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DAS Distributed Annotation System
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DAS Advance Searchand its prototype implementation in MyDas
Gustavo Adolfo Salazar Orejuela
Supervised by: Nicola MulderHenning Hermjakob
DAS workshop - 2011
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DASDistributed Annotation System
QuickTime™ and a decompressor
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??
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Proposed Solution Advance query
query: a new argument for the features command should be added, so now the request of this command is defined as:
SERVER/das/DSN/features? [;segment=RANGE]
[;type=TYPE] [;type=TYPE]
[;category=CATEGORY] [;feature_id=ID] [;maxbins=BINS] [;query=DASQUERY]
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Proposed Solution DAS Query Language
Based in LUCENE, A query is broken into terms and operators: Terms
• E.g. "alpha helix" Fields
• E.g. type Condition:
• E.g. type:”alpha helix” Terms Modifiers
• E.g. type:alpha* Operands
• E.g. typeCvId:CV:00001 AND featureLabel:"one Feature" Grouping
• (typeCvId:CV:00001 AND featureLabel:"one Feature") OR typeId:twoFeatureTypeIdOne
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Proposed Solution DAS Query Language
Defined Fields: featureId, featureLabel, segmentId,
segmentLabel, segmentStart, segmentStop, typeId, typeCvId, typeLabel, typeCategory, type, methodId, methodCvId, methodLabel, method, start, stop, score, orientation, phase, note, link, target, parent, part, all
Reporting capability <capability type="das1:advanced-search" />
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Proposed SolutionResponse
The document returned from the features request does not have to be extended because it supports to have more than one segment in it.
From the relax-ng<oneOrMore>
<element name="SEGMENT">…
</element></oneOrMore>
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Proposed Solution Prototype Implementation
MyDas has been extended to support this capability, but so far it is still a beta version, just downloadable through SVN: SNAPSHOT 1.6.4
LUCENE is used to create an index of the data source to add the advance search capability
The capability entry_point is required to be able of going through all the features per each entry point.
LUCENE is also used to construct the data source. This may cause a sync error with the data, but it avoids the requirement of the feature_id capability
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Proposed Solution Prototype Implementation
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Proposed Solution Data Source - Uniprot 2 Probes
It maps microarrays probes to UniprotKB accession numbers http://tomcat-18:21510/das-srv/das/uniprot2probes/features?
segment=Q58EV5 http://tomcat-18:21510/das-srv/das/uniprot2probes/features?
query=segmentId:Q58EV5 http://tomcat-18:21510/das-srv/das/uniprot2probes/features?
feature_id=234173_s_at.affy_hg_u133b http://tomcat-18:21510/das-srv/das/uniprot2probes/features?
query=featureId:234173_s_at.affy_hg_u133b http://tomcat-18:21510/das-srv/das/uniprot2probes/features?
query=typeLabel:affy_mouse430a_2 http://tomcat-18:21510/das-srv/das/uniprot2probes/features?
query=typeLabel:affy_mouse430a_2%20AND%20featureId:1416176*
QuickTime™ and a decompressor
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Pagination of the feature commandClients using this capability.
• JsDas + Advance Search + Uniprot2probes
Proserver implementation?
QuickTime™ and a decompressor
are needed to see this picture. Acknowledgments Supervisors
Doctor Nicola Mulder Henning Hermjakob
University of Cape Town CBIO laboratory
EBI Rafael Jimenez Andy Jenkinson
DAS Communty Jonathan Warren [email protected] http://lists.open-bio.org/mailman/listinfo/das
Questions??