Semantic Computing: Understanding the Meaning of Data with Semantic Web, Slides of Semantics of Programming Languages

Download Semantic Computing: Understanding the Meaning of Data with Semantic Web and more Slides Semantics of Programming Languages in PDF only on Docsity!

1

Semantic Computing

Introduction

Agenda of the Day

 Introduction to Semantic Computing & Semantic Bioinformatics

 Web

 Today’s Web  Semantic Web

 Paradigm Shift

 Today’s Web to Semantic Web

 Semantic Web Technologies

 A Layered Approach (^2)

4

First results are about bats and dolphins

HTML?

7

Nonmonotonic Reasoning: Context- Dependent Reasoning

byV. Marek and M Truszczynski Springer 1993 ISBN 0387976892

HTML?

 Inability to cover any content aspects – HTML

only describes the appearances of documents

and cannot cover any content related aspects. It

is therefore unsuitable for explicit queries.

 Inability for semantic markup – Individual

elements on a page cannot be marked

semantically.

8

How to overcome these limitations

 Currents situation can be improved by adopting following two strategies  Use the content as it is represented today, and to develop techniques based on artificial intelligence and computational linguistics.  This approach has been followed for sometime now, but despite advances that have been made the task still appears too ambitious.

 Represent Web content in a form that is more easily machine processable  Then use intelligent techniques to take advantage of these representations (Semantic Web). 10

What should we do?

 Simple lesson learnt from Basic Computer Science

 Provide a structure to content

11

 Another problem of bioinformatics is the lack of well defined standards.

 Every database or institute has it's own unique identifiers, indexing scheme, data format and tools to deal with them all.

 There is already a big effort to integrate this data but the amount of work to be done with current data models is huge and because data models change quite often, the maintenance of the code base is just not feasible. 13

 One way of solving this problem is to centralize all data in a single database (such as EMBL, UniProtKB etc)

 but for that we still need all other groups to produce the data in the same format (which does not fit all models)

 and we end up having either lack of information (all using the same fixed format) or integration nightmare (different formats). 14

 Of course reasoning can be done using any kind of data format: flat-files, databases, XMLs but for all of them,

 we still need to explain the meaning of assertions and for that we need ontologies and a statement mechanism to connect them.

16

 create the core of a Bioinformatics Semantic Web populated by a number of sample data sources and applications representative of the use of the Web in Bioinformatics

 and to demonstrate novel, reasoning-based solutions dealing with the following problems:  Rules for mediation and to formulate complex queries  Consistent integration of Bioinformatics data  Adaptive portals for molecular biologists 17

 Consider the following scenario: a biologist obtains a novel DNA sequences nothing is known about.

 He or she wants to run an alignment, but has specific requirements for the alignment.

 These requirements are captured as rules and constraints, which are taken into account by the online accessible semantic Web enabled sequence comparison service. 19

 The researcher found a number of significantly similar sequences in yeast for which there is gene expression data available.

 The scientist requests from the semantic Web enabled gene expression database and tool expression data for the relevant genes.

 He or she defines rules, which capture which expression profiles are interesting, e.g. all genes which are highly expressed at the beginning and end of the experiment are of interest. 20