United States Patent and Trademark Office
IPC Advanced Level Subcommittee
Topic: A010
Date: 30 April 2009
Introduction:
United States (US) thanks the Rapporteur for the Definitions Proposal. It was noted by US that
there are minor differences between the proposal and the contents of the Harmony Visit Report.
US can agree with the majority of the definitions proposal with the exception of the following.
Exceptions
1. It would appear the Glossary terms should be alphabetized and associated with the new Main
Group rather than being listed in relation to the proposed subgroups.
2. In the schema definition of subgroup 19/16, the words "drug targeting" are NOT used,
however "drug targeting" is present in the glossary for 19/16.
3. The schema definition of subgroup 19/18 should include "linkage disequilibrium" or
"population genetics" which are at least as important as "genotyping".
4. US would like to offer the following amendments for the definition of "genotyping":
Genotyping - processes of determining the genotype (i.e., the genetic
constitution) of an individual, or an organism by the use of biological assays.
And "genotype"
Genotype - The genetic constitution of an organism with respect to a trait.
5. “Linkage disequilibrium"
Linkage Disequilibrium - The probability in which two or more than two alleles
present together in one chromosome is greater than the probability in which
they are present randomly
Or:
Linkage Disequilibrium - The tendency of alleles located close to each other
on the same chromosome to be inherited together.
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6. Population Genetics
Population Genetics – The mathematical and biological discipline of
evaluating the numerical progress of the relative frequency of various genes
and alleles in a population of interbreeding organisms.
Or:
Population Genetics - The study of the allele frequency distribution and
change under the influence of the four evolutionary processes: natural
selection, genetic drift, mutation and gene flow.
7. Other Annotations by US on Excerpts of the Rapporteur
Definitions Proposal
Title - G06F19/10
Bioinformatics
Definition statement
This main group covers:

methods and 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, and

in this main group, "systems" include apparatus.
Special rules of classification within this main group
In this main group, at each hierarchical level, in the absence of an indication to the contrary,
classification is made in the first appropriate place.
Limiting references
In silico methods of creating virtual chemical libraries
C40B50/02
In silico methods of screening virtual chemical libraries
C40B30/02
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Informative references
Attention is drawn to the following places, which may be of interest for search:
US can also agree with the comments provided by DE in Annex 8.
Title - G06F19/12
For modelling or simulation in systems biology
Definition statement
This subgroup covers:
Documents involving simulation and 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
subgroup. In such cases, see lower subgroups.
Title - G06F19/18
For functional genomics or proteomics
This subgroup covers:
Documents involving assessing 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. This subgroup includes documents involving genotypicphenotypic associations. This includes genotyping and genome annotation, linkage
disequilibrium analysis and association studies, population genetics, alternative splicing and
Short Interfering RNA design (siRNA, RNAi). This subgroup also covers binding site
identification, mutagenesis analysis, protein-protein or protein-nucleic acid interactions. Mere
mention of genetic or protein function is not sufficient to classify in this subgroup. In such
cases, see lower subgroups.
Title - G06F19/24
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For machine learning, data mining or biostatistics
This subgroup covers:
Documents involving discovery and 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. This
subgroup also includes multivariate analysis of protein or gene-related data [e.g. analysis of
variances (ANOVA), principal component analysis (PCA), support vector machines (SVM)].
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Title - G06F19/26
For data visualisation
This subgroup covers:
Documents involving 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.
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Glossary
Note: Glossary definitions are formulated in the context of bioinformatics. Methods and
calculation processes are carried out using computer programs.
G06F19/12
Systems biology simulation and mathematical modelling of relationships and
interactions between molecular entities in subcellular 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.
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