GeneOntologySupplement

Supplemental data and code used for the article "The Gene Ontology of eukaryotic cilia and flagella", Roncaglia, et al. Cilia 6, 10 (2017)

For full disclosure and information see:

Roncaglia, P. et al. The Gene Ontology of eukaryotic cilia and flagella. Cilia 6, 10 (2017). http://dx.doi.org/10.1186/s13630-017-0054-8

The provided files and scripts should allow you to rerun the analyses as described in the article. Below are links to source files used in this analysis that can not be part of the repository due to licencing and ownership. However running the makefile, by simply executing 'make' will download all required files automatically.

Code is provided under MIT license, see LICENSE file.

Ontologizer

The workflow uses the Ontologizer version 2.1, which can be obtained here: http://ontologizer.de/.

Gene ontology files

The relevant .OBO formatted files that were used can be obtained via:

2012-12-01: ftp://ftp.geneontology.org/go/ontology-archive/gene_ontology_edit.obo.2012-12-01.gz

2017-01-01: ftp://ftp.geneontology.org/go/ontology-archive/gene_ontology_edit.obo.2017-01-01.gz

Gene annotation files

The relevant time matched Gene Annotation files where obtained from:

2012-12-01: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/old/HUMAN/gene_association.goa_human.116.gz

2017-01-16: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/old/HUMAN/goa_human.gaf.164.gz

How to rerun the analyses

In linux:

1. Clone this repository by executing 'git clone https://github.com/JohnvanDam/GeneOntologySupplement.git'
2. cd to the cloned repo directory.
3. Execute 'make'.

All relevant files not present will be downloaded, including the Ontologizer, and all analyses will be run automatically.

#Known problems GOA annotation version 164 is current (as of 2017-01-19) and not yet in the legacy ftp folder at ebi.ac.uk. I've tried to make the pipeline future proof, but the goa_human.gaf.164.gz file currently does not yet exist at the ftp site. For now download ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/goa_human.gaf.gz, unzip the file, and rename to gene_association.goa_human.164 I will test and update the code if necessary in the near future.