Add variant effect ontology #261

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fnothaft opened this Issue Jun 8, 2014 · 5 comments

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fnothaft commented Jun 8, 2014

Suggested by @heuermh, see here for examples. This should be added to the VariantAnnotations and variant annotation parser.

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heuermh Jun 8, 2014

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My further suggestion would be to only accept SO term names in ADAM and not worry about mapping between non-SO terms as described on that GEMINI documentation page, i.e. only those values from the column Sequence Ontology terms (column: impact_so) in this table

http://gemini.readthedocs.org/en/latest/content/functional_annotation.html#so-impact-definitions-in-gemini

Although on review that column has some errors in it, e.g. feature elongation should be feature_elongation (SO:0001907), non_coding_exon_variant should be non_coding_transcript_exon_variant (SO:0001792), nc_transcript_variant isn't a valid term, etc.

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heuermh commented Jun 8, 2014

My further suggestion would be to only accept SO term names in ADAM and not worry about mapping between non-SO terms as described on that GEMINI documentation page, i.e. only those values from the column Sequence Ontology terms (column: impact_so) in this table

http://gemini.readthedocs.org/en/latest/content/functional_annotation.html#so-impact-definitions-in-gemini

Although on review that column has some errors in it, e.g. feature elongation should be feature_elongation (SO:0001907), non_coding_exon_variant should be non_coding_transcript_exon_variant (SO:0001792), nc_transcript_variant isn't a valid term, etc.

@tdanford tdanford removed the pick me up! label Jun 9, 2014

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heuermh Jun 11, 2014

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I have been able to fix some of those documentation errors, not sure yet if the GEMINI code also needs to be fixed.

arq5x/gemini#300

In any case, the SO itself should be the source of record for these terms.

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heuermh commented Jun 11, 2014

I have been able to fix some of those documentation errors, not sure yet if the GEMINI code also needs to be fixed.

arq5x/gemini#300

In any case, the SO itself should be the source of record for these terms.

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fnothaft commented Jul 6, 2016

See new schema in bigdatagenomics/bdg-formats#67.

@fnothaft fnothaft added this to the 0.20.0 milestone Jul 6, 2016

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fnothaft Jul 6, 2016

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Closing as dupe of #1044.

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fnothaft commented Jul 6, 2016

Closing as dupe of #1044.

@fnothaft fnothaft closed this Jul 6, 2016

@fnothaft fnothaft removed this from the 0.20.0 milestone Jul 6, 2016

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