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Merge pull request #189 from obo-behavior/ditch-template-pipeline
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Ethology module: Upper level changes by @DitchingIt
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@matentzn
matentzn authored Nov 15, 2023
2 parents e82dbdd + 7fa4052 commit 26867b1
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120 changes: 94 additions & 26 deletions src/ontology/nbo-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -1022,6 +1022,9 @@ Declaration(Class(obo:NBO_0070001))
Declaration(Class(obo:NBO_0070002))
Declaration(Class(obo:NBO_0070003))
Declaration(Class(obo:NBO_0070004))
Declaration(Class(obo:NBO_0070006))
Declaration(Class(obo:NBO_0070007))
Declaration(Class(obo:NBO_0070008))
Declaration(Class(obo:PATO_0000001))
Declaration(Class(obo:PATO_0000014))
Declaration(Class(obo:PATO_0000040))
Expand Down Expand Up @@ -1080,13 +1083,16 @@ Declaration(AnnotationProperty(oboInOwl:hasNarrowSynonym))
Declaration(AnnotationProperty(oboInOwl:hasOBONamespace))
Declaration(AnnotationProperty(oboInOwl:hasRelatedSynonym))
Declaration(AnnotationProperty(oboInOwl:hasSynonymType))
Declaration(AnnotationProperty(oboInOwl:inSubset))
Declaration(AnnotationProperty(oboInOwl:note))
Declaration(AnnotationProperty(oboInOwl:remark))
Declaration(AnnotationProperty(oboInOwl:source))
Declaration(AnnotationProperty(oboInOwl:treat-xrefs-as-equivalent))
Declaration(AnnotationProperty(oboInOwl:xref))
Declaration(AnnotationProperty(rdfs:comment))
Declaration(AnnotationProperty(owl:deprecated))
Declaration(AnnotationProperty(<http://www.w3.org/2004/02/skos/core#exactMatch>))
Declaration(Datatype(xsd:date))

############################
# Object Properties
Expand Down Expand Up @@ -1205,25 +1211,34 @@ SubClassOf(obo:NBO_0000009 obo:NBO_0000644)

# Class: obo:NBO_0000010 (reproductive behavior)

AnnotationAssertion(obo:IAO_0000115 obo:NBO_0000010 "Behavior directly related to the production of offspring [NBO:AC]")
AnnotationAssertion(dc:date obo:NBO_0000010 "2011-04-14T01:03:39Z")
AnnotationAssertion(oboInOwl:created_by obo:NBO_0000010 "George Gkoutos")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:NBO_0000010 "reproduction"@en)
AnnotationAssertion(Annotation(obo:IAO_0000119 "Immelmann, K., & Beer, C. (1989). A dictionary of ethology. Harvard University Press.") Annotation(oboInOwl:hasDbXref "ISBN:0674205065") obo:IAO_0000115 obo:NBO_0000010 "A behavior process that tends to increase, “the propagation of new individuals”.")
AnnotationAssertion(obo:IAO_0000116 obo:NBO_0000010 "Disjointing parental behavior follows original NBO structural intent despite many experts.")
AnnotationAssertion(terms:contributor obo:NBO_0000010 <https://orcid.org/0000-0002-2061-091X>)
AnnotationAssertion(terms:contributor obo:NBO_0000010 <https://orcid.org/0000-0002-4277-2151>)
AnnotationAssertion(terms:date obo:NBO_0000010 "2011-04-14T01:03:39Z"^^xsd:date)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:NBO_0000010 "reproduction")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:NBO_0000010 "reproductive behaviour")
AnnotationAssertion(oboInOwl:hasOBONamespace obo:NBO_0000010 "behavior_ontology")
AnnotationAssertion(oboInOwl:xref obo:NBO_0000010 "GO:0019098")
AnnotationAssertion(oboInOwl:inSubset obo:NBO_0000010 <http://purl.obolibrary.org/obo/nbo#do_not_annotate>)
AnnotationAssertion(oboInOwl:inSubset obo:NBO_0000010 <http://purl.obolibrary.org/obo/nbo#ethology_module>)
AnnotationAssertion(rdfs:comment obo:NBO_0000010 "PRIOR DEFINITION: Behavior directly related to the production of offspring.")
AnnotationAssertion(rdfs:label obo:NBO_0000010 "reproductive behavior")
AnnotationAssertion(<http://www.w3.org/2004/02/skos/core#exactMatch> obo:NBO_0000010 obo:GO_0019098)
SubClassOf(obo:NBO_0000010 obo:NBO_0000313)
DisjointClasses(obo:NBO_0000010 obo:NBO_0000044)

# Class: obo:NBO_0000011 (social behavior)

AnnotationAssertion(obo:IAO_0000115 obo:NBO_0000011 "\"A behavior that occurs predominantly or only, in individuals that are part of a group.\" [Wikipedia:Social_behavior]")
AnnotationAssertion(dc:date obo:NBO_0000011 "2011-04-14T01:03:39Z")
AnnotationAssertion(oboInOwl:created_by obo:NBO_0000011 "George Gkoutos")
AnnotationAssertion(Annotation(obo:IAO_0000119 "Immelmann, K., & Beer, C. (1989). A dictionary of ethology. Harvard University Press.") Annotation(oboInOwl:hasDbXref "ISBN:0674205065") obo:IAO_0000115 obo:NBO_0000011 "A behavior process that interacts with a conspecific or similarly communicating symbiont.")
AnnotationAssertion(terms:contributor obo:NBO_0000011 <https://orcid.org/0000-0002-2061-091X>)
AnnotationAssertion(terms:date obo:NBO_0000011 "2011-04-14T01:03:39Z"^^xsd:date)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:NBO_0000011 "social behaviour")
AnnotationAssertion(oboInOwl:hasOBONamespace obo:NBO_0000011 "behavior_ontology")
AnnotationAssertion(oboInOwl:xref obo:NBO_0000011 "GO:0035176")
AnnotationAssertion(oboInOwl:inSubset obo:NBO_0000011 <http://purl.obolibrary.org/obo/nbo#do_not_annotate>)
AnnotationAssertion(oboInOwl:inSubset obo:NBO_0000011 <http://purl.obolibrary.org/obo/nbo#ethology_module>)
AnnotationAssertion(rdfs:comment obo:NBO_0000011 "PRIOR DEFINITION: \"A behavior that occurs predominantly or only, in individuals that are part of a group.")
AnnotationAssertion(rdfs:label obo:NBO_0000011 "social behavior")
AnnotationAssertion(<http://www.w3.org/2004/02/skos/core#exactMatch> obo:NBO_0000011 obo:GO_0035176)
SubClassOf(obo:NBO_0000011 obo:NBO_0000313)

# Class: obo:NBO_0000012 (seizures/epilepsy)
Expand Down Expand Up @@ -1842,14 +1857,20 @@ AnnotationAssertion(oboInOwl:hasOBONamespace obo:NBO_0000074 "behavior_ontology"
AnnotationAssertion(rdfs:label obo:NBO_0000074 "yawning")
SubClassOf(obo:NBO_0000074 obo:NBO_0000747)

# Class: obo:NBO_0000075 (playing behavior)
# Class: obo:NBO_0000075 (play)

AnnotationAssertion(obo:IAO_0000115 obo:NBO_0000075 "A very broad category including the partial or complete performance of adult functional behaviors in non-functional contexts, as well as interactive behaviors peculiar to immature animals [NBO:AC]")
AnnotationAssertion(dc:date obo:NBO_0000075 "2011-04-14T01:20:02Z")
AnnotationAssertion(oboInOwl:created_by obo:NBO_0000075 "George Gkoutos")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:NBO_0000075 "play"@en)
AnnotationAssertion(Annotation(obo:IAO_0000119 "Held, S. D., & Špinka, M. (2011). Animal play and animal welfare. Animal Behaviour, 81(5), 891–899.") Annotation(oboInOwl:hasDbXref "doi:10.1016/j.anbehav.2011.01.007") obo:IAO_0000115 obo:NBO_0000075 "A behavior process that is self-rewarding, repeated, and initiated when relaxed, but is only partially functional, structured, or timed.")
AnnotationAssertion(terms:contributor obo:NBO_0000075 <https://orcid.org/0000-0002-2061-091X>)
AnnotationAssertion(terms:contributor obo:NBO_0000075 <https://orcid.org/0000-0002-4277-2151>)
AnnotationAssertion(terms:date obo:NBO_0000075 "2011-04-14T01:20:02Z"^^xsd:date)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:NBO_0000075 "playing")
AnnotationAssertion(Annotation(oboInOwl:hasSynonymType obo:OMO_0003008) oboInOwl:hasExactSynonym obo:NBO_0000075 "playing behavior")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:NBO_0000075 "playing behaviour")
AnnotationAssertion(oboInOwl:hasOBONamespace obo:NBO_0000075 "behavior_ontology")
AnnotationAssertion(rdfs:label obo:NBO_0000075 "playing behavior")
AnnotationAssertion(oboInOwl:inSubset obo:NBO_0000075 <http://purl.obolibrary.org/obo/nbo#do_not_annotate>)
AnnotationAssertion(oboInOwl:inSubset obo:NBO_0000075 <http://purl.obolibrary.org/obo/nbo#ethology_module>)
AnnotationAssertion(rdfs:comment obo:NBO_0000075 "PRIOR DEFINITION: A very broad category including the partial or complete performance of adult functional behaviors in non-functional contexts, as well as interactive behaviors peculiar to immature animals.")
AnnotationAssertion(rdfs:label obo:NBO_0000075 "play")
SubClassOf(obo:NBO_0000075 obo:NBO_0000313)

# Class: obo:NBO_0000076 (locomotor play)
Expand Down Expand Up @@ -2011,11 +2032,18 @@ SubClassOf(obo:NBO_0000090 obo:NBO_0000087)

# Class: obo:NBO_0000091 (fear-related behavior)

AnnotationAssertion(Annotation(oboInOwl:source "NBO:GVG") obo:IAO_0000115 obo:NBO_0000091 "An emotional behavior related to a feeling of uneasiness or nervousness triggered by a specified triggering stimulus such as pain or the threat of danger.")
AnnotationAssertion(dc:date obo:NBO_0000091 "2011-03-31T10:00:42Z")
AnnotationAssertion(oboInOwl:created_by obo:NBO_0000091 "George Gkoutos")
AnnotationAssertion(Annotation(obo:IAO_0000119 "Mobbs, D., Adolphs, R., Fanselow, M. S., Barrett, L. F., LeDoux, J. E., Ressler, K., & Tye, K. M. (2019). Viewpoints: Approaches to defining and investigating fear. Nature Neuroscience, 22(8), 1205–1216.") Annotation(oboInOwl:hasDbXref "doi:10.1038/s41593-019-0456-6") obo:IAO_0000115 obo:NBO_0000091 "A behavior process that is cued by a negatively affective external threat.")
AnnotationAssertion(obo:IAO_0000116 obo:NBO_0000091 "There may need to be a future ontology transfer or obsoletion of NBO:0000018 fear/anxiety related behavior, and making fear-related behavior a direct child of NBO:0000313.")
AnnotationAssertion(terms:contributor obo:NBO_0000091 <https://orcid.org/0000-0002-2061-091X>)
AnnotationAssertion(terms:date obo:NBO_0000091 "2011-03-31T10:00:42Z"^^xsd:date)
AnnotationAssertion(oboInOwl:hasDbXref obo:NBO_0000091 "GO:0042596")
AnnotationAssertion(oboInOwl:hasDbXref obo:NBO_0000091 "MFOEM:000026")
AnnotationAssertion(oboInOwl:hasDbXref obo:NBO_0000091 "SIO:000837")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:NBO_0000091 "fear-related behaviour")
AnnotationAssertion(oboInOwl:hasOBONamespace obo:NBO_0000091 "behavior_ontology")
AnnotationAssertion(oboInOwl:inSubset obo:NBO_0000091 <http://purl.obolibrary.org/obo/nbo#do_not_annotate>)
AnnotationAssertion(oboInOwl:inSubset obo:NBO_0000091 <http://purl.obolibrary.org/obo/nbo#ethology_module>)
AnnotationAssertion(rdfs:comment obo:NBO_0000091 "The differentia is the minimum common denominator from a very contested field. PRIOR DEFINITION: An emotional behavior related to a feeling of uneasiness or nervousness triggered by a specified triggering stimulus such as pain or the threat of danger.")
AnnotationAssertion(rdfs:label obo:NBO_0000091 "fear-related behavior")
SubClassOf(obo:NBO_0000091 obo:NBO_0000018)

Expand Down Expand Up @@ -3154,9 +3182,7 @@ AnnotationAssertion(dc:date obo:NBO_0000209 "2011-04-03T08:58:27Z")
AnnotationAssertion(oboInOwl:created_by obo:NBO_0000209 "George Gkoutos")
AnnotationAssertion(oboInOwl:hasOBONamespace obo:NBO_0000209 "behavior_ontology")
AnnotationAssertion(rdfs:label obo:NBO_0000209 "fear conditioning")
EquivalentClasses(obo:NBO_0000209 ObjectIntersectionOf(obo:NBO_0000208 ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/nbo#is_about> obo:NBO_0000091)))
SubClassOf(obo:NBO_0000209 obo:NBO_0000778)
SubClassOf(obo:NBO_0000209 ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/nbo#is_about> obo:NBO_0000091))

# Class: obo:NBO_0000210 (avoidance learning behavior)

Expand Down Expand Up @@ -4374,13 +4400,19 @@ AnnotationAssertion(oboInOwl:hasOBONamespace obo:NBO_0000337 "behavior_ontology"
AnnotationAssertion(rdfs:label obo:NBO_0000337 "pressure related behavior")
SubClassOf(obo:NBO_0000337 obo:NBO_0000330)

# Class: obo:NBO_0000338 (kinesthetic behavior)
# Class: obo:NBO_0000338 (movement behavior)

AnnotationAssertion(obo:IAO_0000115 obo:NBO_0000338 "\"Movement behavior of the body or its parts.\"")
AnnotationAssertion(dc:date obo:NBO_0000338 "2011-04-05T02:08:47Z")
AnnotationAssertion(oboInOwl:created_by obo:NBO_0000338 "George Gkoutos")
AnnotationAssertion(Annotation(obo:IAO_0000119 "Dickinson, M. H., Farley, C. T., Full, R. J., Koehl, M. A. R., Kram, R., & Lehman, S. (2000). How animals move: An integrative view. Science, 288(5463), 100–106.") Annotation(oboInOwl:hasDbXref "doi:10.1126/science.288.5463.100") obo:IAO_0000115 obo:NBO_0000338 "A behavior process that, “exerts a force on the external environment”.")
AnnotationAssertion(obo:IAO_0000116 obo:NBO_0000338 "‘Kinesthetic’ has specific connotations around position sensation; ‘movement’ is a term used in the old definition and is simpler language.")
AnnotationAssertion(terms:contributor obo:NBO_0000338 <https://orcid.org/0000-0002-2061-091X>)
AnnotationAssertion(terms:date obo:NBO_0000338 "2011-04-05T02:08:47Z"^^xsd:date)
AnnotationAssertion(Annotation(oboInOwl:hasSynonymType obo:OMO_0003008) oboInOwl:hasExactSynonym obo:NBO_0000338 "kinesthetic behavior")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:NBO_0000338 "movement behaviour")
AnnotationAssertion(oboInOwl:hasOBONamespace obo:NBO_0000338 "behavior_ontology")
AnnotationAssertion(rdfs:label obo:NBO_0000338 "kinesthetic behavior")
AnnotationAssertion(oboInOwl:inSubset obo:NBO_0000338 <http://purl.obolibrary.org/obo/nbo#do_not_annotate>)
AnnotationAssertion(oboInOwl:inSubset obo:NBO_0000338 <http://purl.obolibrary.org/obo/nbo#ethology_module>)
AnnotationAssertion(rdfs:comment obo:NBO_0000338 "This is not always the same as movement, for example if behavioral efforts to move are unsuccessful. PRIOR DEFINITION: \"Movement behavior of the body or its parts.")
AnnotationAssertion(rdfs:label obo:NBO_0000338 "movement behavior")
SubClassOf(obo:NBO_0000338 obo:NBO_0000313)

# Class: obo:NBO_0000339 (motor coordination)
Expand Down Expand Up @@ -6635,7 +6667,6 @@ AnnotationAssertion(dc:date obo:NBO_0000568 "2011-04-14T08:31:34Z")
AnnotationAssertion(oboInOwl:created_by obo:NBO_0000568 "George Gkoutos")
AnnotationAssertion(oboInOwl:hasOBONamespace obo:NBO_0000568 "behavior_ontology")
AnnotationAssertion(rdfs:label obo:NBO_0000568 "kinesthetic behavior phenotype")
EquivalentClasses(obo:NBO_0000568 ObjectSomeValuesFrom(obo:BFO_0000056 ObjectIntersectionOf(obo:NBO_0000338 ObjectSomeValuesFrom(obo:RO_0000086 obo:PATO_0000001))))
SubClassOf(obo:NBO_0000568 obo:NBO_0000243)

# Class: obo:NBO_0000569 (fatigue)
Expand Down Expand Up @@ -10012,6 +10043,43 @@ AnnotationAssertion(oboInOwl:source obo:NBO_0070004 "Caro TM. The functions of s
AnnotationAssertion(rdfs:label obo:NBO_0070004 "stotting")
SubClassOf(obo:NBO_0070004 obo:NBO_0020077)

# Class: obo:NBO_0070006 (spatial behavior)

AnnotationAssertion(Annotation(obo:IAO_0000119 "Webber, Q. M., Albery, G. F., Farine, D. R., Pinter-Wollman, N., Sharma, N., Spiegel, O., Vander Wal, E., & Manlove, K. (2023). Behavioural ecology at the spatial–social interface. Biological Reviews, 98(3), 868–886.") Annotation(oboInOwl:hasDbXref "doi:10.1111/brv.12934") obo:IAO_0000115 obo:NBO_0070006 "A behavior process that uses geographical attributes to access or face an environmental resource, risk, or condition.")
AnnotationAssertion(terms:contributor obo:NBO_0070006 <https://orcid.org/0000-0002-4277-2151>)
AnnotationAssertion(terms:date obo:NBO_0070006 "2023-08-16T12:00:00Z"^^xsd:date)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:NBO_0070006 "spatial behaviour")
AnnotationAssertion(oboInOwl:hasOBONamespace obo:NBO_0070006 "behavior_ontology")
AnnotationAssertion(oboInOwl:inSubset obo:NBO_0070006 <http://purl.obolibrary.org/obo/nbo#do_not_annotate>)
AnnotationAssertion(oboInOwl:inSubset obo:NBO_0070006 <http://purl.obolibrary.org/obo/nbo#ethology_module>)
AnnotationAssertion(rdfs:label obo:NBO_0070006 "spatial behavior")
SubClassOf(obo:NBO_0070006 obo:NBO_0000313)

# Class: obo:NBO_0070007 (information processing behavior)

AnnotationAssertion(Annotation(obo:IAO_0000119 "Dukas, R. (Ed.). (1998). Introduction. In Cognitive ecology: The evolutionary ecology of information processing and decision making (pp. 1–19). University of Chicago Press.") Annotation(oboInOwl:hasDbXref "ISBN:0226169324") obo:IAO_0000115 obo:NBO_0070007 "A behavior process that translates a, “representation of the environment into adaptive decisions”.")
AnnotationAssertion(terms:contributor obo:NBO_0070007 <https://orcid.org/0000-0002-4277-2151>)
AnnotationAssertion(terms:date obo:NBO_0070007 "2023-08-16T12:00:00Z"^^xsd:date)
AnnotationAssertion(oboInOwl:hasDbXref obo:NBO_0070007 "SIO:000649")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:NBO_0070007 "information processing behaviour")
AnnotationAssertion(oboInOwl:hasOBONamespace obo:NBO_0070007 "behavior_ontology")
AnnotationAssertion(oboInOwl:inSubset obo:NBO_0070007 <http://purl.obolibrary.org/obo/nbo#do_not_annotate>)
AnnotationAssertion(oboInOwl:inSubset obo:NBO_0070007 <http://purl.obolibrary.org/obo/nbo#ethology_module>)
AnnotationAssertion(rdfs:label obo:NBO_0070007 "information processing behavior")
SubClassOf(obo:NBO_0070007 obo:NBO_0000313)

# Class: obo:NBO_0070008 (maintenance behavior)

AnnotationAssertion(Annotation(obo:IAO_0000119 "Ficken, R. W., & Ficken, M. S. (1966). A review of some aspects of avian field ethology. The Auk, 83(4), 637–661.") Annotation(oboInOwl:hasDbXref "doi:10.2307/4083155") obo:IAO_0000115 obo:NBO_0070008 "A behavior process that protects, “the general health and efficiency of the body”.")
AnnotationAssertion(terms:contributor obo:NBO_0070008 <https://orcid.org/0000-0002-4277-2151>)
AnnotationAssertion(terms:date obo:NBO_0070008 "2023-08-16T12:00:00Z"^^xsd:date)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:NBO_0070008 "maintenance behaviour")
AnnotationAssertion(oboInOwl:hasOBONamespace obo:NBO_0070008 "behavior_ontology")
AnnotationAssertion(oboInOwl:inSubset obo:NBO_0070008 <http://purl.obolibrary.org/obo/nbo#do_not_annotate>)
AnnotationAssertion(oboInOwl:inSubset obo:NBO_0070008 <http://purl.obolibrary.org/obo/nbo#ethology_module>)
AnnotationAssertion(rdfs:label obo:NBO_0070008 "maintenance behavior")
SubClassOf(obo:NBO_0070008 obo:NBO_0000313)


DisjointClasses(obo:NBO_0000014 obo:NBO_0000034 obo:NBO_0000078 obo:NBO_0020084 obo:NBO_0020254 obo:NBO_0020298 obo:NBO_0020299)
DisjointClasses(obo:NBO_0000048 obo:NBO_0000087 obo:NBO_0020015 obo:NBO_0020031 obo:NBO_0020037 obo:NBO_0020059 obo:NBO_0020077 obo:NBO_0020079 obo:NBO_0020105 obo:NBO_0020117 obo:NBO_0020139 obo:NBO_0020149 obo:NBO_0020175 obo:NBO_0020199 obo:NBO_0020223 obo:NBO_0020230 obo:NBO_0020245 obo:NBO_0020251 obo:NBO_0020268 obo:NBO_0020287 obo:NBO_0020289)
Expand Down
2 changes: 1 addition & 1 deletion src/ontology/nbo.Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ reports/phenotypes.tsv: nbo.owl
reports:
$(MAKE_FAST) reports/phenotypes.tsv

MERGE_TEMPLATE_URL="https://docs.google.com/spreadsheets/d/e/2PACX-1vRsAXkG-gL6DTCcV6hMZDuBzEiI7C2YqgcwxQn-6lFqnGPBP4egyU2njvErjuTU81p_rmfM7lwMmV-G/pub?gid=1360418429&single=true&output=tsv"
MERGE_TEMPLATE_URL="https://docs.google.com/spreadsheets/d/e/2PACX-1vSvSJAvqeV-YAT9c0g3QupJrrp4kZ2myTma95btJ0aKO7xxXGTmsgtafeTtZkUR-1-QuhflqfD1zt1X/pub?gid=545342398&single=true&output=tsv"
tmp/merge.tsv:
wget $(MERGE_TEMPLATE_URL) -O $@

Expand Down

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