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