Linked biology – from phenotypes towards phylogenetic trees

Linked biology – from phenotypes towards phylogenetic trees Eduardo de
Paula Miranda Advisor: Prof. Dr. André Santanchè Institute of Computing Unicamp November 22, 2013

Outline 2 1.  Introduction a.  Motivation b.  Goal 2.  Related
work 3.  Our approach 4.  Conclusion and Future work

Motivation 3 A large number of studies in biology result
in the production of a huge amount of data, for example: •  Phenotype descriptions •  Trees of species •  Trees of genes •  DNA sequence •  RNA sequence •  etc.

Motivation 4 A large number of studies in biology result
in the production of a huge amount of data, for example: •  Phenotype descriptions •  Trees of species •  Trees of genes •  DNA sequence •  RNA sequence •  etc.

Motivation 5 Phenotype are: •  A set of observable physical
characteristics and behavior of an individual, resulting from the interaction of its genotype (genetic makeup) with the environment.

Motivation 6 Phenotype are: •  A set of observable physical
characteristics and behavior of an individual, resulting from the interaction of its genotype (genetic makeup) with the environment. •  Eye color •  Hair color •  The sound of your voice

Motivation 7 Phenotype descriptions are •  Traditionally documented in natural
language.

Motivation 8 Phenotype descriptions are •  Traditionally documented in natural
language. •  Typically produced as independent entities.

Motivation 9 As a consequence, this wealth of information has
been largely •  Unavailable for computational comparisons across studies. •  Integration with other biological knowledge.

Motivation 10 Ontologies are one of the promising choices to
link and express explicitly the existing knowledge in biology.

Goal 11 Our challenge lies in How to take advantage
of the existing patrimony of data collected and develop techniques for support converting it into a new ontology- based representation.

Mapping CCS → EQ 12 Character / character-state (C,CS)

Mapping CCS → EQ 13 Character / character-state (C,CS) dorsal
fin shape Character

Mapping CCS → EQ 14 Character / character-state (C,CS) dorsal
fin shape semicircular triangular linear Character States

Mapping CCS → EQ 15 Ontology – Phenotype and Trait
Ontology (PATO) shape 2D shape 3D shape morphology size structure semicircular triangular quadrangular aliform subClassOf subClassOf subClassOf subClassOf

Mapping CCS → EQ 16 shape 2D shape 3D shape
morphology size structure semicircular triangular quadrangular aliform subClassOf subClassOf subClassOf subClassOf Ontology – Phenotype and Trait Ontology (PATO) Definition: A 2-D shape quality that have shape or form of half a circle

Mapping CCS → EQ 21 The benefits of using an
ontology include •  Standardization of terminology •  Explicit definitions of concepts •  The creation of structured representations of information that facilitate computability.

Mapping CCS → EQ 22 Ontology : Entity – Quality
(EQ) Anatomical Ontology Phenotype and Trait Ontology (PATO) + Entity Quality

Mapping CCS → EQ 23 Character dorsal fin shape circular
State

Mapping CCS → EQ 24 Vertebrate Skeletal Anatomy Ontology (VSAO)
http://purl.obolibrary.org/obo/VSAO_??????? Character dorsal fin shape circular dorsal fin (VSAO:0000165) State Entity

http://purl.obolibrary.org/obo/VSAO_??????? Character dorsal fin shape circular dorsal fin (VSAO:0000165) State Entity

http://purl.obolibrary.org/obo/VSAO_??????? Phenotype And Trait Ontology (PATO) http://purl.obolibrary.org/obo/PATO_??????? Character dorsal fin shape circular dorsal fin (VSAO:0000165) circular (PATO:0000411) 2D shape (PATO:0002006) subClassOf State Entity Quality shape (PATO:0000052) subClassOf

Mapping CCS → EQ 30 The mapping of character states
into EQs makes this difficult in two ways. 1.  The mapping between a character state and an EQ is not necessarily one-to-one.

into EQs makes this difficult in two ways. 1.  The mapping between a character state and an EQ is not necessarily one-to-one. Pattern of the end of tail banded or uniformly dark uniform pale yellow or white

into EQs makes this difficult in two ways. 2.  In the EQ formalism the attribute that forms part of a traditional character description is implicit in the hierarchical structure of the quality ontology.

into EQs makes this difficult in two ways. 2.  In the EQ formalism the attribute that forms part of a traditional character description is implicit in the hierarchical structure of the quality ontology. Character dorsal fin shape circular dorsal fin (VSAO:0000165) circular (PATO:0000411) 2D shape (PATO:0002006) subClassOf State Entity Quality shape (PATO:0000052) subClassOf

Related work 36 Phenote

Related work 37 Phenex

Our approach 42 We add an intermediate step between semi-
structured descriptions and ontologies, remodeling them to a graph abstraction. Ontology Dataspace Linked Graph

Our approach 43 We add an intermediate step between semi-
structured descriptions and ontologies, remodeling them to a graph abstraction. Ontology Dataspace Linked Graph

Our approach 44 Data interaction Heterogeneous data sources Phenotype descriptions,
morphological data matrices, phylogenetic tree extraction Graph import LSID linking Character association 2 1 3 4 Linked data Ontologies 5 6 7 Data access DataBase TreeBase Dryad etc. Excel XML CSV RDF Book Mashup DBtune DBPedia Jamendo US Census Data Project Guten- berg DBLP FOAF Revyu Music- brainz Geo- names world Fact book

Our approach 53 nostrils' form transversal section of the tail
nuchal scales Varanus albiguralis 2 1 2 Varanus brevicauda 1 2 1 Nostrils' form 1 – well round 2 – oval or split-like Transversal section of the tail 1 – laterally compressed 2 – roundish Nuchal scales 1 – same size than head scales 2 – bigger than head scales Morphological data matrices Characters Character-States Taxon Assigned States

Our approach 58 Structure Descriptive Data (SDD) CategoricalCharacter id=“c6”
States StateDefini9on id=“s12” “well round” “Nostrils look like a quite per...” Label Detail StateDefini9on id=“s13” “oval or split-‐like” “Nostrils are not perfectly rou...” Label Detail “nostrils' form” “Monitors' nostrils may have different forms...” Label Detail Representa9on Dataset Datasets “V. albiguralis” “White-‐throated monitor. DistribuIon: Africa (West...” Label Detail Representa9on CodedDescrip9on id=“D1” SummaryData Categorical ref=“c6” State ref=“s13” Characters Character-States Taxon Assigned States

Our approach Morphological data matrices Structure Descriptive Data (SDD) 63
OTU Type OTU Label Detail Character-State Type State Label Detail Type Character Detail Character Characters Character-States Taxon Assigned States CategoricalCharacter, id=“c6”( States, StateDefini2on, id=“s12”( “well(round”( “Nostrils(look(like(a(quite(per...”( Label, Detail, StateDefini2on, id=“s13”( “oval(or(split<like”( “Nostrils(are(not(perfectly(rou...”( Label, Detail, “nostrils'(form”( “Monitors'(nostrils(may(have(different(forms...”( Label, Detail, Representa2on, Dataset, Datasets, “V.(albiguralis”( “White<throated(monitor.(DistribuIon:(Africa((West...”( Label, Detail, Representa2on, CodedDescrip2on, id=“D1”( SummaryData, Categorical, ref=“c6”( State, ref=“s13”( nostrils' form transversal section of the tail nuchal scales Varanus albiguralis 2 1 2 Varanus brevicauda 1 2 1 Nostrils' form 1 – well round 2 – oval or split-like Transversal section of the tail 1 – laterally compressed 2 – roundish Nuchal scales 1 – same size than head scales 2 – bigger than head scales 1st Conceptual graph based model

7 distinct morphological descriptions: •  genus Varanus •  Varanus gouldii
•  Varanus indicus •  Varanus prasinus •  Varanus salvator •  Varanus spiny •  Varanus timorensis Our approach 66

Our approach 76 Varanus prasinus smooth, unkeeled granular to slightly
keeled triangular keeled, hull-shaped strongly keeled same size than head scales bigger than head scales Varanus beccarii Varanus bogerti Varanus komodoensis nuchal scales nuchal scales nuchal scales nuchal scales nuchal scales nuchal scales Prasinus.sdd Varanus.sdd OTU Type OTU Label Detail Character-State Type State Label Detail Type Character Detail Character

Our approach 77 Varanus prasinus smooth, unkeeled granular to slightly
keeled triangular keeled, hull-shaped strongly keeled same size than head scales bigger than head scales Varanus beccarii Varanus bogerti Varanus komodoensis nuchal scales nuchal scales nuchal scales nuchal scales nuchal scales nuchal scales Prasinus.sdd Varanus.sdd OTU Type OTU Label Detail Character-State Type State Label Detail Type Character Detail Character

Our approach OTU Type OTU Label Detail Character-State Type State
Label Detail Type Character Detail Character 79 Similarity Index 1st Conceptual graph based model

Label Detail Type Character Detail Character 1st Conceptual graph based model 80 Similarity Index 2nd Conceptual graph based model OTU Type OTU Label Detail Character Type Character Label Detail Character-State Type Character-State ! Label Detail

Label Detail Type Character Detail Character 81 Similarity Index 1st Conceptual graph based model 2nd Conceptual graph based model OTU Type OTU Label Detail Character Type Character Label Detail Character-State Type Character-State ! Label Detail

Our approach TreeEdge OTU Type OTU Label Detail Character Type
Character Label Detail HTU Type HTU Type TreeEdge Character-State Type Character-State Label Detail Character-State Type Character-State OTU Type OTU Label Detail Character-State Type State Label Detail Type Character Detail Character 84 Similarity Index 1st Conceptual graph based model 2nd Conceptual graph based model

Our approach 85 Marattia Pseudosporochnus Zygopteris Equisetum Ophioglossum

Our approach 86 Marattia Pseudosporochnus Zygopteris Equisetum Ophioglossum 1

Our approach 87 Marattia Pseudosporochnus Zygopteris Equisetum Ophioglossum 0 1

Our approach 88 Marattia Pseudosporochnus Zygopteris Equisetum Ophioglossum 0 1

Our approach 89 Marattia Pseudosporochnus Zygopteris Equisetum Ophioglossum Webbing within
the LBS Webbing of the terminal units Branchiness of the LBS 0 1

Our approach 90 unbranched Marattia Pseudosporochnus Zygopteris Equisetum Ophioglossum Webbing
within the LBS Webbing of the terminal units Branchiness of the LBS 0 1

Our approach 91 unbranched Marattia Pseudosporochnus Zygopteris Equisetum Ophioglossum Webbing
within the LBS Webbing of the terminal units Branchiness of the LBS 0 1

Our approach 92 Present (leaflets) unbranched Marattia Pseudosporochnus Zygopteris Equisetum
Ophioglossum Webbing within the LBS Webbing of the terminal units Branchiness of the LBS 0 1

Our approach 93 Present (leaflets) unbranched Marattia Pseudosporochnus Zygopteris Equisetum
Ophioglossum Webbing within the LBS Webbing of the terminal units Branchiness of the LBS 0 1

Our approach 94 absent Present (leaflets) unbranched Marattia Pseudosporochnus Zygopteris
Equisetum Ophioglossum Webbing within the LBS Webbing of the terminal units Branchiness of the LBS 0 1

Our approach 95 Similarity Index Computes the similarity degree between
two morphological character descriptions which will represent how close related they are.

Our approach 96 Similarity Index Scenario 1 Extent of the
planated parts within the LBS Pseudosporochnus restricted to the extremities Author A Planation Pseudosporochnus restricted to the extremities Author B

Our approach 97 Similarity Index Scenario 1 Extent of the
planated parts within the LBS Pseudosporochnus restricted to the extremities Author A Planation Pseudosporochnus restricted to the extremities Author B Scenario 2 Planation of vegetative leaves Pseudosporochnus inapplicable Author C Planation of vegetative leaves Pseudosporochnus restricted to the extremities Author D

Our approach 98 Similarity Index 1 2 3 4 5
A B Taxon Character

Our approach 99 Similarity Index 1 2 3 4 5
A B Taxon Character

Our approach 100 Similarity Index – Part I 1 2
3 4 5 A B Taxon Character

3 4 5 A B Taxon Character

3 4 5 A B NA = { 1, 3, 5 } Taxon Character

Our approach 103 1 2 3 4 5 A B
NA = { 1, 3, 5 } Similarity Index – Part I Taxon Character

NA = { 1, 3, 5 } NB = { 2, 4, 5 } Similarity Index – Part I Taxon Character

circular rounded Similarity Index – Part II round Taxon Character

Our approach 107 1 2 3 4 5 B circular
rounded Similarity Index – Part II round A Taxon Character

Our approach 108 1 2 3 4 5 B circular
rounded Similarity Index – Part II round A LA = { circular, rounded, round } Taxon Character

Our approach 109 1 2 3 4 5 A circular
rounded Similarity Index – Part II round LA = { circular, rounded, round } B Taxon Character

rounded Similarity Index – Part II round LA = { circular, rounded, round } LB = { circular, triangular, ovate } B Taxon Character

Our approach 112 Practical Experiment of the Similarity Measure Author
1 •  Cauline cladotaxy •  Protoxylem position within the cauline stele •  Xylem configuration in the rachis •  Xylem configuration in the leaflets •  Development of the LBS •  Organotaxy of the LBS •  Presence of planated parts within the LBS •  Extent of the planation

Our approach 113 Practical Experiment of the Similarity Measure Author
1 •  Cauline cladotaxy •  Protoxylem position within the cauline stele •  Xylem configuration in the rachis •  Xylem configuration in the leaflets •  Development of the LBS •  Organotaxy of the LBS •  Presence of planated parts within the LBS •  Extent of the planation Author 2 •  Cauline cladotaxy •  Protoxylem position within the cauline stele •  Xylem configuration in the rachis •  Xylem configuration in the leaflets •  Development of the foliar organ •  Phyllotaxy •  Planation

Our approach 114 Cauline cladotaxy Protoxylem position w ithin the
cauline stele Organotaxy of the LBS Xylem conguration in the leaets Planation Development of the foliar organ Phyllotaxy Xylem conguration in the rachis Extent of the planation Presence of planated parts w ithin the LBS Development of the LBS

Our approach 117 An algorithm to trace changes in traits
of phylogenetic trees. absent Present (leaflets) unbranched root Marattia Pseudosporochnus Zygopteris Equisetum Ophioglossum Webbing within the LBS Webbing of the terminal units Branchiness of the LBS 0 1

Our approach 118 An algorithm to trace changes in traits
of phylogenetic trees. Marattia Webbing within the LBS Webbing of the terminal units Branchiness of the LBS Pseudosporochnus Zygopteris Equisetum Ophioglossum root EvolvedTrait EvolvedTrait 0 1

Conclusions 119 •  The present work explores the availability of
data that are represented in many standards not often interconnectable and designed and implemented an approach to link and combine these resources. •  Our approach enables us to discover and make explicit the potential semantics raised by linking previously unconnected information.

Contributions 120 •  The design and implementation of a prototype
to transform phenotype descriptions and phylogenetic trees in graph representations. •  An heuristic similarity measure. •  A visual tool prototype to analyze chaacters correlation . •  An algorithm to trace changes in traits.

Publications 121 •  Unifying phenotypes to support semantic descriptions. In
Proceedings of the 6th Seminar on Ontology Research in Brazil, volume 1041, pages 154 – 165, September 2013. •  Coupling phenotype descriptions and phylogenetic trees: from SDD to ontologies via graph databases. Talk at TDWG 2013 Annual Conference Florence, Italy, 28th of October – 1st of November 2013.

Extensions 122 •  The incorporation of morphological descriptions stored in
other knowledge bases. •  Further investigations in the similarity measure. •  Extend the correlations analysis to the relation between character nodes and ontology terms.

Acknowledgments 123 •  Prof. André Santanchè •  Anaïs Grand and
Régine Vignes Lebbe •  Laboratory of Information Systems (LIS) •  IC infrastructure and staff •  Financial support: •  CNPq (grant 138197/2011-3) •  Microsoft Research FAPESP Virtual Institute (NavScales Project) •  CNPq (MuZOO Project and PRONEX-FAPESP) •  INCT in Web Science (CNPq 557.128/2009-9) •  CAPES •  FAPESP

Linked biology – from phenotypes towards phylogenetic trees Eduardo de
Paula Miranda Advisor: Prof. Dr. André Santanchè Institute of Computing Unicamp November 22, 2013

Linked biology – from phenotypes towards phylog...

Linked biology – from phenotypes towards phylogenetic trees

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