Biomatics Thesaurus
From Biomatics.org
In the spirit of the National Library of Medicine's UMLS project, this thesaurus could be used for biomatical informatics purposes.
The scope of the UMLS Semantic Network is broad, allowing for the semantic categorization of a wide range of terminology in multiple domains. Major groupings of semantic types include organisms, anatomical structures, biologic function, chemicals, events, physical objects, and concepts or ideas. The links between the semantic types provide the structure for the network and represent important relationships in the biomedical domain. The primary link between the semantic types is the 'isa' link. The 'isa' link establishes the hierarchy of types within the Network and is used for deciding on the most specific semantic type available for assignment to a Metathesaurus concept. There is also a set of nonhierarchical relationships, which are grouped into five major categories: `physically related to,' `spatially related to,' `temporally related to,' `functionally related to,' and `conceptually related to.'
The information associated with each semantic type includes a unique identifier, a tree number indicating its position in an `isa' hierarchy, a definition, and its immediate parent and children. The information associated with each relationship includes a unique identifier, a tree number, a definition, and the set of semantic types that can plausibly be linked by this relationship.
Exploiting Semantic Relations for LiteratureBased Discovery
Literaturebased discovery (LBD) is a method for automatically generating hypotheses for scientific research by finding overlooked implicit connections in the research literature. Discoveries have the form of relations between two primary concepts, for example a drug as a treatment for a disease or a gene as the cause of a disease. Swanson [1] introduced a paradigm in which such relations are discovered in bibliographic databases by uncovering a third concept (such as a physiologic function) that is related to both the drug and the disease. The discovery of the third concept allows a relation between the primary concepts, which was latent in the literature, to become explicit, thus constituting a potential discovery.
Literaturebased discovery. The methodology in literaturebased discovery relies on the notion of concepts relevant to three literature domains: X, Y, and Z. In a typical scenario, X concepts are those associated with some disease and Z concepts relate to a drug that treats the disease. Y concepts might then be physiological or pathological functions, symptoms, or body measurements. Concepts in X and Y are often discussed together, as are those in Y and Z. However, concepts from X and Z may not appear together in the same research paper. Discovery is facilitated by using particular Y concepts to draw attention to a connection between X and Z that had not been previously noticed.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1839258
WHAT IS ARROWSMITH AND HOW IS IT USED?
ARROWSMITH is interactive software that extends the power of a MEDLINE search. It operates on the output of a conventional search in a way that helps the user see new relationships and form and assess novel scientific hypotheses. It is based on the premise that information developed in one area of research can be of value in another without anyone being aware of the fact.
Abstract Algebra
Algebraic system embodied in a molecule consisting of N atoms
Cube group
Group theory
Multiplication Table under binary operation
Multiply
Artificial Intelligence
Clustering techniques (Clustering COC)
Basic Science
Biology (Biology COC)
Chemistry
Computer science
Engineering
Mathematics
Physics
Biology
Biological systems
Cellular and molecular biology
DNA Microarray Analysis and Gene Expression Profiling
DNA
Evolution
Gene clusters
Histone Proteins (Histone COC)
Larger macromolecules such as DNA
Mathematical biology
Proteincoding genes
The Histone Code
Topoisomerases
Biomatics
Biological information structures
Biological Mathematics
Blueprint for the ontogeny of the species
Cancerous state
Control atoms
Control Group acting on set of Gene Clusters
Creation of artificial life forms
Design and construction (synthesis) of biological objects and machineries under mathematical principles
Development of artificial organs and appendages
Eight clusters of genes
Finite State Disease Models
Fourier transforms of visual data.
Genetic Control Group
Genetic multiplexer
Groups (in the common and strictly mathematical sense) of covalent bonds
Model of genetic control
Molecular Algebra
Philosophical, mechanical and informational understanding of Biome
Protein Folding
Smart molecules
Systems Bioengineering
Tentative definition
The seamless development of mathematics and computation from a few clearly stated axioms and rules of
inference in pure logic as embodied in an atomic/molecular medium
Therapy result vector
Transcription patterns of gene clusters.
Ubiquitination
Biotechnology
Bioinformatics
Biomatics
Development of human machine interfaces
Genomics, Proteomics, and DNA microarray technology
Computer Science
Algorithms
Artificial Intelligence
Computation
Data structures
Digital signals
Discrete gates
Finite State Machines
Graphics
Hardware
Image processing
Informatics
Information storage and processing
Networks
Diseases/Conditions
Asthma
Cancer
Engineering
Finite State Machines
Change of state
Initial state
Genetics
Cluster of genes
Graph Theory
An ordinary die (cube) as it balances on a single corner
Computational Structures
Cube, hypercube or tesseract
How to calculate the number of vertices, edges, squares, and cubes contained in a hypercube
Informatics
Information retrieval from textual data
Logic
Alfred North Whitehead
Bertrand Russell
Formal logic
Philosophy
Logic Design
3to8 converter
A minterm generator to implement logic functions by combining outputs with logic gates (eg OR gates)
Addressing inputs
Basic building blocks in implementing arbitrary switching functions
Binary inputs
Building blocks of logical circuits.
Chip
Circuit symbol
Circuitry
Code conversions
Logic inputs
Logic outputs
Logiccircuit design
Logiccircuit designers
Memory address decoding.
Minterm
Multiplexing
n to 2^{n} decoder
n to 2^{n} Conversion
Outputs.
Routing input data to a specified output line
Standard Integrated circuits
Switching elements (gates)
Timedivision multiplexing
Mathematics
2n possible states
A Mathematician's Apology
A New Kind of Science
A small (fundamental?) mathematical system consisting of a set and an operation on the members of that set
abacus
Abstract algebra
abstract quantities
abstraction
accountancy
addition
aesthetics
Albert Einstein
aleph numbers
algebra
algebraic geometry
All mathematical proofs can be recast as logical proofs.
All mathematical truths can be translated into logical truths.
An attempt at a detailed deduction of mathematics from logic
analysis
analytic geometry
Applied mathematics
Aristotle
Arithmetic
arithmetical operations
art
astronomy
axiomatic system
axiomatization
axioms
beauty
Benjamin Peirce
Bulletin of the American Mathematical Society
calculations
calculus
calculus on manifolds
cardinal numbers
Carl Friedrich Gauss
category theory
change
changing quantity
chaos theory
closed intellectual system
Combinatorics
Common misconceptions
complex analysis
complex numbers
compression
computability theory
computation
computational complexity theory
computational mathematics
computational methods
computer science
computerassisted proofs
computers
continuous
count physical objects
counting
Cryptography
David Hilbert
days
definitions
derivable formulas of an axiomatic system.
differential equations
differential geometry
disciplines within mathematics
Discrete mathematics
division
draws necessary conclusions
dynamical systems
elegance
elegant proof
empirical mathematics of the various sciences
engineering
entropy
Euclidean geometry
Euclid's Elements
Euclid's proof that there are infinitely many prime numbers
Eugene Wigner
Experimental mathematics
experimentally falsifiable
experimentation
expressions
falsificationism
Fermat
Fermat's last theorem
Feynman
Feynman path integral
fiber bundles
field
Fields of mathematics
first abstraction
formal system
formal system that contains basic arithmetic
formulas within set theory
formulate new conjectures
foundations of mathematics
four color theorem
Fourier transform
Fractal geometry (Fractal COC)
fractions
functions
G. H. Hardy
general relativity
generality
generalized
geometry
Georg Cantor
Gödel's incompleteness theorem
Gödel's second incompleteness theorem
Goldbach's conjecture
Gottfried Leibniz
Graph theory
Greek
groups, rings, fields and other abstract systems
Guiseppe Peano
hierarchy of numbers
higherdimensional geometry
Hilbert's program
homeomorphism
human thought
imaginary abstractions
Imre Lakatos
infinitely large sets
infinitesimal calculus
infinity
information theory
integers
integrable
Intuition
Isaac Newton
Isomorphic
J. M. Ziman
Karl Popper
Knowledge
Königin der Wissenschaften
Kurt Heegner
language
Latin
learning
Lie groups
linear algebra
logical consequences of assumptions
logical reasoning
major disciplines within mathematics
Math
Mathematical fluid dynamics
Mathematical language
mathematical logic
mathematical notation
mathematical objects
Mathematical physics
Mathematical Reviews database
mathematical statement or proof
mathematical theorems and their proofs
Maths
Mayan numerals
measure land
measurement
medicine
Mersenne
Methods for defining the irrationals in terms of the rationals
Mikhail B. Sevryuk
model theory
Modern logic
modern notation
motions
multiplication
natural
need to do calculations in commerce, to understand the relationships between numbers, to measure land, and to predict astronomical events
new mathematical discoveries
nonEuclidean geometries
Notation
number system
Number theory
numbers
Numeral systems
Numerical analysis
numerical method
numerology
only
open
open problems
operations research
Optimization
or
Order theory
P=NP? problem
Pascal’s triangle
pattern
Paul Erdős
peer review
philosophers
philosophy of mathematics
physical reality
Poincaré conjecture
polynomial equations
postulates that seem reasonable and intuitive
predict astronomical events
Primitive notions
Probability
proof theory
Pseudomathematics
pseudoscience
pure mathematics
Pythagorean theorem
quantity
quantum mechanics
quarternions and octonions
quipu, a counting device used by the Inca
rational numbers
real analysis
real numbers
realvalued functions
recreational mathematics
recursion theory
Regina Scientiarum
Relation
Relation of divisibility for the partially ordered set (1,2,3,5,6,10,15,30)
relationships
relationships among numbers
relationships between a quantity and its rate of change
Richard Dedekind
Riemann hypothesis
rigor
Rigorous arguments
rigorous deduction from appropriately chosen axioms and definitions
rounding errors
science
science of pattern
scientific method
seasons
selfevident truths
series of abstractions
set theory
shapes
Simplicity
simulation
size
social sciences such as economics
sources of error in computation
space
statisticians
statistics
statistics
Stephen Wolfram
string of symbols
string theory
structural properties
structure
study
subtraction
syntax
system for recording numbers
tallies
The logicist's goal
The topics of Algebraic expansions, combinatorial analysis, and many other mathematical patterns and curiosities
The Unreasonable Effectiveness of Mathematics in the Natural Sciences
theorems
theoretical computer science
theoretical physicist
Theory of the rationals based on his now famous axioms for the natural numbers
time
topological groups
topology
tractability
traditional seven liberal arts
transfinite numbers
Trigonometry
truth
Turing machine
twin prime conjecture
uncertainty
undecidable formulas
unpredictable yet still deterministic behavior
unsolved problems
Vector calculus
vector spaces
vectors
Weierstrass
whether mathematics is created (as in art) or discovered (as in science)
whole numbers
years
Math/Logic
Gottlob Frege
Predicate calculus
Principia Mathematica
To show that all pure mathematics follows from purely logical premises and uses only concepts definable in logical terms
Medicine
Genetic conditions and diseases
Intervention of Aging
Prevention and cure of diseases
Targeted therapy interventions
Organic Chemistry
Acetylation (Acetyltransferase COC)
Covalent bonding
Five basic elements: Carbon, Hydrogen, Nitrogen, Oxygen, and Phosphorus
Methylation
Organic molecules, such as drugs, sugars, proteins, fats, and deoxyribonucleic acids (DNA)
Outer shell
Relatively but not completely stable conformations
Restricted bond rotations, which occur at 120degree intervals
Rotational states
Single molecules
Small organic molecules
State of this single carbon atom
Steric or physical hindrance
Tetrahedral atoms
Thermodynamic barrier to rotation
Trans conformation
Pascal's Triangle
The 1 3 3 1 configuration
Physics
Electrons
Set Theory
Containment
Intersection
Partially ordered set
Set theoretical concepts
Subset
The set (a,b,c).
Union
External Links
An ontology for biological function based on molecular interactions
BITOLA  Biomedical Discovery Support System
http://ibmi.mf.unilj.si/bitola/
Biological text analysis 

