[emboss-dev] Mapping feature types to Sequence Ontology (SO)
p.j.a.cock at googlemail.com
Tue Aug 16 15:03:26 UTC 2011
Dear Peter R. (et al.),
I recall from one of our chats in person that EMBOSS has some
mapping tables to convert the various different data file format's
feature names into a common standard (the Sequence Ontology?),
for the purpose of inter-converting files. e.g. Converting a UniProt/
SwissProt plain text protein file into a GenPept protein file or GFF3
Is that a fair summary?
It seems to match the minutes of this meeting (found with
> DASGFF requires a sequence ontology (or BioSapiens
> ontology) tag for protein features. Peter has updated the
> Efeatures definitions for proteins to use GFF3 sequence
> ontology codes as internal identifiers, and to use GFF3
> as the principle definitions for all protein features. All
> SwissProt feature types (36 in the current Swissprot
> release) are also defined with the closest possible match
> to the sequence ontology. Where there is no exact match,
> an EMBOSS internal type is defined using the closets SO
> code and the original feature type as a suffix. For SwissProt
> output this is converted back to the swissprot feature type.
> For GFF3 output the internal type is an alias for the closest
> (more general) SO term.
Can you point me at these mapping tables in the EMBOSS
source code please?
I'm particularly interested in the SwissProt to SO mapping
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