Revision: 850
http://obo.svn.sourceforge.net/obo/?rev=850&view=rev
Author: mgibson
Date: 2007-08-29 14:17:47 -0700 (Wed, 29 Aug 2007)
Log Message:
-----------
put min-completion-chars="4" into entity fields with lots of ontologies
or 3 or 2
changed some syntax-abbrev to new datatag
Modified Paths:
--------------
phenote/trunk/conf/birn2.cfg
phenote/trunk/conf/demo.cfg
phenote/trunk/conf/flybase.cfg
phenote/trunk/conf/parameciumDB.cfg
phenote/trunk/conf/phenote-config.rnc
phenote/trunk/conf/phenote-config.xsd
phenote/trunk/conf/smart-atlas.cfg
Modified: phenote/trunk/conf/birn2.cfg
===================================================================
--- phenote/trunk/conf/birn2.cfg 2007-08-29 21:02:47 UTC (rev 849)
+++ phenote/trunk/conf/birn2.cfg 2007-08-29 21:17:47 UTC (rev 850)
@@ -23,7 +23,7 @@
<ns:field name="Organism" enable="true" datatag="GT" desc="This is like the genotype; its probably a
mouse strain or some other identifying factor"/>
<ns:field name="Phenotypic Character" enable="true" desc="This is a free-text field for phenotype characters for now, not exactly sure what this captures; it might be just a grouping or it might be conclusions, or something else entirely"/>
- <ns:field name="Entity" datatag="E" enable="true">
+ <ns:field name="Entity" min-completion-chars="4" 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" file="SAO.obo"/>
@@ -43,7 +43,7 @@
<ns:ontology file="http://www.berkeleybop.org/ontologies/obo-all/quality/quality.obo"/>
</ns:field>
- <ns:field name="Add'l Entity" datatag="E2" enable="true">
+ <ns:field name="Add'l Entity" datatag="E2" min-completion-chars="4" 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" file="SAO.obo"/-->
Modified: phenote/trunk/conf/demo.cfg
===================================================================
--- phenote/trunk/conf/demo.cfg 2007-08-29 21:02:47 UTC (rev 849)
+++ phenote/trunk/conf/demo.cfg 2007-08-29 21:17:47 UTC (rev 850)
@@ -33,12 +33,12 @@
"http://www.your-repository.com/your_obo_file.obo"), then this site
will be checked for updates -->
- <ns:field name="Pub" syntax-abbrev="PUB" enable="true"/>
- <ns:field name="Genotype" syntax-abbrev="GT" enable="true"/>
- <ns:field name="Genetic Context" syntax-abbrev="GC" enable="true">
+ <ns:field name="Pub" datatag="PUB" enable="true"/>
+ <ns:field name="Genotype" datatag="GT" enable="true"/>
+ <ns:field name="Genetic Context" datatag="GC" enable="true">
<ns:ontology name="Genetic Context" file="context.obo"/>
</ns:field>
- <ns:field name="Entity" syntax-abbrev="E" enable="true">
+ <ns:field name="Entity" datatag="E" min-completion-chars="3" enable="true">
<ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" repos-subdir="OBO_REL" is-postcomp-rel="true"/>
<ns:ontology name="FMA" file="fma_obo.obo"/>
<ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo"/>
@@ -46,11 +46,11 @@
<ns:ontology name="SO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/so.obo"/>
<ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
</ns:field>
- <ns:field name="Quality" syntax-abbrev="Q" enable="true">
+ <ns:field name="Quality" datatag="Q" enable="true">
<ns:ontology name="PATO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>
<ns:ontology name="MP" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mammalian_phenotype.obo"/>
</ns:field>
- <ns:field name="Add'l Entity" syntax-abbrev="E2" enable="true">
+ <ns:field name="Add'l Entity" datatag="E2" min-completion-chars="3" enable="true">
<ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" is-postcomp-rel="true"/>
<ns:ontology name="FMA" file="fma_obo.obo"/>
<ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo" />
@@ -58,16 +58,16 @@
<ns:ontology name="SO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/so.obo"/>
<ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
</ns:field>
- <ns:field name="Time" syntax-abbrev="T" enable="true"/>
- <ns:field name="Count" syntax-abbrev="C" enable="true"/>
- <ns:field name="Unit" syntax-abbrev="U" enable="true">
+ <ns:field name="Time" datatag="T" enable="true"/>
+ <ns:field name="Count" datatag="C" enable="true"/>
+ <ns:field name="Unit" datatag="U" enable="true">
<ns:ontology name="Unit" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
</ns:field>
- <ns:field name="Abnormal" syntax-abbrev="Tag" enable="true">
+ <ns:field name="Abnormal" datatag="Tag" enable="true">
<ns:ontology name="Abnormal" file="quality.obo" slim="abnormal_slim"/>
</ns:field>
- <ns:field name="Description" syntax-abbrev="Desc" enable="true"/>
- <ns:field name="Evidence" syntax-abbrev="EC" enable="false">
+ <ns:field name="Description" datatag="Desc" enable="true"/>
+ <ns:field name="Evidence" datatag="EC" enable="false">
<ns:ontology name="Evidence" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/evidence_code.obo"/>
</ns:field>
<!-- ******************** REVISION HISTORY *********************** -->
Modified: phenote/trunk/conf/flybase.cfg
===================================================================
--- phenote/trunk/conf/flybase.cfg 2007-08-29 21:02:47 UTC (rev 849)
+++ phenote/trunk/conf/flybase.cfg 2007-08-29 21:17:47 UTC (rev 850)
@@ -29,15 +29,15 @@
<!-- ******************** FIELD DEFINITIONS *********************** -->
- <ns:field name="Pub" syntax-abbrev="PUB"/>
+ <ns:field name="Pub" datatag="PUB"/>
- <ns:field name="Genotype" syntax-abbrev="GT" type="FREE_TEXT"/>
+ <ns:field name="Genotype" datatag="GT" type="FREE_TEXT"/>
- <ns:field name="Genetic Context" syntax-abbrev="GC">
+ <ns:field name="Genetic Context" datatag="GC">
<ns:ontology file="context.obo"/>
</ns:field>
- <ns:field name="Entity" syntax-abbrev="E">
+ <ns:field name="Entity" datatag="E" min-completion-chars="3">
<!-- postcomp relationship-ontology="relationship.obo" repos-subdir="OBO_REL"/ -->
<ns:ontology name="Relationship" is-postcomp-rel="true"
file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
@@ -47,19 +47,19 @@
<ns:ontology name="SP" file="spatial.obo"/>
</ns:field>
- <ns:field name="Quality" syntax-abbrev="Q">
+ <ns:field name="Quality" datatag="Q">
<ns:ontology file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo" />
</ns:field>
- <ns:field name="Absent" syntax-abbrev="Tag">
+ <ns:field name="Absent" datatag="AbsentTag">
<ns:ontology file="quality.obo" slim="absent_slim" />
</ns:field>
- <ns:field name="Abnormal" syntax-abbrev="Tag">
+ <ns:field name="Abnormal" datatag="Tag">
<ns:ontology file="quality.obo" slim="abnormal_slim" />
</ns:field>
- <ns:field name="Description" syntax-abbrev="Desc"/>
+ <ns:field name="Description" datatag="Desc"/>
<!-- ******************** REVISION HISTORY *********************** -->
<!-- 05.24.2007 - Latest update changes relationship.obo to ro.obo;
Modified: phenote/trunk/conf/parameciumDB.cfg
===================================================================
--- phenote/trunk/conf/parameciumDB.cfg 2007-08-29 21:02:47 UTC (rev 849)
+++ phenote/trunk/conf/parameciumDB.cfg 2007-08-29 21:17:47 UTC (rev 850)
@@ -31,7 +31,7 @@
<ns:field name="Description" syntax-abbrev="Desc"/>
- <ns:field name="Entity" syntax-abbrev="E">
+ <ns:field name="Entity" syntax-abbrev="E" min-completion-chars="2">
<ns:ontology name="Paramecium Anatomy" file="http://paramecium.cgm.cnrs-gif.fr/phenote/obo/para.obo"/>
<ns:ontology name="Paramecium Ontology" file="http://paramecium.cgm.cnrs-gif.fr/phenote/obo/paro.obo"/>
<ns:ontology name="Gene Onotology" file="http://paramecium.cgm.cnrs-gif.fr/phenote/obo/go.obo"/>
Modified: phenote/trunk/conf/phenote-config.rnc
===================================================================
--- phenote/trunk/conf/phenote-config.rnc 2007-08-29 21:02:47 UTC (rev 849)
+++ phenote/trunk/conf/phenote-config.rnc 2007-08-29 21:17:47 UTC (rev 850)
@@ -19,7 +19,8 @@
autocomplete-settings,
field*,
group*,
- data-input-servlet
+ data-input-servlet,
+ character-mode
}
## specify how the master config interacts with local/cached config
@@ -71,6 +72,16 @@
attribute obsolete { xsd:boolean }
}
+## what implementation of CharacterI to use, CHARACTER or OBO_ANNOTATION
+character-mode = element character-mode {
+ ## type of character to use
+ attribute mode { "CHARACTER" | "OBO_ANNOTATION" },
+ ## if using OBO_ANNOTATION, then specify the java mapping class to use
+ ## full java class name, eg phenote.datamodel.BasicAnnotationMappingDriver
+ attribute mapping { xsd:string }
+}
+
+## this is pase and should be phased out
obo-repository = element obo-repository { attribute url-dir {xsd:string} }
field =
Modified: phenote/trunk/conf/phenote-config.xsd
===================================================================
--- phenote/trunk/conf/phenote-config.xsd 2007-08-29 21:02:47 UTC (rev 849)
+++ phenote/trunk/conf/phenote-config.xsd 2007-08-29 21:17:47 UTC (rev 850)
@@ -15,6 +15,7 @@
<xs:element minOccurs="0" maxOccurs="unbounded" ref="x:field"/>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="x:group"/>
<xs:element ref="x:data-input-servlet"/>
+ <xs:element ref="x:character-mode"/>
</xs:sequence>
<xs:attribute name="version" use="required" type="xs:string"/>
<xs:attribute name="description" use="required" type="xs:string"/>
@@ -74,6 +75,11 @@
<xs:attribute name="obsolete" use="required" type="xs:boolean"/>
</xs:complexType>
</xs:element>
+ <xs:element name="character-mode">
+ <xs:complexType>
+ <xs:attribute name="mode" use="required" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
<xs:element name="obo-repository">
<xs:complexType>
<xs:attribute name="url-dir" use="required" type="xs:string"/>
Modified: phenote/trunk/conf/smart-atlas.cfg
===================================================================
--- phenote/trunk/conf/smart-atlas.cfg 2007-08-29 21:02:47 UTC (rev 849)
+++ phenote/trunk/conf/smart-atlas.cfg 2007-08-29 21:17:47 UTC (rev 850)
@@ -30,7 +30,7 @@
<ns:field name="Slice Type" datatag="slicetype" enable="true" desc="coronal or sagittal, read only?"/>
<ns:field name="Slice Number" datatag="slicenumber" enable="true" desc="images have many slices(?)"/>
- <ns:field name="Entity" datatag="E" enable="true">
+ <ns:field name="Entity" datatag="E" min-completion-chars="4" 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" file="SAO.obo"/>
@@ -52,7 +52,7 @@
<ns:ontology file="http://www.berkeleybop.org/ontologies/obo-all/quality/quality.obo"/>
</ns:field>
- <ns:field name="Add'l Entity" datatag="E2" enable="true">
+ <ns:field name="Add'l Entity" datatag="E2" min-completion-chars="4" 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" file="SAO.obo"/>
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