GenomeIn the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as regulatory sequences (see non-coding DNA), and often a substantial fraction of junk DNA with no evident function. Almost all eukaryotes have mitochondria and a small mitochondrial genome.
Knowledge representation and reasoningKnowledge representation and reasoning (KRR, KR&R, KR2) is the field of artificial intelligence (AI) dedicated to representing information about the world in a form that a computer system can use to solve complex tasks such as diagnosing a medical condition or having a dialog in a natural language. Knowledge representation incorporates findings from psychology about how humans solve problems and represent knowledge in order to design formalisms that will make complex systems easier to design and build.
Molecular geneticsMolecular genetics is a sub-field of biology that addresses how differences in the structures or expression of DNA molecules manifests as variation among organisms. Molecular genetics often applies an "investigative approach" to determine the structure and/or function of genes in an organism's genome using genetic screens. The field of study is based on the merging of several sub-fields in biology: classical Mendelian inheritance, cellular biology, molecular biology, biochemistry, and biotechnology.
Molecular dynamicsMolecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.
Relational databaseA relational database is a (most commonly digital) database based on the relational model of data, as proposed by E. F. Codd in 1970. A system used to maintain relational databases is a relational database management system (RDBMS). Many relational database systems are equipped with the option of using SQL (Structured Query Language) for querying and updating the database. The term "relational database" was first defined by E. F. Codd at IBM in 1970. Codd introduced the term in his research paper "A Relational Model of Data for Large Shared Data Banks".
Reference genomeA reference genome (also known as a reference assembly) is a digital nucleic acid sequence database, assembled by scientists as a representative example of the set of genes in one idealized individual organism of a species. As they are assembled from the sequencing of DNA from a number of individual donors, reference genomes do not accurately represent the set of genes of any single individual organism. Instead a reference provides a haploid mosaic of different DNA sequences from each donor.
Sequence analysisIn bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. Methodologies used include sequence alignment, searches against biological databases, and others. Since the development of methods of high-throughput production of gene and protein sequences, the rate of addition of new sequences to the databases increased very rapidly.
Schema matchingThe terms schema matching and mapping are often used interchangeably for a database process. For this article, we differentiate the two as follows: schema matching is the process of identifying that two objects are semantically related (scope of this article) while mapping refers to the transformations between the objects. For example, in the two schemas DB1.Student (Name, SSN, Level, Major, Marks) and DB2.Grad-Student (Name, ID, Major, Grades); possible matches would be: DB1.Student ≈ DB2.Grad-Student; DB1.
Literature reviewA literature review is an overview of the previously published works on a topic. The term can refer to a full scholarly paper or a section of a scholarly work such as a book, or an article. Either way, a literature review is supposed to provide the researcher/author and the audiences with a general image of the existing knowledge on the topic under question. A good literature review can ensure that a proper research question has been asked and a proper theoretical framework and/or research methodology have been chosen.
Knowledge managementKnowledge management (KM) is the collection of methods relating to creating, sharing, using and managing the knowledge and information of an organization. It refers to a multidisciplinary approach to achieve organizational objectives by making the best use of knowledge. An established discipline since 1991, KM includes courses taught in the fields of business administration, information systems, management, library, and information science. Other fields may contribute to KM research, including information and media, computer science, public health and public policy.
