[SO-devel] changes regarding reagents and TE's

[Karen E. <ei...@fr...>]

Flybase (via Lynn) requested some new terms to deal with reagents and 
TE's.

Changes to reagent and TEs:

1.	Redundancy with clones and vectors. Previously a vector was part of 
a clone and each type of clone had a vector. There were many types of 
clone, based on the vector and the kind of insert.
I have cleaned this up so that a clone has 2 parts, a vector and an 
insert. There are a couple of subtypes of clone, and so via their is_a 
relationship, they also have the 2 parts, but this relationship is not 
explicit.

2. 	They requested a way to deal with natural and engineered 
Transposble elements.   We had sub typed them based on transmission 
intermediate (DNA or RNA) Either of these kinds of TE could in theory 
be (natural, engineered, transgenic, or foreign)
I have added engineered, foreign, natural, and transgenic as attributes 
of a regions. These are labeled like the adjectives you would describe 
the TE with. Made cross product terms:

[Term]
id: SO:0000798
name: engineered_transposable_element
namespace: sequence
def: "TE that has been modified by manipulations in vitro." [SO:mc]
intersection_of: SO:0000101 ! transposable_element
intersection_of: has_quality SO:0000783 ! engineered

[Term]
id: SO:0000797
name: natural_transposable_element
namespace: sequence
def: "TE that exists (or existed) in nature." [SO:mc]
intersection_of: SO:0000101 ! transposable_element
intersection_of: has_quality SO:0000782 ! natural

[Term]
id: SO:0000799
name: engineered_foreign_transposable_element
namespace: sequence
intersection_of: SO:0000101 ! transposable_element
intersection_of: has_quality SO:0000783 ! engineered
intersection_of: has_quality SO:0000784 ! foreign

[Term]
id: SO:0000720
name: foreign_transposable_element
comment: requested by Michael on 19 Nov 2004
intersection_of: SO:0000101 ! transposable_element
intersection_of: has_quality SO:0000784 ! foreign

[Term]
id: SO:0000796
name: transgenic_transposable_element
namespace: sequence
def: "TE that has been modified in vitro, including insertion of  DNA 
derived from a source other than the originating TE." [SO:mc]
intersection_of: SO:0000101 ! transposable_element
intersection_of: has_quality SO:0000781 ! transgenic


3.	Added engineered_episome
[Term]
id: SO:0000779
name: engineered_episome
comment: Requested by Lynn Crosby Jan 2006
intersection_of: SO:0000768 ! episome
intersection_of: has_quality SO:0000783 ! engineered


4.	Cloned_DNA_segment.  cloned_region, (has synonym cloned segment) is 
part_of a clone insert and also isa reagent. I have added  
clone_attribute has children validated and invalidated

[Term]
id: SO:0000789
name: validated
synonym: "validated_clone" RELATED []
is_a: SO:0000787 ! clone_attribute

[Term]
id: SO:0000790
name: invalidated
synonym: "invalidated_clone" RELATED []
is_a: SO:0000787 ! clone_attribute

[Term]
id: SO:0000808
name: validated_cDNA_clone
namespace: sequence
intersection_of: SO:0000151 ! clone
intersection_of: SO:0000317 ! cDNA_clone
intersection_of: has_quality SO:0000789 ! validated

[Term]
id: SO:0000809
name: invalidated_cDNA_clone
namespace: sequence
intersection_of: SO:0000317 ! cDNA_clone
intersection_of: has_quality SO:0000790 ! invalidated

[Term]
id: SO:0000810
name: chimeric_cDNA_clone
namespace: sequence
intersection_of: SO:0000809 ! invalidated_cDNA_clone
intersection_of: has_quality SO:0000362 ! invalidated_by_chimeric_cDNA

[Term]
id: SO:0000811
name: genomically_contaminated_cDNA_clone
namespace: sequence
intersection_of: SO:0000809 ! invalidated_cDNA_clone
intersection_of: has_quality SO:0000414 ! 
invalidated_by_genomic_contamination

[Term]
id: SO:0000812
name: polyA_primed_cDNA_clone
namespace: sequence
intersection_of: SO:0000809 ! invalidated_cDNA_clone
intersection_of: has_quality SO:0000415 ! 
invalidated_by_genomic_polyA_primed_cDNA

[Term]
id: SO:0000813
name: partially_processed_cDNA_clone
namespace: sequence
intersection_of: SO:0000809 ! invalidated_cDNA_clone
intersection_of: has_quality SO:0000416 ! 
invalidated_by_partial_processing

[Term]
id: SO:0000785
name: cloned_region
comment: Added in response to Lynn Crosby. A clone insert may be 
composed of many cloned regions.
synonym: "cloned segment" RELATED []
is_a: SO:0000695 ! reagent
relationship: part_of SO:0000753 ! clone_insert


5.	Rescue
Rescue has been added as an attribute of a feature and several cross 
product terms added for things commonly used to rescue. At the most 
general level a rescue_region is a length of sequence used to rescue. 
More specifically rescue_gene, rescue_minigene and 
engineered_rescue_region. minigene was added as a child of 
open_reading_frame
[Term]
id: SO:0000794
name: engineered_rescue_region
synonym: "engineered rescue fragment" RELATED []
synonym: "engineered rescue segment" RELATED []
intersection_of: SO:0000411 ! rescue_region
intersection_of: has_quality SO:0000783 ! engineered

[Term]
id: SO:0000795
name: rescue_mini_gene
synonym: "rescue mini-gene" RELATED []
is_a: SO:0000411 ! rescue_region
intersection_of: SO:0000815 ! mini_gene
intersection_of: has_quality SO:0000814 ! rescue

[Term]
id: SO:0000814
name: rescue
namespace: sequence
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000816
name: rescue_gene
namespace: sequence
is_a: SO:0000411 ! rescue_region
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000814 ! rescue

[Term]
id: SO:0000411
name: rescue_region
synonym: "rescue fragment" RELATED []
synonym: "rescue segment" RELATED []
is_a: SO:0000695 ! reagent
intersection_of: SO:0000001 ! region
intersection_of: has_quality SO:0000814 ! rescue


6.	Clone_library was suggested as an attribute of a feature. This has 
not been added to SO at this time

7.	cDNA moved from a locatable_sequence_feature  to polymer_type