3/12/04 Fixed date: JMarch -> March 4/4/04 -> 1.1.8 1. Corrected measurement type: fixed definition to "class to hold instances used a\ s the filler for the property has_measurement_type". 2. Corrected ProtocolType instances: moved instances to ExperimentalProtocolType 3. Changed the biomaterial_provider definition: A descriptor used to describe a ro\ le or factor value for the person or organization that provides a BioMaterial. 4. Added has_disease_location(DiseaseLocation) to DiseaseState 5. Fixed definition of compound_based_treatment: Now reads "...defined chemical or\ biological compound." 6. Deprecated genetic_variation. Was an instance of BioMaterialCharacteristicsCate\ gory but GeneticVariation is no longer a subclass of BioMaterialCharacteristics. 9/6/04 -> 1.1.9 Process of Generating Core1.1.9 Download MGEDOntology Core1.1.8 form MGED Ontology site It was decided to only include the VOW9 information in this version. List of things changed: -Genotype: Add new definition. The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromsomal, plasmid, viral orother genetic material which has been introduced into the organism either prior to or during the experiment. -IndividualGeneticCharacteristic def: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. -Add chromosomal_substitution as an instanceOf GeneticModification def: A state/condition describing a cell, or organism, in which all, or part, of a chromosome from a donor replaces that of the recipient. Examples include strains created by repeated backcrossing as well as those created by recombinant methods. QUESTION: Is this still distinct from gene_knock_in? -Add oligosomy as an instanceOf ChromosomalAbberationClassification def: A state/condition describing a cell or organism that has fewer normal chromosomes, than the usual complement. -Add polysomy as an instanceOf ChromosomalAbberationClassification A state/condition describing a cell or organism that has one or more normal chromosomes, in excess of the usual complement. -Deprecate monosomy by adding the properties deprecated_from_version, filler: version_1.1.9; was_replaced_by, filler: oligosomy; reason_for_deprecation, filler: replaced_term, add as instanceOf DeprecatedTerms -Deprecate trisomy by adding the properties deprecated_from_version, filler: version_1.1.9; was_replaced_by, filler: polysomy; reason_for_deprecation, filler: replaced_term, add as instanceOf DeprecatedTerms -Modifiy definition for GeneticModification: A genetic modification synthetically introduced into the organism from which the biomaterial was derived. Examples of genetic moodification include specification of a transgene, the creation of point mutations by mutagenesis, or knock out of gene function. -Modify definition for gene_knock_out: The modification of an organism that renders a gene non-functional e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods. -Modify definition for gene_knock_in: A modification whereby a functional gene, or a functional part of a gene, is inserted into an organism', e.g. by recombination, P-element insertion. -Modify the definition of class OrganismPart and individual organism_part: The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood- or body location (arm). -Modify definition of BioSourceType The form in which the BioMaterial was obtained/maintained e.g. frozen, fresh etc. Note can be used to describe BioSamples as well as BioSources. -Deprecate individual blood by adding properties deprecated_from_version, filler: version_1.1.9; reason_for_deprecation, filler: deleted_term, add as instanceOf DeprecatedTerms -Deprecate individual feces by adding properties deprecated_from_version, filler: version_1.1.9; reason_for_deprecation, filler: deleted_term, add as instanceOf DeprecatedTerms -Move biopsy to be an instance of ComplexAction -Add fresh_sample as an instanceOf BioSourceType def: A sample freshly obtained from the organism(s). E.g. a liver freshly removed from a rat. -Add freeze_dried_sample as an instanceOf BioSourceType def: A biomaterial that has been lyophilized or dried by freezing under a vacuum. -Add term innate_behavior_design as an instannceOf BiologicalProperty def: The specific actions or reactions of an organism in response to external or internal stimuli. Patterned activity of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions. -Add stimulated_design_type as an instanceOf PertubationalDesign def: A design type in which some behavior(s) of an organism is studied. The behavior can be innate, such as path finding in bees. -Deprecate behavior_design by adding restriction deprecated_from_version, version_1.1.9; reason_for_deprecation, filler: split_term; add as an instanceOf DeprecatedTerms !!Induviduals can not have multiple individuals as filler for property to show what terms it was split into -Deprecate behavior_design_type by adding restriction deprecated_from_version, filler version_1.1.9; reason_for_deprecation, filler: replaced_term; was_replaced_by, filler innate_behavior_design; add an an instanceOf DeprecatedTerms -Add germination as an instanceOf InitialTimePoint def: The physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth (from the GO). -Add fertilization as an instanceOf InitialTimePoint def: The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. (from the GO) !!Overlap with coitus? -Add sowing as an instanceOf InitialTimePoint def: The process of placing a seed or spore in some media with the intention to invoke germination. -Modify definition of planting, instanceOf InitialTimePoint def: The act of placing a plant in media (e.g. soil) to allow it to grow. This excludes sowing. -Add restriction has_species, filler Organism to StrainOrLine -Add temperature as an instanceOf EnvironmentalFactorCategory def: temperature associated with a particular environment -Add properties has_volume, has_length, has_diameter NOTE: has_volume (BibliographicReference) EXISTS!!! Therefore, NOT added yet -Add restrictions has_volume, has_length, has_diameter with filler Measurement for all to BioMetrics -Add term kg_per_m2, instanceOf OtherUnit -Modify definition of Test def: An assay performed on a biomaterial for the purposes of determining one or more biomaterial characteristics e.g. clinical chemistry. QUESTION: Request to make Test a subclassOf OntologyEntry -Fix typo, clone_of_unknown_source -Modify definition, clone_of_unknown_source, instanceOfPhysicalBioSequenceType def: Sequence from some nucleic acid copy and the associated vector for which the source clone supplier is unknown. -Add NASC as instanceOf StrainOrLineDatabase def: The Nottingham Arabidopsis Stock Centre (NASC). Provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. -Add http://arabidopsis.info/catalogue.html as an instanceOf URI -Add restriction has_human_reabable_URI to NASC, filler http://arabidopsis.info/catalogue.html to individual NASC -Add mating_type_h_plus and mating_type_h_minus as instanceOf Sex, def: Mating type of S.pombe. SUGGESTION: add instance mating_type, add restriction has_species, filler Organism, has_mating_type_name, filler string This could serve a generic mechanism to capture any mating type. However, is this something one would want to query on - Yes, probably so this would still lead to free text annotation of something queriable. -Add imprinting_design as an instanceOf BiologicalProperty def: An experiment design type where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared. -Add ChEBI as an instanceOf CompoundDatabase def: A freely available dictionary of small molecular entities. The term molecular entity encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms. -Add http://www.ebi.ac.uk/chebi as an instanceOf URI -Add restriction has_human_readable_URI, filler http://www.ebi.ac.uk/chebi to individual ChEBI -Add dye_swap_replicate as an instanceOf ReplicateDescriptionType def: One of a pair of replicate assays in which LabeledExtracts derived from the same BioMaterial used for both assays (e.g., a hybridization or a 2-D gel run) differ only in that the dyes used for labeling have been reversed, e.g., assay 1: A-Cy3 vs. B-Cy5 , and assay 2: A-Cy5 vs. B-Cy3. The purpose of using dye-swap replicate pairs is to assess or remove dye-specific biases from the combined experimental results. -Spellcheck copy of MGEDOntology using Word -Classify ontology using DIG and commit results ===================== PENDING ACTION ITEMS -percent_count, instanceOf ConcentrationUnitOther -> Helen C will provide definition -has_purity, add as restriction to TargetedCellType, filler ??? (thing or integer) -> Chris S will send definition of property -provide link on MO web site to NIST -> Helen P will send url and either Helen P, Trish or Chris will modify MO web site to add link -definitions for new properties for BioMetrics; has_volume, has_length, has_diameter -kg_per_m2 -> Helen C will provide definition -terms for tumor shpaes -> Liju will look into this PATO reference: http://obo.sourceforge.net/pheno/pheno.html -possibility of publishing MO paper in Nature Biotech, Action item for Helen P to discuss with Chris Gunter -migrate MO to Protege/OWL, Action item for Trish -Chris T. experiment designs in Proteomics look at organelles, may need additional terms -new Units, Action item Laurance ===================== UNDER DISCUSSION: -condition_specificity, instanceOf HigherLevelAnalysisProtocolType, Action item for Chris, Trish and Elisabetta -Transfection - what was the outcome with this definition? -biofilm, Helen P will discuss with NERC and possibly RBSI folks -terms and classes for DataTransformationProtocolType proposed/modifiied by Elisabetta, Trish, Joe, Helen C and Chris T Will discuss at MGED7. -Array CGH, Action item for Mervi and Greg Grant -environmental_design -> Helen P will send to NERC folks to review Will discuss at MGED7 (?) -discuss various modelling strategies (e.g. use of views, use of synonyms) of MO in Protege/OWL, Action item Trish, Liju, Gilberto and others ===================== POSTPONED ITEMS -"percent" as an some type of Unit, needed in order for unit for quantification parameters such as laser power, gain, percent_foreground Requested by TW -term to describe purpose/application of array Requested by PRS -mechanism to point to image metadata for Histology needs Requested by SS HP, JW, TW Proposal - add has_image, has_uri (should be Datatype Property) to Histology. Follow-up in email as this is needed in this version.