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biosustain / cameo

cameo - computer aided metabolic engineering & optimization
http://cameo.bio
Apache License 2.0
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MetaNetX database #122

Closed the-code-magician closed 7 years ago

the-code-magician commented 7 years ago

The search in the database is not very reliable. I already changed it to be lower-case only, which helped. Also, MetaNetX has mapping for things that are redundant, however I can only find one source and one name, where there should be sources and names or synonyms.

I cannot find L-Serine, L-Lactate, etc. There are several algorithms to do this:

phantomas1234 commented 7 years ago 
from cameo import api
cameo.api.products.search('L-serine')

works for me.

                   name   formula charge      mass  \
MNXM53         L-serine   C3H7NO3      0  105.0926   
MNXM694        D-serine   C3H7NO3      0  105.0926   
MNXM4823         serine   C3H7NO3      0  105.0926   
MNXM59326   L-azaserine  C5H8N3O4      1  174.1347   
MNXM59545  L-synephrine  C9H14NO2      1   168.213   

                                                       InChI  \
MNXM53     InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H...   
MNXM694    InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H...   
MNXM4823   InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H...   
MNXM59326  InChI=1S/C5H7N3O4/c6-3(5(10)11)2-12-4(9)1-8-7/...   
MNXM59545  InChI=1S/C9H13NO2/c1-10-6-9(12)7-2-4-8(11)5-3-...

Edit: search has always been fuzzy

                                      SMILES               source  search_rank  
MNXM53             [NH3+][C@@H](CO)C([O-])=O          chebi:33384            0  
MNXM694             [NH3+][C@H](CO)C([O-])=O          chebi:35247            1  
MNXM4823                [NH3+]C(CO)C([O-])=O          chebi:35243            2  
MNXM59326  [NH3+]C(COC(=O)C=[N+]=N)C([O-])=O  metacyc:L-AZASERINE            3  
MNXM59545    C[NH2+]C[C@@H](O)C1=CC=C(O)C=C1          chebi:33016            4
the-code-magician commented 7 years ago 
In[3]: products.search("l-lysine")
Out[3]: 
             name    formula charge      mass  \
MNXM219  allysine   C6H11NO3      0  145.1564   
MNXM78   L-lysine  C6H15N2O2      1  147.1955   
MNXM975  D-lysine  C6H15N2O2      1  147.1955   

                                                     InChI  \
MNXM219  InChI=1S/C6H11NO3/c7-5(6(9)10)3-1-2-4-8/h4-5H,...   
MNXM78   InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1...   
MNXM975  InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1...   

                                    SMILES       source  search_rank  
MNXM219      [H]C(=O)CCCC([NH3+])C([O-])=O  chebi:57988            0  
MNXM78    [NH3+]CCCC[C@H]([NH3+])C([O-])=O  chebi:32551            1  
MNXM975  [NH3+]CCCC[C@@H]([NH3+])C([O-])=O  chebi:32557            2