integrating data with phylogenies, at scale
TRANSCRIPT
![Page 1: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/1.jpg)
Integra(ngdatawithphylogenies,atscale
NicoCellineseUniversityofFlorida
&HilmarLappDukeUniversity
![Page 2: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/2.jpg)
WHAT’SINANAME?
![Page 3: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/3.jpg)
What’sinaname?
Chaos!• NamesandConceptsdonotreconcilethateasily• Namesaretextstrings• Contextislackingorsubjec(ve• Meaningisnotcomputable
![Page 4: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/4.jpg)
Linneannamespointtoconcepts
AntoineLaurentdeJussieuGeneraPlantarum,1789
![Page 5: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/5.jpg)
Linneannamespointtoconcepts
AntoineLaurentdeJussieuGeneraPlantarum,1789
![Page 6: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/6.jpg)
Linneannamespointtoconcepts
AntoineLaurentdeJussieuGeneraPlantarum,1789
Idon’tunderstandanyofthoseconceptswhetherinLaDnorEnglish,butIcansDlllinkthemtotheirnames,asinoneobject
tooneobject
![Page 7: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/7.jpg)
Linneannamespointtoconcepts
AntoineLaurentdeJussieuGeneraPlantarum,1789
…and200+
…and400+
![Page 8: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/8.jpg)
Idiosyncratic Russian dolls syndrome
![Page 9: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/9.jpg)
Idiosyncratic Russian dolls syndrome
![Page 10: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/10.jpg)
Idiosyncratic Russian dolls syndrome
![Page 11: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/11.jpg)
Idiosyncratic Russian dolls syndrome
![Page 12: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/12.jpg)
Idiosyncratic Russian dolls syndrome
![Page 13: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/13.jpg)
Idiosyncratic Russian dolls syndrome
![Page 14: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/14.jpg)
Idiosyncratic Russian dolls syndrome
![Page 15: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/15.jpg)
FromahumanperspecDve,welosetrackofconcepts.Hardtoreconcileallofthem.Weneedhelp!Canwecomputethem?
Idiosyncratic Russian dolls syndrome
![Page 16: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/16.jpg)
Linneannamespointtoconcepts
AntoineLaurentdeJussieuGeneraPlantarum,1789
…and200+
…and400+
![Page 17: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/17.jpg)
![Page 18: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/18.jpg)
• WecanuncluNerconcepts,andtherebynomenclature
• HowdowenavigatealongtheTreeofLiferepurposingLinneannames,whicharelinkedtotradi(onalconcepts?
![Page 19: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/19.jpg)
Darktaxa!
![Page 20: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/20.jpg)
Darktaxa!
Howdoweintegratedatawiththistree?
![Page 21: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/21.jpg)
Tree-thinkingCommondescentàevoluDonatthecenteroftaxonomy
B C D
Branches
Synapomorphies
A
Clades=taxa
Discovery
![Page 22: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/22.jpg)
Tree-thinkingCommondescentàevoluDonatthecenteroftaxonomy
Discovery
CommunicaDonHow??
014
7De
nsity
0.07
0.22
0.72Diversification rate
![Page 23: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/23.jpg)
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
![Page 24: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/24.jpg)
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)
![Page 25: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/25.jpg)
BoththeEncyclopediaofLife(EOL)andtheOpenTreeofLifesuggestthatCampanuloideaeisamisspellingofCampaniloidea(marinegastropods!)GBIFdoesnotcurrentlyhaveCampanuloideaeinitsbackbonetaxonomy.
![Page 26: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/26.jpg)
Areyoukiddingme?
ThesearetheCampanuloideae!
Wangetal.2014
![Page 27: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/27.jpg)
LifeasastreetmapHowtonavigatelifeasamachine
![Page 28: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/28.jpg)
Mappingdatatophylogene(cknowledgespace
![Page 29: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/29.jpg)
![Page 30: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/30.jpg)
Streetsignsservepeople,notmachines
![Page 31: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/31.jpg)
• HowdowebuildareliableGPSforphylogenies?• Howdowereproduciblyfindtherightnodes?
Mappingdatatophylogene(cknowledgespace
![Page 32: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/32.jpg)
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
![Page 33: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/33.jpg)
Phyloreference=
Logicdefini(onofaclade,usingthepropertycommonto
alloflife
![Page 34: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/34.jpg)
PhyloreferencesStatementsformallyexpressingthepaaernswediscover
(analogoustomapcoordinates)
Node-Based Branch-Based Apomorphy-Based
A B C A B C A B C
X
ThecladeoriginaDngwiththelastcommonancestorofBandC.
ThecladeoriginaDngwiththefirstancestorofBthatisnotanancestorofA.
ThecladeoriginaDngwiththefirstancestorofCtoevolveX.
![Page 35: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/35.jpg)
PhyloreferencesyieldacoordinatesystemfortheTreeofLife
• Anynode,branch,subtreeisreferenceable• Referencesareunambiguous• Referencesarecomputable• Referencesareportable• Adaptstonewandchangingknowledge
![Page 36: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/36.jpg)
Manyneededtechnologiesalreadyexist
• OWLontologiesdesignedfor– PhylogeneDcknowledge:
CDAO
– Phenotypicknowledge:Uberon,PATO,…
– Efficientandexpressivereasoners:FaCT++,HermiT,Racer,ELK
![Page 37: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/37.jpg)
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
![Page 38: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/38.jpg)
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
![Page 39: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/39.jpg)
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
![Page 40: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/40.jpg)
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.
![Page 41: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/41.jpg)
Challenges
• OWL-baseddatamodeltosaDsfyphylogeneDctaxonomy,reasoningexpressivity,scalability
• ConvenDonsfordatatransformaDon,andconsequencesofdifferentchoices
• LeastcommonancestorreasoningforOWLdata
• LackofcanonicalspecimenidenDfiersystem• Specifiermappingontologies
![Page 42: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/42.jpg)
TreeofLife,ontologized:Auniversalcoordinatesystem
• TheTreeofLifeisitselfanaggregaDonandintegraDonofourphylogeneDcknowledge.
• Phyloreferencingisaddressingintoaknowledgeuniverse.
• Ontologies,reasoning,andotherKRtechniquesarepowerfultoolsforthis.
![Page 43: Integrating data with phylogenies, at scale](https://reader034.vdocument.in/reader034/viewer/2022042707/58f307f01a28ab895b8b45d7/html5/thumbnails/43.jpg)
Acknowledgements
• NaDonalScienceFoundaDon(DBI-1458484)• KenandLindaMcGurn• Phenoscape• EvoIO