WeST – Web Science & Technologies University of Koblenz ▪ Landau, Germany Building and Using Knowledge Bases Steffen Staab Saqib Mir – European Bioinformatics

WeST – Web Science & TechnologiesUniversity of Koblenz ▪ Landau, Germany

Building and UsingKnowledge Bases

Steffen Staab

Saqib Mir – European Bioinformatics InstituteErmelinda d‘Oro, Massimo Ruffolo – Univ. Calabria, Italy

& WeST Team

Steffen Staab [email protected]

WeST – Web Science & Technologies

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Semantic Web

Web Retrieval

Social Web

Multimedia Web

Software Web

Institut WeST – Web Science & Technologies

GESIS



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PhD thesis trauma 17 years ago

„Nach dem Auspacken der LPS 105 präsentiert sich dem Betrachter ein stabiles Laufwerk, das genauso geringe Außenmaße besitzt wie die Maxtor.“

Having unwrapped the LPS 105 – reveals itself to the onlooker - a stable disk drive, which has similarly small volume as the Maxtor.“



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GENERAL MOTIVATION

General motivation is not information extraction,

but it is solving tasks!



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General objective: Extracting to LOD

hasLivedInuseAsExample

Crucial to know: Ontologies nowadays reflect this structureOntologies are• Modular (vs one to rule them all)• Distributed (vs defined in one place)• Connected (vs isolated templates)• Extensible (vs claimed to be finished)• Lightweight (vs computationally intractable)• Popular ones are used more often (vs people disagreeing)

Ontologies – LEGO style



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Most famous applications

Steve Macbeth (Microsoft): - discussion wrt Schema.org -“about 7% of pages we crawl have mark-up” http://www.w3.org/2012/06/06-schema-minutes.html

LOD Cloud

Google Knowledge Graph Bing gets its own knowledge graph

http://searchengineland.com/bing-britannica-partnership-123930

http://www.w3.org/2012/06/06-schema-minutes.html

http://www.w3.org/2012/06/06-schema-minutes.html



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ANALYSIS OF URBAN PARAMETERS

Example ontology-based application 1:



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General objective: Analysing LOD

hasLivedInuseAsExample



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http://lisa.west.uni-koblenz.de/lisa-demo/

Family‘s analysis of Koblenz LOD + Open Street Map data



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http://lisa.west.uni-koblenz.de/lisa-demo/

Entrepreneur‘s analysis of Koblenz LOD + Open Street Map data

1. PrizeGerman Linked Open Gov Data Competition 2012



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FACETED MULTIMEDIA EXPLORATION

Example ontology-based application :



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Making Web 2.0 More Accessible

Links Location

Persons

Knowledge Tags

low- to midlevel features

xxxxxxxxx

GeoNames[Schenk et al; JoWS 2009]



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Choosing between Koblenz – and Koblenz

Video at: http://vimeo.com/2057249



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Contextual Information



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Tag-based refinement



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A tag view of „Koblenz“ & „Castle“



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Semantic Identity – Festung Ehrenbreitstein



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Persons – Celebrities, FOAFers & Flickr Users

Billion Triples Challenge 1. Prize 2008

[Schenk et al; JoWS 2009]



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OBSERVATIONS ON INFORMATION EXTRACTION

Now on to information extraction:



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Challenges & Opportunities for IE

Not all web pages are created equal



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Some challenges are the same, e.g. finding type instances



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Some challenges are the same, e.g. finding relation instances



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Some contain concepts and their descriptions, some don‘t

No types here,few relation types



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Knowing that they are instances and of which type

Textual indication

Positional indication



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To some extent

positional and layout

indications work across

languages and sites



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owl:sameAs

We should not only think about

Web pages, but about Web sites



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owl:sameAs

We should not only think about

Web pages, but about Web sites



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Comparing related work to our objectives

Related work objectives IE on Web pages Acquiring instances and

relationship instances

IE based on linear text

Our objectives IE on Web sites Acquiring items Classifying items in

Instances Concepts Relation instances Relationships

IE also based on spatial position

There is overlap and of course there are exceptions in related work



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Outline

The Bio-CaseThe Social Media-Case Motivation State-of-the-Art Core idea of SXPath Implementation Evaluation

[Oro et al; VLDB 2010]



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Presentation-oriented documents



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Presentation-oriented documents

• HTML DOM structure is site specific• Spatial arrangements are rarely explicit• Spatial layout is hidden in complex nesting of layout elements• Intricate DOM tree structures are conceptually difficult to query

for the user (or a tool!)



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Related Work

Web Query languages Xpath 1.0 and XQuery1.0

Established Too difficult to use for scraping from intricate DOM structures

Visual languages Spatial Graph Grammars [Kong et al.] are quite complex in

term of both usability and efficiency Algebras for creating and querying multimedia interactive

presentations (e.g. ppt) [Subrahmanian et al.]

Web wrapper induction exploiting visual interface [Gottlob et al.] [Sahuguet et al.]

generate XPath location paths of DOM nodes can benefit from using Spatial XPath



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Outline




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b

e

Representing Spatial Relations between DOM Nodes



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Idea: Use Spatial Relations among DOM Nodes



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Spatial DOM (SDOM)



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SXPath System Architecture



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Querying for Relations Among Nodes

Rectangular Cardinal Relations (RCR)

Topological Relations

r1 E:NE r2

Spatial models allow for expressing disjunctive relations among regions



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XPath Example



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SXPath Example



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From XPath 1.0 towards Spatial Querying with SXPath

SXPath features adopts intuitive path notation:

axis::nodetest [pred]*

adds to XPath spatial axes spatial position functions

natural semantics for spatial querying



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SXPath System Architecture



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Complexity Results

Formal model defined in the paper [Oro et al; VLDB 2010]



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Outline




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SXPath System



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Summative User Study



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Outline

The Bio-Case Motivation The (Biochemical) Deep

Web Contributions

Page-level wrapper induction

Site-wide wrapper generation

Error Correction by Mutual Reinforcement

Conclusions and Future Directions

The Social Media Case Motivation State-of-the-Art Core idea of SXPath SXPath Language

Spatial Data Model Syntax & Semantics Complexity

Implementation Evaluation



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>1000 Life Science DBs, number growing quickly



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Biochemical Web Sites: Observations - 1

Labeled Data

Total Labeled Unlabeled Unlabeled(Redundant)

754 719 19 16

Table 1: Data fields across 20 Biochemical Web sites

Full survey:http://sabio.villa-bosch.de/labelsurvey.html (404)

http://sabio.villa-bosch.de/labelsurvey.html

http://sabio.villa-bosch.de/labelsurvey.html



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Dynamic Web Pages



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Rich Site Structure



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Semantics is often only in the report, not in the underlying relational database

Web Services Survey: 11 of 100 Databases1 provide APIs Incomplete coverage Varying granularity No semantics in the service description

1 Databases indexed by the Nucleic Acids Research Journal (http://www3.oup.co.uk/nar/database/). Complete survey was available at http://sabiork.villa-bosch.de/index.html/survey.html



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Biochemical Web Sites: Extraction Tasks

Induce Wrapper

Induce Wrapper

Induce Wrapper

[Mir et al; DILS 2009][Mir et al; ESWC 2010]



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Contributions

Unsupervised Page-Level Wrapper Induction

Unsupervised Site-Wide Wrapper Induction (Site Structure Discovery)

(Acquiring the Schema/Ontology)

Automatic Error Detection and Correction by Mutual Reinforcement



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Page-Level Wrapper Induction – 1D1 = {C00221, beta-D-Glucose, …, R01520, 1.1.1.47,…}O1 = {Entry, Name,…, Reaction, R00026, Enzyme,…, 3.2.1.21}

D2 = {C00185, Cellobiose,…, R00306, 1.1.99.18,… }O2 = {Entry, Name,…, Reaction, R00026, Enzyme,…, 3.2.1.21}

//*[text()]



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Page-Level Wrapper Induction - 2

Reclassify – Growing Data Regions



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D1´ = {C00221, beta-D-Glucose, …, R01520, 1.1.1.47, 3.2.1.21 …}O1´ = {Entry, Name,…, Reaction, R00026, Enzyme,…,}

D2´ = {C00185, Cellobiose,…, R00306, 1.1.99.18, 3.2.1.21 … }O2´ = {Entry, Name,…, Reaction, R00026, Enzyme,…,}



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Selecting Labels for Datahtml/…./table[1]/tr[8]/td[1]/…/code[1]/a[1] (“1.1.1.47” )

html/…./table[1]/tr[6]/th[1]/…/code[1]/ (“Reaction”)

html/…./table[1]/tr[8]/th[1]/…/code[1]/ (“Enzyme”)



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Anchor the PathEnzyme - html/table[1]/tr[8]/th[1]/code[1]/

html/table[1]/tr[8]/td[1]/code[1]/a[1]html/table[1]/tr[8]/td[1]/code[1]/a[2]

//*[text()=‘Enzyme’] ../…./../td[1]/code[1]/a[position()≥2]/text()

Pivot GeneralizeRelative



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Selected Sources

KEGG, ChEBI, MSDChem Basic qualitative data Popular Overlapping/complementary data



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Wrapper Induction - Evaluation

SOURCE #L #D #S TP FN FP P R

KEGG Compoundhttp://www.genome.jp/kegg/ compound/

10 762 3 411 351 46 89.9 53.9

15 759 3 0 100 99.6

KEGG Reactionhttp://www.genome.jp/kegg/ reaction/

10 205 3 173 32 0 100 84.4

15 205 0 0 100 100

ChEBIhttp://www.ebi.ac.uk/chebi

22 831 3 595 236 41 93.5 71.6

15 829 2 0 100 99.7

MSDChemhttp://www.ebi.ac.uk/msd-srv/msdchem/

30 600 3 600 0 20 96.7 100

15 600 0 20 96.7 100

Average (based on final wrappers for each source) 99.1 99.8

~9 samples – ~99% P, ~98% R

Table 2: Page-level wrapper induction results, 20 test pages(L=Labels, D=Data entries, S=Training pages)



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Site-Wide Wrapper Induction: Observations

Not all pages contain data (e.g. Legal disclaimers, contact pages, navigational menus)

An efficient approach should ignore these pages We dont need to learn the entire site-structure



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Site-Wide Wrapper Induction: Observations - 2

Classified Link-Collections point to data-intensive pages of the same class.



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Site-Wide Wrapper Induction: Observations - 3

Pages belong to the same class describe the same concepts Some concepts are sometimes omitted Ordering is always the same



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Site-Wide Wrapper Induction

1. Start with C0

2. Follow all classified link-collections

3. Generate wrappers for each set of target pages

4. Determine if new class is formed

5. Add navigation step6. Repeat 2 – 5 for each

new class formed in 4

C0

L3

L1

L2

If C0 != Ci (i>0)S=S+Ci;

Navigation StepsW= {(C0 → L1→ C0),(C0 → L2→ C2),(C0 → L3→ C3)}

S={C0}

C1

C3

C2



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Site-Wide Wrapper Induction – Evaluation

SOURCE #C #C’ #D TP FN FP P R

MSDChem 1 1 N/A N/A N/A N/A N/A N/A

ChEBI 3 1 1711 1195 516 0 100 69.8

KEGG 10 7 6223 5044 1179 188 97 81.1

Average 98.5 75.5

Table 3: Site-wide wrapper induction results, 20 test pages for each class(C=Classes, C´=Classes discovered, D=Data entries)



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Error Detection and Correction:Mutual Reinforcement

Observation: Certain data reappear on more than one class of pages



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Error Detection and Correction:Mutual Reinforcement

Reinforcement if reappearing data correctly classified as Data

Otherwise it points to misclassification Label-Data Mismatch

• Correction: Introduce more samples Label-Label Mismatch

• Cannot be detected



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Where to go next?

Reverse engineering production1. LOD

2. Navigation model

3. Interaction model

4. Layout model

Capture this generative model using machine learning Relational learning

• Markov logic programmes?• …?

emitting RDF & RDFS

what belongs to what

(- not treated at all by us so far -)

spatial positioning



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Bibliography

Ermelinda Oro, Massimo Ruffolo, Steffen Staab. SXPath – Extending XPath towards Spatial Querying on Web Documents. In: PVLDB – Proceedings of the VLDB Endowment, 4(2): 129-140, 2010.

S. Mir, S. Staab, I. Rojas. Site-Wide Wrapper Induction for Life Science Deep Web Databases. In: DILS-2009 – Proc. of the Data Integration in the Life Sciences Workshop, Manchester, UK, July 20-22, LNCS, Springer, 2009.

Saqib Mir, Steffen Staab, Isabel Rojas. An Unsupervised Approach for Acquiring Ontologies and RDF Data from Online Life Science Databases. In: 7th Extended Semantic Web Conference (ESWC2010), Heraklion, Greece, May 30-June 3, 2010, pp. 319-333.

WeST – Web Science & TechnologiesUniversity of Koblenz ▪ Landau, Germany

Thank you for your attention!