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From baleen to cleft palate: *an ontological exploration of evolution and disease*

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Information about From baleen to cleft palate: *an ontological exploration of evolution...

Published on July 15, 2014

Author: mhaendel

Source: slideshare.net

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Keynote at the 17th Annual Bio-Ontologies SIG at ISMB
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From baleen to cleft palate: an ontological exploration of evolution and disease Melissa Haendel July 11 , 2014 17th Annual Bio-Ontologies SIG

Baleen whales The baleen whales are characterized by having baleen plates for filtering food from water, rather than teeth like in the toothed whales

Fin whale fetus showing tooth buds in upper jaw Deméré TA et al. 2008© 2008 Society of Systematic Biologists

Changes in enamel genes during evolution of teeth within Cetacea Meredith R W et al. Proc. R. Soc. B 2011;278:993-1002©2011 by The Royal Society

Cleft palate

Cranial neural crest contributes to the jaw and palate Dougherty et al. 2013 Development 140, 76-81 sox10:kaede transgenic zebrafish

Vertebrata Ascidians Arthropoda Annelida Mollusca Echinodermata tetrapod limbs ampullae tube feet parapodia We want to understand gene function across taxa

Anatomy ontologies built for one species will not work for others http://fme.biostr.washington.edu:8080/FME/index.html http://ccm.ucdavis.edu/bcancercd/22/mouse_figure.html

lung lung lobular organ parenchymatous organ solid organ pleural sac thoracic cavity organ thoracic cavity abnormal lung morphology abnormal respiratory system morphology MP MA FMA abnormal pulmonary acinus morphology abnormal pulmonary alveolus morphology lung alveolus organ system respiratory system Lower respiratory tract alveolar sac pulmonary acinus organ system respiratory system EHDAA2 lung lung bud respiratory primordium pharyngeal region develops_from part_of is_a (SubClassOf) surrounded_by So we build species-specific ontologies

lung lung lobular organ parenchymatous organ solid organ pleural sac thoracic cavity organ thoracic cavity abnormal lung morphology abnormal respiratory system morphology MPO MA FMA abnormal pulmonary acinus morphology abnormal pulmonary alveolus morphology lung alveolus organ system respiratory system Lower respiratory tract alveolar sac pulmonary acinus organ system respiratory system EHDAA2 lung lung bud respiratory primordium pharyngeal region But this results in silos develops_from part_of is_a (SubClassOf) surrounded_by

Why not just map ontology terms? Class A Class B Mapped? Useful? FMA: extensor retinaculum of wrist MouseAnatomy: retina Yes No Vivo: legal decision Cognitive Atlas: decision Yes No PlantOntology: Pith MouseAnatomy: medulla Yes No TaxRank: domain NCI: protein domain Yes No ZfishAnat: hypophysis MouseAnatomy: pituitary No Yes TAO:fossa AdverseReactions: depression Yes No FMA: colon GAZ: Colón, Panama Yes No Quality: male Chebi: maleate 2(-) Yes No String matching for mapping can lead to spurious results and semantics of mappings and provenance are not always clear

Fossils, the ultimate silo  Modern diversity only a fraction of evolutionary diversity  Missing evolutionary transitions e.g. fin to limb  Extant ontologies not always compatible with fossil data  Different data sources and resolution between extinct and extant Shubin et al. 2006

Avoiding Silo-ization Use ontologies that are:  open  documented  reusable  interoperable  built according to shared principles  reuse core relations and patterns Problem: How do we re-use in the presence of variability?

Long ago in the world of anatomies CARO FBbt Drosophila MA Adult mouse EMAP embryonic mouse FMA (mostly) adult human EHDAA2 embryonic human ZFA zebrafish XAO Xenopus An anatomical reference ontology was built to help standardize species-specific ontologies

And then came Uberon, created to bridge model organism anatomies CARO FBbt Drosophila MA Adult mouse EMAP embryonic mouse FMA (mostly) adult human EHDAA2 embryonic human ZFA zebrafish XAO Xenopus UBERON

And over time… … additional multi-species ontologies evolved CARO FBbt Drosophila MA Adult mouse EMAP embryonic mouse FMA (mostly) adult human EHDAA2 embryonic human ZFA zebrafish XAO Xenopus TAO Teleost HAO Hymenoptera Arthropod VSAO Vertebrate Skeletal AAO Amphibian UBERON vHOG Vertebrate Homologous Organs Group

CARO FBbt Drosophila MA Adult mouse EMAP embryonic mouse FMA (mostly) adult human EHDAA2 embryonic human ZFA zebrafish XAO Xenopus TAO Teleost HAO Hymenoptera Arthropod VSAO Vertebrate Skeletal AAO Amphibian UBERON vHOG Vertebrate Homologous Organs Group But… …they had a hard time maintaining relationships to one another

And there was asynchrony in the (anatomical) universe

Cross referenced content pre-merge

The new Uberon  Contents: – Over 11,000 classes (terms), 2500+ added in merge. – Many anatomical properties, including subclass, part-of and develops-from  Scope: metazoa (animals) – Current focus is chordates – Includes teleost, amniote, and amphibian specific classes  Uberon classes are generic / species neutral – ‘mammary gland’: you can use this class for any mammal! – ‘lung’: you can use this class for any vertebrate (that has lungs) http://purl.obolibrary.org/obo/uberon/ext.obo http://purl.obolibrary.org/obo/uberon/ext.owl uberon.org

What can you do with the new uberon? Modified from Ahn and Ho 2008  Reason across anatomical variation in extinct and extant taxa  Query for candidate genes relevant to morphological evolution  Use morphological diversity to investigate human malformations kb.phenoscape.orgmonarchinitiative.org Jim Balhoff talk tomorrow: Presence-absence reasoning for evolutionary phenotypes

B6.Cg-Alms1foz/fox/J increased weight, adipose tissue volume, glucose homeostasis altered ALSM1(NM_015120.4) [c.10775delC] + [-] GENOTYPE PHENOTYPE obesity, diabetes mellitus, insulin resistance increased food intake, hyperglycemia, insulin resistance kcnj11c14/c14; insrt143/+(AB) Models recapitulate various phenotypic aspects of disease ?

Representing phenotypes

Post-composed “EQ” phenotype description Entity (Anatomy, Spatial, Gene Ontology) BSPO: anterior region part_of ZFA:head ZFA:heart ZFA:ventral mandibular arch GO:swim bladder inflation Quality (PATO) Small size Edematous Thick Arrested

Human Phenotype Ontology Human Phenotype Ontology used to annotate: • Patients • Disorders • Genotypes • Genes • Sequence variants In human Reduced pancreatic beta cells Abnormality of pancreatic islet cells Abnormality of endocrine pancreas physiology Pancreatic islet cell adenoma Pancreatic islet cell adenoma Insulinoma Multiple pancreatic beta-cell adenomas Abnormality of exocrine pancreas physiology Köhler et al. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 2014 Jan 1;42(1):D966-74. See Peter Robinson’s keynote on PhenoDay

Mammalian Phenotype Ontology Smith et al. (2005). The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol, 6(1). doi:10.1186/gb-2004-6-1-r7 Used to annotate and query: • Genotypes • Alleles • Genes In mice abnormal pancreatic beta cell mass abnormal pancreatic beta cell morphology abnormal pancreatic islet morphology abnormal endocrine pancreas morphology abnormal pancreatic beta cell differentiation abnormal pancreatic alpha cell morphology abnormal pancreatic alpha cell differentiation abnormal pancreatic alpha cell number See Cynthia Smith’s talk on PhenoDay

Phenotype representation requires more than “phenotype ontologies” glucose metabolism (GO:0006006 ) Gene/protein function data glucose (CHEBI:172 34) Metabolomics, toxico- genomics data Disease & phenotype data type II diabetes mellitus (DOID:9352) pyruvate (CHEBI:153 61) Disease Gene Ontology Chemical pancreatic beta cell (CL:0000169 ) Transcript- omics data Cell Expression and phenotype data Pancreas (UBERON:00 01264) Anatomy

The Biological Spatial Ontology  Evolutionary changes in spatial arrangement  Different standards in different communities =>The Biological Spatial Ontology Gross anatomical directions

The Biological Spatial Ontology Non-perpendicular anatomical axes Cellular anatomical directions Dahdul et al. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. In press, JBMS

Spatial ontology content anterior-posterioraxis anatomicalaxis is_a anteriorside starts_axis posteriorside finishes_axis anterior_to posterior_to opposite_to is_a anatomicalside is_a anteriormargin overlaps anatomicalmargin is_a anatomicalregion is_a anteriorregion overlaps is_a anteriorsurface surface_of anatomicalsurface is_a anatomicalentity passes_through immaterialanatomicalentity is_a anatomicalgradientanatomicalplane sagittalplane is_a midsagittalplane is_a dorsal-ventralaxis approximately_ perpendicular_to is_a anterior-posteriorgradient has_axis is_a orthogonal_to left-rightaxis is_a is_a is_ais_a anatomicalstructure is_a materialanatomicalentity is_ais_a is_a anatomicalboundary is_ais_a anatomicalline apical-basalaxis relativetosubstrate is_a is_a apical-basalaxis relativetodirectionofgrowth is_a

Putting it all together

monarchinitiative.org

Uberpheno – building a cross- species semantic framework Köhler et al. (2014) Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research F1000Research 2014, 2:30

Uberpheno construction

Uberpheno construction

Uberpheno construction

Uberpheno construction

Facial features are so specific as to enable image based diagnostics iphone App => Uses HPO for annotations

What genotype-phenotype data do we have? GWAS + ClinVar + OMIM Human genes have poor phenotype coverage What else can we leverage?

Human genes have poor phenotype coverage What else can we leverage? …animal data Orthology via PANTHER v9 What genotype-phenotype data do we have?

Combined, human and model phenotypes can be linked to >75% human genes. Orthology via PANTHER v9 What genotype-phenotype data do we have?

Monarch phenotype data Also in the system: Rat; IMPC; GO annotations; Coriell cell lines; OMIA; MPD; Yeast; CTD; GWAS; Panther, Homologene orthologs; BioGrid interactions; Drugbank; AutDB; Allen Brain …157 sources to date Coming soon: Animal QTLs for pig, cattle, chicken, sheep, trout, dog, horse Species Data source Genes Genotypes Variants Phenotype annotations Diseases mouse MGI 13,433 59,087 34,895 271,621 fish ZFIN 7,612 25,588 17,244 81,406 fly Flybase 27,951 91,096 108,348 267,900 worm Wormbase 23,379 15,796 10,944 543,874 human HPOA 112,602 7,401 human OMIM 2,970 4,437 3,651 human ClinVar 3,215 100,523 445,241 4,056 human KEGG 2,509 3,927 1,159 human ORPHANET 3,113 5,690 3,064 human CTD 7,414 23,320 4,912

r Long hallux Midface retrusion Arthrogryposis multiplex congenita Bowing of the long bones Cleft palate Exaggerated Cupid's bow Protruding ears digit 1 phenotype short snout epiphyseal plate morphology abnormal limb long bone morphology Cleft palate Cleft lip lowered ear position Abnormality of toe abnormal head shape Abnormal joint morphology limb long bone phenotype Cleft palate Abnormality of upper lip prominent ears OWLsim: Phenotype similarity across patients or ….any organism https://code.google.com/p/owltools/wiki/OwlSim

https://www.sanger.ac.uk/resources/databases/exomiser/query/exomiser2

Undiagnosed patient 2731 Behavioural/ Psychiatric Abnormality Thyroid stimulating hormone excess Gait apraxia Spasticity increased exploration in new environment increased dopamine level hyperactivity hyperactivity Behavioral abnormality Abnormality of the endocrine system abnormal locomotor behavior Abnormal voluntary movement Patient phenotypes Sh3kbp1 tm1Ivdi -/-

What if there aren’t any similar diseases or other organisms? YARS MARS IARSIL41L AARSIARS2 Abnormal stereopsis Choreoathetosis Microcephaly Akinesia Visual impairment Myoclonus Microcephaly Myoclonus abnormal visual perception Involuntary movements Microcephaly musculoskeletal movement phenotype Patient phenotypes Combined Oxidative Phosphorylation Deficiency 14 FARS2 WARS2 ? AIMP1 UDP_1166 ➔ Exomiser can utilize phenotypic similarity via the interactome

Forward Genomics http://bejerano.stanford.edu/phenotree/public/html/ Hiller et al. 2012 Cell Reports

Connecting baleen and palates

Conclusions  Uberon integrates anatomy across human, model, and non-model organisms  Anatomy and phenotypes can be represented using modular ontologies  We can use the data annotated to these diverse ontologies to support rare and undiagnosed disease diagnosis and explain morphological evolution  Use of semantic similarity algorithms enables candidate prioritization, model identification, and mechanism exploration  Baleen evolution CAN aid disease diagnostics

Acknowledgments NIH-UDP William Bone Murat Sincan Amanda Links Neal Boerkoel Cyndi Tifft Bill Gahl OHSU Nicole Vasilesky Shahim Essaid Matt Brush Bryan Laraway Phenoscape Jim Balhoff Paula Mabee Hilmar Lapp David Blackburn Alex Dececchi Wasila Dahdul Lawrence Berkeley Nicole Washington Suzanna Lewis Chris Mungall UCSD Amarnath Gupta Jeff Grethe Anita Bandrowski Maryann Martone U of Pitt Chuck Boromeo Jeremy Espino Becky Boes Harry Hochheiser EBI David Osumi-Sutherland U of Lausanne Frederic Bastian Univ of Illinois Robert Druzinsky Sanger Anika Oehlrich Jules Jacobson Damian Smedley JAX Cynthia Smith Charité Sebastian Kohler Sandra Doelken Sebastian Bauer Peter Robinson Toronto Marta Girdea Sergiu Dumitriu Orion Buske Heather Trang Mike Brudno iPlant Ramona Walls Funding: NIH Office of Director: 1R24OD011883 NIH-UDP: HHSN268201300036C NSF DBI-0641025, DBI-1062404,

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