Semantic tools for aggregation of morphological characters across studies
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Transcript of Semantic tools for aggregation of morphological characters across studies
Semantic tools for aggregation of morphological characters across studies
James Balhoff, Alex Dececchi, Paula Mabee, Hilmar Lapp, & Phenoscape team
Rich body of morphological observations – mostly locked up
hybrid map to see if any of these genes were linked to fls. The edargene is located on LG9 within the determined linkage interval forfls (see Methods). We cloned the full-length wild type cDNA of edarand found several polymorphisms in the Tu edar cDNA whencompared to the WIK mapping strain; these polymorphisms weretightly linked with the fls mutation and did not show recombina-tion in 238 meioses (Figure S2).
The edar gene encodes a transmembrane protein with similarityto tumor necrosis factor receptor (TNFR). The Edar proteincontains a conserved TNFR extracellular ligand binding domain
and a cytoplasmic terminal death domain essential for proteininteractions with signaling adaptor complexes. The flste370f
mutation is an A to T transversion at a splice acceptor site,resulting in missplicing of the mRNA leading to a frame shift intranslation and the generation of a premature stop codon(Figure 3B and Figure S2). This allele is a likely molecular nullmutation as only a fragment of the ligand-binding domain ispresent while the transmembrane and cytoplasmic death domains,which are essential for function of this protein, are both absent.The spontaneous mutation flst0sp212 was found to have a splicingdefect leading to the inclusion of intronic sequence. This ispredicted to form a protein with incorrect amino acid sequenceafter residue 212, at the end of the transmembrane domain leadingto a premature termination codon (Figure 3B, Figure S2). The twoalleles generated by the ENU mutagen both have missensemutations resulting in amino acid changes in the death domain(flst3R367W, R367W(C-T); flsdt3Tpl, I428F (A-T)). These mutationswere found at identical positions as seen in familial cases of HEDin humans (Figure 3B, E; [11,12].
The fang Allele Uncovers Dose and Organ SpecificSensitivity to Levels of Eda Signaling
The fang allele of fls was isolated in an allele screen for mutantsthat failed to complement flste370f (Figure 1P). flstfng homozygotes donot show any observable effect on lepidotrichia development yethave a reduction of scales and teeth/rakers as seen in other flsalleles (Figure 1M–O). The fang allele in trans to the te370fputative null allele shows an intermediate phenotype affectinglepidotrichial growth and a further reduction of teeth and scalessuggesting that the fang allele is a hypomorph (Figure 1P–R); flstfng
heterozygotes do not show any differences compared to wild type.The shape and number of the scales in fang is similar to the otherhomozygous fls alleles (Table 1). Analysis of edar RNA fromhomozygous flstfng showed the presence of two distinct transcriptswith an additional larger isoform than seen in wildtype. Analysis ofthe sequence of the novel isoform showed the addition of intronicsequence leading to a premature termination codon (Figure 3C).The predicted protein would be similar to the flst0sp212 allele
Figure 2. The dominant gene Nkt is phenotypically similar, however complements fls mutants. Nkt homozygotes show complete loss ofscales, teeth and gill rakers resembling the fls phenotype (A–C). Heterozygous Nkt zebrafish show an intermediate phenotype of scale loss andpatterning defect (arrows) while no effect on fin development is seen (D). Heterozygous Nkt also show a dominant effect on the number of teeth(arrows, E) and gill rakers (F), showing deficiencies along the posterior branchial arches and formation of rudimentary rakers along ceratobranchial 1and 2 (arrows, F). Cb1-5, ceratobranchial bones.doi:10.1371/journal.pgen.1000206.g002
Table 1. Quantitative effect of fls on scale number and shapeand the effect of background modifiers in Danio rerio strainson flsdt3Tpl.
Phenotype/Genotype Scale #/ stl n Scale DV/AP n
fish scales
+/+ 6.860.18 4 1.1460.15 13
flsdt3Tpl / Tu 3.060.20 ## 2 1.5260.29 # 8
flsdt3Tpl / Tu; mod 5.660.44 # 3 1.460.3 # 12
flsdt3Tpl / WIK 5.8460.66 # 9 1.4360.35 # 32
flstfang / flstfang 0.9760.50 ### 2 1.5760.18 # 7
flste370f / flste370f 0.4160.39 ### 6 1.860.64 # 16
The total number of scales on one side of alizarin red stained adults of differentgenotypes were counted and measured. Counts were normalized for standardlength (stl) of individual fish as shape and number of scales in the mutants mayvary as a measure of size. Shape characteristics of scales were quantified bymeasuring three to four scales from set positions across the flank of each fishand comparing the height (dorsal-ventral; DV) to length (anterior-posterior; AP)ratios. Results are presented as sample average and standard deviation aroundthe mean. mod, inferred genotype of a modifier in Tu background leading to‘‘weak’’ phenotype. The numerical symbol (#) indicates significant differencecompared to wild type values (students t, p,0.05). The different number ofsymbols signifies a significantly different phenotypic classes of scaledevelopment (#, ##, ###).doi:10.1371/journal.pgen.1000206.t001
Zebrafish Model of Human Ectodermal Dysplasia
PLoS Genetics | www.plosgenetics.org 4 October 2008 | Volume 4 | Issue 10 | e1000206
Free text is a barrier to machine-based integration
OMIM query # of records“large bone” 1083“enlarged bone” 224“big bones” 21“huge bones” 4“massive bones” 41“hyperplastic bones” 12“hyperplastic bone” 45“bone hyperplasia” 181“increased bone growth” 879
Lundberg & Akama 2005
Phylogenetic systematics Human genetics
http://www.ncbi.nlm.nih.gov/omim
Integration is key for knowledge synthesis
The Tree of Life and a New Classification of Bony Fishes—Betancur-R. et al. 2013. PLoS Currents Tree of Life
Integration is key for discovery
Phenoscape: making evolutionary morphology computable
+
= Phenoscape KnowledgebaseComparative studies Model organism datasets
How it works: shared ontologies, rich semantics, OWL reasoning
16,000 character states from >120 comparative morphological datasets, linked to 4,000 vertebrate taxa.
Imported genetic phenotype and expression data from ZFIN, Xenbase, MGI, and Human Phenotype project.
Shared semantics: Uberon (anatomy), PATO (phenotypic qualities), Entity–Quality (EQ) OWL axioms (phenotype observations)
Plus a dozen other ontologies ...
Phenoscape KB content
Integrative querying with the Phenoscape KB: scale, absent
Ictalurus punctatus eda gene in Danio rerio
edadt3S243X/dt3S243X — Harris, M.P., Rohner, N., Schwarz, H., Perathoner, S., Konstantinidis, P., and Nüsslein-Volhard, C.. 2008. Zebrafish eda
and edar mutants reveal conserved and ancestral roles of ectodysplasin signaling in vertebrates. PLoS Genetics 4(10):e1000206.
“body: naked”—Kailola, P. J. 2004. A phylogenetic exploration of the catfish family Ariidae (Otophysi; Siluriformes). The Beagle,
Records of the Museums and Art Galleries of the Northern Territory 20:87-166
Can we use reasoning to integrate character matrices across studies?
Would enable the wealth of single-study character analysis methods on any integrated matrix.
Including tree-based comparative phylogenetic methods
Integrating phylogenetic studies
Combined matrix of any character states related to presence/absence of limb/fin structures from studies in Phenoscape KB
Evolution of Sarcopterygian Limb/Fin
Clack, J. A. (2009). The Fin to Limb Transition: New Data, Interpretations, and Hypotheses from Paleontology and Developmental Biology. Annual Review of Earth and Planetary Sciences, 37(1), 163-179
EQ supermatrix synthesis: workflow
1.Use OWL reasoner to group character states by anatomy and quality axes, based on EQ annotations.
2.Export groupings as character matrix, with taxon assignments to states from original data.
3.Supplement presence/absence character state assertions with reasoner-inferred information.
4.Use Phenex data editor to manually consolidate character states where appropriate
Synthesized limb/fin character matrix
1055 Sarcopterygian taxa
494 characters
2-7 states per character
from 55 original studies
Developed several tools for automated character matrix synthesis to make this happen.
EQ supermatrix synthesis: Results
Ontologies and phenotype observation data in OWL
ELK, an OWL-EL reasoner
OWL-DL reasoners are too slow for this
OWL API (Java), programmed primarily using Scala
Bigdata™ RDF triplestore (~ 25 million triples)
Technology stack
For every pair of anatomical term X and quality attribute Y, generate a “character expression” OWL class: (involves some X and involves some Y)
Done programmatically via property chain axioms and OWL reasoning (ELK)
Classify character states to most relevant character expression
Done by OWL reasoner (ELK)
Inferred relationships materialized to triple store
Using reasoning to group character states
Anatomy ontologies and EQ annotation employ rich OWL semantics → best used with a DL reasoner
Classifying and querying over large dataset (~25 million RDF triples) does not scale well
Presently, the only feasible OWL reasoner is ELK
constrained to OWL EL profile → limits kinds of expressions we use
best performance over class axioms only → data must be modeled so as to avoid need for classifying instances
Challenge: scalable reasoning
Want to allow arbitrary selection of structures of interest, using rich semantics:(part_of some (limb/fin or girdle skeleton)) or (connected_to some girdle skeleton)
RDF triplestores provide very limited reasoning expressivity, and scale poorly with large ontologies.
However, ELK can answer class expression queries within seconds.
Challenge: Querying complex expressions
PREFIX rdf: <http://www.w3.org/1999/02/22-‐rdf-‐syntax-‐ns#>PREFIX rdfs: <http://www.w3.org/2000/01/rdf-‐schema#>PREFIX ao: <http://purl.obolibrary.org/obo/my-‐anatomy-‐ontology/>PREFIX owl: <http://www.w3.org/2002/07/owl#>SELECT DISTINCT ?geneWHERE {?gene ao:expressed_in ?structure .?structure rdf:type ?structure_class .# Triple pattern selecting structure:?structure_class rdfs:subClassOf "ao:muscle” .?structure_class rdfs:subClassOf ?restriction?restriction owl:onProperty ao:part_of .?restriction owl:someValuesFrom "ao:head" .}
Instead of something like this (*):
We would really like to do this:PREFIX rdf: <http://www.w3.org/1999/02/22-‐rdf-‐syntax-‐ns#>PREFIX rdfs: <http://www.w3.org/2000/01/rdf-‐schema#>PREFIX ao: <http://purl.obolibrary.org/obo/my-‐anatomy-‐ontology/>PREFIX ow: <http://purl.org/phenoscape/owlet/syntax#>SELECT DISTINCT ?geneWHERE {?gene ao:expressed_in ?structure .?structure rdf:type ?structure_class .# Triple pattern containing an OWL expression:?structure_class rdfs:subClassOf "ao:muscle and (ao:part_of some ao:head)"^^ow:omn .}
owlet interprets OWL class expressions embedded within SPARQL queries
Uses any OWL API-based reasoner to preprocess query.
We use ELK that holds terminology in memory.
Replaces OWL expression with FILTER statement listing matching terms
https://github.com/phenoscape/owlet
owlet: SPARQL query expansion with in-memory OWL reasoner
PREFIX rdf: <http://www.w3.org/1999/02/22-‐rdf-‐syntax-‐ns#>PREFIX rdfs: <http://www.w3.org/2000/01/rdf-‐schema#>PREFIX ao: <http://purl.obolibrary.org/obo/my-‐anatomy-‐ontology/>PREFIX ow: <http://purl.org/phenoscape/owlet/syntax#>SELECT DISTINCT ?geneWHERE {?gene ao:expressed_in ?structure .?structure rdf:type ?structure_class .# Triple pattern containing an OWL expression:?structure_class rdfs:subClassOf "ao:muscle and (ao:part_of some ao:head)"^^ow:omn .}
PREFIX rdf: <http://www.w3.org/1999/02/22-‐rdf-‐syntax-‐ns#>PREFIX rdfs: <http://www.w3.org/2000/01/rdf-‐schema#>PREFIX ao: <http://purl.obolibrary.org/obo/my-‐anatomy-‐ontology/>PREFIX ow: <http://purl.org/phenoscape/owlet/syntax#>SELECT DISTINCT ?geneWHERE {?gene ao:expressed_in ?structure .?structure rdf:type ?structure_class .# Filter constraining ?structure_class to the terms returned by the OWL query:FILTER(?structure_class IN (ao:adductor_mandibulae, ao:constrictor_dorsalis, ...))}
⬇owlet⬇
Inferring presence/absenceCharacter states often do not directly assert, but imply presence or absence.
Most phenotypic descriptions of some feature of a structure implies its presence or absence:
“Humerus slender and elongate: with length more than three times the diameter of its distal end” → humerus must be present
Partonomy axioms in the ontology allow inferring presence or absence:
‘all humerus part_of some forelimb’ → forelimb must be present if humerus is; humerus must be absent if forelimb is
Absence is typically modeled using negation → not (has_part some forelimb)
Negation not part of OWL EL (and thus ELK reasoner)
Solution: programmatic assertion of “absence hierarchy” via classification of negated expressions
Challenge: absence reasoning with OWL EL
A = has_part some forelimb
B = has_part some limb
C = has_part some appendage
⬆
⬆
absentC = not C
absentB = not B
absentA = not A
⬆
⬆
——
——
—re
vers
e——
——
—
Requires precomputation, constraints for on-the-fly use
Challenge: Character state consolidation
Challenge: Character state consolidation
Reduced 1-297 states per character to 2-7.
Result: Reasoning fills in many missing character states
asserted presence/absence with inference
Mesquite “birds-eye view”
Unified matrix enables candidate gene view
Linking evolutionary phenotypes to genes through ontologies, via Phenoscape KB or similarity
Conflicting interpretations in studiessupinator process of humerus: both absent & present in Strepsodus (Zhu et al. 1999 vs. Ruta 2011)
Gaps in knowledgeacetabulum present or absent?
Same term, different meaning?Acanthostega— “radials, jointed” (Swartz 2012)but doesn’t have radials...
Uneven taxon sampling
Integrated data highlight conflict and gaps
Acetabulum of pelvic girdle: present/absent
figure from Parker et al., 2005
http://characterdesignnotes.blogspot.com/2011/04/proper-use-of-reference-and-anatomy-in.html
https://github.com/phenoscape
owlet (SPARQL processor), Phenex (semantic data editor), phenoscape-owl-tools (KB build), others
http://phenoscape.org/wiki/Software
Phenoscape software
National Evolutionary Synthesis Center (NESCent)
Todd Vision (also University of North Carolina at Chapel Hill)Hilmar LappJim BalhoffPrashanti Manda
University of South DakotaPaula MabeeWasila DahdulAlex Dececchi
University of Chicago Paul SerenoNizar Ibrahim
Mouse Genome InformaticsJudith BlakeTerry Hayamizu
Phenoscape project teamUniversity of Oregon (Zebrafish Information Network)
Monte WesterfieldYvonne BradfordCeri Van Slyke
Cincinnati Children's Hospital (Xenbase)Aaron ZornChristina James-ZornVirgilio Ponferrada
California Academy of SciencesDavid Blackburn
University of ArizonaHong Cui
Oregon Health & Science UniversityMelissa Haendel
Lawrence Berkeley National LabsChris Mungall