Date: 01/08/2014

Semantic Web 101:Benefits for geologists

Daniel GarijoOntology Engineering Group,

Departamento de InteligenciaArtificial. Universidad Politécnica de Madrid

What is the Semantic Web?

•Extension of the Web by using World Wide Web Consortium (W3C) Standards

•Generally, a set of techniques for:• Knowledge representation• Improve data sharing• Improve data access• Link distributed resources.

•How? • RDF, vocabularies, ontologies and standards• Linked Data

RDF: The Resource Description Framework

• W3C recommendation

• Useful to represent metadata and describe any type of information in a machine-accesible way.

• Resources are described in terms of properties and property values using RDF statements

• Statements are represented as triples, consisting of a subject, predicate, and object [S,P,O]

Objectproperty

Statement

© Slide adapted from “RDF and RDF Schema”- Raúl García et al.

Subject

RDF: Example

http://example.org/paper1 http://example.org/Tikoff

http://example.org/paper2

“Crustal-scale, en echelon…”

hasTitle

hasAuthor

hasAuthor

Basil Tikoff

hasName

“Preexisting fractures and the formation of an iconic

American landscape …”

hasTitle

Vocabularies and Ontologies

•Vocabulary:• Defines the concepts and relationships used to describe and

represent an area of concern.

• Used to classify the terms that can be used in a particular application, characterize possible relationships, and define possible constraints on using those terms.

•Ontology: • More complex, and possibly quite formal collection of terms.

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

Heterogeneity vs standardization

Image from: http://www.cs.vu.nl/~frankh/spool/ISWC2011Keynote/Slide32.JPG

Freedom of designGuided design (agreed vocabularies + extensions)

Linked Data

1.Use URIs as names for things.

2.Use HTTP URIs so that people can look up those names.

3.When someone looks up a URI, provide useful information.

4.Include links to other URIs.

“Linking Open Data clouddiagram, by Richard Cyganiak and AnjaJentzsch. http://lod-cloud.net/”

Challenges for geologists

How can this help YOU?

Some of the challenges I have discovered so far…

•No standard way to process , store and archive the metadata related to samples•Not straightforward to find the relation between samples and scientific papers•Repository redundancy: difficult to know if samples are duplicated•Repository heterogeinity: difficult to establish links between data repositories•Difficult to query a repository: the same query is not valid for several repositories.•Which license do I add to my data? How do I attach it?•Accessing data: sharing mappings from different authors is often done by direct contact to the author.•Trust in observations: you have to rely on the scientist who did them•Map integration of heterogeneous observations•How reproducible are the methods applied to the data in the analyses for the paper?•….

Some Helpful Standards

+ Linked Data

Sensor Network Ontology (SSN)•Ontology for describing observations•Provenance of the observation (who, where, how)•Other metadata like sensing method

PROV - O •Vocabulary for provenance•Tracking the resources andactivities that influenced on a result•Credit•Attribution•Responsibility

Exposing scientific methods

Text:Narrative of method,

software packages used

Workflow: Workflow/scripts describing

dataflow, codes, and parameters

Data:Key datasets and figures/plots

Typical Published Article

Text:Narrative of method,

software packages used

Data:Key datasets and figures/plots

Reproducible Article: Weaver, GenePattern GRRD, etc.

Exposing scientific methods: Research Objects

Aggregation of resources that bundles together the contents of a research work:

Conclusions

SW can be helpful to

•Enable accessibility to your research (paper) data (Linked Data)

•Facilitate data sharing and consumption (standards +Linked Data)

•Enable proper credit/citation (Provenance)

•Ease Metadata collection (Standards)

•Facilitate reproducibility (Workflows and Research Objects)

References

Useful links

•SSN: http://www.w3.org/2005/Incubator/ssn/XGR-ssn-20110628/(observation module)

•PROV: http://www.w3.org/TR/prov-o/

•Workflows and provenance: http://www.opmw.org/model/OPMW/

•Research Objects: http://www.researchobject.org/

•Which License do I attach to my data? http://creativecommons.org/choose/

•Data repositories: http://figshare.com/, http://zenodo.org/

Date: 01/08/2014

Semantic Web 101:Benefits for geologists

Daniel GarijoOntology Engineering Group,

Departamento de InteligenciaArtificial. Universidad Politécnica de Madrid