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An Advanced Strategy for Integration of Biological Measurement Data

ICBO 2011 July 28-30, 2011 Buffalo, New York,. An Advanced Strategy for Integration of Biological Measurement Data.

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An Advanced Strategy for Integration of Biological Measurement Data

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  1. ICBO 2011July 28-30, 2011 Buffalo, New York, An Advanced Strategy for Integration of Biological Measurement Data Hiroshi Masuya1, Georgios V. Gkoutos2, Nobuhiko Tanaka1, Kazunori Waki1, Yoshihiro Okuda3, Tatsuya Kushida3, Norio Kobayashi4, Koji Doi4, Kouji Kozaki5, Robert Hoehndorf1, Shigeharu Wakana1, Tetsuro Toyoda4 and Riichiro Mizoguchi5 1: RIKEN BioResource Center, Tsukuba, Japan 2: Department of Genetics, University of Cambridge, UK 3: NalaPro Technologies, Inc, Tokyo, Japan 4: RIKEN BASE, Yokohama Japan 5: Department of Knowledge Systems, ISIR, Osaka University, Japan

  2. Motivation of this study Phenotypes represent a broad range of variations in measured qualities Integrated phenotypic information whole Sophisticated informatics infrastructure (ontology) Mining… Biological knowledge To contribute to development of the informatics infrastructure for the description, exchange and mining of phenotypic data.

  3. Phenotypic Quality (PATO): PATO provides a practical basis for vocabulary and semantics for the description of phenotype information across species. • Single hierarchy model of “quality” suite for BFO • Standard of phenotype annotation across species.(“EQ” annotation) • Less confusions than “EAV” annotation for non-ontology-familiar people. • Basis of inferences of cross-species phenotype equivalence with EQ. (e.g. mouse phenotype and disease) E FMA:30316 ! muscle MA:0000015 ! muscle E HP:0003202 ! Amyotrophy MP:0002269 ! muscular atrophy PATO:0001623 ! atrophied PATO:0001623 ! atrophied Q Q

  4. Expansion of PATO We attempted to expand the PATO ontology to ensure a more advanced, explicit and consistent knowledge framework. Objectives: To provide fundamental classification of quality values on the basis of measurement scales. To provide strict data model to operate context-dependencies of ordinal values. To provide model of datum (or description) as a informational entity with the structure of common formalisms.

  5. Fundamental classification of quality-value (1) Refrain from 2-hiearchy model (and EAV formalism) There were a lot of discussions for PATO to take 1-hiearchy and EQ… Number of studies claims that the fundamental classification of values: “scales of measurement” (Stevens S.S, 1946) is beneficial for data integration in the field of experimental science. This classification takes as starting point the mathematical operation!

  6. Fundamental classification of quality-value (2) Foundation of explicit description of change of quality is needed 1 2 Color 1: green to orange Color 2: orange to green t1 1 2 t2 Explicit description of color change is needed. Growing boy and his height quality Qualitative and quantitative descriptions are integrated in a single knowledge framework in DOLCE. For the coordination of ongoing efforts, equivalence mapping of these systems is beneficial.

  7. Model of context-dependency of ordinal value (1) Problem of “large ant and small elephant” I’m big!! How to classify value instances? I’m small.. Context A: simple comparison value C value A “Large” class “Small” class value D value B Threshold X (some value) larger smaller

  8. Model of context-dependency of ordinal value (2) Problem of “large ant and small elephant” I’m big!! How to classify value instances? I’m small.. Context B: deviation based comparison (context of inference of cross-species equivalence of phenotypes) value C value A “abnormally large” class larger deviation smaller Threshold Y1 and Y2(deviation-based value) “normal size” class value D value B larger smaller “abnormally small” class Knowledge model of context dependencies of ordinal scale values is needed!

  9. Model of datum as an informational entity Current version of Current version of DOLCE, BFO and PATO deal only with the primary reality and do not deal with quality description. Distinction of a “true value” and an “empirical measurement” as an approximation is needed. Modeling of informational entities with common formalisms (eg. EQ, EAV and so on) and their relationships would be useful! weight weight Information Reality weight (Unknown…) weight weight EQ Information Reality weight EAV (Unknown...)

  10. Expansion of PATO with YAMATO framework Mapping Interoperability BFO YAMATO DOLCE A reference ontology “PATO2YAMATO” quality Features: • Framework of interoperability of quality-related concepts between top-level ontologies. Support of classification of scales of measurements. • Model of context dependency with “role” • Detailed model of “representation” (an informational object) that involves quality representation. PATO • Equivalence mapping between 1- and 2-hiearcy models • Model of context dependency • Model of datum with common formalisms quale quality-space OBI Practical use based proposals… Yet Another More Advanced Top-Level Ontology (YAMATO: Mizoguchi, 2009)

  11. Equivalence mapping of 1- and 2-hearcy model BFO identical quality (Upper level) property quality YAMATO generic quality (convertible) quality_quantity (Upper level) identical quality value Classification of quality value (scales of measurements : Stevens S.S, 1946) quality space DOLCE identical region (Upper level) quale About 1,000 PATO terms were manually mapped to YAMATO framework.

  12. Modeling of context dependency with “role” I’m a teacher. I’m a husband An entity often plays different “roles” with different characteristics under different contexts (at school) (at home) context role-holder （Entity playing a role) In the distribution for weight, some weight quality values playing large-roles thereby becomes role holders, abnormally heavy Distribution for weight Abnormallyheavy role potential player weight quality value large-role depend on playable heavier than normal value qualitative value for weight Concept model of role and role-holder

  13. Modeling of context dependency with “role” I’m a teacher. I’m a husband An entity often plays different “roles” with different characteristics under different contexts (at school) (at home) In the distribution for weight, some weight quality values playing large-roles thereby becomes role holders, abnormally heavy context Potential player Role-holder Implementation and representation in Hozo ontology editor

  14. Inter-relationships among contexts Classification of organisms Inherit Inherit Inference of classification: ”Abnormally light in elephant is lighter than abnormally heavy in ant” in the simple comparison context. Inference of the Classification of “abnormally heavy”

  15. Coordination of ordinary values under different contexts Abnormally heavy in elephant Normal weight in elephant Abnormally light in elephant Abnormally heavy in ant Normal weight in ant Abnormally light in ant larger Context of distribution of weight in elephant larger Simple comparison context larger larger Context of distribution of weight in ant larger

  16. Quality representation in YAMATO YAMATO provides “quality representation” for the foundation of formalized informational entities such as EQ, EAV and so on. Reality Quality representation Value Generic quality Informational entities Weight EAV formalism Property EP (EQ) formalism Quality (Symbolization) Quality representation is modeled in the consistent way for content bearing informational entity, “representation”. Entity quality representation Basic structure for representation by symbol (Mizoguchi, 2004) *: symbolization operation, #: Class => individual operation (equivalent with punning in OWL 2)

  17. Current status of the reference ontology: PATO2YAMATO • Including about 1,000 PATO terms into YAMATO framework • Basic form of context-dependent ordinal values are defined. They are workable under the classification of organisms. • Basic form of quality representation (EAV and EQ) are already defined in YAMATO. http://www.brc.riken.go.jp/lab/bpmp/ontology/ontology_pato2yato.html Preliminary trial of simple conversion of EQ to EAV 1,450 EQ annotation: (OBO cross-product file for Mammalian Phenotype ontology) reference:PATO2YAMATO EAV-quality representations in YAMATO framework The ontology helps the automatic conversion from EQ to EAV! We are planning full conversion of EQ across multiple species with coordinated EAV-quality representation.

  18. Summary of this talk This study shows: • YAMATO’s framework helps to coordinate different “qualities” for phenotype information in both of reality and description level. • Role-model successfully coordinated ordinal values dependent on multiple contexts (deviation-based and simple comparison). Future views: • Automatic conversion of EQ of multiple species to EAV. • Modeling of contexts of experimental conditions. • Integration of qualitative and quantitative phenotype data. • Coordination of more complicated phenotype data sets from multiple species and experiments.

  19. Acknowledgements RIKEN BioResource Center Nobuhiko Tanaka, Kazunori Waki, Terue Takatsuki University of Cambridge Georgios V. Gkoutos, Robert Hoehndorf NalaPro Technologies Inc Yoshihiro Okuda, Tatsuya Kushida Enegate corp Mamoru Ota RIKEN BASE Norio Kobayashi, Koji Doi, Tetsuro Toyoda Department of Knowledge Systems, ISIR, Osaka University Koji Kozaki, Riichiro mizoguchi

  20. 貴為和以 “Harmony is to be valued.” In “Seventeen-article constitution” (A.D 603, YAMATO imperial court in ancient Japan)Authored by Prince Shōtoku (A.D. 573–621) Thank you !

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