From: <mg...@us...> - 2008-04-22 21:09:26
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Revision: 1759 http://obo.svn.sourceforge.net/obo/?rev=1759&view=rev Author: mgibson Date: 2008-04-22 14:09:16 -0700 (Tue, 22 Apr 2008) Log Message: ----------- taking out term defs from brin.cfg as term defs barf if ontol doesnt have date and SAO doesnt have date Modified Paths: -------------- phenote/trunk/conf/birn.cfg Modified: phenote/trunk/conf/birn.cfg =================================================================== --- phenote/trunk/conf/birn.cfg 2008-04-22 16:14:44 UTC (rev 1758) +++ phenote/trunk/conf/birn.cfg 2008-04-22 21:09:16 UTC (rev 1759) @@ -7,8 +7,9 @@ overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/birn.cfg" /> <!-- ************************* ONTOLOGIES *************************--> - <ns:terminology-definitions update="SOME" > - <ns:ontology-file handle="PATO" type="OBO" filename="quality.obo" location="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/" auto_update="false" /> +<!-- SAO doesnt have date which makes term defs barf - so taking out for now --> + <!-- ns:terminology-definitions update="SOME" > + <ns:ontology-file handle="Quality" type="OBO" filename="quality.obo" location="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/" auto_update="false" /> <ns:ontology-file handle="Relationship" type="OBO" filename="ro.obo" location="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/" auto_update="false"/> <ns:ontology-file handle="GO" type="OBO" filename="gene_ontology_edit.obo" location="ftp://ftp.geneontology.org/pub/go/ontology/" auto_update="false"/> <ns:ontology-file handle="SAO" filename="SAO.obo" type="OBO"/> @@ -19,7 +20,7 @@ <ns:ontology-file handle="CL" filename="cell.obo" type="OBO" location="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/" auto_update="false" /> <ns:ontology-file handle="Spatial" filename="spatial.obo" type="OBO" /> <ns:ontology-file handle="CHEBI" type="OBO" filename="chebi.obo" location="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/" auto_update="false"/> - </ns:terminology-definitions> + </ns:terminology-definitions --> <!--********************* FILE ADAPTERS **************************--> <!--be sure to include at least one enabled file adapter--> @@ -40,7 +41,18 @@ <ns:field name="Entity" datatag="E" enable="true"> <ns:ontology name="Relationship" is-postcomp-rel="true" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/> - <ns:ontology name="SAO"/> + <ns:ontology name="SAO" file="SAO.obo"/> + <ns:ontology name="BIRNLex-Anatomy" file="BIRNLex-Anatomy.obo"/> + <ns:ontology name="BIRNLex" file="BIRNLex.obo"/> + <ns:ontology name="FMA" file="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma_obo.obo"/> + <ns:ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/> + <ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo"/> + <ns:ontology name="CL" file="http://www.berkeleybop.org/ontologies/obo-all/cell/cell.obo"/> + <ns:ontology name="Spatial" file="spatial.obo"/> + <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/> + <!--ns:ontology name="DO" + file="http://www.berkeleybop.org/ontologies/obo-all/disease_ontology/disease_ontology.obo"/--> + <!-- ns:ontology name="SAO"/> <ns:ontology name="BIRNLex-Anatomy"/> <ns:ontology name="BIRNLex" /> <ns:ontology name="FMA" /> @@ -48,13 +60,12 @@ <ns:ontology name="GO" /> <ns:ontology name="CL" /> <ns:ontology name="Spatial" /> - <ns:ontology name="CHEBI" /> - <!--ns:ontology name="DO" - file="http://www.berkeleybop.org/ontologies/obo-all/disease_ontology/disease_ontology.obo"/--> + <ns:ontology name="CHEBI" / --> </ns:field> <ns:field name="Quality" datatag="Q" enable="true"> - <ns:ontology file="http://www.berkeleybop.org/ontologies/obo-all/quality/quality.obo" name="Quality"/> + <ns:ontology name="Quality" + file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/> </ns:field> <ns:field name="Add'l Entity" datatag="E2" enable="true"> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |