https://github.com/alexslemonade/identifier-refinery

Tools and assets for easy gene identifier conversion

https://github.com/alexslemonade/identifier-refinery

Repository

Tools and assets for easy gene identifier conversion

https://github.com/AlexsLemonade/identifier-refinery/blob/master/

![](https://i.imgur.com/GphUr2m.png)
# identifier-refinery [![](https://zenodo.org/badge/DOI/10.5281/zenodo.1322711.svg)](https://zenodo.org/record/1322711)

Tools and assets for easy and reproducible gene identifier conversion.

## Methods

This repository is used to build matrices which can convert between different gene identifiers.

These conversion matrices are built by:

 * Randomly choosing raw CEL files from NCBI GEO for a given platform accession code (in `/cels`)
 * Reading the CEL header and joining Brainarray (e.g., `hgu133plus2hsensgprobe`) and Bioconductor (e.g., `hgu133plus2.db`) (x, y) coordinates
 * Finding intersecting probe identifiers
 * Extracting supported identifiers and probe IDs from the Bioconductor package
 * Filtering on probe IDs and Ensembl Gene IDs in Brainarray
 * Writing the output to a conversion TSV file
 * Check that all output conversion TSV files have a shared SHA1

## Repository Contents

### Source Files

The `cels` directory contains raw CEL files taken from GEO. The list of supported platforms is in `supported_microarray_platforms.csv`. Source files can be acquired by running the `acquire_cels.py` script.

### Docker Image

The conversion scripts are run on custom Docker images. 

Two Dockerfiles are provided in this repository - `base` Docker image, which is used to install the required R dependencies, and the `pd` image, which is used to build the required databases for a given platform.

### Conversion Scripts

A `build_and_convert.py` script is provided, which build a unique Docker image for each package, mount the downloaded CEL files as a volume, and then run the gene conversion script `R/gene_convert.R` inside the image and output the master conversion matrix. Output TSV files live in `cels/out/`.

## Reproducing

The entire process can be reproduced by running the following command script from a fresh checkout of this repository. It will take some time:

```
$ ./generate_matricies_from_scratch.sh
```

You can also choose to only build a specific platform, ex.,:

```
$ ./generate_matricies_from_scratch.sh celegans
```

## Identifiers

Released assets in this repository are availble under the DOI, `10.5281/zenodo.1322711`, which can be seen on Zenodo [here](https://zenodo.org/record/1322711). This accession is up to date as of https://github.com/AlexsLemonade/identifier-refinery/commit/cace2849baf2666f21ec32f5eee6208d6ec19294.

## Related Projects

 * [AlexsLemonade/refinebio](https://github.com/AlexsLemonade/refinebio)

## Copyright

`identifier-refinery` output assets are released under a [CC0 1.0 Universal](https://creativecommons.org/publicdomain/zero/1.0/legalcode) license. All code is released under the BSD 3-clause license. Input assets are property of the original providers to NCBI GEO, but may be [freely downloaded and redistributed](https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html) unless otherwise noted.

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