Date post: | 16-Apr-2017 |
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Integra(ngdatawithphylogenies,atscale
NicoCellineseUniversityofFlorida
&HilmarLappDukeUniversity
WHAT’SINANAME?
What’sinaname?
Chaos!• NamesandConceptsdonotreconcilethateasily• Namesaretextstrings• Contextislackingorsubjec(ve• Meaningisnotcomputable
Linneannamespointtoconcepts
AntoineLaurentdeJussieuGeneraPlantarum,1789
Linneannamespointtoconcepts
AntoineLaurentdeJussieuGeneraPlantarum,1789
Linneannamespointtoconcepts
AntoineLaurentdeJussieuGeneraPlantarum,1789
Idon’tunderstandanyofthoseconceptswhetherinLaDnorEnglish,butIcansDlllinkthemtotheirnames,asinoneobject
tooneobject
Linneannamespointtoconcepts
AntoineLaurentdeJussieuGeneraPlantarum,1789
…and200+
…and400+
Idiosyncratic Russian dolls syndrome
Idiosyncratic Russian dolls syndrome
Idiosyncratic Russian dolls syndrome
Idiosyncratic Russian dolls syndrome
Idiosyncratic Russian dolls syndrome
Idiosyncratic Russian dolls syndrome
Idiosyncratic Russian dolls syndrome
FromahumanperspecDve,welosetrackofconcepts.Hardtoreconcileallofthem.Weneedhelp!Canwecomputethem?
Idiosyncratic Russian dolls syndrome
Linneannamespointtoconcepts
AntoineLaurentdeJussieuGeneraPlantarum,1789
…and200+
…and400+
• WecanuncluNerconcepts,andtherebynomenclature
• HowdowenavigatealongtheTreeofLiferepurposingLinneannames,whicharelinkedtotradi(onalconcepts?
Darktaxa!
Darktaxa!
Howdoweintegratedatawiththistree?
Tree-thinkingCommondescentàevoluDonatthecenteroftaxonomy
B C D
Branches
Synapomorphies
A
Clades=taxa
Discovery
Tree-thinkingCommondescentàevoluDonatthecenteroftaxonomy
Discovery
CommunicaDonHow??
014
7De
nsity
0.07
0.22
0.72Diversification rate
Tree-thinking
Berberidopsidaceae
OpilionesZingiberaceae
HamamelidaceaeSarcolaenaceae
Lingulidae
Hymenoptera
Mammalia
Apocynaceae
Galliformes
Rubiaceae
Anarthriaceae
Lineidae
CrocodylidaeStylosiphonia
Andrenidae Cracidae
Gavialis
Globba
Micrella Rhodoleia
Phalangiidae Tachyglossa
Lyginia
Mediusella
Chamaeclitandra
Tree-thinking
Berberidopsidaceae
OpilionesZingiberaceae
HamamelidaceaeSarcolaenaceae
Lingulidae
Hymenoptera
Mammalia
Apocynaceae
Galliformes
Rubiaceae
Anarthriaceae
Lineidae
CrocodylidaeStylosiphonia
Andrenidae Cracidae
Gavialis
Globba
Micrella Rhodoleia
Phalangiidae Tachyglossa
Lyginia
Mediusella
Chamaeclitandra
ThesenamesarenotgeneratedinanevoluDonary-basedframework(Groupsdefinedbycharactersimilarityvs.commondescent)
BoththeEncyclopediaofLife(EOL)andtheOpenTreeofLifesuggestthatCampanuloideaeisamisspellingofCampaniloidea(marinegastropods!)GBIFdoesnotcurrentlyhaveCampanuloideaeinitsbackbonetaxonomy.
Areyoukiddingme?
ThesearetheCampanuloideae!
Wangetal.2014
LifeasastreetmapHowtonavigatelifeasamachine
Mappingdatatophylogene(cknowledgespace
Streetsignsservepeople,notmachines
• HowdowebuildareliableGPSforphylogenies?• Howdowereproduciblyfindtherightnodes?
Mappingdatatophylogene(cknowledgespace
FEED
Textual Definition –
The hyoglossus is a muscle that attaches to the hyoid and tongue and is innervated by Cranial Nerve XII.
Computable Definition –
('attached to' some 'hyoid bone') and ('attached to' some tongue) and ('innervated by' some 'hypoglossal nerve') and spatially disjoint with 'intrinsic tongue muscle'
Druzinskyetal(2015):LogicdefiniDonsofmammalianfeedingmusclesbymeansofnecessaryandsufficientcondiDonstrueforallmammals
Nomenclature≠Seman(cs
Phyloreference=
Logicdefini(onofaclade,usingthepropertycommonto
alloflife
PhyloreferencesStatementsformallyexpressingthepaaernswediscover
(analogoustomapcoordinates)
Node-Based Branch-Based Apomorphy-Based
A B C A B C A B C
X
ThecladeoriginaDngwiththelastcommonancestorofBandC.
ThecladeoriginaDngwiththefirstancestorofBthatisnotanancestorofA.
ThecladeoriginaDngwiththefirstancestorofCtoevolveX.
PhyloreferencesyieldacoordinatesystemfortheTreeofLife
• Anynode,branch,subtreeisreferenceable• Referencesareunambiguous• Referencesarecomputable• Referencesareportable• Adaptstonewandchangingknowledge
Manyneededtechnologiesalreadyexist
• OWLontologiesdesignedfor– PhylogeneDcknowledge:
CDAO
– Phenotypicknowledge:Uberon,PATO,…
– Efficientandexpressivereasoners:FaCT++,HermiT,Racer,ELK
0.0
Campanula_rotundifolia
Pseudonemacladus_oppositifolius
Lobelia_cardinalis
Campanula_latifolia
Cyphocarpus_rigescens
Wahlenbergia_linifolia
Nemacladus_ramosissmus
Lobelia_coronopifolia
Cyphia_elata
Pentaphragma
Crysanthemum
Sphenoclea
Platycodon_grandiflorus
Cyphia_bulbosa
53
Campanula
1
7
8
9
4
Lobelia
Cyphia
6
1 0
2
Class:Campanulaceae_1889_to_1980EquivalentTo:cdao:has_Descendantvaluetaxon:Campanula_laDfoliaandphyloref:excludes_lineagevaluetaxon:Crysanthemum
0.0
Campanula_rotundifolia
Pseudonemacladus_oppositifolius
Lobelia_cardinalis
Campanula_latifolia
Cyphocarpus_rigescens
Wahlenbergia_linifolia
Nemacladus_ramosissmus
Lobelia_coronopifolia
Cyphia_elata
Pentaphragma
Crysanthemum
Sphenoclea
Platycodon_grandiflorus
Cyphia_bulbosa
53
Campanula
1
7
8
9
4
Lobelia
Cyphia
6
1 0
2
Class:Campanulaceae_1980EquivalentTo:cdao:has_Descendantvaluetaxon:Campanula_laDfoliaandphyloref:excludes_lineagevaluetaxon:Lobelia
0.0
Campanula_rotundifolia
Pseudonemacladus_oppositifolius
Lobelia_cardinalis
Campanula_latifolia
Cyphocarpus_rigescens
Wahlenbergia_linifolia
Nemacladus_ramosissmus
Lobelia_coronopifolia
Cyphia_elata
Pentaphragma
Crysanthemum
Sphenoclea
Platycodon_grandiflorus
Cyphia_bulbosa
53
Campanula
1
7
8
9
4
Lobelia
Cyphia
6
1 0
2
Class:Campanulaceae_aier_1995EquivalentTo:cdao:has_Descendantvaluetaxon:Campanula_laDfoliaandphyloref:excludes_lineagevaluetaxon:Sphenoclea
Phyloreferencesasontologicalexpressions
Phyloreferenceexpressionscanbe:• Easilygeneratedbyanyone
• Canworkonanytree• Namedandregistered
– Topromotereuseandconsistency
– Toimproveusabilityandaccessibility
Class:CampanulaceaeAnnota(ons:rdfs:label“Campanulaceae_aier_1995”dc:descripDon“thecladethatincludesCampanulalaDfoliabutnotSphenoclea”EquivalentTo:cdao:has_Descendantvaluetaxon:Campanula_laDfoliaandphyloref:excludes_lineagevaluetaxon:Sphenoclea
Class:AGF4-SHRU-3560EquivalentTo:cdao:has_Descendantvaluetaxon:Campanula_laDfoliaandphyloref:excludes_lineagevaluetaxon:Sphenoclea
vs.
Challenges
• OWL-baseddatamodeltosaDsfyphylogeneDctaxonomy,reasoningexpressivity,scalability
• ConvenDonsfordatatransformaDon,andconsequencesofdifferentchoices
• LeastcommonancestorreasoningforOWLdata
• LackofcanonicalspecimenidenDfiersystem• Specifiermappingontologies
TreeofLife,ontologized:Auniversalcoordinatesystem
• TheTreeofLifeisitselfanaggregaDonandintegraDonofourphylogeneDcknowledge.
• Phyloreferencingisaddressingintoaknowledgeuniverse.
• Ontologies,reasoning,andotherKRtechniquesarepowerfultoolsforthis.
Acknowledgements
• NaDonalScienceFoundaDon(DBI-1458484)• KenandLindaMcGurn• Phenoscape• EvoIO