---
title: "Creating CompoundDb annotation resources"
package: CompoundDb
output:
  BiocStyle::html_document:
    toc_float: true
vignette: >
  %\VignetteIndexEntry{Creating CompoundDb annotation resources}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteKeywords{Mass Spectrometry, Metabolomics, Infrastructure, Bioinformatics}
  %\VignetteEncoding{UTF-8}
  %\VignettePackage{MsBackendHmdb}
  %\VignetteDepends{Spectra,BiocStyle,MsBackendMgf}
---

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

**Authors**: Johannes Rainer<br />
**Modified**: `r file.info("create-compounddb.Rmd")$mtime`<br />
**Compiled**: `r date()`

# Introduction

Chemical compound annotation and information can be retrieved from a variety of
sources including [HMDB](http://www.hmdb.ca),
[LipidMaps](http://www.lipidmaps.org) or
[ChEBI](https://www.ebi.ac.uk/chebi). The `CompoundDb` package provides
functionality to extract data relevant for (chromatographic) peak annotations in
metabolomics/lipidomics experiments from these sources and to store it into a
common format (i.e. an `CompDb` object/database). This vignette describes how
such `CompDb` objects can be created exemplified with package-internal test
files that represent data subsets from some annotation resources.

The R object to represent the compound annotation is the `CompDb` object. Each
object (respectively its database) is supposed to contain and provide
annotations from a single source (e.g. HMDB or LipidMaps) but it is also
possible to create cross-source databases too.


# Creating `CompDb` databases

`CompDb` databases can be created from existing data resources such as the Human
Metabolome Database (HMDB) by importing all of their data or can alternatively
be *build* by sequentially adding data and information to the database. This
section explains first how data can be loaded from existing resources to create
a `CompDb` database and in the last subsection how an empty `CompDb` can be
sequentially and manually filled with annotation data \@ref(sec:fill).

The `CompoundDb` package provides the `compound_tbl_sdf` and the
`compound_tbl_lipidblast` functions to extract relevant compound annotation from
files in SDF (structure-data file) format or in the json files from LipidBlast
(http://mona.fiehnlab.ucdavis.edu/downloads). `CompoundDb` allows to process SDF
files from:

- Human Metabolome Database (HMDB), http://www.hmdb.ca
- Chemical Entities of Biological Interest (ChEBI): https://www.ebi.ac.uk/chebi
- LIPID MAPS Structure Database (LMSD): http://www.lipidmaps.org
- PubChem: https://pubchem.ncbi.nlm.nih.gov
- MoNa (Massbank of North America): http://mona.fiehnlab.ucdavis.edu (for MoNa
  import see the next section).

Note however that it is also possible to define such a table manually and use
that to create the database. As simple example for this is provided in the
section *`CompDb` from custom input* \@ref(sec:custom) below or the help page of
`createCompDb` for more details on that.


## `CompDb` from HMDB data

Below we use the `compound_tbl_sdf` to extract compound annotations from a SDF
file representing a very small subset of the HMDB database. To generate a
database for the full HMDB we would have to download the *structures.sdf* file
containing all metabolites and load that file instead.

```{r compound_tbl, message = FALSE, warnings = FALSE}
library(CompoundDb)

## Locate the file
hmdb_file <- system.file("sdf/HMDB_sub.sdf.gz", package = "CompoundDb")
## Extract the data
cmps <- compound_tbl_sdf(hmdb_file)
```

The function returns by default a (`data.frame`-equivalent) `tibble` (from the
*tidyverse*'s `tibble` package).

```{r cmps}
cmps
```

The `tibble` contains columns

- `compound_id`: the resource-specific ID of the compound. Can be an `integer`
  or a `character`.
- `name`: the name of the compound, mostly a generic or common name.
- `inchi`: the compound's inchi.
- `inchikey`: the INCHI key.
- `formula`: the chemical formula of the compound.
- `exactmass`: the compounds (monoisotopic) mass.
- `synonyms`: a `list` of aliases/synonyms for the compound.
- `smiles`: the SMILES of the compound.

To create a simple compound database, we could pass this `tibble` along with
additional required metadata information to the `createCompDb` function. In the
present example we want to add however also MS/MS spectrum data to the
database. We thus load below the MS/MS spectra for some of the compounds from
the respective xml files downloaded from HMDB. To this end we pass the path to
the folder in which the files are located to the `msms_spectra_hmdb`
function. The function identifies the xml files containing MS/MS spectra based
on their their file name and loads the respective spectrum data. The folder can
therefore also contain other files, but the xml files from HMDB should not be
renamed or the function will not recognice them. Note also that at present only
MS/MS spectrum xml files from HMDB are supported (one xml file per spectrum);
these could be downloaded from HMDB with the *hmdb_all_spectra.zip* file.

```{r msms_spectra, message = FALSE}
## Locate the folder with the xml files
xml_path <- system.file("xml", package = "CompoundDb")
spctra <- msms_spectra_hmdb(xml_path)
```

Also here, spectra information can be manually provided by adhering to the
expected structure of the `data.frame` (see `?createCompDb` for details).

At last we have to create the metadata for the resource. The metadata
information for a `CompDb` resource is crucial as it defines the origin of the
annotations and its version. This information should thus be carefully defined
by the user. Below we use the `make_metadata` helper function to create a
`data.frame` in the expected format. The organism should be provided in the
format e.g. `"Hsapiens"` for human or `"Mmusculus"` for mouse, i.e. capital
first letter followed by lower case characters without whitespaces.

```{r metadata, message = FALSE}
metad <- make_metadata(source = "HMDB", url = "http://www.hmdb.ca",
                       source_version = "4.0", source_date = "2017-09",
                       organism = "Hsapiens")
```

With all the required data ready we create the SQLite database for the HMDB
subset. With `path` we specify the path to the directory in which we want to
save the database. This defaults to the current working directory, but for this
example we save the database into a temporary folder.

```{r createCompDb}
db_file <- createCompDb(cmps, metadata = metad, msms_spectra = spctra,
                        path = tempdir())
```

The variable `db_file` is now the file name of the SQLite database. We can pass
this file name to the `CompDb` function to get the `CompDb` objects acting as
the interface to the database.

```{r CompDb}
cmpdb <- CompDb(db_file)
cmpdb
```

To extract all compounds from the database we can use the `compounds`
function. The parameter `columns` allows to choose the database columns to
return. Any columns for any of the database tables are supported. To get an
overview of available database tables and their columns, the `tables` function
can be used:

```{r}
tables(cmpdb)
```

Below we extract only selected columns from the *compounds* table.

```{r compounds}
compounds(cmpdb, columns = c("name", "formula", "exactmass"))
```

Analogously we can use the `Spectra` function to extract spectrum data from the
database. The function returns by default a `Spectra` object from the
`r Biocpkg("Spectra")` package with all spectra metadata available as
*spectra variables*.

```{r spectra, message = FALSE}
library(Spectra)
sps <- Spectra(cmpdb)
sps
```

The available *spectra variables* for the `Spectra` object can be retrieved with
`spectraVariables`:

```{r spectraVariables}
spectraVariables(sps)
```

Individual spectra variables can be accessed with the `$` operator:

```{r}
sps$collisionEnergy
```

And the actual m/z and intensity values with `mz` and `intensity`:

```{r}
mz(sps)

## m/z of the 2nd spectrum
mz(sps)[[2]]
```

Note that it is also possible to retrieve specific spectra, e.g. for a provided
compound, or add compound annotations to the `Spectra` object. Below we use the
filter expression `~ compound_id == "HMDB0000001"`to get only MS/MS spectra for
the specified compound. In addition we ask for the `"name"` and
`"inchikey"` of the compound.

```{r spectra-selected}
sps <- Spectra(cmpdb, filter = ~ compound_id == "HMDB0000001",
               columns = c(tables(cmpdb)$msms_spectrum, "name",
                           "inchikey"))
sps
```

The available spectra variables:

```{r}
spectraVariables(sps)
```

The compound's name and INCHI key have thus also been added as spectra
variables:

```{r}
sps$inchikey
```

To share or archive the such created `CompDb` database, we can also create a
dedicated R package containing the annotation. To enable reproducible research,
each `CompDb` package should contain the version of the originating data source
in its file name (which is by default extracted from the metadata of the
resource). Below we create a `CompDb` package from the generated database
file. Required additional information we have to provide to the function are the
package creator/maintainer and its version.

```{r createCompoundDbPackage, warning = FALSE}
createCompDbPackage(
    db_file, version = "0.0.1", author = "J Rainer", path = tempdir(),
    maintainer = "Johannes Rainer <johannes.rainer@eurac.edu>")
```

The function creates a folder (in our case in a temporary directory) that can be
build and installed with `R CMD build` and `R CMD INSTALL`.

Special care should also be put on the license of the package that can be passed
with the `license` parameter. The license of the package and how and if the
package can be distributed will depend also on the license of the originating
resource.


## `CompDb` from custom data {#sec:custom}

A `CompDb` database can also be created from custom, manually defined
annotations. To illustrate this we create below first a `data.frame` with some
arbitrary compound annotations. According to the `?createCompDb` help page, the
data frame needs to have columns `"compound_id"`, `"name"`, `"inchi"`,
`"inchikey"`, `"formula"`, `"exactmass"`, `"synonyms"`. All columns except
`"compound_id"` can also contain missing values. It is also possible to define
additional columns. Below we thus create a `data.frame` with some compound
annotations as well as additional columns. Note that all these annotations in
this example are for illustration purposes only and are by no means
*real*. Also, we don't provide any information for columns `"inchi"`,
`"inchikey"` and `"formula"` setting all values for these to `NA`.

```{r}
cmps <- data.frame(
    compound_id = c("CP_0001", "CP_0002", "CP_0003", "CP_0004"),
    name = c("A", "B", "C", "D"),
    inchi = NA_character_,
    inchikey = NA_character_,
    formula = NA_character_,
    exactmass = c(123.4, 234.5, 345.6, 456.7),
    compound_group = c("G01", "G02", "G01", "G03")
)
```

Next we add also *synonyms* for each compound. This columns supports multiple
values for each row.

```{r}
cmps$synonyms <- list(
    c("a", "AA", "aaa"),
    c(),
    c("C", "c"),
    ("d")
)
```

We also need to define the *metadata* for our database, which we do with the
`make_metadata` function.  With this information we can already create a first
rudimentary `CompDb` database that contains only compound annotations. We thus
create below our custom `CompDb` database in a temporary directory. We also
manually specify the name of our database with the `dbFile` parameter - if not
provided, the name of the database will be constructed based on information from
the `metadata` parameter. In a real-case scenario, `path` and `dbFile` should be
changed to something more meaningful.

```{r}
metad <- make_metadata(source = "manually defined", url = "",
                       source_version = "1.0.0", source_date = "2022-03-01",
                       organism = NA_character_)

db_file <- createCompDb(cmps, metadata = metad, path = tempdir(),
                        dbFile = "CompDb.test.sqlite")
```

We can now load this toy database using the `CompDb` function providing the full
path to the database file. Note that we load the database in read-write mode by
specifying `flags = RSQLite::SQLITE_RW` - by default `CompDb` will load
databases in read-only mode hence ensuring that the data within the database can
not be compromised. In our case we would however like to add more information to
this database later and hence we load it in read-write mode.

```{r}
cdb <- CompDb(db_file, flags = RSQLite::SQLITE_RW)
cdb
```

We can now retrieve annotations from the database with the `compound` function.

```{r}
compounds(cdb)
```

Or also search and filter the annotations.

```{r}
compounds(cdb, filter = ~ name %in% c("B", "A"))
```

Next we would like to add also MS2 spectra data to the database. This could be
either done directly in the `createCompDb` call with parameter `msms_spectra`,
or with the `insertSpectra` function that allows to add MS2 spectra data to an
existing `CompDb` which can be provided as a `Spectra` object. We thus below
manually create a `Spectra` object with some arbitrary MS2 spectra -
alternatively, `Spectra` can be imported from a variety of input sources,
including MGF or MSP files using e.g. the `r Biocpkg("MsBackendMgf")` or
`r Biocpkg("MsBackendMsp")` packages.

```{r}
#' Define basic spectra variables
df <- DataFrame(msLevel = 2L, precursorMz = c(124.4, 124.4, 235.5))
#' Add m/z and intensity information for each spectrum
df$mz <- list(
    c(3, 20, 59.1),
    c(2, 10, 30, 59.1),
    c(100, 206, 321.1))
df$intensity <- list(
    c(10, 13, 45),
    c(5, 8, 9, 43),
    c(10, 20, 400))
#' Create the Spectra object
sps <- Spectra(df)
```

The `Spectra` object needs also to have a variable (column) called
`"compound_id"` which provides the information with which existing compound in
the database the spectrum is associated.

```{r}
compounds(cdb, "compound_id")
sps$compound_id <- c("CP_0001", "CP_0001", "CP_0002")
```

We can also add additional information to the spectra, such as the instrument.

```{r}
sps$instrument <- "AB Sciex TripleTOF 5600+"
```

And we can now add these spectra to our existing toy `CompDb`. Parameter
`columns` allows to specify which of the *spectra variables* should be stored
into the database.

```{r}
cdb <- insertSpectra(cdb, spectra = sps,
                     columns = c("compound_id", "msLevel",
                                 "precursorMz", "instrument"))
cdb
```

We have thus now a `CompDb` database with compound annotations and 3 MS2
spectra. We could for example also retrieve the MS2 spectra for the compound
with the name *A* from the database with:

```{r}
Spectra(cdb, filter = ~ name == "A")
```



## `CompDb` from MoNA data

MoNa (Massbank of North America) provides a large SDF file with all spectra
which can be used to create a `CompDb` object with compound information and
MS/MS spectra. Note however that MoNa is organized by spectra and the annotation
of the compounds is not consistent and normalized. Spectra from the same
compound can have their own compound identified and data that e.g. can differ in
their chemical formula, precision of their exact mass or other fields.

Similar to the example above, compound annotations can be imported with the
`compound_tbl_sdf` function while spectrum data can be imported with
`msms_spectra_mona`. In the example below we use however the `import_mona_sdf`
that wraps both functions to reads both compound and spectrum data from a SDF
file without having to import the file twice. As an example we use a small
subset from a MoNa SDF file that contains only 7 spectra.

```{r mona-import, message = FALSE}
mona_sub <- system.file("sdf/MoNa_export-All_Spectra_sub.sdf.gz",
                        package = "CompoundDb")
mona_data <- import_mona_sdf(mona_sub)
```

As a result we get a `list` with a data.frame each for compound and spectrum
information. These can be passed along to the `createCompDb` function to create
the database (see below).

```{r mona-metadata}
metad <- make_metadata(source = "MoNa",
                       url = "http://mona.fiehnlab.ucdavis.edu/",
                       source_version = "2018.11", source_date = "2018-11",
                       organism = "Unspecified")
mona_db_file <- createCompDb(mona_data$compound, metadata = metad,
                             msms_spectra = mona_data$msms_spectrum,
                             path = tempdir())
```

We can now load and use this database, e.g. by extracting all compounds as shown
below.

```{r mona-compounds}
mona <- CompDb(mona_db_file)
compounds(mona)
```

As stated in the introduction of this section the `compound` information
contains redundant information and the table has essentially one row per
spectrum. Feedback on how to reduce the redundancy in the ms_compound table is
highly appreciated.


## `CompDb` by sequentially filling with data {#sec:fill}

As an alternative to creating a full database from an existing resource it is
also possible to create an empty `CompDb` database and *sequentially* filling it
with data. This could for example be used to create a laboratory specific
annotation library with compound, ion and fragment spectra of pure standards
measured on a certain LC-MS setup. Below we create an empty `CompDb` database
providing the file name of the database. In the example we store the database to
a temporary file but in a real use case a meaningful file name and file path
should be used instead.

```{r}
dbfile <- tempfile()
mydb <- emptyCompDb(dbfile)
mydb
```

We next define some first compound annotation we want to add to the
database. For compound annotations, fields `"compound_id"` (an arbitrary ID of
the compound), `"name"` (the compound name), `"inchi"`, `"inchikey"`,
`"formula"` (the chemical formula) and `"exactmass"` (the monoisotopic mass) are
expected, but, except of `"compound_id"`, they can also contain missing values
or be completely omitted. Below we define a `data.frame` with annotations for
some compounds and add this annotation to the database using the
`insertCompound` function.

```{r}
cmp <- data.frame(compound_id = c("1", "2"),
                  name = c("Caffeine", "Glucose"),
                  formula = c("C8H10N4O2", "C6H12O6"),
                  exactmass = c(194.080375584, 180.063388116))
mydb <- insertCompound(mydb, cmp)
mydb
```

We next add fragment spectra for the compounds. These could for example
represent MS2 spectra measured for the pure standard of the compound and could
be extracted for example from `xcms` result objects or other sources. Below we
load some fragment spectra for caffeine from an MGF file distributed with this
package. We use the `r BiocStyle::Biocpkg("MsBackendMgf")` package to import
that data into a `Spectra` object.

```{r, message = FALSE}
library(MsBackendMgf)
caf_ms2 <- Spectra(system.file("mgf", "caffeine.mgf", package = "CompoundDb"),
                   source = MsBackendMgf())
caf_ms2
```

We can evaluate what spectra variables are available in the imported data.

```{r}
spectraVariables(caf_ms2)
caf_ms2$rtime
```

There are many variables available, but most of them, like for example the
retention time, or not defined as this information was not provided in the MGF
file. In order to associate these fragment spectra to the caffeine compound we
just added to the database, we need to assign them the ID of the compound (in
our case `"1"`).

```{r}
caf_ms2$compound_id <- "1"
```

We can then add the spectra to the database using the `insertSpectra`
function. With parameter `columns` we specify which of the spectra variables we
actually want to store in the database.

```{r}
mydb <- insertSpectra(mydb, caf_ms2,
                      columns = c("compound_id", "msLevel", "splash",
                                  "precursorMz", "collisionEnergy"))
mydb
```

We thus have now 2 compounds in the database and 2 fragment spectra:

```{r}
compounds(mydb)
sps <- Spectra(mydb)
sps$name
```

With `insertCommpound` and `insertSpectra` further compounds and fragment
spectra could be added to the database. Note that both functions support also to
add additional columns (*fields* or *variables*) to the database. As an example
we define below a compound with an arbitrary additional column and add this to
the database using parameter `addColumns = TRUE`.

```{r}
cmps <- data.frame(compound_id = "3", name = "X003",
                   formula = "C5H2P3O", extra_field = "artificial compound")
mydb <- insertCompound(mydb, cmps, addColumns = TRUE)
compounds(mydb)
```

The additional column is now available in the database. Existing entries in a
`CompDb` can also be deleted using the `deleteCompound` or `deleteSpectra`
functions. Both require as additional input the IDs of the compound(s) (or
spectra) to delete. Below we extract the IDs and names of the compounds from our
database.

```{r}
compounds(mydb, columns = c("compound_id", "name"))
```

We can now delete the compound `"X003"` with `deleteCompound` and the ID of this
compound.

```{r}
mydb <- deleteCompound(mydb, ids = "3")
compounds(mydb)
```

Note that deleting a compound with associated spectra (or ions) will result in
an error, thus it would not be possible to delete caffeine from the database,
because it contains also MS2 spectra for that compound. Using parameter
`recursive = TRUE` in the `deleteCompound` call would however allow to delete
the compound **and all** associated spectra (and/or ions) along with it. Below
we delete thus caffeine and the associated MS2 spectra which leaves us a
`CompDb` with a single compound and no more MS2 spectra.

```{r}
mydb <- deleteCompound(mydb, ids = "1", recursive = TRUE)
compounds(mydb)
Spectra(mydb)
```

Note that these functions can also be used to add or remove annotations to/from
any `CompDb` database, as long as the database is *writeable* (i.e. the database
is loaded by specifying `flags = RSQLite::SQLITE_RW` as additional parameter to
the `CompDb` call to load the database).


# Session information

```{r sessioninfo, echo=FALSE}
sessionInfo()
```
