[InterMine Dev] Questions on keys and merging

JD Wong jdmswong at gmail.com
Fri Jun 29 19:11:21 BST 2012


Hi dev,

I have a few questions:

I notice that in some source key properties
files (bio/sources/<sourcename>/resources/<sourcename>_keys.properties),
properties are defined differently.  For example:

*ensembl_keys.properties*
Organism.key=taxonId
DataSet.key=name
DataSource.key=name
Gene.key=primaryIdentifier
...

*fasta_keys.properties*
Gene.key_primaryidentifier = primaryIdentifier
OntologyTerm.key_name_ontology=name,ontology
Ontology.key_title=name
Organism.key_taxonid = taxonId
Protein.key_primaryidentifier = primaryIdentifier
...

For the sake of understanding I want to make sure I know what's going on
here.  Both these files are defining named indexes for merging the data
types in their respective sources.  If both sources are included, then
multiple redundant indexes will be created for a bunch of data classes
including gene, organism, etc.
In addition, OntologyTerm.key_name_ontology=name,ontology defines a
compound key for ontologyTerm consisting of the combined values of the name
and ontology fields for a record.





Also since it doesn't look like any sources are using the old outdated
method ofdefining keys in a central file described in
http://www.intermine.org/wiki/PrimaryKeys,
does <mine>/dbmodel/resources/genomic_keyDefs.properties do anything
anymore.  Is it still needed? (outside of legacy support)


Have a good weekend!
-JD
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