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vfb.xmi
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<?xml version="1.0" encoding="ASCII"?>
<gep:GeppettoModel
xmi:version="2.0"
xmlns:xmi="http://www.omg.org/XMI"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:gep="https://raw.githubusercontent.com/openworm/org.geppetto.model/development/src/main/resources/geppettoModel.ecore"
xmlns:gep_1="https://raw.githubusercontent.com/openworm/org.geppetto.model/development/src/main/resources/geppettoModel.ecore#//types"
xmlns:gep_2="https://raw.githubusercontent.com/openworm/org.geppetto.model/development/src/main/resources/geppettoModel.ecore#//datasources">
<libraries
id="SWCLibrary"
name="SWC"/>
<libraries
id="OBJLibrary"
name="OBJ"/>
<libraries
id="OWLLibrary"
name="OWL"/>
<libraries
id="ontology"
name="Ontology">
<types xsi:type="gep_1:SimpleType"
id="Individual"
name="Individual"/>
<types xsi:type="gep_1:SimpleType"
id="Class"
name="Class"/>
<types xsi:type="gep_1:SimpleType"
id="Neuron"
name="Neuron"/>
<types xsi:type="gep_1:SimpleType"
id="Neuron_projection_bundle"
name="Neuron Projection Bundle"/>
<types xsi:type="gep_1:SimpleType"
id="Clone"
name="Clone"/>
<types xsi:type="gep_1:SimpleType"
id="Synaptic_neuropil"
name="Synaptic Neuropil"/>
<types xsi:type="gep_1:SimpleType"
id="VFB"
name="Virtual Fly Brain"/>
<types xsi:type="gep_1:SimpleType"
id="Orphan"
name="No Meta Data"/>
<types xsi:type="gep_1:SimpleType"
id="Obsolete"
name="Obsolete"/>
<types xsi:type="gep_1:SimpleType"
id="Synaptic_neuropil_domain"
name="Synaptic Neuropil Domain"/>
<types xsi:type="gep_1:SimpleType"
id="Synaptic_neuropil_subdomain"
name="Synaptic Neuropil Subdomain"/>
<types xsi:type="gep_1:SimpleType"
id="Synaptic_neuropil_block"
name="Synaptic Neuropil Block"/>
<types xsi:type="gep_1:SimpleType"
id="FBDV"
name="FlyBase Development CV"/>
<types xsi:type="gep_1:SimpleType"
id="FBCV"
name="FlyBase Controlled Vocabulary"/>
<types xsi:type="gep_1:SimpleType"
id="FBBI"
name="FlyBase Biological Imaging Methods"/>
<types xsi:type="gep_1:SimpleType"
id="Root"
name="Top Object"/>
<types xsi:type="gep_1:SimpleType"
id="pub"
name="Publication"/>
<types xsi:type="gep_1:SimpleType"
id="Resource"
name="Resource"/>
<types xsi:type="gep_1:SimpleType"
id="VFB_00017894"
name="JFRC2 template"/>
<types xsi:type="gep_1:SimpleType"
id="VFB_00030786"
name="BrainName standard - Ito half brain"/>
<types xsi:type="gep_1:SimpleType"
id="Template"
name="Template"/>
<types xsi:type="gep_1:SimpleType"
id="hasExamples"
name="Has Examples"/>
<types xsi:type="gep_1:SimpleType"
id="Cluster"
name="Cluster"/>
<types xsi:type="gep_1:SimpleType"
id="Ganglion"
name="ganglion"/>
<types xsi:type="gep_1:SimpleType"
id="DataSet"
name="DataSet"/>
<types xsi:type="gep_1:SimpleType"
id="NBLAST"
name="NBLAST"/>
<types xsi:type="gep_1:SimpleType"
id="Neuromere"
name="neuromere"/>
<types xsi:type="gep_1:SimpleType"
id="Expression_pattern"
name="expression pattern"/>
</libraries>
<libraries
id="vfbLibrary"
name="VFB"/>
<dataSources
id="neo4JDataSourceService"
name="neo4j Data Source"
dataSourceService="neo4jDataSource"
url="http://VFB_PDB_SERVER/db/data/transaction"
dependenciesLibrary="//@libraries.3"
targetLibrary="//@libraries.4">
<libraryConfigurations
library="//@libraries.0"
modelInterpreterId="swcModelInterpreterService"
format="swc"/>
<libraryConfigurations
library="//@libraries.1"
modelInterpreterId="objModelInterpreterService"
format="obj"/>
<libraryConfigurations
library="//@libraries.2"
modelInterpreterId="owlModelInterpreterService"
format="owl"/>
<queries
xsi:type="gep_2:CompoundQuery"
name="Get and process example images from Neo4j for class list"
description=""
runForCount="false">
<queryChain
xsi:type="gep_2:SimpleQuery"
name="Get images from Neo4j for class examples"
description="fetch Individual instances from ID list"
runForCount="false"
query="MATCH (n:Class) WHERE n.short_form IN $ARRAY_ID_RESULTS OPTIONAL MATCH (n)<-[:SUBCLASSOF|INSTANCEOF*..]-(i:Individual)<-[:depicts]-(j:Individual)-[k:in_register_with]->(m:Individual) OPTIONAL MATCH (n)-[:SUBCLASSOF]->(c:Class) RETURN n.short_form as class_Id, n.label as class_Name, n.description[0] as class_Desc, COLLECT(DISTINCT c.label) as class_Type, COLLECT (DISTINCT { image_name: i.label, image_id: i.short_form, image_thumb: replace(k.folder,'http:','https:') + '/thumbnailT.png', template_id: m.short_form}) AS inds"
countQuery="MATCH (n:Class) WHERE n.short_form IN $ARRAY_ID_RESULTS RETURN count(n) AS count"/>
<queryChain
xsi:type="gep_2:ProcessQuery"
name="Process images"
queryProcessorId="vfbCreateImagesForQueryResultsQueryProcessor"/>
</queries>
<queries
xsi:type="gep_2:CompoundQuery"
name="Get and process details from Neo4j for list of inds"
description=""
runForCount="false">
<queryChain
xsi:type="gep_2:SimpleQuery"
id="GetMetaForIndList"
name="Get meta from Neo4j"
description="Get images for individual list"
runForCount="false"
query="MATCH (i:Individual) WHERE i.short_form IN $ARRAY_ID_RESULTS OPTIONAL MATCH (i)<-[:depicts]-(:Individual)-[k1:in_register_with]->(:Individual) OPTIONAL MATCH (i:Cluster)<-[:exemplar_of]-(e:Individual) OPTIONAL MATCH (i)-[:INSTANCEOF]->(ic:Class) OPTIONAL MATCH (e)-[:INSTANCEOF]->(ec:Class) with coalesce('Exemplar: ' + ec.label,ic.label) as ct, i, coalesce(replace(k1.folder,'http:','https:') + '/thumbnailT.png','http://flybrain.mrc-lmb.cam.ac.uk/vfb/fc/clusterv/3/' + e.label + '/snapshot.png') as iri, i.description[0] as cd, FILTER(x IN i.synonym WHERE x <> i.label) as syn RETURN i.short_form as id, i.label as name, CASE WHEN not syn = [] THEN cd + replace(' Synonym(s): '+reduce(a='',n in syn|a+n+', ')+')',', )','.') ELSE cd END as def, COLLECT(DISTINCT ct) as type, iri AS file"
countQuery="MATCH(i:Individual) WHERE i.short_form IN $ARRAY_ID_RESULTS RETURN count(i) as count"/>
<queryChain
xsi:type="gep_2:ProcessQuery"
name="Process Images"
runForCount="false"
returnType="//@libraries.3/@types.0"
queryProcessorId="vfbCreateResultListForIndividualsForQueryResultsQueryProcessor"/>
</queries>
<queries
xsi:type="gep_2:CompoundQuery"
name="Get fellow cluster members"
description="">
<queryChain
xsi:type="gep_2:SimpleQuery"
id="GetFellowClusterMembers"
name="Get other cluster members"
description="$NAME's fellow cluster members"
query="MATCH (n:Neuron { short_form: '$ID' } )-[r1:member_of]->(c:Cluster)-[r2:has_member]->(i:Neuron)<-[:depicts]-(j:Individual)-[k:in_register_with]->(m:Individual) OPTIONAL MATCH (i)-[:INSTANCEOF]->(ec:Class) RETURN i.short_form as id, CASE WHEN not i.synonym is null THEN i.label+replace(' ('+reduce(a='',n in i.synonym|a+n+', ')+')',', )',')') ELSE i.label END as name, i.description[0] as def, COLLECT(DISTINCT ec.label) as type, replace(k.folder,'http:','https:') + '/thumbnailT.png' AS file"
countQuery="MATCH (n:Neuron { short_form: '$ID' } )-[r1:member_of]->(c:Cluster)-[r2:has_member]->(i:Neuron) RETURN count(i) as count"/>
<queryChain
xsi:type="gep_2:ProcessQuery"
name="Process Images"
returnType="//@libraries.3/@types.0"
queryProcessorId="vfbCreateResultListForIndividualsForQueryResultsQueryProcessor"/>
</queries>
<queries
xsi:type="gep_2:CompoundQuery"
name="All example images for a class"
description="">
<queryChain
xsi:type="gep_2:SimpleQuery"
name="Fetch all example individuals for Class"
description="Fetch all example Individual instances of this Class or subclasses"
returnType="//@libraries.3/@types.0"
query="MATCH p=(n:Class { short_form: '$ID' } )<-[r:expresses|SUBCLASSOF|INSTANCEOF*..]-(i:Individual)<-[:depicts]-(j:Individual)-[k:in_register_with]->(m:Individual) WITH i, k ORDER BY length(p) asc OPTIONAL MATCH (i)-[:INSTANCEOF]->(c:Class) RETURN distinct i.short_form as id, CASE WHEN not i.synonym is null THEN i.label+replace(' ('+reduce(a='',n in i.synonym|a+n+', ')+')',', )',')') ELSE i.label END as name, i.description[0] as def, COLLECT(DISTINCT c.label) as type, replace(k.folder,'http:','https:') + '/thumbnailT.png' AS file"
countQuery="MATCH (n:VFB:Class { short_form: '$ID' } )<-[r:expresses|SUBCLASSOF|INSTANCEOF*..]-(i:Individual) RETURN count(i) as count"/>
<queryChain
xsi:type="gep_2:ProcessQuery"
name="Process Images"
returnType="//@libraries.3/@types.0"
queryProcessorId="vfbCreateResultListForIndividualsForQueryResultsQueryProcessor"/>
</queries>
<queries
xsi:type="gep_2:CompoundQuery"
id="domainsForTempId"
name="Find domains for template"
description="Doamins for template"
returnType="//@libraries.3/@types.0">
<queryChain
xsi:type="gep_2:SimpleQuery"
id="domainsForTempQuery"
name="Find domain individuals for template id"
description="Find domain individuals for template id"
returnType="//@libraries.3/@types.0"
query="MATCH (n:Template {short_form:'$ID'})<-[:depicts]-(:Template)<-[r:in_register_with]-(dc:Individual)-[:depicts]->(di:Individual)-[:INSTANCEOF]->(d:Class) WHERE has(r.index) RETURN distinct di.short_form as id, di.label as name, coalesce(di.description[0],d.description[0]) as def, COLLECT(DISTINCT d.label) as type, replace(r.folder,'http:','https:') + '/thumbnailT.png' AS file"
countQuery="MATCH (n:Template {short_form:'$ID'})<-[:depicts]-(:Template)<-[r:in_register_with]-(dc:Individual)-[:depicts]->(di:Individual)-[:INSTANCEOF]->(d:Class) WHERE has(r.index) RETURN count(di) as count"/>
<queryChain
xsi:type="gep_2:ProcessQuery"
name="Process Images"
returnType="//@libraries.3/@types.0"
queryProcessorId="vfbCreateResultListForIndividualsForQueryResultsQueryProcessor"/>
</queries>
<queries
xsi:type="gep_2:CompoundQuery"
name="Get cluster members"
description="">
<queryChain
xsi:type="gep_2:SimpleQuery"
id="GetClusterMembers"
name="Get cluster members"
description="$NAME's members"
query="MATCH (c:Cluster { short_form: '$ID' } )-[r2:has_member]->(i:Neuron)<-[:depicts]-(j:Individual)-[k:in_register_with]->(m:Individual) OPTIONAL MATCH (i)-[:INSTANCEOF]->(ec:Class) RETURN i.short_form as id, CASE WHEN not i.synonym is null THEN i.label+replace(' ('+reduce(a='',n in i.synonym|a+n+', ')+')',', )',')') ELSE i.label END as name, i.description[0] as def, COLLECT(DISTINCT ec.label) as type, replace(k.folder,'http:','https:') + '/thumbnailT.png' AS file"
countQuery="MATCH (c:Cluster { short_form: '$ID' } )-[r2:has_member]->(i:Neuron) RETURN count(i) as count"/>
<queryChain
xsi:type="gep_2:ProcessQuery"
name="Process Images"
returnType="//@libraries.3/@types.0"
queryProcessorId="vfbCreateResultListForIndividualsForQueryResultsQueryProcessor"/>
</queries>
<queries
xsi:type="gep_2:CompoundQuery"
id="imagesForDataSet"
name="Find images for dataset"
description="Images in a dataset"
returnType="//@libraries.3/@types.0">
<queryChain
xsi:type="gep_2:SimpleQuery"
id="neoImagesForDataSet"
name="Find images for dataset"
description="Find images for a dataset"
returnType="//@libraries.3/@types.0"
query="MATCH (:DataSet {short_form:'$ID'})<-[:has_source]-(di:Individual)<-[:depicts]-(dc:Individual)-[r:in_register_with]->(:Template) OPTIONAL MATCH (di)-[:INSTANCEOF]->(d:Class) RETURN distinct di.short_form as id, di.label as name, coalesce(di.description[0],di.description[0]) as def, COLLECT(DISTINCT d.label) as type, replace(r.folder,'http:','https:') + '/thumbnailT.png' AS file"
countQuery="MATCH (:DataSet {short_form:'$ID'})<-[:has_source]-(di:Individual) RETURN count(di) as count"/>
<queryChain
xsi:type="gep_2:ProcessQuery"
name="Process Images"
returnType="//@libraries.3/@types.0"
queryProcessorId="vfbCreateResultListForIndividualsForQueryResultsQueryProcessor"/>
</queries>
<queries
xsi:type="gep_2:CompoundQuery"
id="imagesForTempId"
name="Find images aligned to a template"
description="Aligned images for template"
returnType="//@libraries.3/@types.0">
<queryChain
xsi:type="gep_2:SimpleQuery"
id="imagesForTempQuery"
name="Find images aligned to template id"
description="Find images aligned to template id"
returnType="//@libraries.3/@types.0"
query="MATCH (n:Template {short_form:'$ID'})<-[:depicts]-(:Template)<-[r:in_register_with]-(dc:Individual)-[:depicts]->(di:Individual) WHERE not has(r.index) OPTIONAL MATCH (di)-[:INSTANCEOF]->(d:Class) RETURN distinct di.short_form as id, di.label as name, coalesce(di.description[0],d.description[0]) as def, COLLECT(DISTINCT d.label) as type, replace(r.folder,'http:','https:') + '/thumbnailT.png' AS file"
countQuery="MATCH (n:Template {short_form:'$ID'})<-[:depicts]-(:Template)<-[r:in_register_with]-(dc:Individual)-[:depicts]->(di:Individual) WHERE not has(r.index) RETURN count(di) as count"/>
<queryChain
xsi:type="gep_2:ProcessQuery"
name="Process Images"
returnType="//@libraries.3/@types.0"
queryProcessorId="vfbCreateResultListForIndividualsForQueryResultsQueryProcessor"/>
</queries>
<fetchVariableQuery
xsi:type="gep_2:CompoundQuery"
name="The compound query for augmenting a type"
description="">
<queryChain
xsi:type="gep_2:SimpleQuery"
name="Get term info"
description="Fetches essential details."
query="MATCH (n {short_form:'$ID'}) OPTIONAL MATCH (n)-[r]-(o) where not o.short_form starts with 'VFB_internal' WITH n, r, o, startnode(r) as s WITH n, r, o, CASE when s.iri = n.iri then 'node' else 'to' end as starts WHERE starts = 'node' OR type(r) = 'depicts' OR type(r) = 'is a' OR type(r) = 'INSTANCEOF' OR type(r) = 'has_source' OR type(r) = 'expresses' OR type(r) = 'has_license' OPTIONAL MATCH (n:Class)<-[r:SUBCLASSOF]-(o:Class)<-[fr:INSTANCEOF]-(fo:Individual)<-[:depicts]-(:Individual)-[i0:in_register_with]->(:Individual)-[:depicts]->(t0:Individual) OPTIONAL MATCH (o:Individual)<-[:depicts]-(:Individual)-[i1:in_register_with]->(:Template)-[:depicts]->(t1:Individual) WHERE NOT o:Template OPTIONAL MATCH (o:Individual)-[i2:in_register_with]->(:Template)-[:depicts]->(t2:Individual) OPTIONAL MATCH (o:Template)<-[i3:in_register_with]-(:Individual)-[:depicts]->(t3:Individual)-[:INSTANCEOF {label:'type'}]->(dc:Class) WHERE has(i3.index) WITH n, r, starts, coalesce(i1,i3,i2,i0) as i, coalesce(t1,t3,t2,t0) as t, dc, o, fr, fo ORDER BY t.short_form ASC RETURN 0 as order, labels(n) as labels, n as node, COLLECT({edge:coalesce(fr,r),types:type(coalesce(fr,r)),start:starts,to:coalesce(fo,dc,o),labels:labels(coalesce(fo,o)),tempIm:i,temp:t}) as links UNION ALL MATCH (pi:Individual:Synaptic_neuropil {short_form:'$ID'})-[pr:INSTANCEOF {label:'type'}]->(n:Class) MATCH (n)-[r]->(o) WHERE NOT type(r) = 'REFERSTO' RETURN 1 as order, labels(n) as labels, n as node, COLLECT({edge:r,types:type(r),start:'node',to:o,labels:labels(o),tempIm:null,temp:null}) as links ORDER BY order ASC UNION ALL MATCH (pi:Individual:Cluster {short_form:'$ID'})-[pr:has_exemplar]->(n:Individual) MATCH (n)-[r]->(o) WHERE NOT type(r) = 'REFERSTO' RETURN 1 as order, labels(n) as labels, n as node, COLLECT({edge:r,types:type(r),start:'node',to:o,labels:labels(o),tempIm:null,temp:null}) as links ORDER BY order ASC"
countQuery="MATCH (n { short_form: '$ID' } ) RETURN count(n) as count"/>
<queryChain
xsi:type="gep_2:ProcessQuery"
name="Process Term Info"
description="Process Term Info"
queryProcessorId="vfbProcessTermInfo"/>
</fetchVariableQuery>
</dataSources>
<dataSources
id="aberOWLDataSource"
name="Aber OWL Data Source"
dataSourceService="aberOWLDataSource"
url="http://VFB_OWL_SERVER/api/runQuery.groovy"
dependenciesLibrary="//@libraries.3"
targetLibrary="//@libraries.4"/>
<dataSources
id="owleryDataSourceSubclass"
name="owlery Data Source (subclasses)"
dataSourceService="owleryDataSource"
url="http://VFB_OWL_SERVER/kbs/vfb/subclasses"
dependenciesLibrary="//@libraries.3"
targetLibrary="//@libraries.4">
<queries
xsi:type="gep_2:SimpleQuery"
name="Owlery Part of"
description="Part of $NAME"
query="object=%3Chttp://purl.obolibrary.org/obo/BFO_0000050%3E%20some%20%3Chttp://purl.obolibrary.org/obo/$ID%3E&direct=false&includeDeprecated=false&includeEquivalent=true"
countQuery=""/>
<queries
xsi:type="gep_2:SimpleQuery"
name="Owlery Neuron class with part here"
description="Neurons with some part here"
query="object=%3Chttp://purl.obolibrary.org/obo/FBbt_00005106%3E%20and%20%3Chttp://purl.obolibrary.org/obo/RO_0002131%3E%20some%20%3Chttp://purl.obolibrary.org/obo/$ID%3E&direct=false&includeDeprecated=false&includeEquivalent=true"
countQuery=""/>
<queries
xsi:type="gep_2:SimpleQuery"
name="Owlery Neurons Synaptic"
description="Neurons with synaptic terminals here"
query="object=%3Chttp://purl.obolibrary.org/obo/FBbt_00005106%3E%20and%20%3Chttp://purl.obolibrary.org/obo/RO_0002130%3E%20some%20%3Chttp://purl.obolibrary.org/obo/$ID%3E&direct=false&includeDeprecated=false&includeEquivalent=true"
countQuery=""/>
<queries
xsi:type="gep_2:SimpleQuery"
name="Owlery Neurons Presynaptic"
description="Neurons with presynaptic terminals here"
query="object=%3Chttp://purl.obolibrary.org/obo/FBbt_00005106%3E%20and%20%3Chttp://purl.obolibrary.org/obo/RO_0002113%3E%20some%20%3Chttp://purl.obolibrary.org/obo/$ID%3E&direct=false&includeDeprecated=false&includeEquivalent=true"
countQuery=""/>
<queries
xsi:type="gep_2:SimpleQuery"
name="Owlery Neurons Postsynaptic"
description="Neurons with postsynaptic terminals here"
query="object=%3Chttp://purl.obolibrary.org/obo/FBbt_00005106%3E%20and%20%3Chttp://purl.obolibrary.org/obo/RO_0002110%3E%20some%20%3Chttp://purl.obolibrary.org/obo/$ID%3E&direct=false&includeDeprecated=false&includeEquivalent=true"
countQuery=""/>
<queries
xsi:type="gep_2:ProcessQuery"
id="owlPassIdListOnly"
name="Owlery Pass id list only"
description="Keep nothing slimply pass ids"
queryProcessorId="owleryIdOnlyQueryProcessor"/>
<queries
xsi:type="gep_2:SimpleQuery"
id="AberNeuronClassesFasciculatingHere"
name="Owlery Neuron classes fasciculating here"
description="Neuron classes fasciculating here"
returnType="//@libraries.3/@types.1"
query="object=%3Chttp://purl.obolibrary.org/obo/FBbt_00005106%3E%20and%20%3Chttp://purl.obolibrary.org/obo/RO_0002101%3E%20some%20%3Chttp://purl.obolibrary.org/obo/$ID%3E&direct=false&includeDeprecated=false&includeEquivalent=true"
countQuery=""/>
<queries
xsi:type="gep_2:SimpleQuery"
id="innervatesX"
name="Owlery tracts in"
description="tracts in"
returnType="//@libraries.3/@types.1"
query="object=%3Chttp://purl.obolibrary.org/obo/FBbt_00005099%3E%20and%20%3Chttp://purl.obolibrary.org/obo/RO_0002134%3E%20some%20%3Chttp://purl.obolibrary.org/obo/$ID%3E&direct=false&includeDeprecated=false&includeEquivalent=true"
countQuery=""/>
<queries
xsi:type="gep_2:SimpleQuery"
id="subclasses"
name="Owlery Subclasses of"
description="Subclasses of $NAME"
returnType="//@libraries.3/@types.1"
query="object=%3Chttp://purl.obolibrary.org/obo/$ID%3E&direct=false&includeDeprecated=false&includeEquivalent=true"
countQuery=""/>
<queries
xsi:type="gep_2:SimpleQuery"
id="TransgenesExpressedInX "
name="Owlery Transgenes expressed in "
description="Transgenes expressed in "
returnType="//@libraries.3/@types.1"
query=""/>
<queries
xsi:type="gep_2:SimpleQuery"
id="lineageClones"
name="Owlery Lineage Clones"
description="Lineage clones found in"
query="object=%3Chttp://purl.obolibrary.org/obo/FBbt_00007683%3E%20and%20%3Chttp://purl.obolibrary.org/obo/RO_0002131%3E%20some%20%3Chttp://purl.obolibrary.org/obo/$ID%3E&direct=false&includeDeprecated=false&includeEquivalent=true"
countQuery=""/>
</dataSources>
<dataSources
id="owleryDataSourceRealise"
name="owlery Data Source (instances)"
dataSourceService="owleryDataSource"
url="http://VFB_OWL_SERVER/kbs/vfb/instances"
dependenciesLibrary="//@libraries.3"
targetLibrary="//@libraries.4">
<queries
xsi:type="gep_2:SimpleQuery"
id="ImagesOfNeuronsWithSomePartHereClustered"
name="Owlery Images of neurons with some part here (clustered)"
description="Images of neurons with some part here (clustered)"
returnType="//@libraries.3/@types.22"
query="object=%3Chttp://purl.obolibrary.org/obo/C888C3DB-AEFA-447F-BD4C-858DFE33DBE7%3E%20some%20(%3Chttp://purl.obolibrary.org/obo/FBbt_00005106%3E%20and%20%3Chttp://purl.obolibrary.org/obo/RO_0002131%3E%20some%20%3Chttp://purl.obolibrary.org/obo/$ID%3E)&direct=false&includeDeprecated=false"
countQuery=""/>
<queries
xsi:type="gep_2:SimpleQuery"
id="ImagesOfNeuronsWithSomePartHere"
name="Owlery Images of neurons with some part here"
description="Images of neurons with some part here"
returnType="//@libraries.3/@types.2"
query="object=%3Chttp://purl.obolibrary.org/obo/FBbt_00005106%3E%20and%20%3Chttp://purl.obolibrary.org/obo/RO_0002131%3E%20some%20%3Chttp://purl.obolibrary.org/obo/$ID%3E&direct=false&includeDeprecated=false"
countQuery=""/>
<queries
xsi:type="gep_2:SimpleQuery"
id="Owlery_individual_parts"
name="Owlery individual parts"
description="Find individuals that are part of some X (useful for finding expression pattern parts)."
returnType="//@libraries.3/@types.0"
query="object=%3Chttp://purl.obolibrary.org/obo/BFO_0000050%3E%20some%20%3Chttp://virtualflybrain.org/reports/$ID%3E&direct=false&includeDeprecated=false"
countQuery=""/>
<queries
xsi:type="gep_2:ProcessQuery"
id="owlPassIdListOnlyInstances"
name="Owlery Pass id list only Instances"
description="Keep nothing slimply pass ids"
returnType="//@libraries.3/@types.0"
queryProcessorId="owleryIdOnlyQueryProcessor"/>
</dataSources>
<dataSources
id="opencpuDataSource"
name="NBLAST Data Source"
dataSourceService="opencpuDataSource"
url="http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast/json"
dependenciesLibrary="//@libraries.3"
targetLibrary="//@libraries.4">
<queries
xsi:type="gep_2:SimpleQuery"
id="nblastSimilarTo"
name="NBLAST similar to"
description="Similar to $NAME"
query=""query":"$ID","target":"FlyCircuit","n":25,"vfb_ids":true,"normalisation":"mean""
countQuery="">
<matchingCriteria
type="//@libraries.3/@types.0 //@libraries.3/@types.2 //@libraries.3/@types.25"/>
</queries>
<queries
xsi:type="gep_2:SimpleQuery"
id="nblastGal4To"
name="NBLAST Transgene for"
description="NBLAST for potential GAL4 patterns targetting $NAME"
returnType="//@libraries.3/@types.0"
query=""query":"$ID","target":"GMR-Gal4","n":25,"vfb_ids":true"
countQuery="">
<matchingCriteria
type="//@libraries.3/@types.0 //@libraries.3/@types.2 //@libraries.3/@types.25"/>
</queries>
<queries
xsi:type="gep_2:ProcessQuery"
id="nblastPassIdAndScores"
name="NBLAST pass ids and scores"
description="Keep nothing slimply pass ids and scores"
queryProcessorId="nblastQueryProcessor"/>
</dataSources>
<queries xsi:type="gep_2:CompoundRefQuery"
id="ListAllExamples"
name="List all example images for class with examples"
description="List all example images of $NAME"
returnType="//@libraries.3/@types.0"
queryChain="//@dataSources.0/@queries.3">
<matchingCriteria
type="//@libraries.3/@types.21 //@libraries.3/@types.1"/>
</queries>
<queries xsi:type="gep_2:CompoundRefQuery"
id="CompSubclasses"
name="Subclasses of"
description="Subclasses of $NAME"
returnType="//@libraries.3/@types.1"
queryChain="//@dataSources.2/@queries.8 //@dataSources.2/@queries.5 //@dataSources.0/@queries.0">
<matchingCriteria
type="//@libraries.3/@types.1"/>
</queries>
<queries xsi:type="gep_2:CompoundRefQuery"
id="partsof"
name="Parts of"
description="Parts of $NAME"
returnType="//@libraries.3/@types.1"
queryChain="//@dataSources.2/@queries.0 //@dataSources.2/@queries.5 //@dataSources.0/@queries.0">
<matchingCriteria
type="//@libraries.3/@types.1"/>
</queries>
<queries xsi:type="gep_2:CompoundRefQuery"
id="CompNeuronClassesFasciculatingHere"
name="Neuron classes fasciculating here"
description="Neurons fasciculating in $NAME"
returnType="//@libraries.3/@types.1"
queryChain="//@dataSources.2/@queries.6 //@dataSources.2/@queries.5 //@dataSources.0/@queries.0">
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.3"/>
</queries>
<queries xsi:type="gep_2:CompoundRefQuery"
id="ImagesNeurons"
name="Images of neurons with some part here"
description="Images of neurons with some part in $NAME"
returnType="//@libraries.3/@types.2"
queryChain="//@dataSources.3/@queries.1 //@dataSources.3/@queries.3 //@dataSources.0/@queries.1">
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.5"/>
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.23"/>
</queries>
<queries xsi:type="gep_2:CompoundRefQuery"
id="ImagesNeuronsClustered"
name="Images of neurons with some part here (clustered)"
description="Images of neurons with some part in $NAME (clustered)"
returnType="//@libraries.3/@types.22"
queryChain="//@dataSources.3/@queries.0 //@dataSources.3/@queries.3 //@dataSources.0/@queries.1">
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.5"/>
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.23"/>
</queries>
<queries xsi:type="gep_2:CompoundRefQuery"
id="neuronsparthere"
name="Neurons with any part here"
description="Neurons with some part in $NAME"
queryChain="//@dataSources.2/@queries.1 //@dataSources.2/@queries.5 //@dataSources.0/@queries.0">
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.5"/>
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.26"/>
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.23"/>
</queries>
<queries xsi:type="gep_2:CompoundRefQuery"
id="epFrag"
name="Images of expression pattern fragments"
description="Images of fragments of $NAME"
queryChain="//@dataSources.3/@queries.2 //@dataSources.3/@queries.3 //@dataSources.0/@queries.1">
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.27"/>
</queries>
<queries xsi:type="gep_2:CompoundRefQuery"
id="neuronssynaptic"
name="Neurons Synaptic"
description="Neurons with synaptic terminals in $NAME"
queryChain="//@dataSources.2/@queries.2 //@dataSources.2/@queries.5 //@dataSources.0/@queries.0">
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.5"/>
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.26"/>
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.23"/>
</queries>
<queries xsi:type="gep_2:CompoundRefQuery"
id="neuronspresynaptic"
name="Neurons Presynaptic"
description="Neurons with presynaptic terminals in $NAME"
queryChain="//@dataSources.2/@queries.3 //@dataSources.2/@queries.5 //@dataSources.0/@queries.0">
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.5"/>
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.26"/>
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.23"/>
</queries>
<queries xsi:type="gep_2:CompoundRefQuery"
id="neuronspostsynaptic"
name="Neurons Postsynaptic"
description="Neurons with postsynaptic terminals in $NAME"
queryChain="//@dataSources.2/@queries.4 //@dataSources.2/@queries.5 //@dataSources.0/@queries.0">
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.5"/>
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.26"/>
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.23"/>
</queries>
<queries xsi:type="gep_2:CompoundRefQuery"
id="ListClustMembers"
name="Cluster Members"
description="Neurons in $NAME"
returnType="//@libraries.3/@types.2"
queryChain="//@dataSources.0/@queries.5">
<matchingCriteria
type="//@libraries.3/@types.0 //@libraries.3/@types.22"/>
</queries>
<queries xsi:type="gep_2:CompoundRefQuery"
id="paintedDomains"
name="Show all painted domains for template"
description="List all painted anatomy available for $NAME"
returnType="//@libraries.3/@types.0"
queryChain="//@dataSources.0/@queries.4">
<matchingCriteria
type="//@libraries.3/@types.20 //@libraries.3/@types.0"/>
</queries>
<queries xsi:type="gep_2:CompoundRefQuery"
id="datasetImages"
name="Show all images for a dataset"
description="List all images included in $NAME"
returnType="//@libraries.3/@types.0"
queryChain="//@dataSources.0/@queries.6">
<matchingCriteria
type="//@libraries.3/@types.24"/>
</queries>
<queries xsi:type="gep_2:CompoundRefQuery"
id="CompNeuronClassesInnervatingHere"
name="Tracts/nerves innervating synaptic neuropil"
description="Tracts/nerves innervating $NAME"
returnType="//@libraries.3/@types.1"
queryChain="//@dataSources.2/@queries.7 //@dataSources.2/@queries.5 //@dataSources.0/@queries.0">
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.5"/>
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.23"/>
</queries>
<queries xsi:type="gep_2:CompoundRefQuery"
id="componentsOf"
name="Components of"
description="Components of $NAME"
returnType="//@libraries.3/@types.1"
queryChain="//@dataSources.2/@queries.0 //@dataSources.2/@queries.5 //@dataSources.0/@queries.0">
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.4"/>
</queries>
<queries xsi:type="gep_2:CompoundRefQuery"
id="lineageClonesIn"
name="Lineage clones found here"
description="Lineage clones found in $NAME"
returnType="//@libraries.3/@types.4"
queryChain="//@dataSources.2/@queries.10 //@dataSources.2/@queries.5 //@dataSources.0/@queries.0">
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.5"/>
<matchingCriteria
type="//@libraries.3/@types.1 //@libraries.3/@types.23"/>
</queries>
<queries xsi:type="gep_2:CompoundRefQuery"
id="similarto"
name="NBLAST Similar to"
description="NBLAST Similar to $NAME"
returnType="//@libraries.3/@types.2"
queryChain="//@dataSources.4/@queries.0 //@dataSources.4/@queries.2 //@dataSources.0/@queries.1">
<matchingCriteria
type="//@libraries.3/@types.0 //@libraries.3/@types.2 //@libraries.3/@types.25"/>
</queries>
<queries xsi:type="gep_2:CompoundRefQuery"
id="targeting"
name="NBLAST GAL4 tragetting"
description="NBLAST potential GAL4's targetting $NAME"
returnType="//@libraries.3/@types.0"
queryChain="//@dataSources.4/@queries.1 //@dataSources.4/@queries.2 //@dataSources.0/@queries.1">
<matchingCriteria
type="//@libraries.3/@types.0 //@libraries.3/@types.2 //@libraries.3/@types.25"/>
</queries>
<queries xsi:type="gep_2:CompoundRefQuery"
id="alignedImages"
name="Show all images aligned to template"
description="List all images aligned to $NAME"
returnType="//@libraries.3/@types.0"
queryChain="//@dataSources.0/@queries.7">
<matchingCriteria
type="//@libraries.3/@types.20 //@libraries.3/@types.0"/>
</queries>
</gep:GeppettoModel>