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

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Doctor Nicola Mulder Henning Hermjakob

University of Cape Town CBIO laboratory

EBI Rafael Jimenez Andy Jenkinson

DAS Communty Jonathan Warren das@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/das

Questions??