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From: Karen E. <ei...@fr...> - 2006-02-23 22:41:20
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Changes requested by Gillian: See comments On Feb 8, 2006, at 3:52 AM, Gillian Millburn wrote: > > > Here they are (have discussed these changes with Michael) > > 1. > > [Term] > id: SO:0000042 > name: pseudogene_attribute > def: "An attribute of a pseudogene (SO\:0000336)." [SO:ma] > is_a: SO:0000009 ! gene_class > > > please could the name of this term be changed to : > > name: pseudogene_class > > It reads nicer for biologists, and makes more sense if when annotating > a > genes file you have a gene you know is a pseudogene but not which > subclass its is. > > I guess that the definition will need changing/deleting too, as it > doesn't make much sense to me. > I do not think that SO is doing the best job with pseudogenes. Will get back to you about this when I see how the other cross product terms are received. > > 2. suggestions for tidying up the "engineered_gene" section. > > the section of terms that has "engineered" in them needs a bit of > rejigging to be able to cope with all the transgenic situations that > happen in the fly. I have made an attribute "engineered". Now we can make cross product terms of engineered features as needed. > > a. not all engineered bits in flies are a gene, but just a sequence, so > we need a couple of new generic terms to accommodate that: > > [Term] > id: SO:NEW > name: engineered_sequence > is_a: SO:0000400 ! sequence_attribute > [Term] id: SO:0000804 name: engineered_region namespace: sequence synonym: "engineered sequence" RELATED [] intersection_of: SO:0000001 ! region intersection_of: has_quality SO:0000783 ! engineered > > [Term] > id: SO:NEW > name: engineered_foreign_sequence > is_a: SO:NEW ! engineered_sequence > [Term] id: SO:0000805 name: engineered_foreign_region namespace: sequence intersection_of: SO:0000001 ! region intersection_of: has_quality SO:0000783 ! engineered intersection_of: has_quality SO:0000784 ! foreign > > b. it also makes sense to delete the following SO term: > > [Term] > id: SO:0000283 > name: engineered_foreign_transposable_element_gene > is_a: SO:0000111 ! transposable_element_gene > is_a: SO:0000280 ! engineered_gene > > since this SO term seems to be combining two separate concepts - > foreign-ness and TE_gene-ness and in general SO tries to get away from > that. > > it can be accommodated by the following two terms: > > engineered_foreign_gene ; SO:0000281 > transposable_element_gene ; SO:0000111 I am not sure if this makes a lot of sense, but I made this term a cross product too. [Term] id: SO:0000283 name: engineered_foreign_transposable_element_gene intersection_of: SO:0000111 ! transposable_element_gene intersection_of: has_quality SO:0000783 ! engineered intersection_of: has_quality SO:0000784 ! foreign > > c. similar to b above, delete the following SO term: > > [Term] > id: SO:0000293 > name: engineered_foreign_repetitive_element > is_a: SO:0000280 ! engineered_gene > is_a: SO:0000292 ! repetitive_element > > > since it can be accommodated by: > > repetitive_element ; SO:0000292 > engineered_foreign_sequence; SO:NEW > And this one... > d. it then makes sense to add an is_a relationship for engineered_gene > ; > SO:0000280 so that it and all its children are under > engineered_sequence > as well as gene_class: > > [Term] > id: SO:0000280 > name: engineered_gene > is_a: SO:NEW ! engineered_sequence > is_a: SO:0000009 ! gene_class Added engineered_gene > [Term] id: SO:0000280 name: engineered_gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000783 ! engineered > > 3. we need one more SO term to be able to accommodate a class of > foreign > sequences that they put in the fly - they have this habit of attaching > epitope/subcellular location "tags" to Drosophila genes and we need a > term for that type of thing: > > [Term] > id: SO:NEW > name: engineered_tag_sequence > def: "Sequence used in transgenes to mark genes or their products. > Includes epitope tags\, sequence tags\, function tags (such as > subcellular localisation sequences\, enzymes)." [FB:gm] > is_a: SO:NEW ! engineered_sequence > Added engineered_tag [Term] id: SO:0000807 name: engineered_tag namespace: sequence intersection_of: SO:0000324 ! tag intersection_of: has_quality SO:0000783 ! engineered > > 4. the following 4 SO terms have been obsoleted, but we have > chromosomal > aberrations of these classes in our files, so need to use the terms. > Could they be resurrected again ? > I have resurrected these terms from the dead and added the definitions you gave me. They have new ids. > [Term] > id: SO:0000437 > name: assortment_derived_duplication > is_obsolete: true > > [Term] > id: SO:0000554 > name: assortment_derived_deficiency_plus_duplication > is_obsolete: true > > > [Term] > id: SO:0000052 > name: assortment_derived_deficiency > synonym: "assortment-derived_deficiency" [] > is_obsolete: true > > > [Term] > id: SO:0000058 > name: assortment_derived_aneuploid > synonym: "assortment-derived_aneuploid" [] > is_obsolete: true > > > > If you could let me know when you have made the changes, or if you > disagree with them (!) that would be great, as I need the new terms (or > some equivalent) before I can start adding SO terms into the FlyBase > files, thanks, > > Gillian |