Evolving terminology for emerging technologies
Comments? Questions? Revisions? mchitty@healthtech.com
Last revised November 29, 2001
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affinity based data mining: Algorithms & data management glossary

CML Chemical Markup Language: Chemical Markup Language brings the power of XML (Computers glossary)  to the management of chemical information. In simple terms it is "HTML with Molecules", but there is a great deal more. CML, and associated tools, allows for the conversion of current files without semantic loss, structured documents including chemical publications, and precise location of information within files. CML has been designed carefully so that it is as easy as possible for the 'average chemist' to understand it.  [XML- CML.ORG - The Site for Chemical Markup Language] http://www.xml-cml.org/

chemical information: Many people view chemoinformatics as an extension of chemical information, which is a well established concept covering many areas that employ chemical structures, data storage and computational methods, such as compound registration databases, on- line chemical literature, SAR analysis and molecule- property calculation. [Timothy Ritchie "Chemoinformatics; manipulating chemical information to facilitate decision- making in drug discovery" Drug Discovery Today 6(16): 813-814, Aug. 2001]

chemical information system: Must include registration, computed and measured properties, chemical descriptors and inventory. The primary purpose is to be able to identify a chemical substance, find compounds similar to the target compound and determine the location of the compound. To effectively build it, an object definition of the chemical sample is paramount…The hub [central database] of the chemical information system is the inventory system. [Frank Brown "Chemoinformatics: What is it and How does it Impact Drug Discovery" Annual Reports in Medicinal Chemistry 33: 375-384, 1998]

cheminformatics: The practice of  finding the "best- fitting" compounds to address particular targets. The field encompasses diversity analysis and library design, virtual screening, rational drug design, and tools and approaches for predicting activity and other properties from structure. [CHI Bioinformatics]

Going by the numbers in  Google.com cheminformatics seems to be the currently most used form of this word, overtaking chemoinformatics. See the Glossary FAQ question #2 for details and methodology.

chemi-informatics: See chemoinformatics.

chemoinformatics: There are many sources of chemical data; registered chemical structures with stereochemistry, synthesis records, spectral data including NMR, purity determinations, not to mention the volume of data generated by HTS, SAR studies and the calculation of physiochemical properties. While gathering, storage and registration of data transforms it to information, it is accessibility, manipulation, and data mining of chemical information that translates it to knowledge for smarter drug development. This conference will showcase chemoinformatic tools for storage, design and mining of chemical databases/ information and present case examples of its success in lead identification and optimization. Chemoinformatics is about presenting and integrating a vast and complex array of information so that people who make the decisions in drug discovery can make the correct choices quickly and easily. Chemoinformatics: Intelligent Drug Discovery May 6-8, 2002 Philadelphia PA

Chemoinformatics is an integral part of the discipline of knowledge management. [Nicholas J. Hrib, Norton P. Peet "Chemoinformatics: are we exploiting these new science?" Drug Discovery Today 5 (11): 483-485, Nov. 2000]

An emerging area, which annotates small molecules and also libraries with structure – function, synthesis, and all other relevant data used to design and develop better drugs. ["Combinatorial Chemistry" Nature Biotechnology 18:  Supplement Oct. 2000, from Nature Biotechnology 16, 691–693 (1998)]

Increasingly incorporates "compound registration into databases, including library enumeration; access to primary and secondary scientific literature; QSAR Quantitative Structure Activity Relationships) and similar tools for relating activity to structure; physical and chemical property calculations; chemical structure and property databases, chemical library design and analysis; structure- based design and statistical methods. Because these techniques have traditionally been considered the realms of scientists from different disciplines, differences in computer systems and terminology provide a barrier to effective communication. This is probably the single most challenging problem that chemoinformatics must solve. [M Hann and R Green "Chemoinformatics – a new name for an old problem?" Current Opinion in Chemical Biology 3:379-383, 1999]

Mixing of information technology and management to transform data into information and information into knowledge for the intended purpose of making better decisions faster in the arena of drug lead identification and optimization. ..In Chemoinformatics there are really only two [primary] questions: 1.) what to test next and 2.) what to make next. The main processes within drug discovery are lead identification, where a lead is something that has activity in the low micromolar range, and lead optimization, which is the process of transforming a lead into a drug candidate. [Frank Brown  "Chemoinformatics: What is it and How does it Impact Drug Discovery" Annual Reports in Medicinal Chemistry 33: 375-384, 1998] Related terms cheminformatics, chemi-informatics, chemometrics, computational chemistry.  

chemometrics: The application of statistics to the analysis of chemical data (from organic, analytical or medicinal chemistry) and design of chemical experiments and simulations. [IUPAC Computational]

 The science of relating measurements made on a chemical system or process to the state of the system via application of mathematical or statistical methods. [International Society of Chemometrics "ISC symbol and definition of chemometrics" 1997] http://www.emsl.pnl.gov:2080/docs/incinc/chemdef.html

Related terms 3D-QSAR, comparative molecular field analysis (CoMFA, QSAR Algorithms & data management glossary

cLogP: Algorithms & data management glossary

computational chemistry: A discipline using mathematical methods for the calculation of molecular properties or for the simulation of molecular behavior.  It also includes, e.g., synthesis planning, database searching, combinatorial library manipulation (Hopfinger, 1981; Ugi et al., 1990). [IUPAC Computational] Related term Molecular modeling molecular graphics

data mining: Nontrivial extraction of implicit, previously unknown and potentially useful information from data, or the search for relationships and global patterns that exist in databases. [Bob Klevecz "The Whole EST Catalog" Scientist 12 (2): 22 Jan 18 1999]  Extended definition and related terms see Algorithms & data management

data warehouse: Algorithms & data management

GUI Graphical User Interface: The two most useful GUI’s are the Query interface to the database and the Report/Analysis interfaces…each interface should do only a handful of tasks. The most common mistake is to keep adding functionality to an interface rather than creating a new interface…The Query tools are just starting to emerge…The unmet need of querying data is in the area of joining internal and external data …The other emerging concept for the query tool is the need for relationships between the data. The most critical need is to have consistent terms used to describe the data. This is often a very difficult task to get scientists across a multi-site company to agree on one. The other complication is legacy data, either having the wrong terms or no terms at all. [Frank Brown "Chemoinformatics: What is it and How does it Impact Drug Discovery" Annual Reports in Medicinal Chemistry 33: 375-384, 1998]

genetic algorithm GA:  Algorithms & data management glossary

Immersive Virtual Reality IVR: New futuristic technique [which] enables the user to literally become a part of his or her data and to use additional senses. Although IVR has not yet enjoyed widespread use in scientific disciplines, it has been cost- effective in architectural design. [Nicholas J. Hrib, Norton P. Peet "Chemoinformatics: are we exploiting these new science?" Drug Discovery Today 5 (11): 483-485, Nov. 2000]

in silico: Molecular modeling glossary

Lipinski’s rules of five: See rules of five.

"plug and play" systems: Required for effective chemoinformatics systems. Must be designed backward from the answer to the data to be captured and systems should be in components where each component has one simple task…modular systems that can "plug and play" into other systems. [Frank Brown "Chemoinformatics: What is it and How does it Impact Drug Discovery" Annual Reports in Medicinal Chemistry 33: 375-384, 1998]

predictive data mining: Algorithms & data management glossary

Principal Components Analysis PCA: ALGORITHMs & data management glossary In-depth

rules of five: Lipinski’s rules. Set of criteria for predicting the oral bioavailability of a compound on the basis of simple molecular features (molecular weight,  CLogP, numbers of  hydrogen- bond donors and acceptors). Often used to profile a library or virtual library with respect to the proportion of drug- like members  which it contains. [IUPAC Combinatorial] From the 1997 article in Advanced Drug Delivery Research 23: 3-25 by Christopher A. Lipinski and colleagues, in which the cutoff numbers are five or multiples of five.

SAR Structure Activity Relationship: Drug discovery & development glossary

"silo systems": Legacy method for many information systems, a system built to collect, store and report one laboratory’s data. Each "silo system" holds the data differently and may be in a different technology … the results of the systems cannot easily be interchanged … This is as much a corporate structure and resource problem as it is a technical problem. Contrast with "plug and play". [Frank Brown "Chemoinformatics: What is it and How does it Impact Drug Discovery" Annual Reports in Medicinal Chemistry 33: 375-384,1998]   

stereochemical formula (stereoformula): A three- dimensional view of a molecule either as such or in a projection. [IUPAC Compendium]

stereochemistry: See stereochemical formula (stereoformula):

Structure Activity Relationship (SAR): The relationship between chemical structure and pharmacological activity for a series of compounds. [IUPAC Medicinal Chemistry] See also Drug Discovery & Development

virtual library: A library which has no physical existence, being constructed solely in electronic form or on paper. The building blocks required for such a library may not exist, and the chemical steps for such a library may not have been tested. These libraries are used in the design and evaluation of possible libraries. [IUPAC Combinatorial Chemistry] Related term in silico

virtual database assembly: A crucial activity as it enables access to the large number of drug- like molecules that could theoretically be made... can serve several purposes: for example, to generate a maximally diverse virtual library for lead generation, a biased library aimed at a specific target or target family, or a lead optimization library. [Nicholas J. Hrib, Norton P. Peet "Chemoinformatics: are we exploiting these new science?" Drug Discovery Today 5 (11): 483-485, Nov. 2000]

virtual molecules: It has also become clear that even the most efficient combinatorial chemistry approaches can generate only a minute fraction of the 1 x 10⁴⁰ virtual drug molecules that could be prepared. [Timothy Ritchie "Chemoinformatics; manipulating chemical information to facilitate decision- making in drug discovery" Drug Discovery Today 6(16): 813-814, 16 Aug. 2001]

virtual screening: Molecular modeling glossary.

Bibliography

Alpha glossary index

IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.