bridgedb / bridgedb/Goliath

Metabolite ID conversion gives different results, based on auto-select yes/no

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bug
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PHP
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Description

Hi @nunogit ;

I'm testing goliath with the list of HMDb IDs that Freddie was working on:
HMDB00112
HMDB00295
HMDB00901
HMDB00935
HMDB01275
HMDB01877
HMDB13037

When I do autoselect, I get these results:
![image](https://user-images.githubusercontent.com/26277832/54908606-96269180-4ee8-11e9-9729-130397a28814.png)

When I say I want to convert from HMDb to CHEBI, the results change (I have no mappings left):
![image](https://user-images.githubusercontent.com/26277832/54908572-8444ee80-4ee8-11e9-86eb-dd8de38dd89e.png)

And, when I change the IDs of HMDb from old to new ID structure, I get the following results:
![image](https://user-images.githubusercontent.com/26277832/54908708-d128c500-4ee8-11e9-965c-a30d4239aa5b.png)

(every ID but the last is similar... this could be due to mapping issues).

And with HMDB selected as primary database to map from (some mappings, but most do not work):
![image](https://user-images.githubusercontent.com/26277832/54908782-f4537480-4ee8-11e9-80e7-dee74426fe0b.png)

And last but not least, the ID that keeps giving "undefined" as a result, does exist in HMDB:
http://www.hmdb.ca/metabolites/HMDB0000901 . I can check if it is also part of our mapping files (could be that the webservice is still running on quite old data right?)...

Contributor guide

No contributing guide indexed for this repository

Research direction

Reproduce the conversion using the listed HMDB IDs, comparing autoselect, explicit HMDB-to-CHEBI conversion, old-to-new IDs, and HMDB as the primary database. Check the mapping files and webservice data mentioned in the report; done means the same valid mappings are returned consistently and HMDB0000901 no longer produces undefined.

Written by the indexing model from the issue text.

Assessment

Tech stack
php
Domain
data, databases
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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