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@eduardszoecs
eduardszoecs committed Aug 25, 2015
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Expand Up @@ -26,6 +26,7 @@ PubChem | `get_cid()`, `cid_compinfo()` | [link](https://pubchem.ncbi.nlm.nih.go
[Allan Wood's Compendium of Pesticide Common Names](http://www.alanwood.net/pesticides/) | `allanwood()` | none | none
[PHYSPROP Database](http://www.srcinc.com/what-we-do/environmental/scientific-databases.html) | `physprop()` | none | none
[ETOX](http://webetox.uba.de/webETOX/index.do) | `get_etoxid()`, `etox_basic()`. `etox_targets()`, `etox_tests()` | none | none
[PPDB](http://sitem.herts.ac.uk/aeru/iupac/search.htm) | `ppdb_query()` | none | none

#### API keys
ChemSpider functions require a security token.
Expand Down Expand Up @@ -62,28 +63,34 @@ Use `first` to return only the first hit.

```r
cir_query('Triclosan', 'cas')
#> [1] "3380-34-5" "112099-35-1" "88032-08-0"
#> Operation in progressfailed to load external entity "http://cactus.nci.nih.gov/chemical/structure/Triclosan/cas/xml"
#> [1] NA
cir_query('Triclosan', 'cas', first = TRUE)
#> [1] "3380-34-5"
#> Operation in progressfailed to load external entity "http://cactus.nci.nih.gov/chemical/structure/Triclosan/cas/xml"
#> [1] NA
cir_query('Triclosan', 'mw')
#> [1] "289.5451"
#> Operation in progressfailed to load external entity "http://cactus.nci.nih.gov/chemical/structure/Triclosan/mw/xml"
#> [1] NA
```

Query SMILES and InChIKey from CAS (Triclosan).
Inputs might by ambiguous and we can specify where to search using `resolver=`.

```r
cir_query('3380-34-5', 'smiles')
#> [1] "C1=CC(=CC(=C1OC2=CC=C(C=C2Cl)Cl)O)Cl"
#> Operation in progressfailed to load external entity "http://cactus.nci.nih.gov/chemical/structure/3380-34-5/smiles/xml"
#> [1] NA
cir_query('3380-34-5', 'stdinchikey', resolver = 'cas_number')
#> [1] "InChIKey=XEFQLINVKFYRCS-UHFFFAOYSA-N"
#> Operation in progressfailed to load external entity "http://cactus.nci.nih.gov/chemical/structure/3380-34-5/stdinchikey/xml?resolver=cas_number"
#> [1] NA
```

Query the number of rings using the InChiKey (Triclosan)

```r
cir_query('XEFQLINVKFYRCS-UHFFFAOYSA-N', 'ring_count')
#> [1] "2"
#> Operation in progressfailed to load external entity "http://cactus.nci.nih.gov/chemical/structure/XEFQLINVKFYRCS-UHFFFAOYSA-N/ring_count/xml"
#> [1] NA
```


Expand Down Expand Up @@ -206,17 +213,7 @@ info[1:5]
```r
pan_list <- pan('lambda-Cyhalothrin', first = TRUE)
pan_list[c("CAS Number", "Chemical Class", "Water Solubility (Avg, mg/L)", "Adsorption Coefficient (Koc)" )]
#> $`CAS Number`
#> [1] "91465-08-6"
#>
#> $`Chemical Class`
#> [1] "Pyrethroid"
#>
#> $`Water Solubility (Avg, mg/L)`
#> [1] "0.0050"
#>
#> $`Adsorption Coefficient (Koc)`
#> [1] "157000"
#> [1] NA NA NA NA
```


Expand Down Expand Up @@ -264,30 +261,7 @@ You can use `physprop()` to query this database using a CAS number:

```r
physprop('50-00-0')
#> $cas
#> [1] "50-00-0"
#>
#> $cname
#> [1] "FORMALDEHYDE"
#>
#> $mw
#> [1] "30.026"
#>
#> $prop
#> variable value unit temp
#> 1 Water Solubility 400000 mg/L 20 deg C
#> 2 Log P (octanol-water) 0.35 25 deg C
#> 3 Vapor Pressure 3886 mm Hg 25 deg C
#> 4 pKa Dissociation Constant 13.27 25 deg C
#> 5 Henry's Law Constant 0.000000337 atm-m3/mol 25 deg C
#> 6 Atmospheric OH Rate Constant 0.00000000000937 cm3/molecule-sec 25 deg C
#> type ref
#> 1 EXP PICKRELL,JA ET AL. (1983)
#> 2 EXP HANSCH,C ET AL. (1995)
#> 3 EXT BOUBLIK,T ET AL. (1984)
#> 4 EXP SERJEANT,EP & DEMPSEY,B (1979)
#> 5 EXP BETTERTON,EA & HOFFMAN,MR (1988)
#> 6 EXP KWOK,ESC & ATKINSON,R (1994)
#> [1] NA
```


Expand Down Expand Up @@ -424,6 +398,74 @@ tests[ , c('Organism', 'Effect', 'Duration', 'Time_Unit','Endpoint', 'Value', 'U
```


#### PPDB
The PPDB holds a lot of chemical and ecotoxicological information.
In webchem we provide a function to query this database by a CAS number.


```r
out <- ppdb_query('1071-83-6')
```

The informaion output is enormous, I show here only a small part, the countries where the compound is approved:


```r
out[[3]]
#> variable
#> 1 Pesticide type
#> 2 Substance group
#> 3 Substance origin
#> 4 Mode of action
#> 5 CAS RN
#> 6 EC number
#> 7 CIPAC number
#> 8 US EPA chemical code
#> 9 Chiral molecule
#> 10 Chemical formula
#> 11 SMILES
#> 12 International Chemical Identifier key (InChIKey)
#> 13 International Chemical Identifier (InChI)
#> 14 Structure diagram/image available?
#> 15 Molecular mass (g mol-1)
#> 16 PIN (Preferred Identification Name)
#> 17 IUPAC name
#> 18 CAS name
#> 19 Other status information
#> 20 Herbicide Resistance Classification (HRAC)
#> 21 Herbicide Resistance Classification (WSSA)
#> 22 Insecticide Resistance Classification (IRAC)
#> 23 Fungicide Resistance Classification (FRAC)
#> 24 Physical state
#> 25 Related substances & organisms
#> value
#> 1 Herbicide
#> 2 Phosphonoglycine
#> 3 Synthetic
#> 4 Broad-spectrum, systemic, contact action translocated and non-residual. Inhibition of EPSP synthase.
#> 5 1071-83-6
#> 6 213-997-4
#> 7 284
#> 8 417300
#> 9 No
#> 10 C3H8NO5P
#> 11 C(C(=O)[O-])NCP(=O)(O)O
#> 12 XDDAORKBJWWYJS-UHFFFAOYSA-N
#> 13 InChI=1S/C3H8NO5P/c5-3(6)1-4-2-10(7,8)9/h4H,1-2H2,(H,5,6)(H2,7,8,9)
#> 14 Yes
#> 15 169.1
#> 16 -
#> 17 N-(phosphonomethyl)glycine
#> 18 N-(phosphonomethyl)glycine
#> 19 Risk of herbicide resistance developing - anti-resistance management required
#> 20 G
#> 21 9
#> 22 Not applicable
#> 23 Not applicable
#> 24 Colourless crystals
#> 25 diflufenican \n ethoxylated tallow amine \n polyacrylamide \n 8-hydroxyquinoline
```




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