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Accessing Data via the Biomart
dazoakley edited this page Jul 13, 2011
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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…
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 |
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 |