in 5 entires. The column on extreme left indicates the row numbers in the file.

13017                                             bigg:pi            MNXM9  identity  Phosphate
13018                                           bigg:M_pi            MNXM9  identity  Phosphate
235265  envipath:32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/...            MNXM9  identity  Phosphate
241251  envipath:5882df9c-dae1-4d80-a40e-db4724271456/...            MNXM9  identity  Phosphate
241885  envipath:5882df9c-dae1-4d80-a40e-db4724271456/...            MNXM9  identity  Phosphate

Couldn't find sabio compound id. Could you please let me know where to look for SabioCompoundID?

Many thanks,

Deepa

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[Ulrike Wittig]

Hi Deepa,

if you search the file for MNXM9 which is the MetaNetX ID for Phosphate you will find all other mappings from other databases including SABIO-RK.

sabiork:36    MNXM9    identity    Orthophosphate|Phosphate|Phosphoric acid|Pi

Best,

Ulrike

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[Deepa]

Thank you so much

Deepa

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