From: <ba...@us...> - 2008-06-11 14:09:22
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Revision: 1835 http://obo.svn.sourceforge.net/obo/?rev=1835&view=rev Author: balhoff Date: 2008-06-11 07:09:09 -0700 (Wed, 11 Jun 2008) Log Message: ----------- Modified Paths: -------------- phenote/trunk/conf/phenoscape.cfg Added Paths: ----------- phenote/trunk/conf/phenoscape_character.cfg phenote/trunk/conf/phenoscape_taxon.cfg Modified: phenote/trunk/conf/phenoscape.cfg =================================================================== --- phenote/trunk/conf/phenoscape.cfg 2008-06-10 22:44:51 UTC (rev 1834) +++ phenote/trunk/conf/phenoscape.cfg 2008-06-11 14:09:09 UTC (rev 1835) @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<ns:phenote-configuration version="1.9" xmlns:ns="phenote/config/xml" name="PhenoMaP Configuration" author="Jim Balhoff" description="This configuration is used by curators with the PhenoMaP project at NESCent."> +<ns:phenote-configuration version="1.11" xmlns:ns="phenote/config/xml" name="Phenoscape Configuration" author="Jim Balhoff" description="This configuration is used by curators with the Phenoscape project at NESCent."> <!-- *********************** SETTINGS **************************** --> <ns:master-to-local-config mode="WIPEOUT" when="ALWAYS"/> @@ -12,8 +12,8 @@ <!-- ********************* FILE ADAPTERS ***************************--> <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/> <ns:dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="true"/> + <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="true"/> - <!--************************* ONTOLOGIES *************************--> <ns:terminology-definitions update="SOME" > <ns:ontology-file handle="Quality" type="OBO" filename="quality.obo" @@ -46,7 +46,7 @@ <!-- ******************** FIELD DEFINITIONS *********************** --> <ns:field name="Publication" datatag="PUB" enable="true" groups="default taxon-list"/> - <ns:field name="Valid Taxon" datatag="GT" enable="true" groups="default taxon-list"> + <ns:field name="Valid Taxon" datatag="GC" enable="true" groups="default taxon-list"> <ns:ontology name="Taxon"/> </ns:field> <ns:field name="Publication Taxon" datatag="pubtaxon" enable="true" groups="default taxon-list"/> @@ -68,9 +68,6 @@ <ns:ontology name="Spatial Aspect"/> <ns:ontology name="Anatomy"/> </ns:field> - <ns:field name="Spatial Aspect" datatag="SP" enable="true" groups="default"> - <ns:ontology name="Spatial Aspect"/> - </ns:field> <ns:field name="Additional Entity" datatag="E2" enable="true" groups="default"> <ns:ontology name="Relationship" is-postcomp-rel="true"/> <ns:ontology name="Relationship-proposed" is-postcomp-rel="true"/> Added: phenote/trunk/conf/phenoscape_character.cfg =================================================================== --- phenote/trunk/conf/phenoscape_character.cfg (rev 0) +++ phenote/trunk/conf/phenoscape_character.cfg 2008-06-11 14:09:09 UTC (rev 1835) @@ -0,0 +1,72 @@ +<?xml version="1.0" encoding="UTF-8"?> +<ns:phenote-configuration version="1.0" xmlns:ns="phenote/config/xml" name="Phenoscape Character Configuration" author="Jim Balhoff" description="This configuration is used by curators with the Phenoscape project at NESCent to create EQ annotations for character states."> + + <!-- *********************** SETTINGS **************************** --> + <ns:master-to-local-config mode="WIPEOUT" when="ALWAYS"/> + <ns:uvic-graph enable="false"/> + <ns:term-history enable="false"/> + <ns:field-panel-tabs enable="false"/> + <ns:autocomplete-settings term="true" synonym="true" definition="false" obsolete="false"/> + + + <!-- ********************* FILE ADAPTERS ***************************--> + <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/> + + + <!--************************* ONTOLOGIES *************************--> + <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="Relationship-proposed" type="OBO" filename="ro_proposed.obo" + location="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/" auto_update="false"/> + <ns:ontology-file handle="Anatomy" type="OBO" filename="teleost_anatomy.obo" + location="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/" auto_update="false"/> + <ns:ontology-file handle="Spatial Aspect" type="OBO" filename="spatial.obo" + location="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/" auto_update="false"/> + <ns:ontology-file handle="Unit" type="OBO" filename="unit.obo" + location="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/" auto_update="false"/> + <ns:ontology-file handle="Evidence" type="OBO" filename="evidence_code.obo" + location="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/" auto_update="false"/> + </ns:terminology-definitions> + + + <!-- ******************** FIELD GROUPS *********************** --> + <ns:group name="default" title="Main" container="window" interface="default" allowEmptyCharacters="true"/> + + + <!-- ******************** FIELD DEFINITIONS *********************** --> + <ns:field name="Publication" datatag="PUB" enable="true" groups="default"/> + <ns:field name="Character Number" datatag="character-number" enable="true" groups="default"/> + <ns:field name="State Number" datatag="character-number" enable="true" groups="default"/> + <ns:field name="Textual Description" datatag="Desc" enable="true" groups="default"/> + <ns:field name="Entity" datatag="E" enable="true" groups="default"> + <ns:ontology name="Relationship" is-postcomp-rel="true"/> + <ns:ontology name="Relationship-proposed" is-postcomp-rel="true"/> + <ns:ontology name="Anatomy"/> + <ns:ontology name="Quality"/> + <ns:ontology name="Spatial Aspect"/> + </ns:field> + <ns:field name="Quality" datatag="Q" enable="true" groups="default"> + <ns:ontology name="Relationship" is-postcomp-rel="true"/> + <ns:ontology name="Relationship-proposed" is-postcomp-rel="true"/> + <ns:ontology name="Quality"/> + <ns:ontology name="Spatial Aspect"/> + <ns:ontology name="Anatomy"/> + </ns:field> + <ns:field name="Additional Entity" datatag="E2" enable="true" groups="default"> + <ns:ontology name="Relationship" is-postcomp-rel="true"/> + <ns:ontology name="Relationship-proposed" is-postcomp-rel="true"/> + <ns:ontology name="Anatomy"/> + <ns:ontology name="Quality"/> + <ns:ontology name="Spatial Aspect"/> + </ns:field> + <ns:field name="Count" datatag="C" enable="true" groups="default"/> + <ns:field name="Measurement" datatag="M" enable="true" groups="default"/> + <ns:field name="Unit" datatag="U" enable="true" groups="default"> + <ns:ontology name="Unit"/> + </ns:field> + <ns:field name="Curator Notes" datatag="Notes" enable="true" groups="default"/> + +</ns:phenote-configuration> \ No newline at end of file Added: phenote/trunk/conf/phenoscape_taxon.cfg =================================================================== --- phenote/trunk/conf/phenoscape_taxon.cfg (rev 0) +++ phenote/trunk/conf/phenoscape_taxon.cfg 2008-06-11 14:09:09 UTC (rev 1835) @@ -0,0 +1,46 @@ +<?xml version="1.0" encoding="UTF-8"?> +<ns:phenote-configuration version="1.0" xmlns:ns="phenote/config/xml" name="Phenoscape Taxon Configuration" author="Jim Balhoff" description="This configuration is used by curators with the Phenoscape project at NESCent to create taxon and specimen lists."> + + <!-- *********************** SETTINGS **************************** --> + <ns:master-to-local-config mode="WIPEOUT" when="ALWAYS"/> + <ns:uvic-graph enable="false"/> + <ns:term-history enable="false"/> + <ns:field-panel-tabs enable="false"/> + <ns:autocomplete-settings term="true" synonym="true" definition="false" obsolete="false"/> + + + <!-- ********************* FILE ADAPTERS ***************************--> + <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/> + + + <!--************************* ONTOLOGIES *************************--> + <ns:terminology-definitions update="SOME" > + <ns:ontology-file handle="Taxon" type="OBO" filename="teleost_taxonomy.obo" + location="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/" 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="Relationship-proposed" type="OBO" filename="ro_proposed.obo" + location="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/" auto_update="false"/> + <ns:ontology-file handle="Collection Code" type="OBO" filename="fish_collection_abbreviation.obo"/> + </ns:terminology-definitions> + + + <!-- ******************** FIELD GROUPS *********************** --> + <ns:group name="default" title="Main" container="window" allowEmptyCharacters="true" interface="default" /> + <ns:group name="compound-specimen" title="Specimens" interface="default" allowEmptyCharacters="true" useFieldPanel="false"/> + + + <!-- ******************** FIELD DEFINITIONS *********************** --> + <ns:field name="Publication" datatag="PUB" enable="true" groups="default"/> + <ns:field name="Valid Taxon" datatag="GT" enable="true" groups="default"> + <ns:ontology name="Taxon"/> + </ns:field> + <ns:field name="Publication Taxon" datatag="pubtaxon" enable="true" groups="default"/> + <ns:field name="Taxon Comments" datatag="taxoncomments" enable="true" groups="default"/> + <ns:field name="Specimens" datatag="specimens" enable="true" isList="true" groups="default" componentsGroup="compound-specimen"/> + <ns:field name="Collection Code" datatag="collection-code" enable="true" groups="compound-specimen"> + <ns:ontology name="Collection Code"/> + </ns:field> + <ns:field name="Specimen ID" datatag="specimen-id" enable="true" groups="compound-specimen"/> + +</ns:phenote-configuration> \ No newline at end of file This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |