Presentation(malak eshtawi)

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This is a student talk presented as part of a Knowledge Engineering course summarizing a synthesis paper on bioinformatics and protein ontologies. The talk introduces the protein phosphatase family and discusses the development of a phosphatase ontology to classify protein sequences. It then describes the materials and methods used for bioinformatics analysis of protein phosphatases, including extracting phosphatase gene products, performing domain analysis, and identifying class membership. Finally, it discusses translating the ontology into OWL and loading protein instances to systematically classify proteins into phosphatase classes.

Knowledge Engineering Course (SCOM7348)
University of Birzeit, Palestine
December, 2012

Synthesis Paper Talk

Bioinformatics and protein ontologies

Malak Eshtawi.
(Student)
Master of Computing, Birzeit University
meshtawi@ymail.com
This is a student talk, at the Knowledge Engineering course, each student is is
asked to present his/her synthesis paper.
Course Page: http://jarrar-courses.blogspot.com/2011/09/knowledgeengineering-fall2011.html

1

Content

Introduction.

The protein phosphatase family.

Phosphatase ontology.

Materials and methods.

Translation into OWL.

2

Introduction
 Classiﬁcation of proteins is a central process in
understanding the molecular biology of an
organism. Sequencing is a ﬁrst step in revealing
the molecular machinery of a cell, but the
sequences need to be characterised and
classiﬁed, at DNA and protein levels, before
biologists can start more thorough investigations.
 Techniques involved in sequencing, especially the
high throughput sequencing of whole genomes,
have improved dramatically in recent years.
Consequently, classiﬁcation and analysis of data
is now the rate-limiting step.

3

The protein phosphatase family

Protein phosphatases and protein kinases
control phosphorylation events in the cell, which
regulate many different aspects of cell life and
cell interactions with the environment.Recent
reviews on the protein phosphatase family focus
on either :-
i. tyrosine phosphatases .
ii. serine/threonine phosphatases.

4

Phosphatase ontology

 An ontology attempts to describe what exists in
the world; an ontology of protein phosphatases
describes what protein phosphatases exist. In
computer science, an ontology creates a model of
what a community understands about its domain
as a highly interconnected hierarch of concepts
and relationships. By agreeing upon an ontology
and the terms within it, a community can create a
shared understanding of their domain of study.

5

Materials and methods
The bioinformatics analyses necessary for classification of
a protein sequence as a protein phosphatase can be divided
into the following stages :-
I. Extract the protein phosphatase gene products from the
genome in a pre-screening step, without extracting any
non-phosphatase proteins .
II. Perform an InterproScan on each protein phosphatase to
determine its p-domain composition.
III. Use the pattern of p-domain composition to identify to
which class of phosphatases each protein belongs.

6

Translation into OWL

 It requires implicit knowledge of the ontology. In
this case, the use of naming conventions within
the ontology made this transformation simple.
Once translated, all descriptions of protein
instances were loaded into the Instance Store.
We then systematically asked the instance store
which proteins belonged to which class of
phosphatase.

7

References

• Please make sure you list all references,
and to specify them correctly
 Allen,J.E., Pertea,M. and Salzberg,S.L. (2004) Computational gene prediction using
multiple sources of evidence.. Genome Res., 14(1), 142–8.

 Alonso,A., Sasin,J., Bottini,N., Friedberg,I., Friedberg,I., Osterman,A., Godzik,A.,
Hunter,T., Dixon,J. and Mustelin,T. (2004) Protein tyrosine phosphatases in the
human genome. Cell, 117(6), 699–711, Review.

 OWL Web Ontology Language Reference http://www.w3.org/TR/owl-ref/
Pillutla,R.C., Shimamoto,A., Furuichi,Y. and Shatkin,A.J. (1998) Human mRNA
capping enzyme (RNGTT), cap methyltransferase (RNMT) map to 6q16 and
18p11.22-p11.23, respectively. Genomics, 154(2), 351–3.

8

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Presentation(malak eshtawi)

1. Knowledge Engineering Course (SCOM7348) University of Birzeit, Palestine December, 2012 Synthesis Paper Talk Bioinformatics and protein ontologies Malak Eshtawi. (Student) Master of Computing, Birzeit University meshtawi@ymail.com This is a student talk, at the Knowledge Engineering course, each student is is asked to present his/her synthesis paper. Course Page: http://jarrar-courses.blogspot.com/2011/09/knowledgeengineering-fall2011.html 1

2. Content Introduction. The protein phosphatase family. Phosphatase ontology. Materials and methods. Translation into OWL. 2

3. Introduction  Classification of proteins is a central process in understanding the molecular biology of an organism. Sequencing is a first step in revealing the molecular machinery of a cell, but the sequences need to be characterised and classified, at DNA and protein levels, before biologists can start more thorough investigations.  Techniques involved in sequencing, especially the high throughput sequencing of whole genomes, have improved dramatically in recent years. Consequently, classification and analysis of data is now the rate-limiting step. 3

4. The protein phosphatase family Protein phosphatases and protein kinases control phosphorylation events in the cell, which regulate many different aspects of cell life and cell interactions with the environment.Recent reviews on the protein phosphatase family focus on either :- i. tyrosine phosphatases . ii. serine/threonine phosphatases. 4

5. Phosphatase ontology  An ontology attempts to describe what exists in the world; an ontology of protein phosphatases describes what protein phosphatases exist. In computer science, an ontology creates a model of what a community understands about its domain as a highly interconnected hierarch of concepts and relationships. By agreeing upon an ontology and the terms within it, a community can create a shared understanding of their domain of study. 5

6. Materials and methods The bioinformatics analyses necessary for classification of a protein sequence as a protein phosphatase can be divided into the following stages :- I. Extract the protein phosphatase gene products from the genome in a pre-screening step, without extracting any non-phosphatase proteins . II. Perform an InterproScan on each protein phosphatase to determine its p-domain composition. III. Use the pattern of p-domain composition to identify to which class of phosphatases each protein belongs. 6

7. Translation into OWL  It requires implicit knowledge of the ontology. In this case, the use of naming conventions within the ontology made this transformation simple. Once translated, all descriptions of protein instances were loaded into the Instance Store. We then systematically asked the instance store which proteins belonged to which class of phosphatase. 7

8. References • Please make sure you list all references, and to specify them correctly  Allen,J.E., Pertea,M. and Salzberg,S.L. (2004) Computational gene prediction using multiple sources of evidence.. Genome Res., 14(1), 142–8.  Alonso,A., Sasin,J., Bottini,N., Friedberg,I., Friedberg,I., Osterman,A., Godzik,A., Hunter,T., Dixon,J. and Mustelin,T. (2004) Protein tyrosine phosphatases in the human genome. Cell, 117(6), 699–711, Review.  OWL Web Ontology Language Reference http://www.w3.org/TR/owl-ref/ Pillutla,R.C., Shimamoto,A., Furuichi,Y. and Shatkin,A.J. (1998) Human mRNA capping enzyme (RNGTT), cap methyltransferase (RNMT) map to 6q16 and 18p11.22-p11.23, respectively. Genomics, 154(2), 351–3. 8

9. Thank You 9

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