Version 13 (modified by 14 years ago) (diff) | ,
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Biobanks missing from server
Create from scratch (molgenis distro ) the Biobanks (BBMRI), Fill database
this will be faster and more complete : adjust pheno--> http://gbic.target.rug.nl:8080/Biobanks/molgenis.do
GCC project
- Add gcc integrated bbmri project in gbic server.: http://gbic.target.rug.nl:8080/bbmri_gcc/molgenis.do
- Database contents cannot be shown .!
D2R on gcc model: : Materials conflict
$$$ mv molgenis-rdf-mapping.n3 molgenis-rdf-mapping_gcc.n3 $$$ d2r-server molgenis-rdf-mapping_gcc.n3
- Fix missing classes: (despoina)
- * de.fuberlin.wiwiss.d2rq.D2RQException: Object for d2rq:refersToClassMap not found at d2rq:PropertyBridge map:Biobank_materials (E21) *
- Biobank material table exists in DB :
- * mysql> describe Biobank_materials;
- +-----------+---------+------+-----+---------+----------------+
- | Field | Type | Null | Key | Default | Extra |
- +-----------+---------+------+-----+---------+----------------+
- | autoid | int(11) | NO | PRI | NULL | auto_increment |
- | Materials | int(11) | NO | MUL | NULL | |
- | Biobank | int(11) | NO | MUL | NULL | |
- +-----------+---------+------+-----+---------+------------ *
- In magetab_sdrf.xml :
<entity name="Material" extends="!ObservationTarget"> <field name="SourceMaterials" xref_name="SourceTarget" type="mref" xref_entity="Material" description="The source materials that this material was derived from. These are the edges in the experimental design graph." /> <field name="protocolApplications" type="mref" xref_entity="ProtocolApplication" description="The protocols used to produce this material" />
- The only reference in Material in the rdf mapping file is
- * 1388 map:Biobank_materials a d2rq:PropertyBridge;
- 1389 d2rq:belongsToClassMap map:Biobank;
- 1390 d2rq:property vocab:Biobank_Materials;
- 1391 d2rq:propertyDefinitionLabel "Materials";
- 1392 d2rq:propertyDefinitionComment "Materials";
- 1393 d2rq:refersToClassMap map:OntologyTerm;
- 1394 d2rq:join "Biobank.id <= Biobank_Materials.Biobank";
- 1395 d2rq:join "Biobank_Materials.Materials => OntologyTerm.id";
- 1396 .
- Add material in mappings file .
- *