IPC Definitions - January 01, 2012

G06F 19/10 - Definition fr

Definition statement

This group covers:

Methods or systems for genetic or protein related data processing in computational molecular biology.

Bioinformatics methods or systems where digital data processing is inherent or implicit, but not explicitly mentioned.

References relevant to classification in this group

This group does not cover:

In silico methods of screening virtual chemical libraries

C40B 30/02

In silico or mathematical methods of creating virtual chemical libraries

C40B 50/02

Informative references

Attention is drawn to the following places, which may be of interest for search:

Medical diagnosis

A61B 5/00

Manufacture of microarrays, DNA chips

B01J 19/00, C12M 1/34

PCR apparatus per se

B01L 7/00, C12M 1/38

Macromolecular X-ray crystallographic or NMR structures per se

C07K 14/00

Genetic engineering involving nucleic acids

C12N 15/00

Chemical reactions involving the use of microarrays, DNA chips

C12Q 1/68

Sequencing using PCR

C12Q 1/68

Gel electrophoresis apparatus per se

G01N 27/447

Sequencing using electrophoresis

G01N 27/447

Sequencing using chromatography

G01N 30/00

Sequencing using mass spectrometry

G01N 33/68

Pattern recognition

G06K 9/00

Computer input/output arrangements

G06F 3/00

Computer architectures or program control

G06F 9/00

Information retrieval, databases per se

G06F 17/30

Computer systems using neural network models per se

G06N 3/02

Computer systems using knowledge representation per se, e.g. expert systems

G06N 5/02

Computer systems using probabilistic models per se

G06N 7/00

Finding positions and orientations in microarray images by image processing

G06T 7/00

Mass spectrometry apparatus per se

H01J 49/00

Special rules of classification

In this group, the first place priority rule is applied, i.e. at each hierarchical level, classification is made in the first appropriate place.

Glossary of terms

In this group, the following terms or expressions are used with the meaning indicated:

data mining

discovery and analysis of patterns within a vast amount of genetic or protein-related data

data visualisation

generation and/or display of graphical representations of genetic and protein-related data

domain

domain of a protein is an element of the overall molecular structure that is self-stabilising and often folds independently of the rest of a polypeptide chain

drug targeting

drug design strategy aiming at optimising the properties of a medicinal compound, based on the 3-dimensional structure of a target, for delivery to a particular tissue or organ in the body

fragment assembly

method by which linear portions of sequence information are assembled to obtain full length gene sequence data

functional genomics

experimental analyses aiming at assessing the function of genes in determining traits, physiology and/or development of an organism, making use of computational and high-throughput technologies

gene expression

process by which proteins are made or transcribed from the instructions encoded in DNA

gene expression profiling

determination of the pattern of genes expressed, i.e. transcribed, under specific circumstances or in a specific cell line

gene finding

method of searching genomic DNA sequences to identify open reading frames which encode proteins

genome annotation

allocation of functions to individual genes in the genome

genotype

genetic makeup or profile of an organism with respect to a trait

genotyping

analysis of an organism's genotype

haplotype

set of one or more polymorphisms (sequence variations) that may be found at a particular genetic location on the same chromosome

homology

indication of the amount of similarity between two sequences; homology determinations can include allowance for gaps, insertions, deletions and mismatches between the aligned sequences

linkage disequilibrium

tendency of alleles located close to each other on the same chromosome to be inherited together

microarray

plurality of nucleic acid probes attached to a substrate, which form an ordered pattern

molecular structure

2-dimensional or 3-dimensional arrangement of atoms, groups of atoms or domains in nucleic aids, proteins, peptides and amino acids

motif

specific nucleotide or amino acid sequence pattern

noise correction model

model that accounts for non-signal data, such as for microarrays: optical noise, quality control problems and cross hybridisation

ontology

classification methodology for formalising a subject’s knowledge in a structured and controlled vocabulary

orthologue

homologous sequence found in different species and derived from a common ancestor

paralogue

homologous sequence in the same organism derived from gene duplication

pedigree

family tree describing the occurrence of heritable traits across generations

phylogenetic tree

tree-like graphical representation of phylogenetic relationships

phylogeny

reconstruction of an evolutionary development and history of a species or higher taxonomic grouping of organisms; typically represented as a phylogenetic tree; methods for creating phylogenetic trees

population genetics

study of genetic variation and genetic evolution of populations

probe design and optimisation for microarrays

designing and selecting (i) optimal, highly specific probes, e.g. oligonucleotides, cDNA, fragments for hybridisation experiments with microarrays and (ii) optimal sets of probes, e.g. oligonucleotides, cDNA, to be chemically attached to a solid support to form an array

programming tools or database systems

computer software to assist programming procedures within bioinformatics and database systems for managing genetic/ protein-related data

protein folding

process by which a polypeptide chain folds into a specific 3-dimensional structure

proteomics

large-scale study of the functions of proteins and their interactions with other molecular entities in a biological system

sequence comparison

process of comparing nucleic or amino acid sequences, generally by a linear alignment in such a way that equivalent positions in adjacent sequences are brought into the correct alignment with each other by introducing insertions in suitable positions, in order to identify similarities and/or differences amongst the compared sequences

sequencing by hybridisation

DNA sequencing technique in which an array of short sequences of nucleotides is brought in contact with a solution of a target DNA sequence, a biochemical method determines a subset of probes that bind to the target sequence and a combinatorial method is then used to reconstruct the DNA sequence from the spectrum

SNP

single nucleotide polymorphism: a DNA sequence variation that involves a change in a single nucleotide and is commonly present in a part of a population

structure alignment

form of alignment to establish structural and functional equivalences between two or more proteins based on their secondary or tertiary structures

syntenic regions

corresponding regions in a species to an observed grouping of genes in the same order and on the same chromosome in another species

systems biology

simulation and mathematical modelling of relationships and interactions between molecular entities in sub-cellular systems integrating genetic and/or protein-related data to describe the dynamic behaviour of, for example, protein-protein/protein-ligand interactions, regulatory networks and metabolic networks

taxonomy

classification of organisms to show their evolutionary relationships to other organisms