PharmGKB XML Schema Version History

This page contains the change history for the PharmGKB XML schema in reverse chronological order.

Version 4.0 (5/12/2004)

Major non-backwards compatible changes (affects all submitters):

• <sample> should now be used instead of <subject> when reporting genotyping results
• <sampleSet> is now a set of <sample> instead of a set of <subject>
• Renamed <genotypesInSubject> to <genotypesInSample>; it cross-references a <sample> instead of a <subject>
• Removed <pcrResult> under <genotypesInSample> (previously known as <genotypesInSubject>); <sequencingResult> should be used instead
• Moved <referenceSequence> from under <gene> to the top under <pharmgkb>
• The <name> subelement in <feature> is now used to name the feature, as opposed to specifying its type. Use the new <type> subelement instead to provide the same infomation <name> used to provide.
• <firstAllele> and <secondAllele> in <variant> replaced with 1 or more <allele>.

Minor non-backwards compatible changes (never/not commonly used):

• Removed <isAlternativeSplicing> from <featureSet>
• Renamed <namedAlleleSet> to <namedAllele>
• <haplotype> under <gene> is effectively replaced by the new top-level element <haplotypeSet>
• Renamed <pharmacogeneticRelationship> to <literatureAnnotation>
• Replaced <genotypeInSampleSet> with <pooledGenotypes>
• Add support for different types of organisms (human, mouse and rat), which resulted in changes to <organism>

Changes:

• Added <sample>
• Added <studyGroup>
• Added <geneStructure>
• Added <spliceSet>
• Added <rna>
• Added <protein>
• Added <polymorphism>
• Added <haplotypeSet>
• Added the ability to name more elements
• Added the ability to annotate more elements with cross-references via <xref> elements (e.g. in <featureSet> and <feature>)
• Added the ability to annoate elements with ontology terms via <term> elements.
• <experiment> can now cross-reference more than one <sampleSet>

Version 3.3 (6/23/2003)

This release deals with the problems what were introduced in version 3.1 with the addition of the <assay> element and adds more support for haplotypes and named alleles.

• Replaced <assay> with <sequencingAssay> and <genotypingAssay>
• Added <sequencingResult>
• Reverted <genotypingResult> to old behavior and only allow one <variant>.
• Removed many subelements in <subject> that are not used and do not make sense (originally added for dbSTS support).
• Properly escaped "-" in regular expression since Xerces 2.4 complains.
• Added <namedAlleleSet>.
• Extended <haplotype>.

Version 3.2 (5/21/2003)

This release removes two deprecated subelements.

• Removed <sampleSet> in favor of <sampleSetXref> under <experiment>
• Removed <subject> in favor of <subjectXref> under <experiment>

Version 3.1 (4/25/2003)

• Added <pcrSizingAssay> under <experiment>
• Added <assay> under <experiment>
• <genotypingResult> now only allows one <assayXref>
• <genotypingResult> now allows multiple <variant>
• <forwardPrimer> and <reversePrimer> are no longer required within <pcrAssay>
• Added "MutDB" to the list of accepted xref resources
• Renamed <pharmacogeneticKnowledge> to <pharmacogeneticRelationship>
• Added <evidenceLocation> under <pharmacogeneticRelationship>
• Added <phenotypeDataset> under <pharmgkb> (this is brand new and has not been nailed down yet)
• A lot more documentation and clarifications