Notes To Document Changes in MGEDOntology version 1.1.4 Additions: - pcr_amplification -> instance of ProtocolType def - The procedure of amplifying specific nucleic acids in vitro. - labeling_and_amplification From Helen - protocols have only 1 type, and we are getting information on both of these -- EXPLAIN - sample_treatment - request for generic treatment Question - is this what specified_biomaterial_action is for? - hatching - added as instance of IntitialTimePoint def - NONE - eclosion - added as instance of InitialTimePoint def - NONE - unknown_substrate_type -> instance of SubstrateType def - SubstrateType of unknown type. - unknown_surface_type -> instance of SurfaceType def - SurfaceType of unknown type. - unknown_protocol_type -> instance of ProtocolType def - ProtocolType of unknown type. - unknown_experiment_design_type -> instance of ExperimentDesignType (added as an instance to all subclasses of ExperimentDesignType). def - ExperimentDesignType of unknown type. - MatingType -> subclass of Sex def - NONE - mating_type_a -> instance of MatingType - mating_type_alpha -> instance of MatingType Question - are mixed_mating_type and unknown_mating_type appropriate - F+, F- and Hfr -> instances of MatingType - optimization_design -> instance of MethodologicalDesign def - An optimization experiment design type is where different protocols or protocol parameters are compared. - ad libitum - removed space in name - specified_biomaterial_action -> remove as instance of Action and make it an instance of AtomicAction and ComplexAction? - remove organism_part, genetic_variation, and sex as instances of BiologicalFactorCategory - add extract and not-extract as instances of BioSampleType - ZoneDefect - added property has_type DefectType - ReplicateDescriptionType -- biological_replicate - added as instance of ReplicateDescriptionType def - A replicate that consists of independent biological replicates made from different individual biosources. -- technical_replicate - added as instance of ReplicateDescriptionType def - A replicate where the same biomaterial is used (e.g as in a dye_swap_design). - QualityControlDescriptionType -- dye_swap_quality_control - added instance def - NONE -- peer_review_quality_control - added instance def - NONE -- spike_quality_control - added instance def - NONE Moved the following: non_targeted_transgenic_variation_design -> PertubationalDesign FactorValueSet -> ExperimentPackage Modifications: - snRNA -> snRNA_gene - reference_design -> remove MethodologicalFactorCategory as class that this instance belongs to, therefore instance of only class MethodologicalDesign