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Showing metabocard for Medemo (HMDB0254401)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 13:40:51 UTC
Update Date2021-09-26 23:08:22 UTC
HMDB IDHMDB0254401
Secondary Accession NumbersNone
Metabolite Identification
Common NameMedemo
DescriptionMedemo, also known as EDMM, belongs to the class of organic compounds known as trialkylamines. These are organic compounds containing a trialkylamine group, characterized by exactly three alkyl groups bonded to the amino nitrogen. Based on a literature review very few articles have been published on Medemo. This compound has been identified in human blood as reported by (PMID: 31557052 ). Medemo is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Medemo is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0254401 (Medemo)

  Mrv1652309112115412D          

 12 11  0  0  0  0            999 V2000
    0.4125    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    3.5724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    2.8579    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    2.4454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  4  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
M  END
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3D MOL for HMDB0254401 (Medemo)

HMDB0254401
     RDKit          3D
Medemo
 30 29  0  0  0  0  0  0  0  0999 V2000
    3.8924    2.0494   -0.6774 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3630    0.6417   -0.2981 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4936    0.1963    0.7030 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1032   -0.4955   -0.0422 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.1400   -2.2587    0.1128 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0336   -0.0889   -1.4823 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5735    0.4572    1.0183 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0491   -0.1824    0.9709 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1341    0.6778    0.2912 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4397    0.1794    0.7594 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6079   -1.2397    0.4108 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4250    0.8821   -0.1032 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6081    2.8239   -0.5928 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9441    2.2609   -0.0900 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5339    1.9986   -1.7690 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7436    0.0139   -1.0291 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3188    0.8997    0.3748 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7154   -2.6604   -0.7761 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5528   -2.5756    1.0649 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0762   -2.6184   -0.0456 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9444   -1.0080    0.0107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3785   -0.7779    1.7717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0224    0.7731   -0.7516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0781    1.7292    0.7301 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3154   -1.8062    1.3977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7138   -1.3865    0.3698 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0045   -1.5575   -0.4020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4140    0.4605    0.1847 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2047    0.6705   -1.1946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3604    1.9414    0.0996 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  2  0
  4  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 10 12  1  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  2 16  1  0
  2 17  1  0
  5 18  1  0
  5 19  1  0
  5 20  1  0
  8 21  1  0
  8 22  1  0
  9 23  1  0
  9 24  1  0
 11 25  1  0
 11 26  1  0
 11 27  1  0
 12 28  1  0
 12 29  1  0
 12 30  1  0
M  END
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3D SDF for HMDB0254401 (Medemo)

  Mrv1652309112115412D          

 12 11  0  0  0  0            999 V2000
    0.4125    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    3.5724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    2.8579    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    2.4454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  4  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0254401

> <DATABASE_NAME>
hmdb

> <SMILES>
CCOP(C)(=O)SCCN(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C7H18NO2PS/c1-5-10-11(4,9)12-7-6-8(2)3/h5-7H2,1-4H3

> <INCHI_KEY>
PKDYQTANBZBIRM-UHFFFAOYSA-N

> <FORMULA>
C7H18NO2PS

> <MOLECULAR_WEIGHT>
211.26

> <EXACT_MASS>
211.079586996

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
22.229388664461926

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
ethyl {[2-(dimethylamino)ethyl]sulfanyl}(methyl)phosphinate

> <ALOGPS_LOGP>
0.78

> <JCHEM_LOGP>
0.49173670366666605

> <ALOGPS_LOGS>
-1.16

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
9.450942758029942

> <JCHEM_POLAR_SURFACE_AREA>
29.54

> <JCHEM_REFRACTIVITY>
55.51960000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.47e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ethyl [2-(dimethylamino)ethyl]sulfanyl(methyl)phosphinate

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0254401 (Medemo)

HMDB0254401
     RDKit          3D
Medemo
 30 29  0  0  0  0  0  0  0  0999 V2000
    3.8924    2.0494   -0.6774 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3630    0.6417   -0.2981 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4936    0.1963    0.7030 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1032   -0.4955   -0.0422 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.1400   -2.2587    0.1128 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0336   -0.0889   -1.4823 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5735    0.4572    1.0183 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0491   -0.1824    0.9709 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1341    0.6778    0.2912 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4397    0.1794    0.7594 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6079   -1.2397    0.4108 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4250    0.8821   -0.1032 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6081    2.8239   -0.5928 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9441    2.2609   -0.0900 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5339    1.9986   -1.7690 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7436    0.0139   -1.0291 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3188    0.8997    0.3748 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7154   -2.6604   -0.7761 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5528   -2.5756    1.0649 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0762   -2.6184   -0.0456 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9444   -1.0080    0.0107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3785   -0.7779    1.7717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0224    0.7731   -0.7516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0781    1.7292    0.7301 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3154   -1.8062    1.3977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7138   -1.3865    0.3698 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0045   -1.5575   -0.4020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4140    0.4605    0.1847 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2047    0.6705   -1.1946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3604    1.9414    0.0996 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  2  0
  4  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 10 12  1  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  2 16  1  0
  2 17  1  0
  5 18  1  0
  5 19  1  0
  5 20  1  0
  8 21  1  0
  8 22  1  0
  9 23  1  0
  9 24  1  0
 11 25  1  0
 11 26  1  0
 11 27  1  0
 12 28  1  0
 12 29  1  0
 12 30  1  0
M  END
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PDB for HMDB0254401 (Medemo)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       0.770   9.336   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   8.002   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.770   6.668   0.000  0.00  0.00           O+0
HETATM    4  P   UNK     0       1.540   5.335   0.000  0.00  0.00           P+0
HETATM    5  O   UNK     0       0.206   4.565   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       2.874   6.105   0.000  0.00  0.00           C+0
HETATM    7  S   UNK     0       2.310   4.001   0.000  0.00  0.00           S+0
HETATM    8  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       1.540   0.000   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6    7                                             
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    4    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END
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3D PDB for HMDB0254401 (Medemo)

COMPND    HMDB0254401
HETATM    1  C1  UNL     1       3.892   2.049  -0.677  1.00  0.00           C  
HETATM    2  C2  UNL     1       4.363   0.642  -0.298  1.00  0.00           C  
HETATM    3  O1  UNL     1       3.494   0.196   0.703  1.00  0.00           O  
HETATM    4  P1  UNL     1       2.103  -0.496  -0.042  1.00  0.00           P  
HETATM    5  C3  UNL     1       2.140  -2.259   0.113  1.00  0.00           C  
HETATM    6  O2  UNL     1       2.034  -0.089  -1.482  1.00  0.00           O  
HETATM    7  S1  UNL     1       0.574   0.457   1.018  1.00  0.00           S  
HETATM    8  C4  UNL     1      -1.049  -0.182   0.971  1.00  0.00           C  
HETATM    9  C5  UNL     1      -2.134   0.678   0.291  1.00  0.00           C  
HETATM   10  N1  UNL     1      -3.440   0.179   0.759  1.00  0.00           N  
HETATM   11  C6  UNL     1      -3.608  -1.240   0.411  1.00  0.00           C  
HETATM   12  C7  UNL     1      -4.425   0.882  -0.103  1.00  0.00           C  
HETATM   13  H1  UNL     1       4.608   2.824  -0.593  1.00  0.00           H  
HETATM   14  H2  UNL     1       2.944   2.261  -0.090  1.00  0.00           H  
HETATM   15  H3  UNL     1       3.534   1.999  -1.769  1.00  0.00           H  
HETATM   16  H4  UNL     1       4.744   0.014  -1.029  1.00  0.00           H  
HETATM   17  H5  UNL     1       5.319   0.900   0.375  1.00  0.00           H  
HETATM   18  H6  UNL     1       2.715  -2.660  -0.776  1.00  0.00           H  
HETATM   19  H7  UNL     1       2.553  -2.576   1.065  1.00  0.00           H  
HETATM   20  H8  UNL     1       1.076  -2.618  -0.046  1.00  0.00           H  
HETATM   21  H9  UNL     1      -0.944  -1.008   0.011  1.00  0.00           H  
HETATM   22  H10 UNL     1      -1.379  -0.778   1.772  1.00  0.00           H  
HETATM   23  H11 UNL     1      -2.022   0.773  -0.752  1.00  0.00           H  
HETATM   24  H12 UNL     1      -2.078   1.729   0.730  1.00  0.00           H  
HETATM   25  H13 UNL     1      -3.315  -1.806   1.398  1.00  0.00           H  
HETATM   26  H14 UNL     1      -4.714  -1.387   0.370  1.00  0.00           H  
HETATM   27  H15 UNL     1      -3.005  -1.557  -0.402  1.00  0.00           H  
HETATM   28  H16 UNL     1      -5.414   0.461   0.185  1.00  0.00           H  
HETATM   29  H17 UNL     1      -4.205   0.671  -1.195  1.00  0.00           H  
HETATM   30  H18 UNL     1      -4.360   1.941   0.100  1.00  0.00           H  
CONECT    1    2   13   14   15
CONECT    2    3   16   17
CONECT    3    4
CONECT    4    5    6    6    7
CONECT    5   18   19   20
CONECT    7    8
CONECT    8    9   21   22
CONECT    9   10   23   24
CONECT   10   11   12
CONECT   11   25   26   27
CONECT   12   28   29   30
END
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SMILES for HMDB0254401 (Medemo)

CCOP(C)(=O)SCCN(C)C
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INCHI for HMDB0254401 (Medemo)

InChI=1S/C7H18NO2PS/c1-5-10-11(4,9)12-7-6-8(2)3/h5-7H2,1-4H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
EDMMHMDB
O-Ethyl S-(2-dimethylaminoethyl) methylphosphonothioateHMDB
O-Ethyl S-(2-dimethylaminoethyl) methylphosphonothioate oxalate (1:1) saltHMDB
Methylethoxy(2-dimethylaminoethylthio)phosphine oxideHMDB
Methylthiophosphorous acid O-ethyl S-2-dimethylamianoethyl esterHMDB
Chemical FormulaC7H18NO2PS
Average Molecular Weight211.26
Monoisotopic Molecular Weight211.079586996
IUPAC Nameethyl {[2-(dimethylamino)ethyl]sulfanyl}(methyl)phosphinate
Traditional Nameethyl [2-(dimethylamino)ethyl]sulfanyl(methyl)phosphinate
CAS Registry NumberNot Available
SMILES
CCOP(C)(=O)SCCN(C)C
InChI Identifier
InChI=1S/C7H18NO2PS/c1-5-10-11(4,9)12-7-6-8(2)3/h5-7H2,1-4H3
InChI KeyPKDYQTANBZBIRM-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as trialkylamines. These are organic compounds containing a trialkylamine group, characterized by exactly three alkyl groups bonded to the amino nitrogen.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassAmines
Direct ParentTrialkylamines
Alternative Parents
Substituents
  • Tertiary aliphatic amine
  • Sulfenyl compound
  • Organothiophosphorus compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organosulfur compound
  • Organophosphorus compound
  • Organooxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID92416
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound102302
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]