Tidymass MassDatabase

https://massdatabase.tidymass.org/
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### Example: Get Reaction Data as List

Source: https://massdatabase.tidymass.org/reference/request_bigg_universal_reaction

Demonstrates retrieving reaction data in a list format. This is useful for inspecting the detailed structure of the returned information.

```R
x <- request_bigg_universal_reaction(reaction_id = "ADA", return_form = "list")
x
```

--------------------------------

### Example GITHUB_PAT Configuration

Source: https://massdatabase.tidymass.org/articles/install

This is an example of how to add your GitHub Personal Access Token to the `.Renviron` file. Replace `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` with your actual token.

```text
GITHUB_PAT=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
```

--------------------------------

### Example: Request Compound as List

Source: https://massdatabase.tidymass.org/reference/request_foodb_compound

Demonstrates how to call the function to get compound data in list format and access its first two elements.

```R
x = request_foodb_compound( compound_id = "FDB000004", return_form = "list")
x[1:2]
```

--------------------------------

### Install massdatabase from GitHub

Source: https://massdatabase.tidymass.org/articles/install

Use this command to install the massdatabase package directly from its GitHub repository. Ensure `dependencies` are set to `TRUE` to include necessary packages.

```r
remotes::install_github("tidymass/massdatabase", dependencies = TRUE)
```

--------------------------------

### Install massDatabase from GitLab

Source: https://massdatabase.tidymass.org/

Installs the remotes package if not already present, then installs the massDatabase package from GitLab.

```r
if(!require(remotes)){
install.packages("remotes")
}
remotes::install_gitlab("jaspershen/massdatabase")
```

--------------------------------

### Install massDatabase from GitHub

Source: https://massdatabase.tidymass.org/

Installs the massDatabase package from GitHub using the remotes package.

```r
remotes::install_github("tidymass/massdatabase")
```

--------------------------------

### Install massdatabase from GitLab

Source: https://massdatabase.tidymass.org/articles/install

Use this command to install the massdatabase package directly from its GitLab repository. Ensure `dependencies` are set to `TRUE` to include necessary packages.

```r
remotes::install_gitlab("tidymass/massdatabase", dependencies = TRUE)
```

--------------------------------

### Example Usage of request_foodb_compound_info_crawler

Source: https://massdatabase.tidymass.org/reference/request_foodb_compound_info_crawler

This example shows a practical use case for the `request_foodb_compound_info_crawler` function, fetching data for the first page and then displaying the head of the resulting data frame. This is useful for testing the function or inspecting a small subset of the data.

```r
x = request_foodb_compound_info_crawler(pages = 1)
#> 1  
head(x)
#>    FooDB ID                                    Name         CAS
#> 1 FDB000004     Cyanidin 3-(6''-acetyl-galactoside) 350602-26-5
#> 2 FDB000013     Cyanidin 3-(6''-succinyl-glucoside) 216692-08-9
#> 3 FDB000014 Pelargonidin 3-(6''-succinyl-glucoside)            
#> 4 FDB000024  Petunidin 3-O-(6''-acetyl-galactoside)            
#> 5 FDB000025     Peonidin 3-(6''-acetyl-galactoside)     75-07-0
#> 6 FDB000027     Malvidin 3-(6''-acetyl-galactoside)     75-07-0
#>          FormulaWeight  Mono Mass
#> 1   C23H23O12491.4215 491.1189512
#> 2 C25H25O14549.4576 549.124430508
#> 3 C25H25O13533.4582 533.129515886
#> 4 C24H25O13521.4475 521.129515886
#> 5 C24H25O12505.4481 505.134601264
#> 6  C25H27O13535.4741 535.14516595
#>                                                 Foods Structure
#> 1                 Highbush blueberryLowbush blueberry        NA
#> 2                                          Strawberry        NA
#> 3              CloudberryRed raspberryStrawberryWheat        NA
#> 4                 Highbush blueberryLowbush blueberry        NA
#> 5                 Highbush blueberryLowbush blueberry        NA
#> 6 Canada blueberryHighbush blueberryLowbush blueberry        NA
```

--------------------------------

### Example usage of request_foodb_compound_info

Source: https://massdatabase.tidymass.org/reference/request_foodb_compound_info

Demonstrates how to call the `request_foodb_compound_info` function with default arguments and display the head of the resulting data frame.

```r
x = request_foodb_compound_info()
head(x)
```

--------------------------------

### Example: Request Compound as Data Frame

Source: https://massdatabase.tidymass.org/reference/request_foodb_compound

Shows how to request compound data as a data frame and display the first few rows using head().

```R
y = request_foodb_compound(compound_id = "FDB000004", return_form = "data.frame")
head(y)
```

--------------------------------

### Show Progresser Example

Source: https://massdatabase.tidymass.org/reference/show_progresser

Demonstrates how to use the show_progresser function with a specified index range and progresser values. This function is useful for visualizing loop progress.

```R
show_progresser(
  index = 1:1000,
  progresser = c(1, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100)
)
```

--------------------------------

### Example Usage of request_chebi_compound

Source: https://massdatabase.tidymass.org/reference/request_chebi_compound

Demonstrates how to call the `request_chebi_compound` function with a specific compound ID and displays the returned structured information.

```R
request_chebi_compound(compound_id = "CHEBI:18358")
```

--------------------------------

### Example: Request Reaction with ID '1'

Source: https://massdatabase.tidymass.org/reference/request_hmdb_reaction

Demonstrates retrieving reaction information for reaction ID '1'. The output includes the reaction equation and associated enzymes.

```r
request_hmdb_reaction(reaction_id = "1")
#>                                                              equation
#> 1 A 3-beta-hydroxy-Delta(5)-steroid+NAD=a 3-oxo-Delta(5)-steroid+NADH
#>                                                            Enzymes
#> 1 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type 1
#>   External_Links            Status Comments
#> 1             NA Experimental Data       NA
```

--------------------------------

### Example: Requesting 'Wax' Lipid Class Data

Source: https://massdatabase.tidymass.org/reference/request_lipidbank_lipid_class

This example demonstrates how to request data for a specific lipid class, 'Wax', from the Lipidbank. The output is a data frame containing details about various waxes.

```r
x = request_lipidbank_lipid_class(lipid_class = "Wax")
head(x)
```

--------------------------------

### Request information for Glucose

Source: https://massdatabase.tidymass.org/reference/request_wikipedia_compound

This example shows how to request information for a different compound, 'Glucose', using the same function. The output is a tibble with compound details.

```R
request_wikipedia_compound(compound_id = "Glucose")
```

--------------------------------

### Get All Pathway Information

Source: https://massdatabase.tidymass.org/articles/kegg_pathway

Retrieves a summary of all pathways available in KEGG for a specified organism. This is useful for getting an overview of metabolic pathways.

```APIDOC
## request_kegg_pathway_info

### Description
Get the information of all pathways in KEGG (https://www.genome.jp/kegg/pathway.html).

### Method
`request_kegg_pathway_info`

### Parameters
#### Query Parameters
- **organism** (string) - Required - The organism code (e.g., "hsa" for Homo sapiens).

### Request Example
```R
library(massdatabase)
pathway_info <- request_kegg_pathway_info(organism = "hsa")
head(pathway_info)
```

### Response
#### Success Response (200)
Returns a data frame containing KEGG pathway IDs and their names.
```

--------------------------------

### Inspect Returned Reaction Data

Source: https://massdatabase.tidymass.org/reference/request_bigg_universal_reaction_info

After fetching universal reaction data, this example demonstrates how to check the dimensions and view the first few rows of the resulting data frame to understand its structure and content.

```r
x <- request_bigg_universal_reaction_info()
dim(x)
#> [1] 28302     3
head(x)
#>        bigg_id                                       name model_bigg_id
#> 1 10FTHF5GLUtl     5-glutamyl-10FTHF transport, lysosomal     Universal
#> 2 10FTHF5GLUtm 5-glutamyl-10FTHF transport, mitochondrial     Universal
#> 3 10FTHF6GLUtl     6-glutamyl-10FTHF transport, lysosomal     Universal
#> 4 10FTHF6GLUtm 6-glutamyl-10FTHF transport, mitochondrial     Universal
#> 5 10FTHF7GLUtl     7-glutamyl-10FTHF transport, lysosomal     Universal
#> 6 10FTHF7GLUtm 7-glutamyl-10FTHF transport, mitochondrial     Universal

```

--------------------------------

### Display massdatabase Package Information

Source: https://massdatabase.tidymass.org/reference/massdatabase_logo

Call the massdatabase_logo() function to display the package version, installation date, website, and ASCII logo.

```R
massdatabase_logo()
```

--------------------------------

### Requesting Information for a Different Compound

Source: https://massdatabase.tidymass.org/reference/request_chebi_compound

Shows an example of using the `request_chebi_compound` function to fetch data for a different ChEBI compound, illustrating its reusability.

```R
request_chebi_compound(compound_id = "CHEBI:18377")
```

--------------------------------

### Retrieve Metabolite Data as a List

Source: https://massdatabase.tidymass.org/reference/request_bigg_universal_metabolite

This example demonstrates how to use `request_bigg_universal_metabolite` to fetch metabolite data and store it as an R list. The output shows the structure of the returned list, including metabolite ID, name, formula, and associated database links.

```r
x <- request_bigg_universal_metabolite(metabolite_id = "g3p", return_form = "list")
x
```

--------------------------------

### Create GitHub Personal Access Token

Source: https://massdatabase.tidymass.org/articles/install

If you encounter API rate limit errors during GitHub installation, use this function to create a personal access token. This token will be used to authenticate your requests and increase the rate limit.

```r
usethis::create_github_token()
```

--------------------------------

### Example Usage of Request BIGG Universal Metabolite Info

Source: https://massdatabase.tidymass.org/reference/request_bigg_universal_metabolite_info

Demonstrates how to call the function and inspect the returned data. The output is a data frame containing metabolite IDs, names, and model IDs.

```R
x <- request_bigg_universal_metabolite_info()
dim(x)
#> [1] 9088    3
head(x)
#>        bigg_id                                 name model_bigg_id
#> 1       10fthf            10-Formyltetrahydrofolate     Universal
#> 2   10fthf5glu   10-formyltetrahydrofolate-[Glu](5)     Universal
#> 3   10fthf6glu   10-formyltetrahydrofolate-[Glu](6)     Universal
#> 4   10fthf7glu   10-formyltetrahydrofolate-[Glu](7)     Universal
#> 5 10fthfglu__L 10-Formyltetrahydrofolyl L-glutamate     Universal
#> 6    10m3ouACP       10-methyl-3-oxo-undecanoyl-ACP     Universal

```

--------------------------------

### Load Required Libraries for massdatabase

Source: https://massdatabase.tidymass.org/articles/read_convert_functions

Load the necessary R libraries for working with metabolic databases and pathways. Ensure these packages are installed before running.

```r
library(metid)
library(massdatabase)
library(metpath)
```

--------------------------------

### Download MassBank Compound Database

Source: https://massdatabase.tidymass.org/articles/download_functions

Use this function to download the MassBank compound database. Specify the source, for example, 'nist'.

```r
download_massbank_compound(source = "nist")
```

--------------------------------

### Request All KEGG Reaction Class Information

Source: https://massdatabase.tidymass.org/reference/request_kegg_rclass_info

Call the request_kegg_rclass_info() function to retrieve all reaction class information from KEGG. No setup or imports are required.

```R
request_kegg_rclass_info()
```

--------------------------------

### Request All KEGG Pathway Information

Source: https://massdatabase.tidymass.org/articles/request_functions

Fetches a list of all available KEGG pathways for a specified organism. Useful for getting an overview of metabolic pathways present in a given species.

```r
x <- 
  request_kegg_pathway_info(organism = "hsa")
dim(x)
#> [1] 347   2
head(x)
#>    KEGG.ID                                                    Pathway.name
#> 1 hsa00010             Glycolysis / Gluconeogenesis - Homo sapiens (human)
#> 2 hsa00020                Citrate cycle (TCA cycle) - Homo sapiens (human)
#> 3 hsa00030                Pentose phosphate pathway - Homo sapiens (human)
#> 4 hsa00040 Pentose and glucuronate interconversions - Homo sapiens (human)
#> 5 hsa00051          Fructose and mannose metabolism - Homo sapiens (human)
#> 6 hsa00052                     Galactose metabolism - Homo sapiens (human)
```

--------------------------------

### Get KEGG Reaction Class Info

Source: https://massdatabase.tidymass.org/articles/request_functions

Retrieves all reaction class information from KEGG. The output is a data frame with KEGG IDs and their corresponding names. Use this function to get a comprehensive list of reaction classes for analysis.

```r
x <- 
  request_kegg_rclass_info()
dim(x)
#> [1] 3180    2
head(x)
#>   KEGG.ID                                                            name
#> 1 RC00001 C1x-C8x:*-*:C2x+C2y-C8x+C8y N1y-N5y:*-*:C1y+C2x+C2x-C1y+C8x+C8x
#> 2 RC00002                                           O1c-O2c:*-P1b:P1b-P1b
#> 3 RC00003                                    S0-S2a:C1a-*:C1b+C1b-C1b+C1b
#> 4 RC00004                                           S1a-S2a:*-C5a:C1b-C1b
#> 5 RC00005                                           O1c-O2b:*-C1y:P1b-P1b
#> 6 RC00006                             C1c-C5a:N1a+*-*+O5a:C1b+C6a-C1b+C6a
```

--------------------------------

### Get Specific Compound Information from Wikipedia

Source: https://massdatabase.tidymass.org/articles/request_functions

Retrieves detailed information for a specific compound using its ID from Wikipedia.

```R
x <- 
  request_wikipedia_compound(compound_id = "Microcystin-LR")
dim(x)
#> [1] 36  2
head(x)
#> # A tibble: 6 × 2
#>   name                                                                     value
#>   <chr>                                                                    <chr>
#> 1 "Names"                                                                  "Nam…
#> 2 "IUPAC name
(5R,8S,11R,12S,15S,18S,19S,22R)-15-[3-(diaminomethylidenea… "IUP…
#> 3 "Other names
5-L-Arginine-microcystin LA"                               "Oth…
#> 4 "Identifiers"                                                            "Ide…
#> 5 "CAS Number"                                                             "101…
#> 6 "3D model (JSmol)"                                                       "Int…
```

--------------------------------

### Get LipidBank Lipid Class

Source: https://massdatabase.tidymass.org/articles/request_functions

Retrieves lipid class information from LipidBank. Ensure you have an active internet connection.

```R
x <- 
  request_lipidbank_lipid_class(lipid_class = "Wax")
#> Check your internet.
dim(x)
#> NULL
head(x)
#> NULL
```

--------------------------------

### List all packages in massdatabase

Source: https://massdatabase.tidymass.org/reference/massdatabase_packages

Lists all packages in the massdatabase. Use include_self = TRUE to also include the massdatabase package itself.

```R
massdatabase_packages(include_self = TRUE)

massdatabase_packages(include_self = TRUE)
```

```R
massdatabase_packages()
#>  [1] "crayon"       "plyr"         "readr"        "tidyr"        "ggplot2"     
#>  [6] "dplyr"        "utils"        "rvest"        "XML"          "Rdisop"      
#> [11] "stringr"      "stringdist"   "magrittr"     "curl"         "purrr"       
#> [16] "metid"        "masstools"    "tibble"       "xml2"         "tidyselect"  
#> [21] "progress"     "ChemmineR"    "KEGGREST"     "metpath"      "rjson"       
#> [26] "rstudioapi"   "massdatabase"
```

--------------------------------

### Get Specific Lipid Information from LipidMaps

Source: https://massdatabase.tidymass.org/articles/request_functions

Fetches detailed information for a specific lipid using its ID from the LIPID MAPS database.

```R
x <- 
  request_lipidmaps_lipid(lipid_id = "LMFA01030001")
x
#>                                                                                                                                                                      Synonyms
#> 2 5Z,8Z,11Z,14Z-icosatetraenoic acid{}AA{}Arachidonate{}cis-5,8,11,14-Eicosatetraenoic acid{}(all-Z)-5,8,11,14-Eicosatetraenoic acid{}all-cis-5,8,11,14-Eicosatetraenoic acid
#>        Common_Name                     Systematic_Name        LM_ID Status
#> 2 Arachidonic acid 5Z,8Z,11Z,14Z-eicosatetraenoic acid LMFA01030001 Active
#>   Exact_Mass  Formula  Abbrev         Category
#> 2   304.2402 C20H32O2 FA 20:4 Fatty Acyls [FA]
#>                          Main.Class                        Sub.Class
#> 2 Fatty Acids and Conjugates [FA01] Unsaturated fatty acids [FA0103]
#>                      InChiKey
#> 2 YZXBAPSDXZZRGB-DOFZRALJSA-N
#>                                                                                                                                                            InChi
#> 2 InChI=1S/C20H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20(21)22/h6-7,9-10,12-13,15-16H,2-5,8,11,14,17-19H2,1H3,(H,21,22)/b7-6-,10-9-,13-12-,16-15-
#>                                        SMILES         Curated.from
#> 2 C(O)(=O)CCC/C=C\C/C=C\C/C=C\C/C=C\CCCCC Homo sapiens (#9606)
#>   NCBI.taxonomy.class        Wikipedia KEGG.ID     HMDB.ID CHEBI.ID
#> 2   Mammalia (#40674) Arachidonic acid  C00219 HMDB0001043    15843
#>   LIPIDBANK.ID PubChem.CID PlantFA.ID SwissLipids.ID Cayman.ID  NA.
#> 2      DFA0213      444899      10144  SLM:000000296  10007268 <NA>
```

--------------------------------

### Display First Few Rows of KEGG Reaction Information

Source: https://massdatabase.tidymass.org/reference/request_kegg_reaction_info

Use `head()` with `request_kegg_reaction_info()` to display the first few entries of the reaction data frame. This is useful for a quick overview of the data structure and content.

```r
head(request_kegg_reaction_info(), 3)
```

--------------------------------

### Download KEGG Reaction Class Database

Source: https://massdatabase.tidymass.org/articles/download_functions

Use this function to download the KEGG reaction class database. No specific parameters are required for this download.

```r
download_kegg_rclass()
```

--------------------------------

### Download, Read, and Convert KEGG Pathway Database

Source: https://massdatabase.tidymass.org/articles/read_convert_functions

Downloads the KEGG pathway database for a specified organism (e.g., human 'hsa'), reads the data, and converts it to a metpath format. This facilitates the analysis of metabolic pathways.

```r
download_kegg_pathway(path = ".", organism = "hsa")
data <- 
  read_kegg_pathway(path = ".")
kegg_pathway_database <-
  convert_kegg2metpath(data = data, path = ".")
```

--------------------------------

### Get Scientific Classification of a Species from Wikipedia

Source: https://massdatabase.tidymass.org/articles/request_functions

Fetches the scientific classification (Kingdom, Phylum, Class, etc.) for a given species ID from Wikipedia.

```R
x <- 
  request_wikipedia_scientific_classification(species_id = "Aaptos ciliata")
dim(x)
#> [1] 7 2
x
#>      name        value
#> 1 Kingdom     Animalia
#> 2  Phylum     Porifera
#> 3   Class Demospongiae
#> 4   Order   Suberitida
#> 5  Family  Suberitidae
#> 6   Genus       Aaptos
#> 7 Species   A. ciliata
```

--------------------------------

### Request Metabolite as List

Source: https://massdatabase.tidymass.org/reference/request_hmdb_metabolite

Demonstrates how to request metabolite information and receive it as an R list object. The output shows the first two elements of the returned list.

```R
x = request_hmdb_metabolite(metabolite_id = "HMDB0000001", return_form = "list")
x[1:2]
```

--------------------------------

### Request ChEBI Compound Information

Source: https://massdatabase.tidymass.org/articles/request_functions

Retrieves information for a specific ChEBI compound using its ID. The example shows a case where the compound might not be found.

```r
x <- 
  request_chebi_compound(compound_id = "CHEBI:18358")
#> Can't find CHEBI:18358, check it.
names(x)
#> NULL
x$base_info
#> NULL
```

--------------------------------

### Display First Few Rows of KEGG Drug Information

Source: https://massdatabase.tidymass.org/reference/request_kegg_drug_info

Use `head()` with `request_kegg_drug_info()` to display the first 3 entries of the KEGG drug information data frame, showing the KEGG.ID and Synonyms columns.

```R
head(request_kegg_drug_info(), 3)
```

--------------------------------

### Download BIGG Model Data

Source: https://massdatabase.tidymass.org/reference/download_bigg_model

Use this function to download data for a specified model ID from the BIGG database. Ensure you have the necessary R packages installed.

```r
download_bigg_model(model_id = "iND750")
```

--------------------------------

### Download KEGG Compound Database

Source: https://massdatabase.tidymass.org/articles/download_functions

Use this function to download the KEGG compound database. Specify the download path.

```r
download_kegg_compound(path = ".")
```

--------------------------------

### Request BIGG model information

Source: https://massdatabase.tidymass.org/articles/request_functions

Retrieves a summary of all available BIGG models. Use this to get an overview of models, including gene, reaction, and metabolite counts.

```R
library(massdatabase)
x <- 
  request_bigg_model_info()
```

```R
dim(x)
#> [1] 108   5
head(x)
#>       bigg_id gene_count reaction_count
#> 1 e_coli_core        137             95
#> 2 iAB_RBC_283        346            469
#> 3     iAF1260       1261           2382
#> 4    iAF1260b       1261           2388
#> 5      iAF692        692            690
#> 6      iAF987        987           1285
#>                                    organism metabolite_count
#> 1 Escherichia coli str. K-12 substr. MG1655               72
#> 2                              Homo sapiens              342
#> 3 Escherichia coli str. K-12 substr. MG1655             1668
#> 4 Escherichia coli str. K-12 substr. MG1655             1668
#> 5        Methanosarcina barkeri str. Fusaro              628
#> 6           Geobacter metallireducens GS-15             1109
```

--------------------------------

### Download KEGG Reaction Class Database

Source: https://massdatabase.tidymass.org/reference/download_kegg_rclass

This function downloads the KEGG reaction class database. It requires a path for saving the file and an optional sleep interval between requests.

```r
download_kegg_rclass(path = ".", sleep = 1)
```

--------------------------------

### Load massdatabase Package

Source: https://massdatabase.tidymass.org/articles/download_functions

Loads the massdatabase R package. Ensure this is run before using any download functions.

```r
library(massdatabase)
```

--------------------------------

### Request BIGG Reaction Info for a Specific Model

Source: https://massdatabase.tidymass.org/reference/request_bigg_reaction_info

Call `request_bigg_reaction_info` with a specific model's BIGG ID to get its reaction data. The default is the human model 'iAB_RBC_283'.

```R
request_bigg_reaction_info(model_bigg_id = "iAB_RBC_283")
```

--------------------------------

### Display First 3 Rows of KEGG Reaction Class Info

Source: https://massdatabase.tidymass.org/reference/request_kegg_rclass_info

Use head() with request_kegg_rclass_info() to display the first 3 rows of the returned data frame. This is useful for a quick preview of the data structure and content.

```R
head(request_kegg_rclass_info(), 3)
```

--------------------------------

### download_chebi_compound

Source: https://massdatabase.tidymass.org/reference/download_chebi_compound

Downloads the CHEBI compound database from a specified URL to a given path.

```APIDOC
## download_chebi_compound

### Description
Downloads the CHEBI compound database from a specified URL to a given path.

### Arguments

* **url** (string) - The URL to download the database from. Defaults to "https://ftp.ebi.ac.uk/pub/databases/chebi/Flat_file_tab_delimited/".
* **path** (string) - The directory path where the downloaded files will be saved. Defaults to ".".

### Value
Downloaded files.

### Author
Xiaotao Shen shenxt1990@outlook.com
```

--------------------------------

### Request Universal Reaction Information and Inspect

Source: https://massdatabase.tidymass.org/reference/request_bigg_reaction_info

Retrieve all universal reaction information and then check its dimensions and the first few rows. This is useful for understanding the scope of available reaction data.

```R
x <- request_bigg_universal_reaction_info()
dim(x)
#> [1] 28302     3
head(x)
#>        bigg_id                                       name model_bigg_id
#> 1 10FTHF5GLUtl     5-glutamyl-10FTHF transport, lysosomal     Universal
#> 2 10FTHF5GLUtm 5-glutamyl-10FTHF transport, mitochondrial     Universal
#> 3 10FTHF6GLUtl     6-glutamyl-10FTHF transport, lysosomal     Universal
#> 4 10FTHF6GLUtm 6-glutamyl-10FTHF transport, mitochondrial     Universal
#> 5 10FTHF7GLUtl     7-glutamyl-10FTHF transport, lysosomal     Universal
#> 6 10FTHF7GLUtm 7-glutamyl-10FTHF transport, mitochondrial     Universal
```

--------------------------------

### R Example: Calculate Similarity Between Two Words

Source: https://massdatabase.tidymass.org/reference/get_words_similarity

Demonstrates how to use the get_words_similarity function to compute the similarity score between two chemical compound names. The function utilizes stringdist::stringsim() for the calculation.

```R
get_words_similarity(word1 = "(2S)-2-Amino-3-(1-methyl-1H-imidazol-4-yl)propanoic acid",
word2 = "(2S)-2-Amino-3-(1-methyl-1H-imidazol-4-yl)propanoate")
#> [1] 0.8809524
```

--------------------------------

### Inspect First Few Rows of KEGG Compound Info

Source: https://massdatabase.tidymass.org/reference/request_kegg_compound_info

Use `head` to view the first few rows of the data frame returned by `request_kegg_compound_info`. This helps in understanding the structure and content of the retrieved data.

```r
head(request_kegg_compound_info(), 3)
#>   KEGG.ID
#> 1  C00001
#> 2  C00002
#> 3  C00003
#>                                                                                             Synonyms
#> 1                                                                                         H2O; Water
#> 2                                                                     ATP; Adenosine 5'-triphosphate
#> 3 NAD+; NAD; Nicotinamide adenine dinucleotide; DPN; Diphosphopyridine nucleotide; Nadide; beta-NAD+
```

--------------------------------

### Get Specific Pathway Information

Source: https://massdatabase.tidymass.org/articles/kegg_pathway

Retrieves detailed information about a specific KEGG pathway using its unique pathway ID. This includes entry details, name, description, class, associated modules, drugs, and genes.

```APIDOC
## request_kegg_pathway

### Description
Get the information of one pathway.

### Method
`request_kegg_pathway`

### Parameters
#### Query Parameters
- **pathway_id** (string) - Required - The KEGG pathway ID (e.g., "hsa00010").

### Request Example
```R
pathway <- request_kegg_pathway(pathway_id = "hsa00010")
pathway
```

### Response
#### Success Response (200)
Returns a list containing detailed information about the specified pathway, including:
- ENTRY: Pathway identifier.
- NAME: Full name of the pathway.
- DESCRIPTION: Detailed description of the pathway.
- CLASS: Classification of the pathway.
- PATHWAY_MAP: Mapping information.
- MODULE: Associated KEGG modules.
- NETWORK: Network information.
- DRUG: Associated drug identifiers.
- DBLINKS: Database links.
- ORGANISM: Organism information.
- GENE: Associated genes.
```

--------------------------------

### Download CHEBI Compound Database

Source: https://massdatabase.tidymass.org/reference/download_chebi_compound

Use this function to download the CHEBI compound database. Specify the URL and the local path for saving the files.

```r
download_chebi_compound(
  url = "https://ftp.ebi.ac.uk/pub/databases/chebi/Flat_file_tab_delimited/",
  path = "."
)
```

--------------------------------

### Download KEGG Reaction Database

Source: https://massdatabase.tidymass.org/reference/download_kegg_reaction

Use this function to download the KEGG reaction database. Specify the desired path for saving the database and an optional sleep interval between requests.

```r
download_kegg_reaction(path = ".", sleep = 1)
```

--------------------------------

### Download, Read, and Convert KEGG Compound Database

Source: https://massdatabase.tidymass.org/articles/read_convert_functions

Downloads the KEGG compound database, reads the data, and converts it to a metid format. This is useful for integrating KEGG compound information into your analysis.

```r
download_kegg_compound(path = ".")
data <- 
  read_kegg_compound(path = ".")
kegg_database <-
  convert_kegg2metid(data = data, path = ".")
```

--------------------------------

### Display Session Information

Source: https://massdatabase.tidymass.org/articles/install

This command displays detailed information about your current R session, including the R version, platform, locale, and loaded packages. This is useful for debugging and ensuring compatibility.

```r
sessionInfo()
#> R version 4.2.1 (2022-06-23)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur ... 10.16
#>
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
#>
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#>
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#>
#> loaded via a namespace (and not attached):
#>  [1] rprojroot_2.0.3   digest_0.6.29     R6_2.5.1          jsonlite_1.8.0   
#>  [5] magrittr_2.0.3    evaluate_0.15     stringi_1.7.6     rlang_1.0.3      
#>  [9] cachem_1.0.6      cli_3.3.0         rstudioapi_0.13   fs_1.5.2         
#> [13] jquerylib_0.1.4   bslib_0.3.1       ragg_1.2.2        rmarkdown_2.14   
#> [17] pkgdown_2.0.5     textshaping_0.3.6 desc_1.4.1        tools_4.2.1      
#> [21] stringr_1.4.0     purrr_0.3.4       yaml_2.3.5        xfun_0.31        
#> [25] fastmap_1.1.0     compiler_4.2.1    systemfonts_1.0.4 memoise_2.0.1    
#> [29] htmltools_0.5.2   knitr_1.39        sass_0.4.1
```

--------------------------------

### Read and Convert FooDB Compound Database

Source: https://massdatabase.tidymass.org/articles/read_convert_functions

Download, read, and convert the FooDB compound database. This allows for the incorporation of food constituent data into metabolic studies.

```r
download_foodb_compound(compound_id = "all", path = ".")
data <-
  read_foodb_compound(path = ".")
foodb_dataabse <-
  convert_foodb2metid(data = data, path = ".")
```

--------------------------------

### Download ChEBI Compound Database

Source: https://massdatabase.tidymass.org/articles/download_functions

Downloads the ChEBI compound database. Specify the desired local path for the downloaded data.

```r
download_chebi_compound(path = ".")
```

--------------------------------

### Download KEGG Drug Database

Source: https://massdatabase.tidymass.org/articles/download_functions

Use this function to download the KEGG drug database. Specify the download path.

```r
download_kegg_drug(path = ".")
```

--------------------------------

### Request KEGG Compound Info as List

Source: https://massdatabase.tidymass.org/articles/kegg_compound

Retrieve detailed information for a KEGG compound ID and return it as an R list. Useful for accessing all available fields.

```r
x <- request_kegg_compound(compound_id = "C02886", return_form = "list")
x
```

--------------------------------

### Session Information

Source: https://massdatabase.tidymass.org/articles/request_functions

Displays the current R session information, including version, platform, and loaded packages.

```R
sessionInfo()
#> R version 4.2.1 (2022-06-23)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur ... 10.16
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] massdatabase_0.99.14
#> 
#> loaded via a namespace (and not attached):
#>   [1] readxl_1.4.0                circlize_0.4.15            
#>   [3] systemfonts_1.0.4           selectr_0.4-2              
#>   [5] igraph_1.3.2                plyr_1.8.7                 
#>   [7] lazyeval_0.2.2              BiocParallel_1.30.3        
#>   [9] listenv_0.8.0               ChemmineR_3.48.0           
#>  [11] GenomeInfoDb_1.32.2         ggplot2_3.3.6              
#>  [13] Rdisop_1.56.0               digest_0.6.29              
#>  [15] foreach_1.5.2               yulab.utils_0.0.5          
#>  [17] htmltools_0.5.2             viridis_0.6.2              
#>  [19] massdataset_1.0.5           fansi_1.0.3                
#>  [21] magrittr_2.0.3              memoise_2.0.1              
#>  [23] metpath_0.99.4              cluster_2.1.3              
```

--------------------------------

### Convert FOODB Compound Data to metID Format

Source: https://massdatabase.tidymass.org/reference/convert_foodb2metid

Use this function to convert FOODB compound data into the metID database format. Ensure the input `data` is a data frame obtained from `read_foodb_compound`. The `path` argument specifies the directory for output, and `threads` controls parallel processing.

```r
convert_foodb2metid(data, path = ".", threads = 5)
```

--------------------------------

### Display First Few Rows of Pathway Info

Source: https://massdatabase.tidymass.org/reference/request_kegg_pathway_info

Shows the first 3 rows of the data frame returned by `request_kegg_pathway_info`. This is useful for quickly inspecting the structure and content of the retrieved data.

```r
head(request_kegg_pathway_info, 3)
```

--------------------------------

### Read and Convert ChEBI Compound Database

Source: https://massdatabase.tidymass.org/articles/read_convert_functions

Download, read, and convert the ChEBI compound database. This function is useful for integrating chemical entity information into metabolic analyses.

```r
download_chebi_compound(path = ".")
data <-
  read_chebi_compound(path = ".")
chebi_database <-
  convert_chebi2metid(data = data, path = ".")
```
Tokens:
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