department of computer science semantic web meets biology · department of computer science. 3....

Department of Computer Science


Prof. Eero Hyvönen, directorSemantic Computing Research Group (SeCo)Aalto University and University of HelsinkiHelsinki Centre for Digital Humanities (HELDIG)http://seco.cs.aalto.fi/ http://heldig.fi/

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

http://seco.cs.aalto.fi/

http://heldig.gi/

Digital Humanities

Social SciencesHumanities

ComputerScience

Digital Humanities

Digital Biology

BiologyHumanities

ComputerScience

Digital Biology


Big Data


Interoperability


ArtificialIntelligence


Study Biologyas Data


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


Semantic weband Linked Data

Semantic Web Activity at W3C Started 2001

Web of PagesWWW

Web of DataGGG

(Giant Global Graph)

WWW Document:Semantic portal HealthFinland

Corresponding GGG graph (in RDF)

LODStats 2018 (http://stats.lod2.eu/): 10000 datasets,150 billion triples

Linked Open Data Clound 2018

GGG: Big Boys Have Entered the Game …http://schema.org

• Google Knowledge Graph

• Microsoft Satori Knowledge Base

http://schema.org/

2001

(Hyvönen, ed., 2002)

Building Semantic Web Infrastructurein Finland with Applications

Ca. 50 funding organizations, including LUOMUS

• National Finnish Ontology Project 2003-2012

• Linked Data Finland 2012-

• Linked Open Science 2014-2017


Linked Data for Managing Distributed

Collections

Problem 1: Content Compexity- Heterogenous and Interlinked

Encyclopedia

Artefacts

Maps

Videos

Buildings

Fine arts

Narratives

Literature

Cultural sites

Music

http://images.google.com/imgres?imgurl=http://www.raivaaja.org/fribrg_kalevala.jpg&imgrefurl=http://leatherhead.livejournal.com/&h=964&w=692&sz=35&hl=en&start=18&sig2=3kxXguNSuWI-EIZPFTe79Q&tbnid=KTRLksgbMKObHM:&tbnh=148&tbnw=106&ei=tMVGSJ3rDIb20ATot9z9Bg&prev=/images?q%3Dkalevala%26gbv%3D2%26hl%3Den%26sa%3DG


http://images.google.fi/imgres?imgurl=http://pater.kul.lublin.pl/wystawy/pamietnik_wystaw/kalevala/obrazki/obrona_sampo.jpg&imgrefurl=http://pater.kul.lublin.pl/wystawy/pamietnik_wystaw/kalevala/wizualizacja_kalevali.htm&h=292&w=300&sz=43&tbnid=xTVe_NzoyZoJ:&tbnh=108&tbnw=111&hl=fi&start=13&prev=/images?q%3Dsampo%26svnum%3D10%26hl%3Dfi%26lr%3D%26sa%3DG


Problem 2: Cultural Content Production System- Distributed and Independent

Museums

Libraries

Archieves

Land survey

Linked Data

Web 2.0 sites

Media

Citizens

”Sampo” Model for Semantic Portals

Ontology & Data Infrastructure

SemanticMetadata

ContentProviders

Land survey Museums

Archieves

Linked DataCitizens

Libraries

Web 2.0 sites

Media





”Intellectuals solve problems - geniuses prevent them”

Albert Einstein

Why infrastructure?

https://www.google.fi/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&docid=SX6tp-_4uO-yzM&tbnid=KJ0X_PVNReiOxM:&ved=0CAcQjRw&url=https://plus.google.com/+AboutAlbertEinstein&ei=gqkVVOKPKYvhywOHmYDQDg&bvm=bv.75097201,d.bGQ&psig=AFQjCNGrfVGofT7PMfaXQjNpLZ0LFuxSqg&ust=1410792188884092

https://www.google.fi/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&docid=SX6tp-_4uO-yzM&tbnid=KJ0X_PVNReiOxM:&ved=0CAcQjRw&url=https://plus.google.com/+AboutAlbertEinstein&ei=gqkVVOKPKYvhywOHmYDQDg&bvm=bv.75097201,d.bGQ&psig=AFQjCNGrfVGofT7PMfaXQjNpLZ0LFuxSqg&ust=1410792188884092

Traditional Infras: (rail)roads, electricity, …

Semantic Content Infra:Ontologies, data, metadata

‹#›

How Does Linked Data Work in Practise?

http://images.google.fi/imgres?imgurl=http://users.tkk.fi/sergei/aalto_logo.jpg&imgrefurl=http://users.tkk.fi/sergei/heading.html&usg=__U6qNyTYkgFi5mUBUl6FV1oxZCSc=&h=120&w=144&sz=5&hl=fi&start=24&um=1&tbnid=MKbjjoSBqbn_EM:&tbnh=78&tbnw=94&prev=/images?q%3Daalto%2Buniversity%2Blogo%26ndsp%3D18%26hl%3Dfi%26sa%3DN%26start%3D18%26um%3D1


‹#›

Biographical Registries Collect Data about Persons

henkilö nimi ammatti syntymapaikka ...H1 Akseli Gallen-Kallela taiteilija LemuH2 Gustaf Mannerheim marsalkka Askainen

...

H1

Lemu

ArtistPerson

”Akseli Gallen-Kallela”

H2

Askainen

Marshall

”Gustaf Mannerheim”

type

type

name

nanme

profession

profession

birthPlace

birthPlace

Biography Center

Person Name Profession Birth Place



‹#›

Art Museum Catalogs Paintings

...

T1

1929

Painting

creator

time

type

”Gustaf Mannerheim”nimi

subject

name”Akseli Gallen-Kallela”

teos nimi tekijä aika aihe ...T1 Mannerheimin muotokuva Akseli Gallen-Kallela 1929 Gustaf MannerheimT2 Aino-triptyykki Akseli Gallen-Kallela 1891 Aino, Kalevala

...

Art Museum Collection



‹#›

Land Survey Organizations Know Places

Varsinais-Suomen lääni Finland

Askainen

Lemu

Turku

kunta lääniAskainen Varsinais-Suomen lääniHelsinki Uudenmaan lääniLemu Varsinais-Suomen lääniTurku Varsinais-Suomen lääni...

part-ofpart-of

part-of

part-of

County

type

Province

type...

type Land Survey



‹#›

Ontologies are Developed by Semantic Web Researchers

ArtistPerson

Marshall

Painting

Concept

Endurant

Place

Profession CountysubClassOf

TimePeriod

AbstractPerdurant

PhysicalObject

Province

KOKO-ontologySubclass Hierarchy

FinnONTO

subClassOf

subClassOf

subClassOf

subClassOf



‹#›

RDF Connects and Harmonizes Linked Data into a GGG

H1

Lemu

ArtistPerson


H2

Askainen

Marshall


type

type

name

name

profession

profession

birthPlace

birthPlace

T1

1929

maalaus

tekijä

aiheaika

tyyppi

Varsinais-Suomen lääni Finland

Turku

part-of part-of

part-of part-of

Concept

Endurant

Place

Profession County

type

type

type

subClassOf

subClassOf

subClassOf

subClassOf

yläluokka

Time

subClassOfA bstractPerdurant

PhysicalObject

Province

yläluokka

...

PortalTriplestore



‹#›

1+1>2



‹#›

AI



‹#›

WarSampoFinnish WW II on the Semantic Web

http://sotasampo.fi

Presenter

Presentation Notes

- presentation - topic



http://sotasampo.fi/en

‹#›

https://vimeo.com/212249404



https://vimeo.com/212249404

‹#›

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!



‹#›

Concepts (IDs) and Data Model Glue Data TogetherSolution: Shared Ontology Infrastructure

P1

Lemu

artistperson


P2

Askainen

marshal


type

type

name

name

occupation

occupation

birth place

birth place

W1

1929

painting

creator

topictime

type

Varsinais-Suomi Finland

Turku

part-of part-of

part-of part-of

concept

endurant

place

occupation municipality

type

type

type

subclassOf

subclassOf

subclassOf

subclassOf

subclassOf

time

subclassOfabstractperdurant

physical object

province

subclassOf

...



Components of a Semantic Web Intrastructure

RDF

Metadata Models

Domain Ontologies

Datasets


1. Metadata Modelsfor 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


TaxMeOn Metaontology:The big picture

OWL/RDF(S)

TaxMeOn

Ontology

Metadata

Data


Three parts of the model

Environmentalauthorities, ecologists

Biological research results Specieslists

Commonnames

Researchers

Hobbyists, journalists, translators

Pterotarsus

Elateridae

GalbapotentialRelation

Publication

Lameere, 1900

publishedIn

Split

Balgus

Fleutiaux, 1920

Eucnemidaebefore

after

after

Galbites

Fleutiaux,1918

changeInTaxonomicConcept

Fleutiaux, 1945

Muona,1987

isPartOfHigherTaxon

Elateridae

Pterotarsus

Publication Publication

Eucnemidae

PterotarsuschangeInTaxonomicConcept

Eucnemidae

Galbites

Eucnemidae


Publication

Fleutiaux1920

Publication

Eucnemidae

Publication

Schenkling1928 Crowson,

1967

Throscidae

BalguscongruentTaxon

Publication

isOlderThan

Cobos,1961

Elateridae

Balgus

Publication

Publication

Guerin-Meneville,1831

Publication

Publication

1 2 3

4a 4b 4c

5a 5b 5c

4d

Galba

tuberculata

Eucnemidae

Guerin-Meneville,1830

Guerin-Meneville,1838. In the illustrations of the book were publishe later and Galba tuberculata had a name Pterotarsus marmorata

historio

Publication


Fleutiaux,1945

isPartOfHigherTaxon

(Tuominen, Laurenne, Hyvönen, ESWC 2011)

Research Case Study:Modeling False Click Beetles

http://schema.onki.fi/taxmeon


2. Domain Ontologiesfor 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, …)

❏ …

Resolving Identities: URIs

(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

2. Information Indexers- Support indexing concept finding- Keyword disambiguation- Support indexing patterns

Nokia:company or city?

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


Department ofComputer Science

48

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

http://finto.fi/


3. Datasetsfor 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, …


Example Application: BirdWatch

● ”Tiira.fi” citizen science observations / GBIF -> RDF● Birds of the World ontology● Ontology of Finnish bird characteristics● Geographical places & maps (Google)


http://seco.cs.aalto.fi/applications/birdwatch/ESWC WS, 2013

http://seco.cs.aalto.fi/applications/birdwatch/


Filling in Observation Form


● 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

Conclusions

57

More Info – Questions?

https://www.amazon.com/Publishing-Cultural-Heritage-Synthesis-Technology/dp/1608459977

Semantic Web & Linked Datahttp://www.w3.org/standards/semanticweb/Sampo Model & Applicationshttp://seco.cs.aalto.fi/publications

https://www.gaudeamus.fi/semanttinen-web/

https://www.amazon.com/Publishing-Cultural-Heritage-Synthesis-Technology/dp/1608459977

http://www.w3.org/standards/semanticweb/

http://seco.cs.aalto.fi/publications

https://www.gaudeamus.fi/semanttinen-web/

department of computer science semantic web meets biology · department of computer science. 3....

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