IPC Revision WG – Definition Project
Rapporteur Proposal
Project: A019
Group: G06F 19/10
Date : 10-11-2009
G06F 19/10
Bioinformatics --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
In silico or mathematical methods of creating virtual chemical
libraries
C40B 30/02
C40B 50/02
Informative references
Attention is drawn to the following places, which may be of interest for search:
Medical diagnosis
A61B 5/00
B01J 19/00
Manufacture of microarrays, DNA chips
C12M 1/34
B01L 7/00
PCR apparatus per se
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.
G06N 5/02
expert systems
Computer systems using probabilistic models per se
G06N 7/00
Finding positions and orientations in microarray images by
image processing
Mass spectrometry apparatus per se
G06T 7/00
H01J 49/00
Special rules of classification within this group
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
data visualisation
domain
drug targeting
fragment assembly
functional genomics
gene expression
gene expression profiling
gene finding
genome annotation
genotype
genotyping
haplotype
homology
linkage disequilibrium
discovery and analysis of patterns within a vast amount
of genetic or protein-related data
generation and/or display of graphical representations of
genetic and protein-related data
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 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
method by which linear portions of sequence
information are assembled to obtain full length gene
sequence data
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
process by which proteins are made or transcribed from
the instructions encoded in DNA
determination of the pattern of genes expressed, i.e.
transcribed, under specific circumstances or in a
specific cell line
method of searching genomic DNA sequences to
identify open reading frames which encode proteins
allocation of functions to individual genes in the
genome
genetic makeup or profile of an organism with respect
to a trait
analysis of an organism's genotype
set of one or more polymorphisms (sequence variations)
that may be found at a particular genetic location on the
same chromosome
indication of the amount of similarity between two
sequences; homology determinations can include
allowance for gaps, insertions, deletions and
mismatches between the aligned sequences
tendency of alleles located close to each other on the
microarray
molecular structure
motif
noise correction model
ontology
orthologue
paralogue
pedigree
phylogenetic tree
phylogeny
population genetics
probe design and
optimisation for
microarrays
programming tools or
database systems
protein folding
proteomics
sequence comparison
sequencing by
hybridisation
same chromosome to be inherited together
plurality of nucleic acid probes attached to a substrate,
which form an ordered pattern
2-dimensional or 3-dimensional arrangement of atoms,
groups of atoms or domains in nucleic aids, proteins,
peptides and amino acids
specific nucleotide or amino acid sequence pattern
model that accounts for non-signal data, such as for
microarrays: optical noise, quality control problems and
cross hybridisation
classification methodology for formalising a subject’s
knowledge in a structured and controlled vocabulary
homologous sequence found in different species and
derived from a common ancestor
homologous sequence in the same organism derived
from gene duplication
family tree describing the occurrence of heritable traits
across generations
tree-like graphical representation of phylogenetic
relationships
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
study of genetic variation and genetic evolution of
populations
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
computer software to assist programming procedures
within bioinformatics and database systems for
managing genetic/ protein-related data
process by which a polypeptide chain folds into a
specific 3-dimensional structure
large-scale study of the functions of proteins and their
interactions with other molecular entities in a biological
system
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
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
SNP
structure alignment
syntenic regions
systems biology
taxonomy
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
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
form of alignment to establish structural and functional
equivalences between two or more proteins based on
their secondary or tertiary structures
corresponding regions in a species to an observed
grouping of genes in the same order and on the same
chromosome in another species
simulation and mathematical modelling of relationships
and interactions between molecular entities in subcellular systems integrating genetic and/or proteinrelated data to describe the dynamic behaviour of, for
example, protein-protein/protein-ligand interactions,
regulatory networks and metabolic networks
classification of organisms to show their evolutionary
relationships to other organisms
G06F 19/12
for modelling or simulation in systems biology --Definition statement
This group covers:
Simulation or mathematical modelling of relationships and interactions between molecular entities
on a subcellular level, integrating genetic and/or protein-related data to describe the dynamic
behaviour of protein-protein/protein-ligand interactions, regulatory or metabolic networks.
Mere mention of modelling or simulation is not sufficient to classify in this group. In such cases,
see the other subgroups of group G06F 19/10 following this one in the scheme.
G06F 19/14
for phylogeny or evolution --Definition statement
This group covers:
Analysis of orthologous, paralogous, syntenic or taxonomic relationships.
Generation of pedigrees and phylogenetic trees.
Mere mention of evolutionary data is not sufficient to classify in this group. In such cases, see the
other subgroups of group G06F 19/10 following this one in the scheme.
G06F 19/16
for molecular structure --Definition statement
This group covers:
Structural architecture of proteins, peptides, amino acids and nucleic acids and the prediction
thereof.
Processes including structural alignment, protein folding, domain topology, molecular modelling,
receptor-ligand modelling, docking methods, structural-functional relationships and drug targeting
using structure data, as well as two- and three-dimensional structure prediction and/or analysis.
The structure types include secondary, tertiary and quaternary structures.
Mere mention of structural data is not sufficient to classify in this group. In such cases, see the other
subgroups of group G06F 19/10 following this one in the scheme.
G06F 19/18
for functional genomics or proteomics --Definition statement
This group covers:
Assessment of the function of genes and proteins in determining traits, physiology and/or
development of an organism, making use of computational and large scale, high-throughput
technologies.
Genotypic-phenotypic associations, including genotyping and genome annotation, linkage
disequilibrium analysis and association studies, population genetics, alternative splicing and Short
Interfering RNA design (siRNA, RNAi).
Binding site identification, mutagenesis analysis, protein-protein or protein-nucleic acid
interactions.
Mere mention of gene or protein function is not sufficient to classify in this group. In such cases,
see the other subgroups of group G06F 19/10 following this one in the scheme.
G06F 19/20
for hybridisation or gene expression ---
Definition statement
This group covers:
Analysis of gene expression information. This includes microarray analysis, gel electrophoresis
analysis and sequencing by hybridisation. Further covered technologies include probe design and
probe optimisation, microarray normalisation, expression profiling, noise correction models,
expression ratio estimation.
Mere mention of hybridisation or gene expression is not sufficient to classify in this group. In such
cases, see the other subgroups of group G06F 19/10 following this one in the scheme.
Relationship between large subject matter areas
This group does not cover base calling or sequencing methods per se. These are covered by the
relevant places listed under section Informative References for group G06F 19/10.
G06F 19/22
for sequence comparison involving nucleotides or amino acids --Definition statement
This group covers:
Comparison of sequence information, wherein the sequences are nucleic acids or amino acids. The
comparisons include methods of alignment, homology identification, motif identification, SNP
(Single-Nucleotide Polymorphism) discovery, haplotype identification, fragment assembly, gene
finding.
Mere mention of sequence data is not sufficient to classify in this group. In such cases, see the other
subgroups of group G06F 19/10 following this one in the scheme.
G06F 19/24
for machine learning, data mining or biostatistics --Definition statement
This group covers:
Discovery and/or analysis of patterns within a vast amount of genetic or protein-related data,
wherein the emphasis is placed on the method of analysis and is largely independent of the type of
bioinformatic data. Covered methods include bioinformatic pattern finding, knowledge discovery,
rule extraction, correlation, clustering and classification.
Multivariate analysis of protein or gene-related data, e.g. analysis of variances (ANOVA), principal
component analysis (PCA), support vector machines (SVM).
G06F 19/26
for data visualisation --Definition statement
This group covers:
Visual representations specifically adapted to bioinformatic data, wherein the emphasis is placed on
the method of visualisation and is largely independent of the type of bioinformatic data.
Visualisation of bioinformatic data specifically includes, for example, graphics generation, map
display and network display.
G06F 19/28
for programming tools or database systems --Definition statement
This group covers:
Computer software specifically adapted to assist programming procedures within bioinformatics
and database systems specifically adapted for managing bioinformatic data. This includes
ontologies, heterogeneous data integration, data warehousing, computing architectures.