ICBO 2011 July 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 Motivation of this study Phenotypes represent a broad range of variations in measured qualities Integrated phenotypic information whole Organism A Organism B Organism C Organism D Sophisticated informatics infrastructure (ontology) Mining… Biological knowledge To contribute to development of the informatics infrastructure for the description, exchange and mining of phenotypic data. 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 MP:0002269 ! muscular atrophy Q MA:0000015 ! muscle PATO:0001623 ! atrophied FMA:30316 ! muscle PATO:0001623 ! atrophied E Q HP:0003202 ! Amyotrophy Expansion of PATO We attempted to expand the PATO ontology to ensure a more advanced, explicit and consistent knowledge framework. Objectives: 1. To provide fundamental classification of quality values on the basis of measurement scales. 2. To provide strict data model to operate contextdependencies of ordinal values. 3. To provide model of datum (or description) as a informational entity with the structure of common formalisms. 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… 1. 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. length temperature 20cm 37℃ - 310.15K Long, short high, low color red, blue.. This classification takes as starting point the mathematical operation! Fundamental classification of quality-value (2) 2. Foundation of explicit description of change of quality is needed Color 1: green to orange Color 2: orange to green 1 2 t1 t2 1 Growing boy and his height quality Ontology System of quality Formalism BFO, PATO 1-hiearchy EQ DOLCE 2-hiearchy EAV 2 Explicit description of color change is needed. 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. 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 smaller Threshold X (some value) larger 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 A value C “abnormally large” class larger deviation Threshold Y1 and Y2 (deviation-based value) smaller value B value D “normal size” class larger smaller “abnormally small” class Knowledge model of context dependencies of ordinal scale values is needed! Model of datum as an informational entity Current version of DOLCE, BFO and PATO deal only with the primary reality and do not deal with quality description. 1. Distinction of a “true value” and an “empirical measurement” as an approximation is needed. weigh t weigh t Reality Information weigh t (Unknown…) 2. Modeling of informational entities with common formalisms (eg. EQ, EAV and so on) and their relationships would be useful! weigh t Reality (Unknown...) EQ EAV weigh t Information weigh t Expansion of PATO with YAMATO framework BFO quality PATO Mapping Interoperability YAMATO DOLCE A reference ontology “PATO2YAMATO” •Equivalence mapping between 1- and 2-hiearcy models •Model of context dependency OBI quale quality-space •Model of datum with common formalisms Practical use based proposals… Yet Another More Advanced Top-Level Ontology (YAMATO: Mizoguchi, 2009) 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. Equivalence mapping of 1- and 2-hearcy model BFO (Upper level) quality identical property quality YAMATO (Upper level) quality_ quantity (convertible) generic quality identical quality value quality space DOLCE (Upper level) Classification of quality value (scales of measurements : Stevens S.S, 1946) identical region quale About 1,000 PATO terms were manually mapped to YAMATO framework. Modeling of context dependency with “role” I’m a teacher. (at school) (at home) In the distribution for weight, some weight quality values playing large-roles thereby becomes role holders, abnormally heavy context role-holder （Entity playing a role) Distribution for weight role Abnormally heavy large-role depend on Concept model of role and role-holder I’m a husband An entity often plays different “roles” with different characteristics under different contexts playable heavier than normal value potential player weight quality value qualitative value for weight 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 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” Coordination of ordinary values under different contexts Abnormally heavy in elephant Context of distribution of weight in elephant larger Normal weight in elephant larger Abnormally light in elephant larger Abnormally heavy in ant larger Context of distribution of weight in ant Normal weight in ant larger Abnormally light in ant Simple comparison context Quality representation in YAMATO YAMATO provides “quality representation” for the foundation of formalized informational entities such as EQ, EAV and so on. Informational entities Reality Quality representation Weight Quality (Symbolization) Quality representation is modeled in the consistent way for content bearing informational entity, “representation”. Basic structure for representation by symbol (Mizoguchi, 2004) quality representation EP (=EQ) (BFO, PATO) EAV (DOLCE) Sentence of natural language Coding of genetic information Tupple Triple natural language nucleotide sequence *entity, #property *entity, #generic quality, value alphabet molecular symbol quality measurement quality measurement anything… Specification of gene product *: symbolization operation, #: Class => individual operation (equivalent with punning in OWL 2) 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 EAVquality representation. 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. 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 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 !