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Ntr allelopath issue809 #815

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Ntr allelopath issue809 #815

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a46bc61
added 'has allelopath' as inverse of 'allelopath of'
mdrishti Aug 20, 2024
3538798
added 'has allelopath' as inverse of 'allelopath of'. Fixes #809
mdrishti Aug 20, 2024
fda13e4
Update ro-idranges.owl to include ranges for mdrishti
mdrishti Oct 15, 2024
6060298
Update ro-edit.owl to include hasAllelopath (fixes oborel#809)
mdrishti Oct 15, 2024
7cfbb5d
Update ro-edit.owl.
mdrishti Oct 15, 2024
61a51a1
Update ro-edit.owl
mdrishti Oct 15, 2024
58fdac2
Update ro-edit.owl
mdrishti Nov 6, 2024
70141d0
Upd ro-edit.owl, kept direction-neutral information in the primary di…
mdrishti Dec 3, 2024
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46 changes: 29 additions & 17 deletions src/ontology/ro-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -52,6 +52,7 @@ Declaration(Class(obo:UPHENO_0001001))
Declaration(Class(foaf:image))
Declaration(ObjectProperty(obo:BFO_0000050))
Declaration(ObjectProperty(obo:BFO_0000051))
Declaration(ObjectProperty(obo:RO_0020301))
Declaration(ObjectProperty(obo:RO_0000058))
Declaration(ObjectProperty(obo:RO_0000300))
Declaration(ObjectProperty(obo:RO_0000301))
Expand Down Expand Up @@ -1306,6 +1307,14 @@ AnnotationAssertion(oboInOwl:inSubset obo:BFO_0000066 obo:valid_for_go_ontology)
AnnotationAssertion(oboInOwl:inSubset obo:BFO_0000066 obo:valid_for_gocam)
AnnotationAssertion(rdfs:seeAlso obo:BFO_0000066 "https://wiki.geneontology.org/Occurs_in"^^xsd:anyURI)

# Object Property: obo:RO_0020301 (has allelopath)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0020301 <https://orcid.org/0009-0005-5515-1230>)
AnnotationAssertion(obo:IAO_0000115 obo:RO_0020301 "inverse of allelopath of")
AnnotationAssertion(rdfs:label obo:RO_0020301 "has allelopath"@en)
AnnotationAssertion(rdfs:seeAlso obo:RO_0020301 "https://en.wikipedia.org/wiki/Allelopathy")
SubObjectPropertyOf(obo:RO_0020301 obo:RO_0002574)
InverseObjectProperties(obo:RO_0020301 obo:RO_0002555)

# Object Property: obo:RO_0000052 (characteristic of)

SubObjectPropertyOf(obo:RO_0000052 obo:RO_0002314)
Expand Down Expand Up @@ -3887,8 +3896,8 @@ SubObjectPropertyOf(obo:RO_0002433 obo:RO_0002131)
# Object Property: obo:RO_0002434 (interacts with)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0002434 "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.")
AnnotationAssertion(obo:IAO_0000116 obo:RO_0002434 "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI)
AnnotationAssertion(obo:IAO_0000116 obo:RO_0002434 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.")
AnnotationAssertion(obo:IAO_0000116 obo:RO_0002434 "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002434 <https://orcid.org/0000-0002-6601-2165>)
AnnotationAssertion(obo:IAO_0000232 obo:RO_0002434 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0002434 "in pairwise interaction with")
Expand Down Expand Up @@ -4837,11 +4846,14 @@ SubObjectPropertyOf(obo:RO_0002554 obo:RO_0002453)
# Object Property: obo:RO_0002555 (allelopath of)

AnnotationAssertion(obo:IAO_0000117 obo:RO_0002555 <https://orcid.org/0000-0002-6601-2165>)
AnnotationAssertion(obo:IAO_0000115 obo:RO_0002555 "A relationship between organisms where one organism is influenced by the biochemicals produced by another.")
AnnotationAssertion(obo:IAO_0000119 obo:RO_0002555 "http://en.wikipedia.org/wiki/Allelopathy")
AnnotationAssertion(oboInOwl:inSubset obo:RO_0002555 subsets:ro-eco)
AnnotationAssertion(rdfs:comment obo:RO_0002555 "Allelopathy is a phenomenon in which one organism releases chemicals to positively or negatively influence the growth, survival or reproduction of other organisms in its vicinity.")
AnnotationAssertion(rdfs:label obo:RO_0002555 "allelopath of")
AnnotationAssertion(rdfs:seeAlso obo:RO_0002555 "http://eol.org/schema/terms/allelopathyYes")
AnnotationAssertion(rdfs:seeAlso obo:RO_0002555 "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y")
AnnotationAssertion(rdfs:seeAlso obo:RO_0002555 "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10172429/")
AnnotationAssertion(rdfs:seeAlso obo:RO_0002555 "x is an allelopath of y if x produces one or more biochemicals that influence the growth, survival, and reproduction of y")
SubObjectPropertyOf(obo:RO_0002555 obo:RO_0002574)

# Object Property: obo:RO_0002556 (pathogen of)
Expand Down Expand Up @@ -6638,10 +6650,10 @@ ObjectPropertyRange(obo:RO_0017005 obo:COB_0000121)

# Object Property: obo:RO_0017006 (has maximum capacity)

AnnotationAssertion(obo:IAO_0000112 obo:RO_0017006 "anticoagulant-containing test tube has maximum capacity 10 ml.")
AnnotationAssertion(obo:IAO_0000115 obo:RO_0017006 "A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume.")
AnnotationAssertion(terms:contributor obo:RO_0017006 <https://orcid.org/0000-0002-2999-0103>)
AnnotationAssertion(terms:contributor obo:RO_0017006 <https://orcid.org/0000-0002-5714-991X>)
AnnotationAssertion(obo:IAO_0000112 obo:RO_0017006 "anticoagulant-containing test tube has maximum capacity 10 ml.")
AnnotationAssertion(rdfs:label obo:RO_0017006 "has maximum capacity"@en)
ObjectPropertyDomain(obo:RO_0017006 obo:OBI_0000967)
ObjectPropertyRange(obo:RO_0017006 obo:COB_0000121)
Expand Down Expand Up @@ -7286,19 +7298,19 @@ DLSafeRule(Annotation(rdfs:seeAlso <https://github.com/oborel/obo-relations/issu
DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable(<urn:swrl:var#B>) Variable(<urn:swrl:var#C>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl:var#A>) Variable(<urn:swrl:var#B>)) ObjectPropertyAtom(obo:RO_0002013 Variable(<urn:swrl:var#D>) Variable(<urn:swrl:var#C>)))Head(ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl:var#A>) Variable(<urn:swrl:var#D>))))
DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable(<urn:swrl:var#B>) Variable(<urn:swrl:var#C>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl:var#A>) Variable(<urn:swrl:var#B>)) ObjectPropertyAtom(obo:RO_0002014 Variable(<urn:swrl:var#D>) Variable(<urn:swrl:var#C>)))Head(ObjectPropertyAtom(obo:RO_0002630 Variable(<urn:swrl:var#A>) Variable(<urn:swrl:var#D>))))
DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable(<urn:swrl:var#B>) Variable(<urn:swrl:var#C>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl:var#A>) Variable(<urn:swrl:var#B>)) ObjectPropertyAtom(obo:RO_0002015 Variable(<urn:swrl:var#D>) Variable(<urn:swrl:var#C>)))Head(ObjectPropertyAtom(obo:RO_0002629 Variable(<urn:swrl:var#A>) Variable(<urn:swrl:var#D>))))
DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#eff>)) ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl:var#eff>) Variable(<urn:swrl:var#in>)))Head(ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#in>))))
DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#eff>)) ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#in>)))Head(ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl:var#eff>) Variable(<urn:swrl:var#in>))))
DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#mf2>)) ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#eff>)))Head(ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl:var#eff>) Variable(<urn:swrl:var#mf2>))))
DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#eff>)) ObjectPropertyAtom(obo:RO_0002629 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#mf2>)))Head(ObjectPropertyAtom(obo:RO_0002629 Variable(<urn:swrl:var#eff>) Variable(<urn:swrl:var#mf2>))))
DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom(obo:RO_0002630 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#mf2>)) ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#eff>)))Head(ObjectPropertyAtom(obo:RO_0002630 Variable(<urn:swrl:var#eff>) Variable(<urn:swrl:var#mf2>))))
DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002131 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)) ObjectPropertyAtom(obo:RO_0002404 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)))Head(ClassAtom(owl:Nothing Variable(<urn:swrl:var#y>)) ClassAtom(owl:Nothing Variable(<urn:swrl:var#x>))))
DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002131 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)) ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)))Head(ClassAtom(owl:Nothing Variable(<urn:swrl:var#y>)) ClassAtom(owl:Nothing Variable(<urn:swrl:var#x>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002211 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>)) ObjectPropertyAtom(obo:RO_0012011 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>)))Head(ObjectPropertyAtom(obo:RO_0012012 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)) ObjectPropertyAtom(obo:RO_0002213 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)))Head(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)) ObjectPropertyAtom(obo:RO_0019002 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)))Head(ObjectPropertyAtom(obo:RO_0019001 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)) ObjectPropertyAtom(obo:RO_0002213 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)))Head(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)) ObjectPropertyAtom(obo:RO_0002264 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)))Head(ObjectPropertyAtom(obo:RO_0002263 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>)) ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#q>) Variable(<urn:swrl:var#u>)))Head(ObjectPropertyAtom(obo:RO_0012011 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#u>))))
DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl:var#eff>) Variable(<urn:swrl:var#in>)) ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#eff>)))Head(ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#in>))))
DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#in>)) ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#eff>)))Head(ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl:var#eff>) Variable(<urn:swrl:var#in>))))
DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#eff>)) ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#mf2>)))Head(ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl:var#eff>) Variable(<urn:swrl:var#mf2>))))
DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom(obo:RO_0002629 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#mf2>)) ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#eff>)))Head(ObjectPropertyAtom(obo:RO_0002629 Variable(<urn:swrl:var#eff>) Variable(<urn:swrl:var#mf2>))))
DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#eff>)) ObjectPropertyAtom(obo:RO_0002630 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#mf2>)))Head(ObjectPropertyAtom(obo:RO_0002630 Variable(<urn:swrl:var#eff>) Variable(<urn:swrl:var#mf2>))))
DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002404 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)) ObjectPropertyAtom(obo:RO_0002131 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)))Head(ClassAtom(owl:Nothing Variable(<urn:swrl:var#x>)) ClassAtom(owl:Nothing Variable(<urn:swrl:var#y>))))
DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)) ObjectPropertyAtom(obo:RO_0002131 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)))Head(ClassAtom(owl:Nothing Variable(<urn:swrl:var#x>)) ClassAtom(owl:Nothing Variable(<urn:swrl:var#y>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0012011 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>)) ObjectPropertyAtom(obo:RO_0002211 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>)))Head(ObjectPropertyAtom(obo:RO_0012012 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002213 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)) ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)))Head(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0019002 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)) ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)))Head(ObjectPropertyAtom(obo:RO_0019001 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002213 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)) ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)))Head(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002264 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)) ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)))Head(ObjectPropertyAtom(obo:RO_0002263 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#q>) Variable(<urn:swrl:var#u>)) ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>)))Head(ObjectPropertyAtom(obo:RO_0012011 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#u>))))
AnnotationAssertion(owl:deprecated obo:BFO_0000060 "true"^^xsd:boolean)
AnnotationAssertion(obo:IAO_0000115 obo:RO_0000092 "inverse of has disposition")
AnnotationAssertion(oboInOwl:inSubset obo:RO_0000092 obo:RO_0002259)
Expand All @@ -7312,4 +7324,4 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002086 subsets:ro-eco)
AnnotationAssertion(oboInOwl:inSubset obo:RO_0002089 subsets:ro-eco)
AnnotationAssertion(oboInOwl:inSubset obo:RO_0002093 subsets:ro-eco)
AnnotationAssertion(Annotation(rdfs:comment "This is an experimental annotation") obo:IAO_0000589 rdfs:isDefinedBy "is defined by")
)
)
4 changes: 4 additions & 0 deletions src/ontology/ro-idranges.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -119,3 +119,7 @@ EquivalentTo: xsd:integer[> 20100 , <= 20200]
Datatype: idrange:27
Annotations: allocatedto: "Ray Stefancsik"
EquivalentTo: xsd:integer[> 20201 , <= 20300]

Datatype: idrange:28
Annotations: allocatedto: "Disha Tandon"
EquivalentTo: xsd:integer[> 20301 , <= 20325]