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Biomatics Thesaurus - Biomatics.org

Biomatics Thesaurus

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In the spirit of the National Library of Medicine's UMLS project, this thesaurus could be used for biomatical informatics purposes.  

Structure and Content of the UMLS Semantic Network

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 non-hierarchical 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 Literature-Based Discovery

Literature-based 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.

Literature-based discovery. The methodology in literature-based 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.


WELCOME TO ARROWSMITH 3.0


Contents

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
                Protein-coding 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

     
                   Mechanics

 

 

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

 
                     3-to-8 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
                      Logic-circuit design
                      Logic-circuit designers
                     Memory address decoding.
                     Minterm
                     Multiplexing
                      n to 2n decoder
                      n to 2n Conversion
                      Outputs.
                      Routing input data to a specified output line
                      Standard Integrated circuits
                      Switching elements (gates)
                      Time-division 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

computer-assisted 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

Group theory

groups, rings, fields and other abstract systems

Guiseppe Peano 

hierarchy of numbers

higher-dimensional 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

non-Euclidean 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

real-valued 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

self-evident 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 120-degree 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.uni-lj.si/bitola/


Biological text analysis
  • AcroMed - A computer generated database of biomedical acronyms and the associated long forms extracted from the recent Medline abstracts
  • BioMinT - Mining the biomedical literature
  • GPSDB - Gene and Protein Synonym DataBase
  • MedMiner - Extract and organize relevant sentences in the literature based on a gene, gene-gene or gene-drug query
  • XplorMed - Explore a set of abstracts derived from a bibliographic search in MEDLINE
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