Hi Julian,
Futhermore, For URL linking jsut as Ensembl does with BioMart, you can
use the format exaplained and examples below. By default it supports
HTML format only.
====== URL BASED QUERY FORMAT
?VIRTUALSCHEMANAME=<VSName>
&ATTRIBUTES=<datasetInternalName>.<Interface>.<AttributePageInternalName>.<AtrributeInternalName>."<OPTIONAL:
comma separated list of values-this deals with attributeFilters such upstream
downstream Sequence Flanks>"
&FILTERS=<datasetInternalName>.<Interface>.<FilterPageInternalName>.<FilterInternalName>."<comma
separated list of values-this deals with attributeFilters such upstream
downstream Sequence Flanks>"
====== NOTES
- All params must be supplied unless they are OPTIONAL.
- &FILTERS: is OPTIONAL
- When using FilterInternalName for Container type filters
e.g DropDownMenu with Only/exculded choice [ENSEMBL HUMAN ID LIST
FILTERS]
OR DropDownMenu with TEXTField for values [ENSEMBL HUMAN ID list
limit]
the FilterInternalName should be the internalName of option in dropdown
and
value in double quotes would be internal name only/excluded OR any
value
should you wish to appear in text field. This is just as in XML based
queries.
- incase you don't have a virtualSchema in registry, then use default
- incase yow don't have any interface for a dataset, use default
======= EXAMPLES
?VIRTUALSCHEMANAME=default&ATTRIBUTES=msd.default.feature_page.pdb_id&FILTERS=msd.default.filters.experiment_type."Electron
diffraction,Electron microscopy"
?VIRTUALSCHEMANAME=default&ATTRIBUTES=msd.default.feature_page.pdb_id|
msd.default.feature_page.experiment_type|
msd.default.feature_page.assembly_code&FILTERS=msd.default.filters.experiment_type."Electron
diffraction,Electron microscopy"
?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.strand|hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id&FILTERS=hsapiens_gene_ensembl.default.filters.chromosome_name."4"
?VIRTUALSCHEMANAME=default&ATTRIBUTES=mmusculus_gene_ensembl.default.feature_page.strand|mmusculus_gene_ensembl.default.feature_page.ensembl_gene_id&FILTERS=mmusculus_gene_ensembl.default.filters.chromosome_name."Y"
?VIRTUALSCHEMANAME=default&ATTRIBUTES=msd.default.feature_page.assembly_code|hsapiens_gene_ensembl.default.structure.biotype|msd.default.feature_page.pdb_id|hsapiens_gene_ensembl.default.structure.exon_stable_id|hsapiens_gene_ensembl.default.structure.gene_stable_id|msd.default.feature_page.experiment_type&FILTERS=msd.default.filters.experiment_type."Electron
diffraction,Electron microscopy"
?VIRTUALSCHEMANAME=default&ATTRIBUTES=msd.default.feature_page.assembly_code|hsapiens_gene_ensembl.default.feature_page.strand|msd.default.feature_page.pdb_id|hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id|msd.default.feature_page.experiment_type&FILTERS=msd.default.filters.experiment_type."Electron
diffraction,Electron
microscopy"|hsapiens_gene_ensembl.default.filters.chromosome_name."4"
------------- with AttributeFilters Upstream downstream flanks
?VIRTUALSCHEMANAME=default&ATTRIBUTES=msd.default.feature_page.assembly_code|hsapiens_gene_ensembl.default.sequences.gene_flank|hsapiens_gene_ensembl.default.sequences.upstream_flank."140"|msd.default.feature_page.pdb_id|hsapiens_gene_ensembl.default.sequences.biotype|hsapiens_gene_ensembl.default.sequences.gene_stable_id|msd.default.feature_page.experiment_type
?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.sequences.gene_flank|msd.default.feature_page.assembly_code|hsapiens_gene_ensembl.default.sequences.upstream_flank."140"|msd.default.feature_page.pdb_id|hsapiens_gene_ensembl.default.sequences.biotype|hsapiens_gene_ensembl.default.sequences.gene_stable_id|msd.default.feature_page.experiment_type&FILTERS=hsapiens_gene_ensembl.default.filters.chromosome_name."4"
?VIRTUALSCHEMANAME=default&ATTRIBUTES=msd.default.feature_page.assembly_code|hsapiens_gene_ensembl.default.sequences.cdna|hsapiens_gene_ensembl.default.sequences.exon_stable_id|hsapiens_gene_ensembl.default.sequences.gene_stable_id
------------- with peptide
?VIRTUALSCHEMANAME=default&ATTRIBUTES=msd.default.feature_page.assembly_code|hsapiens_gene_ensembl.default.sequences.peptide|msd.default.feature_page.pdb_id|hsapiens_gene_ensembl.default.sequences.exon_stable_id|hsapiens_gene_ensembl.default.sequences.gene_stable_id
Queries with CONTAINER TYPE FILTERS filter
?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.strand|hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id&FILTERS=hsapiens_gene_ensembl.default.filters.with_ccds."only"
?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.strand|hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id&FILTERS=hsapiens_gene_ensembl.default.filters.with_ipi."only"
?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.strand|hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id&FILTERS=hsapiens_gene_ensembl.default.filters.with_ipi."excluded"|hsapiens_gene_ensembl.default.filters.chromosome_name."4"
?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.strand|hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id&FILTERS=hsapiens_gene_ensembl.default.filters.biotype."miRNA,Mt_rRNA"
?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.strand|hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id&FILTERS=hsapiens_gene_ensembl.default.filters.band_start."p36.33"|hsapiens_gene_ensembl.default.filters.band_end."p31.3"
?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.strand|hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id&FILTERS=hsapiens_gene_ensembl.default.filters.encode_region."16:1:500000"
?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.strand|hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id
?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.strand|hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id&FILTERS=hsapiens_gene_ensembl.default.filters.chromosome_name."Y"
?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.strand|hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id&FILTERS=hsapiens_gene_ensembl.default.filters.start."4000"
?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.strand|hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id&FILTERS=hsapiens_gene_ensembl.default.filters.chromosome_name."4"
?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.strand|hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id&FILTERS=hsapiens_gene_ensembl.default.filters.pathology_term."neoplasia"
?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.strand|hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id&FILTERS=hsapiens_gene_ensembl.default.filters.pathology_term."neoplasia"|hsapiens_gene_ensembl.default.filters.chromosome_name."4"
?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.strand|hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id|msd.default.feature_page.assembly_code&FILTERS=hsapiens_gene_ensembl.default.filters.chromosome_name."4"|msd.default.filters.has_cath."only"
?VIRTUALSCHEMANAME=default&ATTRIBUTES=msd.default.feature_page.assembly_code|hsapiens_gene_ensembl.default.feature_page.strand|hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id&FILTERS=hsapiens_gene_ensembl.default.filters.chromosome_name."4"|msd.default.filters.has_cath."only"
Feel free to write back if you need further assistance.
Kind Regards
Syed
On Mon, 2007-03-12 at 09:56 +0000, Arek Kasprzyk wrote:
> On 12 Mar 2007, at 03:48, Julian Catchen wrote:
>
> > Hello,
> >
> > Does anyone have any example XML queries they are using to poll the
> > Ensembl biomart interface? I have gotten some simple examples working
> > that pull down lists of ensembl IDs by using examples from the
> > documentation. However, I can't seem to find any examples of how to
> > query for FASTA formatted cDNA sequences or translations. Also, I
> > can't find any documentation of how to request gzipped data.
> >
>
> Hi Julian,
> please go to www.biomart.org/biomart/martview, create your favourite
> query using MView and click
> XML button. This will give you the exact xml format required for your
> web service query. In principle anything
> that you can do with MView you should be also able to do with
> webservice XML. If not, that we need
> to fix it.
>
> In order to invoke a formatter you simply need to add
> 'formatter="FASTA' to your xml query.
>
> For example the below query will give you peptides from chromosome 22
> in FASTA format:
>
>
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE Query>
> <Query virtualSchemaName = "default" Header = "1" count = ""
> softwareVersion = "0.5" formatter="FASTA" >
>
> <Dataset name = "hsapiens_gene_ensembl" interface = "default" >
> <Attribute name = "peptide" />
> <Attribute name = "str_chrom_name" />
> <Attribute name = "gene_stable_id" />
> <Attribute name = "biotype" />
> <Filter name = "chromosome_name" value = "22"/>
> </Dataset>
> </Query>
>
>
>
> you can run this query using the webExample.pl script:
>
>
> http://cvs.sanger.ac.uk/cgi-bin/viewcvs.cgi/biomart-perl/scripts/
> webExample.pl?view=markup
>
>
>
>
> > I used to have all of these automated through simple URL GET queries
> > that no longer seem to work with Ensembl post version 41.
> >
>
> URL GET query still work but the format has changed. We have not yet
> documented it properly.
>
> I am cc-ing your email to mart-dev so someone from there will send you
> a few examples
>
> hope that helps,
> a.
>
>
> > Any pointers to examples or documentation for XML queries would be
> > appreciated.
> >
> > Thanks,
> >
> > julian
> >
>
>
> ------------------------------------------------------------------------
> -------
> Arek Kasprzyk
> EMBL-European Bioinformatics Institute.
> Wellcome Trust Genome Campus, Hinxton,
> Cambridge CB10 1SD, UK.
> Tel: +44-(0)1223-494606
> Fax: +44-(0)1223-494468
> ------------------------------------------------------------------------
> -------
>
>
--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
