Rmd file that retrieves and parses ENA's XML specification for NGS experiments

ena_controlled_vocabulary.Rmd

---
title: "Controlled vocabulary for sequencing experiments"
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

```{r setup}
library(magrittr)
library(stringr)
library(xml2)
```

## ENA's annotation schema

The European Nucleotide Archive (ENA) has published a 
[schema](ftp://ftp.ebi.ac.uk/pub/databases/ena/doc/xsd/sra_1_5/SRA.experiment.xsd)
with the controlled vocabulary for annotation of sequencing experiments.
This document highlights the available terms for the

- `library_strategy`
- `library_source`
- `library_selection`
- `library_layout`

annotation fields. Please choose `Keywords` from the following tables:

```{r}
url <- paste0("ftp://ftp.ebi.ac.uk/pub/databases/ena/doc/xsd/sra_1_5/",
              "SRA.experiment.xsd")
root <- xml2::read_xml(url)
nodes <- xml2::xml_children(root)
```

### Library strategy

```{r results='asis'}
terms <- nodes %>%
  xml_find_all("//*[@name='typeLibraryStrategy']") %>%
  xml_children() %>%
  xml_find_all("xs:enumeration")

lib_strategy <- data.frame(
  Keyword = terms %>%
    xml_attr("value", default = NA_character_),
  Description = terms %>%
    xml_text() %>%
    str_squish()
)
knitr::kable(lib_strategy)
```

### Library source

```{r results='asis'}
terms <- nodes %>%
  xml_find_all("//*[@name='typeLibrarySource']") %>%
  xml_children() %>%
  xml_find_all("xs:enumeration")

lib_source <- data.frame(
  Keyword = terms %>%
    xml_attr("value", default = NA_character_),
  Description = terms %>%
    xml_text() %>%
    str_squish()
)
knitr::kable(lib_source)
```

### Library selection

```{r results='asis'}
terms <- nodes %>%
  xml_find_all("//*[@name='typeLibrarySelection']") %>%
  xml_children() %>%
  xml_find_all("xs:enumeration")

lib_selection <- data.frame(
  Keyword = terms %>%
    xml_attr("value", default = NA_character_),
  Description = terms %>%
    xml_text() %>%
    str_squish()
)
knitr::kable(lib_selection)
```

### Library layout

```{r results='asis'}
terms <- nodes %>%
  xml_find_all("//*[@name='LIBRARY_LAYOUT']") %>%
  xml_find_all("./xs:complexType") %>%
    xml_children() %>%
    xml_find_all("./xs:element")

lib_layout <- data.frame(
  Keyword = terms %>%
    xml_attr("name", default = NA_character_),
  Description = terms %>%
    xml_text() %>%
    str_squish()
)
knitr::kable(lib_layout)
```

## Reproducibility

<details>
<summary>
Session Information
</summary>

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

</details>