Mapping compund name to SabioCompoundID

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Deepa

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Jul 24, 2019, 6:10:17 AM7/24/19
to SABIO-RK

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

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Jul 24, 2019, 9:15:55 AM7/24/19
to SABIO-RK
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

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Jul 24, 2019, 11:26:14 AM7/24/19
to Ulrike Wittig, SABIO-RK
Hi Ulrike,

Thanks a lot for the response. That helps.

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Deepa

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Jul 24, 2019, 12:01:10 PM7/24/19
to Ulrike Wittig, SABIO-RK
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

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Jul 24, 2019, 3:16:57 PM7/24/19
to SABIO-RK
Hi Deepa,

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

Best,
Ulrike
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Deepa

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Jul 25, 2019, 3:51:11 AM7/25/19
to Ulrike Wittig, SABIO-RK
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

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Jul 25, 2019, 4:09:55 AM7/25/19
to SABIO-RK
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

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Jul 25, 2019, 7:47:06 AM7/25/19
to Ulrike Wittig, SABIO-RK
Thank you so much

Deepa

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