On Mon, 2007-04-02 at 10:16 +0100, Richard Holland wrote:
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Hi
> I believe that the only way to do this at present is to construct a GET
> request URL string, exactly like the mart links on the left panel of
> Ensembl's ComparaView. This supports only a limited range of functions,
> e.g. only a single dataset can be queried at once.
It supports 2 dataset queries as well, and supports most of the
functions (any possible combination of attributes and datasets), yes,
you cannot specify the formatter. However, I am not sure how this could
be useful in your case. Kindly have a look at the following file David,
might help you in making URL links. Any further assistance, please do
write.
You can try the examples against the www.biomart.org.
Kind Regards
Syed
>
> The ability to use Mart XML as an access path into MartView is something
> that has cropped up before, but I'm not sure if we ever implemented it.
>
> Syed or Arek will be able to tell you for sure.
>
> cheers,
> Richard
>
> David Croft wrote:
> > Hi,
> >
> > I just had a slapping my hand on my forhead and saying duh moment.
> >
> > It occurred to me that, instead of feeding the results of a martservice
> > query to some kind of HTML results page, I could, theoretically, send
> > it to a regular martview page. That would give me the full flexibility
> > of BioMart, plus a standardized GUI that I already know how to
> > use.
> >
> > I'm guessing that what I would need to do is to set some hidden
> > parameters and then do a POST. In fact, thinking about it, maybe
> > I wouldn't even need the martservice call at all, if I can send the query
> > directly to a martview page and tell it to run the query.
> >
> > What do the experts think?
> >
> > Cheers,
> >
> > David.
> >
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--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
====== 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, the 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"
=========== EXCEPTIONS TESTING - delibrate breaking
?ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.strand|hsapiens_gene_ensembl3.default.feature_page.ensembl_gene_id|hsapiens_gene_ensembl2.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_ensembl3.default.feature_page.ensembl_gene_id|hsapiens_gene_ensembl2.default.feature_page.ensembl_gene_id&FILTERS=hsapiens_gene_ensembl.default.filters.encode_region."16:1:500000"
