# 4. Tutorial: Working with Human Protein Atlas (HPA) xml files offline

Anh N. Tran1*

1DataGrata LLC

*trannhatanh89@gmail.com

#### 6/7/2019

    library(BiocStyle)
    library(HPAanalyze)
    library(dplyr)
    library(xml2)

# 1 The case

The Human Protein Atlas allow you to download very detailed data for each protein in the form of an xml file, and `hpaXmlGet` and `hpaXml` allow you to retrieve those files automatically from HPA server and parse them. However, due to technical limitation, you will not be able to save those `"xml_document"/"xml_node"` objects. The question is: How do you keep a version of these files to use when you are not connected to the internet, or for reproducibility?

# 2 The solution

## 2.1 Download and keep a local version of the xml files for yourself

Look at the “Downloadable data” page from HPA website, you will see how these files are downloaded. Basically, you add `[ensembl_id].xml` to `http://www.proteinatlas.org` to download individual entries (that’s what `hpaXmlGet` does behind the scene), or download the whole big set.

From there, you can import the file using `xml2::read_xml()`. The output should be exactly the same as `hpaXmlGet`.

    ## same as hpaXmlGet("ENSG00000134057")
    CCNB1xml <- xml2::read_xml("data/ENSG00000134057.xml")

## 2.2 Business as usual with `hpaXml` functions

Since the umbrella function `hpaXml` take either the ensembl id or the imported `xml_document` object, you can feed what you just imported to it and get the expected result.

    CCNB1_parsed <- hpaXml(CCNB1xml)

You can obviously use other `hpaXml` functions as well.

    hpaXmlProtClass(CCNB1xml)
    hpaXmlTissueExprSum(CCNB1xml)
    hpaXmlAntibody(CCNB1xml)
    hpaXmlTissueExpr(CCNB1xml)

## 2.3 Save your parsed objects

It is recommended that you save your parsed objects for reproducibility. Unlike the `xml_document` object, these parsed objects are just regular R lists of standard vectors or data frames. You can save them just as usual.

    saveRDS(CCNB1_parsed, "data/CCNB1_parsed.rds")

# 3 Copyright

Anh Tran, 2018-2023

Please cite: Tran, A.N., Dussaq, A.M., Kennell, T. et al. HPAanalyze: an R package that facilitates the retrieval and analysis of the Human Protein Atlas data. BMC Bioinformatics 20, 463 (2019) https://doi.org/10.1186/s12859-019-3059-z