Last modified 20 months ago
Last modified on 30/09/10 16:21:02
Core Model Changes
Below is a summary of the changes made to the data model in InterMine 0.94.
Deleted
- Analysis
- AnalysisResult
- BioEntity
- curated
- relations
- BioProperty
- Chromosome
- genes
- exons
- features
- Clone
- Comment.source
- ComputationalAnalysis
- ComputationalResult
- Contig
- CpIsland
- CrossGenomeMatch
- DistanceRelation
- Evidence
- Experiment
- ExperimentalResult
- ExperimentSubmission
- GenePart
- GenomeRegion
- InfoSource
- Location
- phase
- endPhase
- endIsPartial
- startIsPartial
- Organism.abbreviation
- OverlapRelation
- PartialLocation
- RankedRelation
- Relation
- Scaffold
- SimpleRelation
- SuperContig
- SymmetricalRelation
- SyntenicRegion
- Synonym.type, Synonym.isPrimary
- TFBSCluster
- Transcript.exonCount / MRNA.exonCount
Renamed
| old name | new name |
| Annotation | OntologyAnnotation |
| BioEntity.annotations | BioEntity.ontologyAnnotations |
| BioEntity.evidence | BioEntity.dataSets |
| BioEntity.subjects | BioEntity.locatedFeatures |
| BioEntity.objects | BioEntity.locations |
| BlastMatch.object | |
| BlastMatch.subject | |
| DataSet.title | DataSet.name |
| ESTCluster | OverlappingESTSet |
| EST.ESTClusters | EST.overlappingESTSets |
| InteractionExperiment.interactionDetectionMethod | InteractionExperiment.interactionDetectionMethods |
| LocatedSequenceFeature | SequenceFeature |
| Location.object | Location.locatedOn |
| Location.subject | Location.feature |
| MicroarrayOligo | MicroArrayOligo |
| Ontology.title | name |
Remodeled
- OntologyTerm.dataSets
- OntologyTerm doesn't extend BioProperty any more
- MicroArrayExperiment.publication
- Experiment object removed
- SequenceFeature.symbol to BioEntity
- SequenceFeature.featureType to SequenceFeature.sequenceOntologyTerm
- mRNA is a subclass of Transcript
New
- Organism.commonName
- CrossReference
- Added Sequence Ontology source
FlyMine-specific
| FlyMine | SO | status |
| Amplicon | pcr_product | change class name |
| Deletion | chromosomal_deletion | change class name (should be done already!) |
| Motif | dna_motif | keep class name, use SO term |
| NuclearDNA | nuclear_sequence | delete |
| TFModule | CRM | change class name (should be done already!) |
| Transposition | chromosomal_transposition | change class name |
| Vector | vector_replicon | delete |
Other changes
| old | new |
| Allele.annotations | Allele.phenotypeAnnotation |
| ArtificialDeletion | ChromosomalDeletion |
| CDS.polypeptides | proteins |
| FlyAtlasResult.source | dataSets |
| Gene.chromosomeLocation | locations |
