Release Notes for MO version 1.3.1.1

-Deprecate the following terms:
-PCR_amplicon, ctDNA, mtDNA
-to each term add the following properties:
--add parent class of DeprecatedTerms
--remove old parent of PhysicalBioSequenceType
--add annotation property deprecation_old_parent, value PhysicalBioSequenceType
--add annotation property deprecation_in_version, value 1.2.0
--add annotation property deprecation_reason, value deleted_term
--add annotation property deprecation_replacement_term, value PhysicalBioSequenceType

-consensus_DNA, consensus_mRNA, gene_fragment, predicted_gene, transcript, exemplar_mRNA
-to each term add the following properties:
--add parent class of DeprecatedTerms
--remove old parent of PhysicalBioSequenceType
--add annotation property deprecation_old_parent, value TheoreticalBioSequenceType
--add annotation property deprecation_in_version, value 1.2.0
--add annotation property deprecation_reason, value deleted_term
--add annotation property deprecation_replacement_term, value TheoreticalBioSequenceType

-add restriction "has_measurement", filler "Measurement"
to the class Compound

-add individual:cell_component_comparison_design
--definition:A design in which RNA from different cell components is examined.
--parent term: BiologicalProperty
--unique_identifier: MO_1019

-add class:CellularComponent
--definition: A structure within a cell, such as an anatomical structure (e.g. rough endoplasmic reticulum or nucleus) or a gene product group (e.g. ribosome, proteasome or a protein dimer).
--parent term:BioMaterialCharacteristics
--add restriction has_database, filler CellularComponentDatabase
--unique_identifier: MO_1020
--class_role: abstract
--class_source: ontology

-add class:CellularComponentDatabase
--definition: A resource for terms to describe cellular components, e.g. GO Cellular Component ontology.
--parent term: Database
--unique_identifier:MO_1021
--class_role: concrete
--class_source: ontology

-add individual GeneOntology
--add property: has_machine_readable_URI
--value:http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo
--parent: CellularComponentDatabase
--unique_identifier: MO_1022

-remove Unicode characters from the term french_railway_distance (child of NodeValueType), RMA  (child of DerivedBioAssayType)

-add unique_identifier property to the following terms:
--deleted_term, MO_1023
--flag_filter, MO_1024
--merged_term, MO_1025
--replaced_term, MO_1026
--split_term, MO_1027
--oligosomy, MO_1028
--physiological_process_design, MO_1029
--polysomy, MO_1030
--version_1.1.7, MO_1031
--version_1.1.9, MO_1032
--version_1.2.0, MO_1033
--version_1.3.1, MO_1034

-Add definition to term version_1.3.1

-Add prefix for value of unique_identifier for the term IU

LAST USED IDENTIFIER IN THE FILE: 1034

## Notes for MO 1.3.1 ##

-Removed HTML characters for the definitions for:
--in_vitro_design 
--sampling_time_point

-Removed Unicode characters for the definitions for the terms:
--"RMA" the words "perfect match" are enclosed in a by the UTF-8 symbols U+00D4 and U+00D5  (a pair of capital Os with differing accents).                                                                    

--"french_railway_distance" both occurrences of the word "Paris" are    enclosed in a by the UTF-8 symbols U+00D2 and U+00D3  (again, a pair of  capital Os decorated with different accents).  

-Add Datatype Annotation property called unique_identifier to be added to all classes, properties (within MO namespace) and individuals

-Remove HTML characters from definition for in_vitro_design, MethodologicalDesign

-Remove use of enumerated lists
--DiseaseLocation - change filler of the restriction has_cancer_site from metastatic_site, primary_site to CancerSite which contains the above terms as Individuals
--remove the parent of owl:Thing from metastatic_site, primary_site

--Measurement - change filler of restriction has_measurement_type from absolute, change_biomaterial_characteristics, relative to MeasurementType which contains the above terms as Individuals
--remove the parent of owl:Thing from absolute, change_biomaterial_characteristics, relative

--PathogenTest - change filler for restriction has_result from inconclusive, negative, positive to Result which has the above terms as Individuals
--remove the parent of owl:Thing from inconclusive, negative, positive

--DeprecationReason, remove the parent of owl:Thing from the children of this class, deleted_term, merged_term, replaced_term, split_term

-Update Metadata to indicate that the value for the tag dc:versionInfo is 1.3.1

-Add definition to the object property, has_diameter

-Run script over the file to add the property unique_identifier
LAST USED IDENTIFIER as added by script: 1004 (for programmatic addition of the property and value). See below for the LAST USED IDENITIFIER added to the file.

-Replace MO usage XML Schema datatype thing with string, integer etc. as appropriate.
--BibliographicReference, restrictions:
has_authors - change to some string
has_editor - change to some string
has_issue - change to some string
has_publication - change to some string
has_publisher - change to some string
has_volume - change to some string
has_pages - change to some string
has_year - change to some date

--Contact
has_email - change to some string
has_address - change to some string
has_phone - change to some string
has_fax - change to some string
has_toll_free_phone - change to some string

--Database
has_version - change to some string

--FactorValueDependency 
has_value - change to some string

-FactorValueSet 
has_value - change to some string

-GrowthCondidtion
has_value - change to some string

-IndividualGeneticCharacteristics
has_value - change to some string

-Measurement
has_value - change to some string

-OntologyEntry
has_value - change to some string

-TestResult - Filler is Not owl:Thing, but Measurement, can't have this as a
filler with a Datatype. Apply the property 'has_measurement' with the filler
Measurement to the class TestResult

--Hardware
has_make - change to some string
has_model - change to some string

--Individual
has_ID - Used by multiple classes, check MAGE doc before changing. All classes are class_source=ontology or part of MGEDExtendedOntology: Individual, MGEDCoreOntology, User.  
Property not added back to Individual since it was already inherited.

--OntologyEntry
has_accession - change to some string
has_accession_version - change to some string

--Organization
has_name - change to some string

--Person
has_last_name - change to some string
has_first_name - change to some string
has_mid_initials - change to some string

--Final check for changes in XML Schema Datatype are that they are the same as indicated in the MAGE document. DONE.
-check has_URI -> for BibliographicReference, Contact the filler is a string
in MAGE. Is the class URI left-over from DAML+OIL representation? It is
applied as such to Database, Image and Protocol as well.

- Add synonym property to those terms that contain a synonym in the definition. Format: Class, individual - Synonym(s)
--Sex, hermaphrodite - intersex 
--ExperimentalProtocolType - change_biomaterial_characteristics - change growth condition, change environment (Non-exact synonyms)
--StrandType, reverse - "-"
--MaterialType, syntheticRNA - cRNA, complementary RNA, aRNA, amplified RNA(Non-exact synonyms)
--LightUnit, candela - candle power
--MaterialType, synthetic_DNA - cDNA (Non-exact synonym)
--PhysicalBioSequenceType, ctDNA - chloroplast DNA
--MaterialType, polyA_RNA - polyA+_RNA and mRNA (Non-exact synonym)
--EnvironmentalFactorCategory, light_duration - photoperiod
--SoftwareType, feature_extraction_software - image analysis software, image quantification software
--OtherUnit, kg_per_m2 - kg/m2
--SoftwareType, bioassay_data_transformation_software - normalization software (Non-exact synonym)
--ComplexAction, pool - combine
--InitialTimePoint, coitus - copulation, insemination
--StrandType, forward - "+"
--ComplexAction, split - sample (Non-exact synonym)
--DeprecatedTerms/TheoreticalBioSequenceType, tRNA_gene - transfer RNA gene
--HardwareType, thermal_cycler - thermocycler
--MethodologicalDesign, dye_swap_design - flip dye, dye flip
--AtomicAction, spin - centrifuge
--BioMolecularAnnotation, co-expression_design - guilt by association
--MethodologicalDesign, loop_design - circular design
--ExperimentalProtocolType, feature_extraction - image analysis, image quantification
--BioMolecularAnnotation, binding_site_identification_design - chromatinIP
--TheoreticalBioSequenceType/DeprecatedTerms, rRNA_gene - ribosomal RNA gene
--DeprecatedTerms/TheoreticalBioSequenceType, snRNA_gene - small nuclear RNA gene
--PhysicalBioSequenceType/DeprecatedTerms, cDNA_clone - cDNA, complementary DNA (Non-exact synonyms)
--PhysicalBioSequenceType/DeprecatedTerms, BAC - bacterial artificial chromosome
--ExperimentalProtocolType, linear_amplification - Eberwine procedure (Non-exact synonym)
--SoftwareType, image_acquisition_software - scanning software

=-=-=-=
-deprecate the term 'activity_units_per_ml' (Individual of the class OtherUnit)
--added Individual version_1.3.1 as child of MGEDOntologyVersion
--applied property 'deprecated_from_version', filler 'version_1.3.1', 
--applied property 'has_reason_for_deprecation', filler 'deleted_term'

-update URL for individual CABRI_Human_and_Animal_Cell_lines to http://www.cabri.org/HyperCat/cells/all.htm

=-=-=-=
-add Individual CABRI_HLA_typed_B_Cell_lines as a child of CellLineDatabase
--add the property 'has_human_readable_URI', filler http://www.cabri.org/HyperCat/cells/hla.htm
--add property unique_identifier, value MO_1005


Add definition and url to terms 
-add Individual CABRI_Hybridomas as a child of CellLineDatabase
--add the property 'has_human_readable_URI', filler http://www.cabri.org/HyperCat/cells/hybrid.htm
--add property unique_identifier, value MO_1006


-add Individual CLDB_Human_and_Animal_Cell_Lines as a child of CellLineDatabase
--add the property 'has_human_readable_URI', filler http://www.biotech.ist.unige.it/cldb/indexes.html
--add property unique_identifier, value MO_1007


-add Individual CABRI_Bacteria_and_Archaea_Strains as a child of StrainOrLineDatabase
--add the property 'has_human_readable_URI', filler http://www.cabri.org/HyperCat/bact/all_A.htm
--add property unique_identifier, value MO_1008


-add Individual CABRI_Filamentous_Fungi_Strains as a child of StrainOrLineDatabase
--add the property 'has_human_readable_URI', filler http://www.cabri.org/HyperCat/fun/all_A.htm
--add property unique_identifier, value MO_1009


-add Individual CABRI_Yeasts_Strains as a child of StrainOrLineDatabase
--add the property 'has_human_readable_URI', filler http://www.cabri.org/HyperCat/yeast/all_A.htm
--add property unique_identifier, value MO_1010

-add Individual IU as a child of QuantityUnit
--add property unique_identifier, value MO_1011
--add Datatype Annotation property synonym, value UI
--add Datatype Annotation property synonym, value International Unit

-in response to mail from Kjell on the mged-ontologies list, the use of the one-of construct was removed as the filler for the property 'has_reason_for_deprecation' and replaced with the class 'DeprecationReason' as applied to the class 'DeprecatedTerms'

-leave the filler for the other classes that have the property 'has_reason_for_deprecation' as the individual term that exists as an individual of the class DeprecationReason. Same is true for the filler for the property 'deprecated_from_version'
--change the use of the properties 'has_reason_for_deprecation' and 'deprecated_from_version' from using 'someValues' to 'hasValue' so that the oneOf construct is not used for the classes: ChromosomalAberration, FactorValueDependency, FactorValueSet, IndividualChromosomalAbnormality

=-=-=-=
Implement new Deprecation Policy as stated at:
https://www.cbil.upenn.edu/magewiki/index.php/TermDeprecationPolicy

-add new properties to be used to indicate Deprecated Terms
--deprecation_replacement_term, type:ObjectAnnotationProperty

--deprecation_reason, type: DatatypeAnnotationProperty 

--deprecation_in_version, type:DatatypeAnnotationProperty
Would like to have a better name!!!

--deprecation_old_restriction, type:DatatypeAnnotationProperty

--deprecation_old_parent, type: ObjectAnnotationProperty

--add split_to_term, type:ObjectAnnotationProperty

--add replaced_with_term, type;ObjectAnnotationProperty

Apply to Deprecated Classes
-apply properties to ChromosomalAberration
--need to set Deprecation flag

-apply properties to FactorValueDependency
--need to set Deprecation flag

-apply to FactorValueSet
--need to set Deprecation flag

--apply to IndividualChromosomalAbnormality
-need to set Deprecation flag

Apply to Deprecated Individuals - Do the properties to indicate the Deprecation Status using the old method need to be captured as part of the state using the new method since they are already accounted for using the new method???
--apply to BAC, added deprecation_reason, deprecation_version

--apply to bedding

--apply to behavior_design
---deprecation_in_version,1.1.9; deprecation_reason,split_term; split_to_term, innate_behavior_design; split_to_term, stimulated_design_type; deprecation_old_parent, BiologicalProperty

--apply to behavioral_design_type
---deprecation_in_version,1.1.9; deprecation_reason,replaced_term; replaced_with_term, innate_behavior_design; deprecation_old_parent, PerturbationalDesign

--apply to blood

--apply to cDNA

--apply to chromosome

--apply to circadian_rhythm_design, see properties for Replaced Term (Individual)

--apply to cosmid

--apply to ds_oligo

--apply to EST

--apply to exon

--apply to feces

--apply to gene

--apply to genetic_variation

--apply to Hfr

--apply to infect

--apply to intergenic

--apply to intron

--apply to low_intensity_filter

--apply to mean_and_confidence_indicators

--apply to monosomy

--apply to NCI_Thesaurus

--apply to no
---not able to find values for deprecation_old_parent and deprecation_replacement_term

--apply to operon

--apply to ORF

--apply to PAC

--apply to PCR_primer

--apply to PCR_primer_forward

--apply to PCR_primer_reverse

--apply to plasmid

--apply to polypeptide

--apply to promoter

--apply to rRNA_gene

--apply to signal_log_ratio

--apply to slice_analysis

--apply to snRNA_gene

--apply to ss_oligo

--apply to tau_rank_correlation

--apply to total_intensity_normalization

--apply to trisomy

--apply to tRNA_gene

--apply to vector

--apply to YAC

--apply to yes
---not able to find values for properties deprecation_replacement_term and deprecation_old_parent


LAST USED IDENTIFIER IN THE FILE: 1018