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Accessing Data via the Biomart

dazoakley edited this page Jul 13, 2011 · 3 revisions

The purpose of this page is to give a very brief overview of how you can use the webservices in the IKMC Biomart to gain programatic access to the data contained within iMits.

There are two ways of interacting with a biomart via webservices: the XML api or SOAP, the basic information about these services can be found here.

Alternatively, there is a Perl API (shipped with the biomart codebase itself) or a Ruby API (documentation) that you can use to gain easy access to the data.

All you need to know now is what Filters and Attributes are available…

Available Filters and Attributes

Filters

Name Display Name
blastocyst_strain Blastocyst Strain
colony_background_strain Colony Background Strain
colony_prefix Colony Prefix
distribution_centre Distribution Centre
escell_clone Escell clone
marker_symbol Marker Symbol
mgi_accession_id MGI Accession ID
microinjection_status Micro-Injection Status
pipeline Pipeline
production_centre Production Centre
qc_five_prime_cassette_integrity 5’ Cassette Integrity
qc_five_prime_lr_pcr 5’ LR-PCR
qc_homozygous_loa_sr_pcr Homozygous Loss of WT Allele (LOA) SR-PCR
qc_lacz_sr_pcr lacZ SR-PCR
qc_loa_qpcr Loss of WT Allele (LOA) qPCR
qc_loxp_confirmation LoxP Confirmation
qc_mutant_specific_sr_pcr Mutant Specific SR-PCR
qc_neo_count_qpcr Neo Count (qPCR)
qc_neo_sr_pcr Neo SR-PCR
qc_southern_blot Southern Blot
qc_three_prime_lr_pcr 3’ LR-PCR
qc_tv_backbone_assay Targeting Vector Backbone Assay
test_cross_strain Test Cross Strain

Attributes

Name Display Name
allele_symbol_superscript Allele Symbol Superscript
blastocyst_strain Blastocyst Strain
colony_background_strain Colony Background Strain
colony_prefix Colony Prefix
deposited_material Deposited Material
distribution_centre Distribution Centre
emma Suitable for EMMA?
escell_clone ES Cell Clone
is_active Microinjection Active?
marker_symbol Marker Symbol
mgi_accession_id MGI Accession ID
microinjection_date Microinjection date
microinjection_status Microinjection Status
mouse_allele_symbol_superscript Mouse Allele Symbol Superscript
pipeline Pipeline
production_centre Production Centre
qc_five_prime_cassette_integrity 5’ Cassette Integrity
qc_five_prime_lr_pcr 5’ LR-PCR
qc_homozygous_loa_sr_pcr Homozygous Loss of WT Allele (LOA) SR-PCR
qc_lacz_sr_pcr lacZ SR-PCR
qc_loa_qpcr Loss of WT Allele (LOA) qPCR
qc_loxp_confirmation LoxP Confirmation
qc_mutant_specific_sr_pcr Mutant Specific SR-PCR
qc_neo_count_qpcr Neo Count (qPCR)
qc_neo_sr_pcr Neo SR-PCR
qc_southern_blot Southern Blot
qc_three_prime_lr_pcr 3’ LR-PCR
qc_tv_backbone_assay Targeting Vector Backbone Assay
test_cross_strain Test Cross Strain