OBO versus Slim
there are confusion yeast subset, GOSLIm (is the a subset of yeast GO or full-genome coverage). Guo think Goslim is a partial coverage of the yeast genome. The http://geneontology.org/docs/go-subset-guide/ seem to suggest that yeast genome-GO is call "slim".
It seems OBO is a human readable format.
http://geneontology.org/docs/go-subset-guide/
http://geneontology.org/docs/download-ontology/#subsets
Ghafari suggests:
https://sites.google.com/view/yeastgenome-help/useful-sgd-links?authuser=0 which linked to a FTP site at sgd: http://sgd-archive.yeastgenome.org/. and https://downloads.yeastgenome.org/latest/sgd.gaf.gz
Guo confirmed that *gaf file is what he used.
GAF format is at
http://geneontology.org/docs/go-annotation-file-gaf-format-2.1/
But, GAF files is gene-2-GO mapping. Not the GO_tree.
It seems JASON files contain 'graph', 'node' in its structure.
https://ontobio.readthedocs.io/en/latest/notebooks.html
Jupyternoteook https://github.com/biolink/ontobio
TODO: read graph based DNN to see how graph is converted to connection of layers.
Guo suggests GO-CAM, a nature comment with download link
http://current.geneontology.org/products/ttl/index.html
No comments:
Post a Comment