Semantic Web meets biology: Finnish experiences in modelling, managing, and using biological linked data

Transcription

1 Department of Computer Science Semantic Web meets biology: Finnish experiences in modelling, managing, and using biological linked data Prof. Eero Hyvönen, director Semantic Computing Research Group (SeCo) Aalto University and University of Helsinki Helsinki Centre for Digital Humanities (HELDIG) Department of Computer Science

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3 Digital Humanities Computer Science Digital Humanities Humanities Social Sciences

4 Digital Biology Computer Science Digital Biology Humanities Biology

5 Department of Computer Science Big Data

6 Interoperability Department of Computer Science

7 Artificial Intelligence Department of Computer Science

8 Study Biology as Data Department of Computer Science

9 Contents 1. Semantic Web and Linked Data 2. Problem: Aggregating and publishing distributed collection data 3. Solution: Shared Semantic Web infrastructure 4. What is needed for an infrastructure? 5. Examples of applications Department of Computer Science

10 Semantic web and Linked Data

11 Semantic Web Activity at W3C Started 2001

12 Web of Pages WWW Web of Data GGG (Giant Global Graph)

13 WWW Document: Semantic portal HealthFinland

14 Corresponding GGG graph (in RDF)

15 Linked Open Data Clound 2018 LODStats 2018 ( datasets,150 billion triples

16 GGG: Big Boys Have Entered the Game Google Knowledge Graph Microsoft Satori Knowledge Base

17 2001 (Hyvönen, ed., 2002)

18 Building Semantic Web Infrastructure in Finland with Applications National Finnish Ontology Project Linked Data Finland Linked Open Science Ca. 50 funding organizations, including LUOMUS

19 Linked Data for Managing Distributed Collections

20 Problem 1: Content Compexity - Heterogenous and Interlinked Narratives Maps Encyclopedia Videos Buildings Artefacts Music Cultural sites Fine arts Literature

21 Problem 2: Cultural Content Production System - Distributed and Independent Land survey Museums Web 2.0 sites Archieves Media Linked Data Citizens Libraries

22 Sampo Model for Semantic Portals Land survey Museums Content Providers Archieves Semantic Metadata Ontology & Data Infrastructure Web 2.0 sites Media Linked Data Citizens Libraries

23 Why infrastructure? Intellectuals solve problems - geniuses prevent them Albert Einstein

24 Traditional Infras: (rail)roads, electricity, Semantic Content Infra: Ontologies, data, metadata

25 How Does Linked Data Work in Practise? #

26 Biographical Registries Collect Data about Persons Person Name Profession Birth Place henkilö nimi ammatti syntymapaikka... H1 Akseli Gallen-Kallela taiteilija Lemu H2 Gustaf Mannerheim marsalkka Askainen... name Akseli Gallen-Kallela Person type H1 profession Artist birthplace Lemu Biography Center type nanme Gustaf Mannerheim H2 profession Marshall birthplace Askainen #

27 Art Museum Catalogs Paintings teos nimi tekijä aika aihe... T1 Mannerheimin muotokuva Akseli Gallen-Kallela 1929 Gustaf Mannerheim T2 Aino-triptyykki Akseli Gallen-Kallela 1891 Aino, Kalevala... name Akseli Gallen-Kallela Art Museum Collection creator T1 type Painting... time 1929 subject nimi Gustaf Mannerheim #

28 Land Survey Organizations Know Places kunta Askainen Helsinki Lemu Turku... lääni Varsinais-Suomen lääni Uudenmaan lääni Varsinais-Suomen lääni Varsinais-Suomen lääni County Lemu type type Province Land Survey part-of type part-of... part-of Varsinais-Suomen lääni Finland Askainen Turku part-of #

29 Ontologies are Developed by Semantic Web Researchers KOKO-ontology Subclass Hierarchy Endurant subclassof Concept Perdurant Abstract PhysicalObject subclassof Place subclassof subclassof TimePeriod Profession County Person Artist subclassof FinnONTO Province Painting Marshall #

30 RDF Connects and Harmonizes Linked Data into a GGG Concept Endurant subclassof Perdurant subclassof A bstract subclassof PhysicalObject subclassof Place yläluokka Person type type subclassof Akseli Gallen-Kallela name profession Artist H1 birthplace Lemu tekijä tyyppi maalaus T1 Time type type Profession County Province type Portal Triplestore yläluokka... aihe aika 1929 part-of Varsinais-Suomen lääni part-of Finland H2 Gustaf Mannerheim name profession Marshall part-of part-of birthplace Askainen Turku #

31 1+1>2 #

32 AI #

33 WarSampo Finnish WW II on the Semantic Web #

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35 In Principle a Piece of Cake but How to align concepts (URIs) used by different organizations? How to align metadata models used by different organization? SHARED INFRA NEEDED! #

36 Concepts (IDs) and Data Model Glue Data Together Solution: Shared Ontology Infrastructure concept endurant subclassof perdurant subclassof abstract subclassof physical object subclassof place subclassof subclassof time occupation municipality name Akseli Gallen-Kallela type person type type P1 occupation artist birth place Lemu creator type W1 painting type province type subclassof... topic time 1929 part-of Varsinais-Suomi part-of Finland P2 Gustaf Mannerheim name occupation marshal part-of part-of birth place Askainen Turku #

37 Components of a Semantic Web Intrastructure Datasets Metadata Models RDF Domain Ontologies

38 1. Metadata Models for Modeling the Domain of Discourse Object and document centric Traditional approach in museums E.g. Darwin Core Event-centric harmonizing models E.g. CIDOC CRM, FRBRoo Department of Computer Science

39 TaxMeOn Metaontology: The big picture OWL/RDF(S) TaxMeOn Ontology Metadata Data Department of Computer Science

40 Three parts of the model Researchers Biological research results Species lists Environmental authorities, ecologists Common names Hobbyists, journalists, translators Department of Computer Science

41 Research Case Study: Modeling False Click Beetles Schenkling Fleutiaux Fleutiaux, 1945 Crowson, 1967 Cobos, 1961 Publication Publication Publication Publication Publication Eucnemidae Throscidae Elateridae Eucnemidae ispartof HigherTaxon Elateridae Galba changein Pterotarsus Taxonomic Concept tuberculata historio Publication Guerin-Meneville, 1830 Publication Guerin- Meneville, 1831 Guerin-Meneville, In the illustrations of the book were publishe later and Galba tuberculata had a name Pterotarsus marmorata ispartof HigherTaxon potential Relation publishedin Elateridae Galba Publication Lameere, 1900 before after Split after 5a 5b 5c Balgus Pterotarsus Publication Fleutiaux, 1920 congruent Taxon Eucnemidae changein Taxonomic Concept Balgus Eucnemidae Galbites Publication Fleutiaux, 1918 isolder Than 4a 4b 4c Balgus Eucnemidae Pterotarsus changein Taxonomic Concept Publication Fleutiaux, d Eucnemidae Galbites changein Taxonomic Concept Publication Muona, 1987 (Tuominen, Laurenne, Hyvönen, ESWC 2011)

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43 2. Domain Ontologies for Populating Metadata Schemas Tangible Objects Intangible Subject Matter Contemporaty Places & Historical places Actors (Persons, Groups, Organizations) Events (historical and provenance) Nomenclatures (e.g. taxonomies, chemical compounds, ) Department of Computer Science

44 Resolving Identities: URIs

45 (Centralized)g ONKI Ontology Services 1. Ontology Developers - Colloborative development of interdependent ontologies - Versioning and support for updates 2. Information Searchers - Support concept-based search - Keyword disambiguation - Finding the right search concepts Nokia: company or city? 2. Information Indexers - Support indexing concept finding - Keyword disambiguation - Support indexing patterns

46 ONKI widget for using ontologies in mashup applications Ontology services are automatically available after publishing a vocabulary or ontology with ONKI Simple AJAX-based widget for creating mash-ups 46

47 Department of Computer Science

48 Department of Computer Science Department of Computer Science 48

49 ONKI Light deployed January 2014 by the National Library as Finto Permanent free national service funded by Ministry of Education and Culture and Ministry of Finance from the state budget

50 3. Datasets for Research and Applications Museum collections Observations (e.g., GBIF) Environmental measurements Encyclopedic data about biology & sciences Geographical data, biotype data, etc Weather data Legal data, regulations, red lists, Department of Computer Science

51 Example Application: BirdWatch Tiira.fi citizen science observations / GBIF -> RDF Birds of the World ontology Ontology of Finnish bird characteristics Geographical places & maps (Google) Department of Computer Science

52 Department of Computer Science ESWC WS, 2013

53 Filling in Observation Form Department of Computer Science

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56 Conclusions Big data about biology is available Cannot be investigated manually Enriched big data provide new insights For the public in semantic portals For researchers in data analysis Linked data is a promising approach Data harmonization Data aggregation Knowledge-based analysis Department of Computer Science

57 More Info Questions? Semantic Web & Linked Data Sampo Model & Applications Cultural-Heritage-Synthesis- Technology/dp/