---
title: "MassBank Data for AnnotationHub"
author: "Johannes Rainer"
graphics: no
package: AHMassBank
output:
    BiocStyle::html_document:
      toc_float: true
vignette: >
    %\VignetteIndexEntry{Provide EnsDb databases for AnnotationHub}
    %\VignetteEngine{knitr::rmarkdown}
    %\VignetteEncoding{UTF-8}
    %\VignetteDepends{CompoundDb,AnnotationHub}
---

```{r style, echo = FALSE, results = 'asis', message=FALSE}
BiocStyle::markdown()
```

**Authors**: `r packageDescription("AHMassBank")[["Author"]] `<br />
**Compiled**: `r date()`

# Introduction

MassBank is an open access, community maintained annotation database for small
compounds. Annotations provided by this database comprise names, chemical
formulas, exact masses and other chemical properties for small compounds
(including metabolites, medical treatment agents and others). In addition,
fragment spectra are available which are crucial for the annotation of
untargeted mass spectrometry data. The `r BiocStyle::Biocpkg("CompoundDb")`
Bioconductor package supports conversion of MassBank data into the `CompDb`
(SQLite) format which enables a simplified distribution of the resource and easy
integration into Bioconductor-based annotation workflows.


# Fetch MassBank `CompDb` Databases from `AnnotationHub`

The `AHMassBank` package provides the metadata for all `CompDb` SQLite databases
with [MassBank](https://massbank.eu/MassBank) annotations in `r
Biocpkg("AnnotationHub")`. To get and use MassBank annotations we first we
load/update the `AnnotationHub` resource.

```{r load-lib, message = FALSE}
library(AnnotationHub)
ah <- AnnotationHub()
```

Next we list all *MassBank* entries from `AnnotationHub`.

```{r}
query(ah, "MassBank")
```

We fetch the `CompDb` with MassBank annotations for release *2021.03*.

```{r load-ensdb}
qr <- query(ah, c("MassBank", "2021.03"))
cdb <- qr[[1]]
```


# Creating `CompDb` Databases from MassBank

MassBank provides its annotation database as a MySQL dump. To simplify its usage
(also for users not experienced with MySQL or with the specific MassBank
database layout), MassBank annotations can also be converted into the
(SQLite-based) `CompDb` format which can be easily used with the 
`r Biocpkg("CompoundDb")` package. The steps to convert a MassBank MySQL
database to a `CompDb` SQLite database are described below.

First the MySQL database dump needs to be downloaded from the MassBank [github
page](https://github.com/MassBank/MassBank-data/releases). This database needs
to be installed into a local MySQL/MariaDB database server (using `mysql -h
localhost -u <username> -p < MassBank.sql` with `<username>` being the name of
the user with write access to the database server).

To transfer the MassBank data into a `CompDb` database a helper function from
the `CompoundDb` package can be used.

```{r, eval = FALSE}
library(RMariaDB)
con <- dbConnect(MariaDB(), host = "localhost", user = <username>,
                 pass = <password>, dbname = "MassBank")
source(system.file("scripts", "massbank_to_compdb.R", package = "CompoundDb"))
massbank_to_compdb(con)
```


# Session Information

```{r}
sessionInfo()
```