From 452cb4f9ad7f1409de9e6c69a4f1f9e99769cb8b Mon Sep 17 00:00:00 2001 From: c1au6i0 Date: Fri, 6 Dec 2024 09:51:21 -0500 Subject: [PATCH] fix [skipci] --- README.Rmd | 1 + README.md | 348 ++++++++++-------- docs/index.html | 336 +++++++++-------- docs/news/index.html | 2 +- docs/pkgdown.yml | 2 +- docs/reference/extr_comptox.html | 2 +- docs/reference/write_dataframes_to_excel.html | 2 +- docs/search.json | 2 +- 8 files changed, 366 insertions(+), 329 deletions(-) diff --git a/README.Rmd b/README.Rmd index 3d11576..86d3495 100644 --- a/README.Rmd +++ b/README.Rmd @@ -13,6 +13,7 @@ knitr::opts_chunk$set( ) ``` +# extractox logo [![R-CMD-check](https://github.com/c1au6i0/extractox/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/c1au6i0/extractox/actions/workflows/R-CMD-check.yaml) diff --git a/README.md b/README.md index f118d17..e6303d2 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,8 @@ + + +# extractox logo + [![R-CMD-check](https://github.com/c1au6i0/extractox/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/c1au6i0/extractox/actions/workflows/R-CMD-check.yaml) @@ -25,21 +29,25 @@ To communicate with Pubchem, `extractox` relies on the package`webchem`. Install the package `extractox` from CRAN. - # From CRAN - install.packages("extractox") +``` r +# From CRAN +install.packages("extractox") +``` ### Development Version To get a bug fix or to use a feature from the development version, you can install the development version of `extractox` from GitHub. - # Install pak if not already installed - if (!requireNamespace("pak", quietly = TRUE)) { - install.packages("pak") - } +``` r +# Install pak if not already installed +if (!requireNamespace("pak", quietly = TRUE)) { + install.packages("pak") +} - # Install the package from GitHub - pak::pkg_install("c1au6i0/extractox") +# Install the package from GitHub +pak::pkg_install("c1au6i0/extractox") +``` ## Features @@ -53,21 +61,23 @@ and computational models. `extr_ice` provides access to NTP’s ICE database for toxicological and exposure-related data. - library(extractox) - ice_data <- extr_ice(casrn = c("50-00-0"), assays = NULL) # assays is null so all assays are retrieved - #> ℹ Checking Internet Connection... - #> ℹ Internet connection OK... - #> Sending request to ICE database... - #> Request succeeded with status code: 200 - names(ice_data) - #> [1] "assay" "endpoint" "substanceType" - #> [4] "casrn" "qsarReadyId" "value" - #> [7] "unit" "species" "receptorSpecies" - #> [10] "route" "sex" "strain" - #> [13] "lifeStage" "tissue" "lesion" - #> [16] "location" "assaySource" "inVitroAssayFormat" - #> [19] "reference" "referenceUrl" "dtxsid" - #> [22] "substanceName" "pubMedId" +``` r +library(extractox) +ice_data <- extr_ice(casrn = c("50-00-0"), assays = NULL) # assays is null so all assays are retrieved +#> ℹ Checking Internet Connection... +#> ℹ Internet connection OK... +#> Sending request to ICE database... +#> Request succeeded with status code: 200 +names(ice_data) +#> [1] "assay" "endpoint" "substanceType" +#> [4] "casrn" "qsarReadyId" "value" +#> [7] "unit" "species" "receptorSpecies" +#> [10] "route" "sex" "strain" +#> [13] "lifeStage" "tissue" "lesion" +#> [16] "location" "assaySource" "inVitroAssayFormat" +#> [19] "reference" "referenceUrl" "dtxsid" +#> [22] "substanceName" "pubMedId" +``` ### IRIS @@ -80,18 +90,20 @@ information. of Chemical Abstracts Service Registry Number (CASRN) or International Union of Pure and Applied Chemistry (IUPAC) names of chemicals. - iris_info <- extr_iris(c("glyphosate", "50-00-0")) - #> ℹ Checking Internet Connection... - #> ℹ Internet connection OK... - #> Quering glyphosate to EPA IRIS database... - #> Request succeeded with status code: 200 - #> Quering 50-00-0 to EPA IRIS database... - #> Request succeeded with status code: 200 - names(iris_info) - #> [1] "chemical_name" "casrn" - #> [3] "exposure_route" "assessment_type" - #> [5] "critical_effect_or_tumor_type" "woe_characterization" - #> [7] "toxicity_value_type" "toxicity_value" +``` r +iris_info <- extr_iris(c("glyphosate", "50-00-0")) +#> ℹ Checking Internet Connection... +#> ℹ Internet connection OK... +#> Quering glyphosate to EPA IRIS database... +#> Request succeeded with status code: 200 +#> Quering 50-00-0 to EPA IRIS database... +#> Request succeeded with status code: 200 +names(iris_info) +#> [1] "chemical_name" "casrn" +#> [3] "exposure_route" "assessment_type" +#> [5] "critical_effect_or_tumor_type" "woe_characterization" +#> [7] "toxicity_value_type" "toxicity_value" +``` ### CompTox @@ -104,39 +116,43 @@ assessments. both CASRN and IUPAC names of chemicals and returns a list of **dataframes**. - info_comptox <- extr_comptox(ids = c("Aspirin", "50-00-0")) - #> ℹ Sending request to CompTox... - #> Request succeeded with status code: 202 - #> ℹ Getting info from CompTox... - #> - #> Request succeeded with status code: 200 - names(info_comptox) - #> [1] "comptox_cover_sheet" "comptox_main_data" - #> [3] "comptox_abstract_sifter" "comptox_synonym_identifier" - #> [5] "comptox_related_relationships" "comptox_toxcast_assays_ac50" - #> [7] "comptox_toxval_details" "comptox_chemical_properties" +``` r +info_comptox <- extr_comptox(ids = c("Aspirin", "50-00-0")) +#> ℹ Sending request to CompTox... +#> Request succeeded with status code: 202 +#> ℹ Getting info from CompTox... +#> +#> Request succeeded with status code: 200 +names(info_comptox) +#> [1] "comptox_cover_sheet" "comptox_main_data" +#> [3] "comptox_abstract_sifter" "comptox_synonym_identifier" +#> [5] "comptox_related_relationships" "comptox_toxcast_assays_ac50" +#> [7] "comptox_toxval_details" "comptox_chemical_properties" +``` ### Tox Info The function `extr_tox` is a wrapper used to call all the above-mentioned functions and retrieve a list of dataframes. - info_tox <- extr_tox(casrn = c("Aspirin", "50-00-0")) - #> ℹ Checking Internet Connection... - #> ℹ Internet connection OK... - #> ℹ Getting PubChem IDS... - #> Querying Aspirin. OK (HTTP 200). - #> Querying 2244. OK (HTTP 200). - #> ℹ Getting PubChem IDS... - #> Querying 50-00-0. OK (HTTP 200). - #> Querying 712. OK (HTTP 200). - #> ℹ Sending request to CompTox... - #> Request succeeded with status code: 202ℹ Getting info from CompTox... - #> Request succeeded with status code: 200ℹ Checking Internet Connection... - #> ℹ Internet connection OK... - #> Sending request to ICE database...Request succeeded with status code: 200ℹ Checking Internet Connection... - #> ℹ Internet connection OK... - #> Quering Aspirin to EPA IRIS database...Request succeeded with status code: 200Quering 50-00-0 to EPA IRIS database...Request succeeded with status code: 200 +``` r +info_tox <- extr_tox(casrn = c("Aspirin", "50-00-0")) +#> ℹ Checking Internet Connection... +#> ℹ Internet connection OK... +#> ℹ Getting PubChem IDS... +#> Querying Aspirin. OK (HTTP 200). +#> Querying 2244. OK (HTTP 200). +#> ℹ Getting PubChem IDS... +#> Querying 50-00-0. OK (HTTP 200). +#> Querying 712. OK (HTTP 200). +#> ℹ Sending request to CompTox... +#> Request succeeded with status code: 202ℹ Getting info from CompTox... +#> Request succeeded with status code: 200ℹ Checking Internet Connection... +#> ℹ Internet connection OK... +#> Sending request to ICE database...Request succeeded with status code: 200ℹ Checking Internet Connection... +#> ℹ Internet connection OK... +#> Quering Aspirin to EPA IRIS database...Request succeeded with status code: 200Quering 50-00-0 to EPA IRIS database...Request succeeded with status code: 200 +``` ### CTD Database @@ -149,37 +165,39 @@ A series of functions interact with the CTP database. `extr_ctd` extracts information related to chemical-gene or pathway associations. - input_terms <- c("50-00-0", "64-17-5", "methanal", "ethanol") - ctd_association <- extr_ctd( - input_terms = input_terms, - category = "chem", - report_type = "genes_curated", - input_term_search_type = "directAssociations", - action_types = "ANY", - ontology = c("go_bp", "go_cc") - ) - #> ℹ Checking Internet Connection... - #> ℹ Internet connection OK... - #> Sending request to CTD database... - #> Request succeeded with status code: 200 - - - # Get expresssion data - ctd_expression <- extr_ctd( - input_terms = input_terms, - report_type = "cgixns", - category = "chem", - action_types = "expression" - ) - #> ℹ Checking Internet Connection... - #> ℹ Internet connection OK... - #> Sending request to CTD database...Request succeeded with status code: 200 - - names(ctd_expression) - #> [1] "x_input" "chemical_name" "chemical_id" - #> [4] "cas_rn" "gene_symbol" "gene_id" - #> [7] "organism" "organism_id" "interaction" - #> [10] "interaction_actions" "pub_med_i_ds" +``` r +input_terms <- c("50-00-0", "64-17-5", "methanal", "ethanol") +ctd_association <- extr_ctd( + input_terms = input_terms, + category = "chem", + report_type = "genes_curated", + input_term_search_type = "directAssociations", + action_types = "ANY", + ontology = c("go_bp", "go_cc") +) +#> ℹ Checking Internet Connection... +#> ℹ Internet connection OK... +#> Sending request to CTD database... +#> Request succeeded with status code: 200 + + +# Get expresssion data +ctd_expression <- extr_ctd( + input_terms = input_terms, + report_type = "cgixns", + category = "chem", + action_types = "expression" +) +#> ℹ Checking Internet Connection... +#> ℹ Internet connection OK... +#> Sending request to CTD database...Request succeeded with status code: 200 + +names(ctd_expression) +#> [1] "x_input" "chemical_name" "chemical_id" +#> [4] "cas_rn" "gene_symbol" "gene_id" +#> [7] "organism" "organism_id" "interaction" +#> [10] "interaction_actions" "pub_med_i_ds" +``` Tetramers are computationally generated information units that interrelate four data types from the CTP: a chemical, gene product, @@ -189,22 +207,24 @@ health. `extr_tetramer` extract info related to tetramers from CTD. - tetramer_data <- extr_tetramer( - chem = c("50-00-0", "ethanol"), - disease = "", - gene = "", - go = "", - input_term_search_type = "directAssociations", - qt_match_type = "equals" - ) - #> Sending request to CTD database for tetramer data for 50-00-0... - #> Request succeeded with status code: 200 - #> Sending request to CTD database for tetramer data for ethanol... - #> Request succeeded with status code: 200 - - names(tetramer_data) - #> [1] "query" "chemical" "chemical_id" "gene" "gene_id" - #> [6] "phenotype" "phenotype_id" "disease" "disease_id" +``` r +tetramer_data <- extr_tetramer( + chem = c("50-00-0", "ethanol"), + disease = "", + gene = "", + go = "", + input_term_search_type = "directAssociations", + qt_match_type = "equals" +) +#> Sending request to CTD database for tetramer data for 50-00-0... +#> Request succeeded with status code: 200 +#> Sending request to CTD database for tetramer data for ethanol... +#> Request succeeded with status code: 200 + +names(tetramer_data) +#> [1] "query" "chemical" "chemical_id" "gene" "gene_id" +#> [6] "phenotype" "phenotype_id" "disease" "disease_id" +``` ### PubChem Database @@ -221,64 +241,66 @@ The function `extr_chem_info` retrieves chemical information of IUPAC-named chemicals. A warning is displayed if the chemical is not found. - chem_info <- extr_chem_info(IUPAC_names = c("Formaldehyde", "Aflatoxin B1")) - #> ℹ Checking Internet Connection... - #> ℹ Internet connection OK... - #> Querying Formaldehyde. OK (HTTP 200). - #> Querying Aflatoxin B1. OK (HTTP 200). - #> ℹ Checking Internet Connection... - #> ℹ Internet connection OK... - #> ℹ Querying 712 and 186907. - names(chem_info) - #> [1] "cid" "iupac_name" - #> [3] "cas_rn" "cid_all" - #> [5] "cas_rn_all" "molecular_formula" - #> [7] "molecular_weight" "canonical_smiles" - #> [9] "isomeric_smiles" "in_ch_i" - #> [11] "in_ch_i_key" "iupac_name_y" - #> [13] "x_log_p" "exact_mass" - #> [15] "monoisotopic_mass" "tpsa" - #> [17] "complexity" "charge" - #> [19] "h_bond_donor_count" "h_bond_acceptor_count" - #> [21] "rotatable_bond_count" "heavy_atom_count" - #> [23] "isotope_atom_count" "atom_stereo_count" - #> [25] "defined_atom_stereo_count" "undefined_atom_stereo_count" - #> [27] "bond_stereo_count" "defined_bond_stereo_count" - #> [29] "undefined_bond_stereo_count" "covalent_unit_count" - #> [31] "volume3d" "x_steric_quadrupole3d" - #> [33] "y_steric_quadrupole3d" "z_steric_quadrupole3d" - #> [35] "feature_count3d" "feature_acceptor_count3d" - #> [37] "feature_donor_count3d" "feature_anion_count3d" - #> [39] "feature_cation_count3d" "feature_ring_count3d" - #> [41] "feature_hydrophobe_count3d" "conformer_model_rmsd3d" - #> [43] "effective_rotor_count3d" "conformer_count3d" - #> [45] "fingerprint2d" "query" +``` r +chem_info <- extr_chem_info(IUPAC_names = c("Formaldehyde", "Aflatoxin B1")) +#> ℹ Checking Internet Connection... +#> ℹ Internet connection OK... +#> Querying Formaldehyde. OK (HTTP 200). +#> Querying Aflatoxin B1. OK (HTTP 200). +#> ℹ Checking Internet Connection... +#> ℹ Internet connection OK... +#> ℹ Querying 712 and 186907. +names(chem_info) +#> [1] "cid" "iupac_name" +#> [3] "cas_rn" "cid_all" +#> [5] "cas_rn_all" "molecular_formula" +#> [7] "molecular_weight" "canonical_smiles" +#> [9] "isomeric_smiles" "in_ch_i" +#> [11] "in_ch_i_key" "iupac_name_y" +#> [13] "x_log_p" "exact_mass" +#> [15] "monoisotopic_mass" "tpsa" +#> [17] "complexity" "charge" +#> [19] "h_bond_donor_count" "h_bond_acceptor_count" +#> [21] "rotatable_bond_count" "heavy_atom_count" +#> [23] "isotope_atom_count" "atom_stereo_count" +#> [25] "defined_atom_stereo_count" "undefined_atom_stereo_count" +#> [27] "bond_stereo_count" "defined_bond_stereo_count" +#> [29] "undefined_bond_stereo_count" "covalent_unit_count" +#> [31] "volume3d" "x_steric_quadrupole3d" +#> [33] "y_steric_quadrupole3d" "z_steric_quadrupole3d" +#> [35] "feature_count3d" "feature_acceptor_count3d" +#> [37] "feature_donor_count3d" "feature_anion_count3d" +#> [39] "feature_cation_count3d" "feature_ring_count3d" +#> [41] "feature_hydrophobe_count3d" "conformer_model_rmsd3d" +#> [43] "effective_rotor_count3d" "conformer_count3d" +#> [45] "fingerprint2d" "query" +``` Two functions are used to extract specific sections of PubChem chemical information using CASRN: -- `extr_pubchem_ghs` extracts Globally Harmonized System (GHS) codes. -- `extr_pubchem_fema` extracts flavor profile data. - - - - ghs_info <- extr_pubchem_ghs(casrn = c("50-00-0", "64-17-5")) - #> ℹ Checking Internet Connection... - #> ℹ Internet connection OK... - #> ℹ Getting PubChem IDS... - #> Querying 50-00-0. OK (HTTP 200). - #> Querying 712. OK (HTTP 200). - #> ℹ Getting PubChem IDS... - #> Querying 64-17-5. OK (HTTP 200). - #> Querying 702. OK (HTTP 200). - fema_info <- extr_pubchem_fema(casrn = c("50-00-0", "123-68-2")) - #> ℹ Checking Internet Connection... - #> ℹ Internet connection OK... - #> Querying 50-00-0. OK (HTTP 200). - #> Querying 712. Not Found (HTTP 404). - #> ℹ FEMA for 50-00-0 not found! - #> Querying 123-68-2. OK (HTTP 200). - #> Querying 31266. OK (HTTP 200). +- `extr_pubchem_ghs` extracts Globally Harmonized System (GHS) codes. +- `extr_pubchem_fema` extracts flavor profile data. + +``` r +ghs_info <- extr_pubchem_ghs(casrn = c("50-00-0", "64-17-5")) +#> ℹ Checking Internet Connection... +#> ℹ Internet connection OK... +#> ℹ Getting PubChem IDS... +#> Querying 50-00-0. OK (HTTP 200). +#> Querying 712. OK (HTTP 200). +#> ℹ Getting PubChem IDS... +#> Querying 64-17-5. OK (HTTP 200). +#> Querying 702. OK (HTTP 200). +fema_info <- extr_pubchem_fema(casrn = c("50-00-0", "123-68-2")) +#> ℹ Checking Internet Connection... +#> ℹ Internet connection OK... +#> Querying 50-00-0. OK (HTTP 200). +#> Querying 712. Not Found (HTTP 404). +#> ℹ FEMA for 50-00-0 not found! +#> Querying 123-68-2. OK (HTTP 200). +#> Querying 31266. OK (HTTP 200). +``` ## Important Note for Linux Users diff --git a/docs/index.html b/docs/index.html index 2690d02..0e680e4 100644 --- a/docs/index.html +++ b/docs/index.html @@ -46,26 +46,32 @@
-
+
+

extractox logo +

+ +

extractox is a comprehensive R package designed to simplify querying various chemical, toxicological, and biological databases such as the Comparative Toxicogenomics Database (CTP) of the MDI Biological Laboratory and NC State University, the Integrated Chemical Environment (ICE) of the National Toxicology Program (NTP), the Integrated Risk Information System (IRIS) of the Environmental Protection Agency (EPA), the CompTox Chemicals Dashboard Resource Hub (CompTox) of EPA, and PubChem of the National Center for Biotechnology Information/National Institures Of Health (NCBI, NIH). The package facilitates interaction with APIs, providing curated and user-friendly outputs.

To communicate with Pubchem, extractox relies on the packagewebchem.

Installation

Install the package extractox from CRAN.

-
# From CRAN
-install.packages("extractox")
+
+# From CRAN
+install.packages("extractox")

Development Version

To get a bug fix or to use a feature from the development version, you can install the development version of extractox from GitHub.

-
# Install pak if not already installed
-if (!requireNamespace("pak", quietly = TRUE)) {
-  install.packages("pak")
-}
-
-# Install the package from GitHub
-pak::pkg_install("c1au6i0/extractox")
+
+# Install pak if not already installed
+if (!requireNamespace("pak", quietly = TRUE)) {
+  install.packages("pak")
+}
+
+# Install the package from GitHub
+pak::pkg_install("c1au6i0/extractox")
@@ -76,77 +82,81 @@

ICE Database
library(extractox)
-ice_data <- extr_ice(casrn = c("50-00-0"), assays = NULL) # assays is null so all assays are retrieved
-#> ℹ Checking Internet Connection...
-#> ℹ Internet connection OK...
-#> Sending request to ICE database...
-#> Request succeeded with status code: 200
-names(ice_data)
-#>  [1] "assay"              "endpoint"           "substanceType"     
-#>  [4] "casrn"              "qsarReadyId"        "value"             
-#>  [7] "unit"               "species"            "receptorSpecies"   
-#> [10] "route"              "sex"                "strain"            
-#> [13] "lifeStage"          "tissue"             "lesion"            
-#> [16] "location"           "assaySource"        "inVitroAssayFormat"
-#> [19] "reference"          "referenceUrl"       "dtxsid"            
-#> [22] "substanceName"      "pubMedId"

+
+library(extractox)
+ice_data <- extr_ice(casrn = c("50-00-0"), assays = NULL) # assays is null so all assays are retrieved
+#> ℹ Checking Internet Connection...
+#> ℹ Internet connection OK...
+#> Sending request to ICE database...
+#> Request succeeded with status code: 200
+names(ice_data)
+#>  [1] "assay"              "endpoint"           "substanceType"     
+#>  [4] "casrn"              "qsarReadyId"        "value"             
+#>  [7] "unit"               "species"            "receptorSpecies"   
+#> [10] "route"              "sex"                "strain"            
+#> [13] "lifeStage"          "tissue"             "lesion"            
+#> [16] "location"           "assaySource"        "inVitroAssayFormat"
+#> [19] "reference"          "referenceUrl"       "dtxsid"            
+#> [22] "substanceName"      "pubMedId"

IRIS

The IRIS database is managed by the EPA and contains information on the health effects of exposure to various substances found in the environment. It provides qualitative and quantitative health risk information.

extr_iris provides access to EPA’s IRIS database and accepts queries of Chemical Abstracts Service Registry Number (CASRN) or International Union of Pure and Applied Chemistry (IUPAC) names of chemicals.

-
iris_info <- extr_iris(c("glyphosate", "50-00-0"))
-#> ℹ Checking Internet Connection...
-#> ℹ Internet connection OK...
-#> Quering glyphosate to EPA IRIS database...
-#> Request succeeded with status code: 200
-#> Quering 50-00-0 to EPA IRIS database...
-#> Request succeeded with status code: 200
-names(iris_info)
-#> [1] "chemical_name"                 "casrn"                        
-#> [3] "exposure_route"                "assessment_type"              
-#> [5] "critical_effect_or_tumor_type" "woe_characterization"         
-#> [7] "toxicity_value_type"           "toxicity_value"
+
+iris_info <- extr_iris(c("glyphosate", "50-00-0"))
+#> ℹ Checking Internet Connection...
+#> ℹ Internet connection OK...
+#> Quering glyphosate to EPA IRIS database...
+#> Request succeeded with status code: 200
+#> Quering 50-00-0 to EPA IRIS database...
+#> Request succeeded with status code: 200
+names(iris_info)
+#> [1] "chemical_name"                 "casrn"                        
+#> [3] "exposure_route"                "assessment_type"              
+#> [5] "critical_effect_or_tumor_type" "woe_characterization"         
+#> [7] "toxicity_value_type"           "toxicity_value"

CompTox

The CompTox Chemistry Dashboard, managed by the EPA, provides access to data on chemical structures, properties, and associated bioactivity data. It integrates data from various sources to support chemical safety assessments.

extr_comptox extracts data from the CompTox Chemistry Dashboard using both CASRN and IUPAC names of chemicals and returns a list of dataframes.

-
info_comptox <- extr_comptox(ids = c("Aspirin", "50-00-0"))
-#> ℹ Sending request to CompTox...
-#> Request succeeded with status code: 202
-#> ℹ Getting info from CompTox...
-#> 
-#> Request succeeded with status code: 200
-names(info_comptox)
-#> [1] "comptox_cover_sheet"           "comptox_main_data"            
-#> [3] "comptox_abstract_sifter"       "comptox_synonym_identifier"   
-#> [5] "comptox_related_relationships" "comptox_toxcast_assays_ac50"  
-#> [7] "comptox_toxval_details"        "comptox_chemical_properties"
+
+info_comptox <- extr_comptox(ids = c("Aspirin", "50-00-0"))
+#> ℹ Sending request to CompTox...
+#> Request succeeded with status code: 202
+#> ℹ Getting info from CompTox...
+#> 
+#> Request succeeded with status code: 200
+names(info_comptox)
+#> [1] "comptox_cover_sheet"           "comptox_main_data"            
+#> [3] "comptox_abstract_sifter"       "comptox_synonym_identifier"   
+#> [5] "comptox_related_relationships" "comptox_toxcast_assays_ac50"  
+#> [7] "comptox_toxval_details"        "comptox_chemical_properties"

Tox Info

The function extr_tox is a wrapper used to call all the above-mentioned functions and retrieve a list of dataframes.

-
info_tox <- extr_tox(casrn = c("Aspirin", "50-00-0"))
-#> ℹ Checking Internet Connection...
-#> ℹ Internet connection OK...
-#> ℹ Getting PubChem IDS...
-#> Querying Aspirin. OK (HTTP 200).
-#> Querying 2244. OK (HTTP 200).
-#> ℹ Getting PubChem IDS...
-#> Querying 50-00-0. OK (HTTP 200).
-#> Querying 712. OK (HTTP 200).
-#> ℹ Sending request to CompTox...
-#> Request succeeded with status code: 202ℹ Getting info from CompTox...
-#> Request succeeded with status code: 200ℹ Checking Internet Connection...
-#> ℹ Internet connection OK...
-#> Sending request to ICE database...Request succeeded with status code: 200ℹ Checking Internet Connection...
-#> ℹ Internet connection OK...
-#> Quering Aspirin to EPA IRIS database...Request succeeded with status code: 200Quering 50-00-0 to EPA IRIS database...Request succeeded with status code: 200
+
+info_tox <- extr_tox(casrn = c("Aspirin", "50-00-0"))
+#> ℹ Checking Internet Connection...
+#> ℹ Internet connection OK...
+#> ℹ Getting PubChem IDS...
+#> Querying Aspirin. OK (HTTP 200).
+#> Querying 2244. OK (HTTP 200).
+#> ℹ Getting PubChem IDS...
+#> Querying 50-00-0. OK (HTTP 200).
+#> Querying 712. OK (HTTP 200).
+#> ℹ Sending request to CompTox...
+#> Request succeeded with status code: 202ℹ Getting info from CompTox...
+#> Request succeeded with status code: 200ℹ Checking Internet Connection...
+#> ℹ Internet connection OK...
+#> Sending request to ICE database...Request succeeded with status code: 200ℹ Checking Internet Connection...
+#> ℹ Internet connection OK...
+#> Quering Aspirin to EPA IRIS database...Request succeeded with status code: 200Quering 50-00-0 to EPA IRIS database...Request succeeded with status code: 200

CTD Database @@ -154,55 +164,57 @@

CTD Database
input_terms <- c("50-00-0", "64-17-5", "methanal", "ethanol")
-ctd_association <- extr_ctd(
-  input_terms = input_terms,
-  category = "chem",
-  report_type = "genes_curated",
-  input_term_search_type = "directAssociations",
-  action_types = "ANY",
-  ontology = c("go_bp", "go_cc")
-)
-#> ℹ Checking Internet Connection...
-#> ℹ Internet connection OK...
-#> Sending request to CTD database...
-#> Request succeeded with status code: 200
-
-
-# Get expresssion data
-ctd_expression <- extr_ctd(
-  input_terms = input_terms,
-  report_type = "cgixns",
-  category = "chem",
-  action_types = "expression"
-)
-#> ℹ Checking Internet Connection...
-#> ℹ Internet connection OK...
-#> Sending request to CTD database...Request succeeded with status code: 200
-
-names(ctd_expression)
-#>  [1] "x_input"             "chemical_name"       "chemical_id"        
-#>  [4] "cas_rn"              "gene_symbol"         "gene_id"            
-#>  [7] "organism"            "organism_id"         "interaction"        
-#> [10] "interaction_actions" "pub_med_i_ds"

+
+input_terms <- c("50-00-0", "64-17-5", "methanal", "ethanol")
+ctd_association <- extr_ctd(
+  input_terms = input_terms,
+  category = "chem",
+  report_type = "genes_curated",
+  input_term_search_type = "directAssociations",
+  action_types = "ANY",
+  ontology = c("go_bp", "go_cc")
+)
+#> ℹ Checking Internet Connection...
+#> ℹ Internet connection OK...
+#> Sending request to CTD database...
+#> Request succeeded with status code: 200
+
+
+# Get expresssion data
+ctd_expression <- extr_ctd(
+  input_terms = input_terms,
+  report_type = "cgixns",
+  category = "chem",
+  action_types = "expression"
+)
+#> ℹ Checking Internet Connection...
+#> ℹ Internet connection OK...
+#> Sending request to CTD database...Request succeeded with status code: 200
+
+names(ctd_expression)
+#>  [1] "x_input"             "chemical_name"       "chemical_id"        
+#>  [4] "cas_rn"              "gene_symbol"         "gene_id"            
+#>  [7] "organism"            "organism_id"         "interaction"        
+#> [10] "interaction_actions" "pub_med_i_ds"

Tetramers are computationally generated information units that interrelate four data types from the CTP: a chemical, gene product, phenotype, and disease. They help in understanding the complex relationships between these entities and their combined impact on human health.

extr_tetramer extract info related to tetramers from CTD.

-
tetramer_data <- extr_tetramer(
-  chem = c("50-00-0", "ethanol"),
-  disease = "",
-  gene = "",
-  go = "",
-  input_term_search_type = "directAssociations",
-  qt_match_type = "equals"
-)
-#> Sending request to CTD database for tetramer data for 50-00-0...
-#> Request succeeded with status code: 200
-#> Sending request to CTD database for tetramer data for ethanol...
-#> Request succeeded with status code: 200
-
-names(tetramer_data)
-#> [1] "query"        "chemical"     "chemical_id"  "gene"         "gene_id"     
-#> [6] "phenotype"    "phenotype_id" "disease"      "disease_id"
+
+tetramer_data <- extr_tetramer(
+  chem = c("50-00-0", "ethanol"),
+  disease = "",
+  gene = "",
+  go = "",
+  input_term_search_type = "directAssociations",
+  qt_match_type = "equals"
+)
+#> Sending request to CTD database for tetramer data for 50-00-0...
+#> Request succeeded with status code: 200
+#> Sending request to CTD database for tetramer data for ethanol...
+#> Request succeeded with status code: 200
+
+names(tetramer_data)
+#> [1] "query"        "chemical"     "chemical_id"  "gene"         "gene_id"     
+#> [6] "phenotype"    "phenotype_id" "disease"      "disease_id"

PubChem Database @@ -210,38 +222,39 @@

PubChem DatabasePubChem is an open chemistry database at the NIH. It provides information on chemical structures, identifiers, chemical and physical properties, biological activities, safety and toxicity information, patents, literature citations, and more.

A series of functions that rely on the webchem package are used to extract chemical information, Globally Harmonized System (GHS) classification data, or flavor classification from PubChem.

The function extr_chem_info retrieves chemical information of IUPAC-named chemicals. A warning is displayed if the chemical is not found.

-
chem_info <- extr_chem_info(IUPAC_names = c("Formaldehyde", "Aflatoxin B1"))
-#> ℹ Checking Internet Connection...
-#> ℹ Internet connection OK...
-#> Querying Formaldehyde. OK (HTTP 200).
-#> Querying Aflatoxin B1. OK (HTTP 200).
-#> ℹ Checking Internet Connection...
-#> ℹ Internet connection OK...
-#> ℹ Querying 712 and 186907.
-names(chem_info)
-#>  [1] "cid"                         "iupac_name"                 
-#>  [3] "cas_rn"                      "cid_all"                    
-#>  [5] "cas_rn_all"                  "molecular_formula"          
-#>  [7] "molecular_weight"            "canonical_smiles"           
-#>  [9] "isomeric_smiles"             "in_ch_i"                    
-#> [11] "in_ch_i_key"                 "iupac_name_y"               
-#> [13] "x_log_p"                     "exact_mass"                 
-#> [15] "monoisotopic_mass"           "tpsa"                       
-#> [17] "complexity"                  "charge"                     
-#> [19] "h_bond_donor_count"          "h_bond_acceptor_count"      
-#> [21] "rotatable_bond_count"        "heavy_atom_count"           
-#> [23] "isotope_atom_count"          "atom_stereo_count"          
-#> [25] "defined_atom_stereo_count"   "undefined_atom_stereo_count"
-#> [27] "bond_stereo_count"           "defined_bond_stereo_count"  
-#> [29] "undefined_bond_stereo_count" "covalent_unit_count"        
-#> [31] "volume3d"                    "x_steric_quadrupole3d"      
-#> [33] "y_steric_quadrupole3d"       "z_steric_quadrupole3d"      
-#> [35] "feature_count3d"             "feature_acceptor_count3d"   
-#> [37] "feature_donor_count3d"       "feature_anion_count3d"      
-#> [39] "feature_cation_count3d"      "feature_ring_count3d"       
-#> [41] "feature_hydrophobe_count3d"  "conformer_model_rmsd3d"     
-#> [43] "effective_rotor_count3d"     "conformer_count3d"          
-#> [45] "fingerprint2d"               "query"
+
+chem_info <- extr_chem_info(IUPAC_names = c("Formaldehyde", "Aflatoxin B1"))
+#> ℹ Checking Internet Connection...
+#> ℹ Internet connection OK...
+#> Querying Formaldehyde. OK (HTTP 200).
+#> Querying Aflatoxin B1. OK (HTTP 200).
+#> ℹ Checking Internet Connection...
+#> ℹ Internet connection OK...
+#> ℹ Querying 712 and 186907.
+names(chem_info)
+#>  [1] "cid"                         "iupac_name"                 
+#>  [3] "cas_rn"                      "cid_all"                    
+#>  [5] "cas_rn_all"                  "molecular_formula"          
+#>  [7] "molecular_weight"            "canonical_smiles"           
+#>  [9] "isomeric_smiles"             "in_ch_i"                    
+#> [11] "in_ch_i_key"                 "iupac_name_y"               
+#> [13] "x_log_p"                     "exact_mass"                 
+#> [15] "monoisotopic_mass"           "tpsa"                       
+#> [17] "complexity"                  "charge"                     
+#> [19] "h_bond_donor_count"          "h_bond_acceptor_count"      
+#> [21] "rotatable_bond_count"        "heavy_atom_count"           
+#> [23] "isotope_atom_count"          "atom_stereo_count"          
+#> [25] "defined_atom_stereo_count"   "undefined_atom_stereo_count"
+#> [27] "bond_stereo_count"           "defined_bond_stereo_count"  
+#> [29] "undefined_bond_stereo_count" "covalent_unit_count"        
+#> [31] "volume3d"                    "x_steric_quadrupole3d"      
+#> [33] "y_steric_quadrupole3d"       "z_steric_quadrupole3d"      
+#> [35] "feature_count3d"             "feature_acceptor_count3d"   
+#> [37] "feature_donor_count3d"       "feature_anion_count3d"      
+#> [39] "feature_cation_count3d"      "feature_ring_count3d"       
+#> [41] "feature_hydrophobe_count3d"  "conformer_model_rmsd3d"     
+#> [43] "effective_rotor_count3d"     "conformer_count3d"          
+#> [45] "fingerprint2d"               "query"

Two functions are used to extract specific sections of PubChem chemical information using CASRN:

-
ghs_info <- extr_pubchem_ghs(casrn = c("50-00-0", "64-17-5"))
-#> ℹ Checking Internet Connection...
-#> ℹ Internet connection OK...
-#> ℹ Getting PubChem IDS...
-#> Querying 50-00-0. OK (HTTP 200).
-#> Querying 712. OK (HTTP 200).
-#> ℹ Getting PubChem IDS...
-#> Querying 64-17-5. OK (HTTP 200).
-#> Querying 702. OK (HTTP 200).
-fema_info <- extr_pubchem_fema(casrn = c("50-00-0", "123-68-2"))
-#> ℹ Checking Internet Connection...
-#> ℹ Internet connection OK...
-#> Querying 50-00-0. OK (HTTP 200).
-#> Querying 712. Not Found (HTTP 404).
-#> ℹ FEMA for 50-00-0 not found!
-#> Querying 123-68-2. OK (HTTP 200).
-#> Querying 31266. OK (HTTP 200).
+
+ghs_info <- extr_pubchem_ghs(casrn = c("50-00-0", "64-17-5"))
+#> ℹ Checking Internet Connection...
+#> ℹ Internet connection OK...
+#> ℹ Getting PubChem IDS...
+#> Querying 50-00-0. OK (HTTP 200).
+#> Querying 712. OK (HTTP 200).
+#> ℹ Getting PubChem IDS...
+#> Querying 64-17-5. OK (HTTP 200).
+#> Querying 702. OK (HTTP 200).
+fema_info <- extr_pubchem_fema(casrn = c("50-00-0", "123-68-2"))
+#> ℹ Checking Internet Connection...
+#> ℹ Internet connection OK...
+#> Querying 50-00-0. OK (HTTP 200).
+#> Querying 712. Not Found (HTTP 404).
+#> ℹ FEMA for 50-00-0 not found!
+#> Querying 123-68-2. OK (HTTP 200).
+#> Querying 31266. OK (HTTP 200).

@@ -273,7 +287,7 @@

Important Note for Linux Usersthis gist for instructions on how to downgrade curl and OpenSSL on Ubuntu.

- +