Depending on experience and cognition of the molecular biological science experts and handiness of research lab trials, genetically germinating diseases, symptoms of those diseases and besides familial interactions are described in greater or lesser item. Ontology is the construct that holding shop sphere cognition of peculiar research group. Therefore the information about diseases, symptoms and cistron interactions are officially described in ontology. I have adapted semantic similar-ity prosodies to mensurate similarity between questions and familial diseases annotated with the usage of biomedical ontology that are published by Open Biological and Biomedical Ontologies Foundry such as Human Phenotype Ontology ( HPO ) , Disease Ontology ( DO ) , Symptom Ontology ( SO ) etc. Besides I am traveling to present a statistical theoretical account to delegate weights to ensuing similarity tonss which can be used to rank the campaigner diseases.
If I describe the advantages of knowledge-bases ( ontology ) instead than the databases, ontology is a computational representation of a sphere of cognition based upon a controlled, standardised vocabulary for depicting entities and the semantic relationships between them. In point of fact ontology is a general construct to show the cognition of a individual who may be an expertness of such sphere. Many ontologies are structured as a directed acyclic graph ( DAG ) , whereby the nodes of the DAG, which are besides called footings of the ontology corresponding of the sphere. After success of the biomedical undertaking Gene Ontology in the past decennary the ontologies have been developed for many Fieldss other than the biomedical scientific discipline. Recent old ages they are published by those domain experts to portion their cognition with others in web.
The attack of the research outperforms simpler consecutive alliance attacks in traditional Bioinformatics that do non see about the interrelatednesss among the diseases ; sphere experts found. Then the attack may non hold the simpler term fiting instead than alignment procedure. The semantic web seeking construct that take the semantic interrelatednesss between footings into history is embedded.
The most of import function of the doctor is doing the clinical diagnosing. Clinical nosologies is frequently ambitious, particularly in the field of medical genetic sciences where the differential diagnosing is complicated by the figure of Mendalian and chromosomal upsets. Each of upsets is characterized by genetically germinating diseases. Not merely the individual cistron fluctuations are affected to the disease but besides the genetic sciences interactions are affected to such diseases.
The figure of familial databases is drastically grown-up and the experimenters have to make such analysis of utilizing those informations for biological intents in an effectual manner. Therefore such new constructs are used for that undertaking such as ontology construct etc. In this attack, the semantic web construct is traveling to be used for such analysis of the informations to foretell the diseases or diagnosing procedure. In the fact of disease anticipation, initial user input is the genome of user. Then harmonizing to mutants of the genome user has been given such filtered-out list of matching clinical characteristics or symptoms to come in whether the user has or non them. Users enter one or more characteristics and are presented with a list of campaigner diagnosings that are characterized by some or all of the characteristics. Then the system uses the semantic hunt modus operandis through biomedical ontologies to foretell the campaigner diseases that can be raised. Finally acquire the consequence of prioritized list of diseases.
Chapter 2 – Literature Reappraisal
Recent few decennaries, Biology becomes in the center of a major theoretical account driven paradigm by the Information Technology. This is the beginning of Bioinformatics. Although Biology is an informational scientific discipline in many facets the field has been quickly going more computational every bit good as analytical. Because of rapid advancement in genetic sciences and biochemistry research combined with the tool provided by modern biotechnology has carried out monolithic volumes of genetic sciences and sequence informations.
Figure: construction of Deoxyribonucleic acid
Bioinformatics has been defined as a agency for analysing, comparing, diagrammatically exposing, patterning, systematizing, hive awaying, seeking and finally administering biological information which includes sequences, constructions, map and evolution. Then Bioinformatics may be defined as a subject that generates computational background for the Biological Science. It comprises the survey of DNA construction and map, cistron and protein look, protein production, construction and map every bit good as the IT applications such as familial regulative systems and clinical applications. Bioinformatics needs the expertness from Computer Science, Mathematics, Statistics, Medicine, and Biology.
Molecular Biology is a specification of Biology ; subdivision of Biology that trades with the nature of Biological Phenomena in molecular degree through the survey of familial information such as DNA, RNA and proteins. Conceptually this overlaps with Biology and Chemistry every bit good as Biochemistry. [ 1 ] Molecular Biology chiefly concerns itself with apprehension and the interactions between the assorted systems of cell, including interactions between the different types of DNA, RNA and protein biogenesis and how these interactions are regulated.
Although the emerging field of genetic sciences was guided by Mendel ‘s jurisprudence of segregation and jurisprudence of independent mixture in the early 20th century, the existent mechanisms of cistron reproduction, mutant and look staying unknown. Thomas Hunt Morgan and his co-workers utilized the fruit fly, Drosophila, as a theoretical account being to analyze the relationship between the cistron and the chromosomes in the familial procedure. A former pupil of Morgan ‘s, Hermann J. Muller, recognized the cistron as a footing of life, [ 2 ] and so put out to look into its construction. Muller discovered the mutagenic consequence of X raies on Drosophila, and utilized this phenomenon as a tool to research the size and nature of the cistron.
Harmonizing to the Aristotle ‘s two characteristics of life Biochemistry was concerned with nutrition or metamorphosis more by and large and Molecular Biology ( along with its more direct predecessor classical genetic sciences ) investigated reproduction [ 2 ] . It traced its roots to animal chemical science and medical chemical science of the 19th century ( Kohler 1982 ) . Much focal point of Biochemistry as the position of familial stuff was on proteins and enzymes. Until find of DNA in 1940s and 50s, the genomic concentration of biochemists is normally rare due to groundss. The find of twenty-some amino acids, constructing blocks of proteins, was major accomplishments of early 20th century biochemistry. After Watson and Crick ‘s find of the construction of DNA, Biochemistry showed increased accent on nucleic acids. [ 3 ] Figure: Friedrich Wohler German chemist who was a pupil of Berzelius. In trying to fix ammonium cyanate from Ag nitrile and ammonium chloride, he by chance synthesized carbamide in 1828. [ 4 ] [ 5 ]
Friedrich Wohler ( Figure2 ) by chance obtained one of the most of import biological compounds called Urea ( NH3 ) , while he was trying to fix Ammonium cyanate in a laboratory reaction. After that construct called Vitalism was falsified in 1828. [ 4 ] In 1833, Anselme Payen became the first to detect an enzyme, diastase amylase. This research was a major turning point opened toward biochemical researches. Subsequently, in 1896, Eduard Buchner demonstrated complex biochemical procedure that can be made to take topographic point outside of a life cell: Alcoholic agitation in cell infusions of barm. Due to development of new techniques such as chromatography, X-ray diffraction, NMR spectrometry, radioisotopic labeling, molecular kineticss simulations, negatron microscopy, the biomedical research field was widely spread in mid-twentieth century. The find of the cistron was happened so Biochemistry is known as Molecular Biology. In the 1950s, James D. Watson, Francis Crick, Rosalind Franklin, and Maurice Wilkins were instrumental in work outing the construction of DNA and proposing its relationship with the familial transportation of information.
The article that was published in Harvard Business Review in 1958, defined a individual term for engineering senses as the words in ; “ the new engineering dosage non yet have a individual established name. We shall name it information engineering ” . That was the documental wise startup of the term information engineering [ 6 ] . Information Technology is the acquisition, processing, storage and airing of vocal, pictural, textual and numerical information by a microelectronics-based combination of calculating and telecommunications. When the sphere of Molecular Biology field becomes wide, it combined with Information Technology towards so that is called Biology + Information Technology = Bioinformatics.
Figure: Molecular construction of the life homo. Cell, Chromosome brace, Genes, DNA and bases are clearly shows here.
The genome of Homo sapiens has been defined as Human Genome which is stored on 23 chromosome braces. Twenty two braces of these are autosomal chromosome braces while other is sex-determining brace. [ 7 ] The molecular construction of the human being such cell, chromosomes, DNA ( Deoxyribonucleic acid ) , bases etc are visibly depicted in Figure3. The mention sequen-ces ( standard euchromatic human genome ) that world-wide used for Biomedical Science researches are supplied by Human Genome Project Harmonizing to Human Genome Project * presently genome has occupies a entire figure of merely over three billion DNA base brace. In other manus there are over 20 three 1000s protein-coding cistrons has been discovered.
Deoxyribonucleic acid is a nucleic acid that shops the smallest direction used in development and operation in life being. Simply as the Deoxyribonucleic acid is the design of a life being. Deoxyribonucleic acid is a long polymer made from reiterating units called bases discovered by James D. Watson and Francis Crik. Single base ( Figure 4 ) has been consisted with Phosphate group, Sugar and Nitrogenous base. There are four types of bases are discovered as Adenin, Cytosin, Guanine and Thymin ; abbreviated by A, C, G, and T severally in Bioinformatics.
From molecular biological science literature reappraisal theses nucleotide bases are structured as dual spiral construction. The dual spiral construction of DNA is stabilized by H bonds between the bases attached to the two strands. Slightly if without H bonds the life can non be in the Earth. As good the Deoxyribonucleic acid has dual spiral construction that shops long-run storage of familial information.
Figure: Structure of a base. It consists with Phosphate group, Sugar and Nitrogenous base.
Then the bearer of the familial information from ascendant to descendants can be identified as cistrons ( Figure 3 ) . A modern definition of a cistron is “ A locatable part of genomic sequence matching to a unit of heritage which is associated with regulative parts, transcribed parts, and or other functional sequence parts ” . [ 9 ] [ 10 ] Today the big figure of Molecular Biology experiments and researches are ongoing with respects to the cistrons and DNA constructs.
Genotype and Phenotype
Wilhelm Johannsen was a Danish phytologist, works physiologist and geneticist who introduced the footings genotype and phenotype in his paper “ Om arvelighed one samfund og I rene linier ” and in his published manus book “ Arvelighedsl?rens Elementer ” * .
Genotype is the internally coded, inheritable information carried by heritage in all life beings. This information is used as a design or set of instructions for edifice and keeping a living animal. These Deoxyribonucleic acid instructions are originated within about all cells, they are written in familial codification or familial sequences, and they are copied at the clip of cell division or reproduction and are inherited to the following coevals. These Deoxyribonucleic acid instructions are implicitly involved with all facets of the life of an being. DNA sequences command everything from the formation of protein supermolecules, to the ordinance of metamorphosis and synthesis. [ 12 ]
Human phenotype is the outward, physical manifestation of the being. These are the physical parts, the amount of the atoms, molecules, supermolecules, cells, constructions, energy use, metamorphosis, tissues, variety meats, physiological reactions and behaviours ; anything that is portion of the discernible construction, map or behaviour of a life being. [ 11 ] [ 12 ] In the sense of definition of genotype and phenotype at that place can re construct up the relationship those types are Phenotype = Genotype + development in the several environment
There are figure of definitions are encountered for disease every bit good as the difference faces of the diseases can be seen in different diaries and books. Some of the definitions are disease is any perturbation or anomalousness in the normal operation of the organic structure that likely has a specific cause and identifiable symptoms. [ 19 ] Diseases are one of the factors endangering us from holding a properly functional life. Throughout our history, epidemics have caused the extinction of whole populations. A disease is an unnatural status impacting the organic structure of an being. It is frequently construed to be a medical status associated with specific symptoms and marks. Over the last century, adult male has discovered many micro-organisms that cause diseases in worlds and animate beings, and has learned how to protect himself from them, by either bar or intervention. It is difficult to number the figure of diseases that are identified in human organic structure every bit good as categorized the diseases in a theoretical mode is really good hard due to find of the diseases is big.
Familial diseases are the specification of the sphere of disease. When find of the human being design called DNA construction in subsequently mid 20th century, there are tonss of researches were done [ 14-18 ] about how the diseases that could be inherited through the DNA design. These built-in diseases are named as familial diseases. Harmonizing to the OMIM, today over 5000 diseases have been discovered. Basically the familial forms are affected to emerge peculiar disease. By comparing with the standard sequences of HGP, if there is familial upsets may impact to such disease.
In May 2001 TimBerners-Lee, James Hendler, OraLassila, defined Semantic Web as an extension of the current web in which information is given chiseled significance, better enabling computing machines and people to work together, in American diary called The Semantic Web, Scientific American. [ 20 ]
Semantic Web is besides identified as Web 3.0 in different articles and publishing houses who involved developing web in a user attractive manner [ 21 ] . As an case the article published in The New York Times in November 2007, newsman John Markoff stated that “ commercial involvement in Web 3.0 or the ‘Semantic Web, ‘ for the thought of adding significance is merely now emerging. ” Although the appellative convention was happened, due to this word picture of Web 3.0 or semantic web caused great confusion with regard to the relationships between the Semantic Web and the Web itself, every bit good as between the Semantic Web and some facets of the alleged Web 2.0. Therefore some research workers wanted to reject the term “ Web 3.0 ” as excessively business-oriented ; others felt that the vision in the article was lone portion of the larger Semantic Web vision, and still others felt that, whatever it was called, the Semantic Web ‘s reaching in the concern subdivision of The New York Times reflected an of import approach of age [ 20,21 ] .
Alternatively the semantic web research workers in contrast accept that paradoxes and unreciprocated inquiries are a monetary value that must be paid to accomplish versatility. We make the linguistic communication for the regulations every bit expressive as needed to let the Web to ground every bit widely as desired. The challenge of the Semantic Web, hence, is to supply a linguistic communication that expresses both informations and regulations for concluding about the informations and that allows regulations from any bing knowledge-representation system to be exported onto the Web.
Semantic Web Technologies
It is of import to reexamine the engineerings and criterion used to carry through the semantic web construct. The some worldwide used criterions are
W3C ( World Wide Web Consortium )
RDF, RDF Schema, SPARQL
RIF ( Rule Interchange Format )
OWL, OWL 2, OWL DL, OWL Full
ISO ( International Standards Organization )
Common Logic ( CLIF )
ISO/IEC 11179 Metadata Registry Std
OMG ( Object Management Group )
Ontology Definition Metamodel ( ODM ) .
Tim Berners-Lee suggested dividing development of sentence structure and semantic of this MEGA-language called Resource Description Framework ( RDF ) that is syntax for paperss of Semantic Web. It uses links to Ontologies Ontology Web Language ( OWL ) is a linguistic communication for ontology description.
The timeline [ 22 ] of the Semantic Web can be regulated as:
1994: Foundation of W3C. They develop criterions such as HTML, URL, XML, HTTP, PNG, SVG, CSS
1998: Tim Berners-Lee published “ Semantic Web Road Map ”
1999: W3C launched groups for planing Semantic Web foundations, the first version of RDF is published
2000: American defence research establishment started probes for ontology descriptions ( DAML+OIL undertaking )
2001: “ The Semantic Web ” paper in Scientific American
2004: New version of RDF, ontology description linguistic communication OWL
2006: Candidate recommendation of SPARQL, a question linguistic communication for Semantic Web
As before mentioned there are two of import engineerings for developing the Semantic Web: extensile Markup Language ( XML ) and the Resource, Description Framework ( RDF ) . XML lets everyone make their ain tags-hidden labels such as & lt ; zip codification & gt ; or & lt ; alma mater & gt ; that annotate Web pages or subdivisions of text on a page. Scripts, or plans, can do usage of these tickets in sophisticated ways, but the book author has to cognize what the page author uses each ticket for. In short, XML allows users to add arbitrary construction to their paperss but says nil about what the constructions mean [ 23 ] .
Meaning is expressed by RDF, which encodes it in sets of three-base hits, each three-base hit being instead like the topic, verb and object of an simple sentence. These three-base hits can be written utilizing XML tickets. In RDF, a papers makes averments that peculiar have belongingss with certain values. This construction turns out to be a natural manner to depict the huge bulk of the informations processed by machines.
The cognition representation in a formalistic mode is conceptualisation: the objects, constructs or relationships among the objects and other entities. Conceptualization is an abstract, simplified position of the universe that we wish to stand for for a figure of intents. In the instance of ontology every cognition base, knowledge-based system, or knowledge-level agent is committed to some conceptualisation, explicitly or implicitly. Ontology is an expressed specification of conceptualisation. The term ontology derived from doctrine where the significance is a systematic history of being.
When the sphere cognition is represented in a declaratory formalisation, the set of categories that can be represented is called the existence of discourse. This set of objects, and the describable relationships among them, are reflected in the representational vocabulary with which a knowledge-based plan represents cognition. This is the instance in the context of Artificial Intelligent ; that can be described the ontology plans by specifying a set of representational footings. In such ontology, definitions associate the names of entities in the existence of discourse ( e.g. , categories, dealingss, maps, or other objects ) with human-readable text depicting what the names mean, and standardized maxims that constrain the reading and grammatical usage of those footings. Formally, ontology is the statement of a logical theory.
As mentioned in earlier, the ontology represents the sphere cognition of such sphere similar to biomedical cognition in biomedical sphere. Research workers, sphere experts, developers defined broad scope of biomedical Ontologies and published via the standardised procedure. One of the biomedical ontology publishing houses is The Open Biological and Biomedical Ontologies Foundry ( hypertext transfer protocol: //obofoundry.org/ ) The OBO Foundry is a collaborative experiment affecting developers of science-based Ontologies who are set uping a set of rules for ontology development with the end of making a suite of extraneous interoperable mention ontologies in the biomedical sphere. The groups developing Ontologies who have expressed an involvement in this end are listed below, followed by other relevant attempts in this sphere. When we visit the hypertext transfer protocol: //obofoundry.org / there are tonss of Ontologies published by the individual in around the universe ( Table 1 )
Chemical entities of biological involvement
chebi.obo A A
quality.obo A A
PRotein Ontology ( PRO )
pro.obo A A
Xenopus anatomy and development
Related Research Works
Annotating the human genome with Disease Ontology
John D Osborne, Jared Flatow, Michelle Holko, Simon M Lin, Warren A Kibbe, Lihua ( Julie ) Zhu, Maria I Danila, Gang Feng and Rex L Chisholm
In this research they used the Unified Medical Language System ( UMLS ) MetaMap Transfer tool to detect gene-disease relationships from the GeneRIF database. The human genome has been extensively annotated with Gene Ontology for Biological maps, but minimally computationally annotated for diseases so they utilized a comprehensive subset of UMLS, which is disease-focused and structured as a directed acyclic graph ( the Disease Ontology ) , to filtrate and construe consequences from MMTx.
From disease ontology to disease-ontology lite: statistical methods to accommodate a all-purpose ontology for the trial of gene-ontology associations
Pan Du, Gang Feng, Jared Flatow, Jie Song, Michelle Holko3, Warren A, Kibbe and Simon M. Lin
They proposed statistical methods to accommodate the general intent, OBO Foundry Disease Ontology ( DO ) for the designation of gene-disease associations. Therefore they need a simplified definition of disease classs derived from implicated cistrons. On the footing of the premise that the DO footings holding similar associated cistrons are closely related, we group DO footings based on the similarity of gene-to-DO function profiles. Two types of binary distance prosodies are defined to mensurate the overall and subset similarity between DO footings. A compactness-scalable fuzzy constellating method is so applied to group similar DO footings. To cut down false bunch, the semantic similarities between DO footings are besides used to restrain clustering consequences. As such, the DO footings are aggregated and the excess DO footings are mostly removed. Using these methods, they constructed a simplified vocabulary list from the DO called Disease Ontology Lite.
Investigating semantic similarity steps across the Gene Ontology: the relationship between sequence and note
P. W. Lord, R. D. Stevens, A. Brass and C. A. Goble
In this paper writers investigate the usage of ontological note to mensurate the similarities in cognition content or ‘semantic similarity ‘ between entries in a information resource. These allow a bioinformatician to execute a similarity step over note in an correspondent mode to those performed over sequences. A step of semantic similarity for the cognition constituent of bioinformatics resources should afford a life scientist a new tool in their repetoire of analyses. They present the consequences from experiments that investigate the cogency of utilizing semantic similarity by comparing with sequence similarity.
Clinical Nosologies in Human Genetics with Semantic Similarity Searches in Ontologies
Sebastian KoA?hler, Marcel H. Schulz, Peter Krawitz, Sebastian Bauer, Sandra DoA?lken, Claus E. Ott, Christine Mundlos, Denise Horn, Stefan Mundlos, and Peter N. Robinson
In this research they used semantic similarity prosodies to mensurate phenotypic similarity between questions and familial diseases annotated with the usage of the Human Phenotype Ontology. They have developed a statistical theoretical account to delegate p values to the ensuing similarity tonss, which can be used to rank the campaigner diseases. They show that this diagnosing attack outperforms simpler term-matching attacks that do non take the semantic interrelatednesss between footings into history.
A semantic web attack applied to integrative bioinformatics experimentation: a biological usage instance with genomics informations.
Lennart J. G. Post, Marco Roos, M. Scott Marshall, Roel new wave Driel and Timo M. Breit
They constructed four OWL cognition theoretical accounts, two RDFS informations theoretical accounts, transformed and mapped relevant informations to the information theoretical accounts, linked the information theoretical accounts to knowledge theoretical accounts utilizing linkage statements, and ran semantic questions. Our biological usage instance demonstrates the relevancy of these sorts of integrative bioinformatics experiments. Our findings show high startup costs for the SWEDI attack, but straightforward extension with similar informations.
Finding disease specific changes in the co-expression of cistrons
Dennis Kostka and Rainer Spang
In this research the writer introduces a mark for differential co-expression and suggests a computationally efficient algorithm for happening high hiting sets of cistrons. The usage of our fresh method is demonstrated in the context of simulations and on existent look informations from a clinical survey.
An illustration of nutrient ontology for diabetes control
Jaime Cantais, David Dominguez, Valeria Gigante, Loredana Laera, and Valentina Tamma
This paper describes our experience in the rapid prototyping of a nutrient ontology oriented to the nutritionary and wellness attention sphere that is used to portion cognition between the different stakeholders involved in the PIPS undertaking.
Towards a Semantic Web for Bioinformatics – ongoing research
With the detonation of online accessible bioinformatics informations and tools, systems integrating has become really of import for farther advancement. Presently, bioinformatics relies to a great extent on the Web. But the Web is geared towards human interaction instead than automated processing. The vision of a Semantic Web facilitates this mechanization by footnoting web content and by supplying equal logical thinking linguistic communications.
Identifying Relationships among Genomic Disease Regions: Predicting Genes at Pathogenic SNP Associations and Rare Deletions
Soumya Raychaudhuri, Robert M. Plenge, Elizabeth J. Rossin, Aylwin C. Y. Ng, International Schizophrenia Consortium, Shaun M. Purcell, Pamela Sklar, Edward M, Scolnick, Ramnik J. Xavier, David Altshuler, Mark J. Daly
In here they describe a statistical method, Gene Relationships among Implicated Loci ( GRAIL ) , which takes a list of disease parts and automatically assesses the grade of relatedness of concerned cistrons utilizing 250,000 PubMed abstracts. They foremost evaluated GRAIL by measuring its ability to place subsets of extremely related cistrons in common tracts from validated lipoid and tallness SNP associations from recent genome-wide surveies. We so tested GRAIL, by measuring its ability to divide true disease parts from many false positive disease parts in two separate practical applications in human genetic sciences. First, we took 74 nominally associated Crohn ‘s disease SNPs and applied GRAIL to place a subset of 13 SNPs with extremely related cistrons. Of these, ten convincingly validated in follow-up genotyping ; genotyping consequences for the staying three were inconclusive. Following, they applied GRAIL to 165 rare omission events seen in schizophrenic disorder instances
Collection of bioinformatics informations utilizing Semantic Web engineering
Susie Stephens, David LaVigna, Mike DiLascio, Joanne Luciano
The integrating of disparate biomedical informations continues to be a challenge for drug find attempts. Semantic Web engineerings provide the capableness to more easy aggregate informations and therefore can be utilized to better the efficiency of drug find. We describe an implement-ation of a Semantic Web substructure that utilizes the scalable Oracle Resource Description Framework ( RDF ) Data Model as the depository and Seamark Navigator for shoping and seeking the information. The paper presents a usage instance that identifies cistron biomarkers of involvement and uses the Semantic Web substructure to footnote the information.
Olivier Bodenreider and Anita Burgun
Ontology design is an of import facet of medical information sciences, and reusability is a cardinal issue that is determined by the degree of compatibility among ontology constructs and among the theories of the biomedical sphere they convey. In this article, we examine OpenGALEN, the UMLS Semantic Network, SNOMED CT, the Foundational Model of Anatomy, and the MENELAS ontology every bit good as descriptions of the biomedical sphere in two general ontologies, OpenCyc and WordNet. Using the representation of Blood in each system, we examine issues in compatibility among these ontologies.