Argot, Lexicon & Lingo

An alphabetical list of terms, words, jargon, patentspeak, concepts, and buzzwords about science, research & development and all things technical. This is a personal advanture. Feel free to use it but these definitions are in arleen-speak, which means no guarantees.

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Abbreviated New Drug Application (ANDA): Generics
An Abbreviated New Drug Application (ANDA) contains data which when submitted to FDA's Center for Drug Evaluation and Research, Office of Generic Drugs, provides for the review and ultimate approval of a generic drug product. Once approved, an applicant may manufacture and market the generic drug product to provide a safe, effective, low cost alternative to the American public.

A substance whose chemical constituents are being identified and measured.
A chemical substance that is the subject of chemical analysis. More broadly, the object that is the subject of a scientific or medical research analysis.
Anatomical Therapeutic Chemical (ATC)
A classification system where the active substances are divided into different groups according to the organ or system on which they act and their therapeutic,pharmacological and chemical properties. Drugs are classified at five different levels. The drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The 2nd, 3rd and 4th levels are often used to identify pharmacological subgroups when that is considered more appropriate than therapeutic or chemical subgroups. (http://www.whocc.no/atc/application_for_atc_codes/)


Basic Logical Alignment System Tool — BLAST
BLAST Search. In bioinformatics, BLAST for Basic Local Alignment Search Tool is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold.
Big Data to Knowledge (BD2K)
NIH's big data initiative.
Biologic License Application (BLA)


Chemistry genomics.
Chimeric antigen receptor (CAR)-expressing T cells (CAR-T)
Adoptive T-cell therapy (ACT), employing a patient’s own cultured T cells, is an emerging paradigm for the treatment of a variety of cancers. The use of genetic engineering approaches to insert antigen-targeted receptors of defined specificity into T cells has greatly extended the potential capabilities of ACT. Chimeric antigen receptors (CARs) are a type of antigen-targeted receptor composed of intracellular T-cell signaling domains fused to extracellular tumor-binding moieties, most commonly single-chain variable fragments (scFvs) from monoclonal antibodies. The current leaders (@ April 2015) in the CAR-T field are Adaptimmune (ADAP), Juno Therapeutics ($JUNO), Novartis ($NVS) and Kite Pharma ($KITE)
Choropleth map
A choropleth map (from Greek χώρο ("area/region") + πλήθος ("multitude")) is a thematic map in which areas are shaded or patterned in proportion to the measurement of the statistical variable being displayed on the map, such as population density or per-capita income. The choropleth map provides an easy way to visualize how a measurement varies across a geographic area or it shows the level of variability within a region. A special type of choropleth map is a prism map, a three-dimensional map in which a given region's height on the map is proportional to the statistical variable's value for that region.
Clinical Data Interchange Standards Consortium (CDISC)
CDISC is a global, open, multidisciplinary, non-profit organization that has established standards to support the acquisition, exchange, submission and archive of clinical research data and metadata. The CDISC mission is to develop and support global, platform-independent data standards that enable information system interoperability to improve medical research and related areas of healthcare. CDISC standards are vendor-neutral, platform-independent and freely available via the CDISC website.
Clinical Research Glossary of Acronymns & Terms
Glossary of acronymns for clinical research
Clinical Trials Transformation Initiative (CTTI)
Competitive Techical Intelligence — CTI
Cooperative Research and Development Agreement (CRADA)
Correlation Maps
In medical research — How many times the same terms show up together.


Database of Genotypes and Phenotype (dbGaP)
Archives and distributes the results of studies that investigate the interaction of genotype and phenotype.
Database of Single Nucleotide Polymorphisms (dbSNP)
Data Considerations (Translational R&D)
Five characteristics for evaluating large data sets for medical research:
  1. Volume — The number of documents/sources being evauated.
  2. Variety — The number of different types of files (PDFs, video, images, etc.) and the number of different sources (different journals, papers, conference proceedings, social media sentiment analysis).
  3. Velocity — The speed at which new data is being created. Also an indication of data "freshness."
  4. Veracity — The level of trust associated with the data. Includes aspects like the reliability of the source, the number of citations by other scientists, and the source — academic papers and the editorials about them; patents and the interpretations of the patent; blogs and comments on the blog. Veracity is increasingly important as researchers must assess external data beyond clinical results created locally — all the results and data are not coming from their lab.
  5. Value — The real value of the content. How useful is it in answering clinical questions.
Data Exclusivity
Drug companies have a period when the data they create to support clinical trials remains their intellectual property and can't be used by others until that period expires. This prevents generic drug makers and competitors from gaining access to their findings to accelerate their own work.
Defined Daily Dose (DDD)
The DDD is the assumed average maintenance dose per day for a drug used for its main indication in adults. A DDD will only be assigned for drugs that already have an ATC code.

Derwent Innovations Index
Derwent Innovations Index covers over 14.3 million basic inventions from 40 worldwide patent-issuing authorities.
Derwent World Patent Index (DWPI)
The Derwent World Patents Index (files WPINDEX/ WPIDS/WPIX) is a comprehensive value-added database of worldwide patents covering all areas of technology. The intellectual value of DWPI is the result of a thorough editorial process of classification, abstracting, and indexing. Original titles and abstracts are rewritten to reveal the actual invention and highlight the main uses and advantages of the technology.


Electronic Medical Records and Genomics Network (eMERGE)
eMERGE is an NIH organized and funded consortium of medical research organizations. Primary goal is to develop, disseminate, ad apply approaches to research that combine DNA biorepositories with electronic medical records for large-scale, high-throughput genetic research.
Engineering Index Compendex (EI Compendex)
Engineering Village comprises 12 engineering literature and patent databases providing comprehensive coverage from a range of trusted, reliable and relevant sources: scholarly journals, conference proceedings, trade publications, patents, and government reports. Currently with over 17 million records across 190 engineering disciplines, Compendex delivers the comprehensive, precise information and insights that researchers need.
The Engineering Index Backfile provides an historical view of engineering developments and innovations described in literature from 1884-1969. Over 1.7 million records have been digitized from the original Engineering Index print indexes. EI Patents contains 12.7 million patents filed with the United States Patent and Trademark Office (USPTO) and 4.4 million patents filed with the European Union Patent Office (EPO).
The study of all of the epigenetic changes in a cell. Epigenetic changes are changes in the way genes are switched on and off without changing the actual DNA sequence. They may be caused by age and exposure to environmental factors, such as diet, exercise, drugs, and chemicals. Epigenetic changes can affect a person’s risk of disease and may be passed from parents to their children.
A persons exposure to events over their life time. CDC and NIOSH refer to this as "insults from environmental and occupational sources" and how these exposures impact our health. Exposomics is the measurement and assessment of this exposure. Events are referred to as exogenous exposures. This can include factors like socioeconomic status, quality of housing, neighborhood, and social relationships, access to services, and experience with discrimination and how these contribute to psychological stress, health and health inequalities.
The internal and external exposure assessment values for exposome events. Assessment of environmental stressors.
European Federation of Pharmaceutical Industries and Associations (EFPIA)


FDA Advisory Committee (FDA Ad Com)
Federal Advisory Committees are committees of outside experts convened to assist FDA in approval/rejection of a New Drug Application (NDA)


The haploid (having a single set of unpaired chromosomes) set of chromosomes in a gamete or microorganism, or in each cell of a multicellular organism, the complete set of genes or genetic material present in a cell or organism.
Genome-Wide Association (GWAS)
A study the identifies the marketers across genomes to find genetic variations associated with a disease or condition. (For example, if you have this genetic mutation you will have this disease.)
The genetic sequence of an individual organism categorized in terms of known genetic variations. (For example — some lung cancer has mutant Efg receptor genotype while others have a wild-tupe or normal Egf receptor genotype)


Hospitalomics is a systems-based approach to revealing patterns of care with the strongest relationship to patient outcomes and costs, with the ultimate goal of generating and disseminating information on how to improve hospital care. Hospitalomics, funded by a 4-year Donaghue Foundation grant, is a multi-disciplinary data-driven approach that combines systems thinking, outcomes sciences, and information sciences to generate information on variation in hospital care and to identify those patterns of care that are strongly associated with the best performance as measured by clinical outcomes (mortality and readmission rates) and hospital costs. Our ultimate goal is to disseminate this information among the hospitals to guide improvement strategies.


Digital information sharing and genomics.
An invaluable resource - 14 million abstracts and specialised indexing to quality research literature in physics and engineering. Inspec is a major indexing database of scientific and technical literature, published by the Institution of Engineering and Technology (IET), and formerly by the Institution of Electrical Engineers (IEE), one of the IET's forerunners. Inspec coverage is extensive in the fields of physics, computing, control, and engineering. Its subject coverage includes astronomy, electronics, communications, computers & computing, computer science, control engineering, electrical engineering, information technology, physics, manufacturing, production and mechanical engineering.
Sample Record
International Classification of Diseases (ICD)
A system established more than 100 years ago that the World Health Organization uses to track disease incidence, physicians use as a basis for standardized diagnoses, and the health-care industry (specifically, clinicians, hospitals, and payers) uses to determine reimbursement for care. ICD, which is currently in its tenth revision, remains the most commonly used categorization of disease (WHO 2007). Published by the World Health Organization (WHO), ICD-10 is used for statistical analyses, reimbursement, and decision support, making it an integral part of health-care systems throughout the world. The publication of ICD-11 in approximately 2015.
International Health Terminology Standards Development Organization (IHTSDO)
Owners of the SNOMED clinical terminology system created by the College of American Pathologists.
International Nonproprietary Name (INN)
An official nonproprietary or generic name given to a pharmaceutical drug, as designated by the World Health Organization (WHO). The plethora of named proprietary preparations containing a given substance can lead to confusion about the identity of the active ingredient. Like other systems of drug nomenclature, INNs facilitate communication by providing a standard name for each substance; they are designed to be unique and distinct so as to avoid confusion in prescribing. WHO issues INNs in English, Latin, French, Russian, Spanish, Arabic, and Chinese. (See USAN and INN)
International Union of Pure and Applied Chemistry (IUPAC)
A chemical nomenclature is a set of rules to generate systematic names for chemical compounds. The nomenclature used most frequently worldwide is the one created and developed by the International Union of Pure and Applied Chemistry (IUPAC).
Investigative New Drug (IND)
FDA Investigative Drug Application. There are three IND types:
  1. An Investigator IND is submitted by a physician who both initiates and conducts an investigation, and under whose immediate direction the investigational drug is administered or dispensed. A physician might submit a research IND to propose studying an unapproved drug, or an approved product for a new indication or in a new patient population.
  2. Emergency Use IND allows the FDA to authorize use of an experimental drug in an emergency situation that does not allow time for submission of an IND in accordance with 21CFR , Sec. 312.23 or Sec. 312.34. It is also used for patients who do not meet the criteria of an existing study protocol, or if an approved study protocol does not exist.
  3. Treatment IND is submitted for experimental drugs showing promise in clinical testing for serious or immediately life-threatening conditions while the final clinical work is conducted and the FDA review takes place.
There are two IND categories:
  1. Commercial
  2. Research (non-commercial)



A type of enzyme



Medical Subject Headings — MeSH
MeSH is used to index 5,400 of the world's leading biomedical journals for MedLine and PubMed. National Library of Medicine controlled vocabulary thesaurus. NLM defines terms in the context of existing vocabulary. NLM indexes its catalog of holdings into MeSH. "Staff collects new terms as they appear in scientific literature or emerging areas of research."An alphabetical and hierarchical thesaurus. It has the following features:
  • A 12 level hierarchy that moves from general to granular subject matter.
  • 27,149 Descriptors
  • 218,000 terms that assist in finding the most appropriate MeSH headings.
  • 219,000 Supplementary Concept Records arranged in a separate thesaurus.

MeSH-P is Primary Medical Subject Headings.
Researchers create their own topic clusters using MeSH headings and thesauri. Also use MeSH Qualifiers — assignment based on human indexer review of full articles.
Primary terms and qualifiers.

Name Stems
Drugs from the same therapeutic or chemical class are usually given names with the same stem. Stems are mostly placed word-finally, but in some cases word-initial stems are used. They are collected in a publication informally known as the Stem Book. (See USAN and INN)
National Counsel for Prescription Drug Programs (NCPDP)
NCPDP provides a forum wherein our diverse membership can develop business solutions, including ANSI-accredited standards, and guidance for promoting information exchanges related to medications, supplies, and services within the healthcare system.
National Institute of Biomedical Imaging and Bioengineering (NIBIB)
NIBIB supports emerging technology research and development within its internal laboratories and through grants, collaborations, and training.
National Institute for Occupational and Safety and Health (NIOSH)
Nano Enabled Drug Delivery — NEDD
National Health and Nutrition Examination Survey — NHANES
New Drug Application — NDA
The NDA application is the vehicle through which drug sponsors formally propose that the FDA approve a new pharmaceutical for sale and marketing in the U.S. The data gathered during the animal studies and human clinical trials of an Investigational New Drug (IND) become part of the NDA.
Newly Emerging Science & Technology (NEST)
New Molecular Entity (NME)
A New Molecular Entity is an active ingredient that has never before been marketed in the United States in any form.
National Library of Medicine.

Nonproprietary Names for Pharmaceuticals
The creation of public names for drugs. MedNet-INN is curated by WHO.


Orange Book
FDA Orange Book of Approved Drug Products with Therapeutic Equivalence Evaluations. The Orange Book also contains extensive information about New Drug Applications and Abbreviated New Drug Application approvals for generic drug applications. USPTO patent applications and FDA drug applications are interwoven in the Pharma commercialization and drug approval processes.


Personalized Medicine Also individualized or precision medicine
Rather than treating a person as [part of] a group, treat the person as an individual, based on [his or her] own genetic material, to enable us to provide individualized, personalized and precise care. Precision medicine envisions collecting enormous amounts of information — not just from humans, but from other species and from basic science research -- and crunching that data to identify ways to diagnose and treat individuals.
Pharmaceutical Drug Labeling Standard
Pharmaceutical Compound Number prefixes details a pharmaceutical drug labeling standard. Pharmaceutical companies produce a large number of compounds, which cannot all be given names. Instead, they are systematically numbered for internal reference. The number is prefixed with a letter code indicating which company synthesized the compound. For example, CP-529414 is the compound number for the recently failed Pfizer experimental drug torcetrapib. If the company or its agents choose to publish information or research results about the drug before it has been assigned a generic name (such as an INN, USAN, or BAN), they will refer to it by this number.
Pharmaceutical Research and Manufacturers of America (PhRMA)
Pharmacogenomics is the study of genetic variations that influence individual response to drugs. Knowing whether a patient carries any of these genetic variations can help prescribers individualize drug therapy, decrease the chance for adverse drug events, and increase the effectiveness of drugs. This determines what the right medicine is for the individual patient based upon the small genetic variations that can be measured by genetic testing.
What a drug does to the body, involves receptor binding, postreceptor effects, and chemical interactions.
What the body does to a drug, refers to the movement of drug into, through, and out of the body—the time course of its absorption (Drug Absorption), bioavailability (Drug Bioavailability), distribution (Drug Distribution to Tissues), metabolism (Drug Metabolism), and excretion (Drug Excretion). Drug pharmacokinetics determines the onset, duration, and intensity of a drug's effect. Formulas relating these processes summarize the pharmacokinetic behavior of most drugs.
The idiosyncratic traits exhibited by an organism categorized in terms of know trait variants. (For example blue eyes and brown eyes are phenotypes exhibited in subsets of humans.
See Public Library of Science
Prescription Drug User Fee Act (PDUFA)
It authorizes FDA to collect fees from companies that produce certain human drug and biological products. Since the passage of PDUFA, user fees have played an important role in expediting the drug approval process.
President’s Council on Advisors on Science and Technology (PCAST)
The entire coplement of proteins and associated modification produced by an organism.
Proteomics is the large-scale study of the way in which proteins control cellular behavior. Proteins are encoded by genes, therefore proteomics is closely linked to genomics.
Public Library of Science (PLoS)
PLOS is a nonprofit open access scientific publishing project aimed at creating a library of open access journals and other scientific literature under an open content license.



Regulatory Information Management (RIM)
Regulatory Information Management (RIM) is defined as the effective and efficient collection, storage, retrieval and communication of regulatory information. RIM processes include defining product authorization targets, managing regulatory submission plans, creating and gathering submission information, producing and submitting the submission output and managing the product registration.
Regulatory Science
The process of translating biomedical discoveries into new therapies has become increasingly complex in light of evolving science and technology, and requires that the science of regulation keep up with the advances in biomedical science and technology. New methodologies or innovative approaches in regulatory science that will ultimately inform the regulatory decisions the Food and Drug Administration (FDA) and others make.
R01 Money
Basic NIH Grant money.


Scientific, Technical and Medical (STM) Publishing
Broad groupings of learned society and peer reviewed journals.
Elsivier's Scopus is the largest abstract and citation database of peer-reviewed literature: scientific journals, books and conference proceedings. Delivering a comprehensive overview of the world's research output in the fields of science, technology, medicine, social sciences, and arts and humanities, Scopus features smart tools to track, analyze and visualize research. 55 million records | 21,915 titles | 5,000 publishers
Systematized Nomenclature of Medicine SNOMED
The Systematized Nomenclature of Medicine developed by the International Health Terminology Standards Development Organization (IHTSDO). SNOMED is a large, clinically focused ontology that uses high-level nodes to aggregate more granular data. SNOMED is owned, maintained, and distributed by the International Health Terminology Standards Development Organization (IHTSDO) a not-for-profit association in Denmark.
SNOMED Clinical Terms
A systematically organized computer processable collection of medical terms providing codes, terms, synonyms and definitions used in clinical documentation and reporting.
Single Nucleotide Polymorphisms (SNPs)
The most common variations in the human genome. There is estimated to be approximately 11 million SNPs in the human population, with an average of one every 1,300 base pairs. An individual's response to a drug is often linked to these common DNA variations. In a similar manner, susceptibility to certain diseases is also influenced by common DNA variations.
A data visualization tool from TIBCO. Heavily used in pharma for use in evidence based R&D decisions.
Synthetic Biology

Synthetic Biology is a) the design and construction of new biological parts, devices and systems and b) the re-design of existing natural biological systems for useful purposes. Synthetic biology involves using plant and human genome data to create new products and services. Synthetic Biology has emerged as a widely open data/open research community and the genome sequencing world.

Scientists seek to do things like coding sequence -- here's a strand of DNA that codes for a protein found in alligators that has antibiotic properties now search the medical/pharma/bioengineering literature and find similar strands of DNA you could hypothetically pair with the alligator antibiotic sequence to amp up production of the alligator antibiotic in bacteria. These techniques are used in a wide range of emerging SynBio industries - pharma, renewable fuels (algae), consumer products like hair products (J&J). SynBio seeks to facilitate the development of bio-based technologies to monitor, remediate and protect our environment with an appropriate balance of efficacy, sustainability and economic viability.

Another definition is: Synthetic biology is the engineering of biology: the synthesis of complex, biologically based (or inspired) systems, which display functions that do not exist in nature. This engineering perspective may be applied at all levels of the hierarchy of biological structures—from individual molecules to whole cells, tissues and organisms. Synthetic Biology should be able to rely on a list of standardized parts (amino acids, bases, proteins, genes, circuits, cells, etc…) whose properties have been characterized quantitatively and on software modeling tools that would help putting parts together to create a new biological function.

Systematized Nomenclature of Medicine SNOMED
the Systematized Nomenclature of Medicine developed by the International Health Terminology Standards Development Organization (IHTSDO). SNOMED is a large, clinically focused ontology that uses high-level nodes to aggregate more granular data.


Technology Opportunities Analyses (TOA)
ThemeScape is a data visualization tool that creates topographic map-style outputs (called "content maps"). The physical distance between peaks on a ThemeScape map represents a relationship score between the two points: the closer the distance, the more closely related the two documents are in terms of subject matter.
sample themescape map ThemeScape is designed to handle large data sets; maps can represent thousands of documents. The feature can handle input from full text patent data, DWPI data, and scientific literature.[2] Users can create a ThemeScape map on Thomson Innovation by first selecting the records you want to include in the map from a result set or work file.
Theranostics is determining if diagnostics can be added to therapeutics.
Therapeutic Area Data Standards (TUAG)
The transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA transcribed in one cell or a population of cells.
Translational Nursing
Term used for the focus on practicing what we know.
Translational Research
Translational research includes two areas of translation. One is the process of applying discoveries generated during research in the laboratory, and in preclinical studies, to the development of trials and studies in humans. The second area of translation concerns research aimed at enhancing the adoption of best practices in the community. Cost-effectiveness of prevention and treatment strategies is also an important part of translational science.

Translational R&D is an emerging area that seeks to accelerate delivery of new medicine by bridging the gap between basic R&D and clinical pharma delivery. Translational research requires development of interdisciplinary teams, many from different subspecialties, to execute research projects. Major drug companies like GSK and Novartis have significant on-going Translational R&D efforts. Johns Hopkins and other medical schools are supporting Translational R&D by merging their engineering and medical school research efforts to increase the amount of cross-discipline research. This offers a significant opportunity for COBE as a tool to facilitate that interdisciplinary research improving outcomes and reducing time and cost.


US Adopted Names (USAN)
The generic name is officially called the United States Adopted Name (USAN) and serves as an important and unique designation for the active ingredient. It appears with the company's trade name on drug labels, advertisements, and other information and is also requested on FDA applications and in drug substance chemical descriptions. Because most journals request that authors use the generic name in clinical trial reports, it is used in publishing scientific data about investigational and established therapies. The USAN is also much shorter, easier to remember and pronounceable than the systematic chemical name.

By definition, nonproprietary names are not subject to proprietary trademark rights but are entirely in the public domain. This distinguishes them from the trademarked names that have been registered for private use.

Unlike generic names, brand names vary from company to company and from country to country. In rare instances, a brand name may be used for two different active ingredients in different countries. More commonly, a company uses different brand names in different countries for the same drug, or two countries may market the same substance under different brand names. Finally, as part of "brand extension" business strategies, companies use the same brand name to refer to two different active ingredients.

USAN will be provided for the following:
  • small molecule drugs
  • biotechnology drugs including monoclonal antibodies, therapeutic vaccines, proteins and peptides, DNA, RNA, nucleoside and nucleotide therapies
  • gene therapies
  • cellular therapies
  • other biological substances deemed appropriate to be assigned a USAN by the USANC
  • contact lens materials
  • active ingredients in sunscreens
  • veterinary products intended to control diseases in animals
  • the base, salt, solvate, ester or other chemical derivative of a substance that has received a USAN
USAN will not be provided for the following:
  • mixtures that do not have an IND number or do not require approval for human use by the FDA
  • drug delivery mechanisms
  • excipients alone
  • prophylactic vaccines
  • product formulations* (emulsions, suspensions, etc.)
  • medical devices
  • manufacturing processes
  • combination drug products
Sample Brand Names and Generic Names for Active Ingredients

Brand:  Cialis
Generic:  tadalafil

Brand:  Colemin, Lipex, Zocor, Vytorin
Generic:  simvastatin

Brand:  Gleevec, Glivec
Generic:  imatinib mesylate

USAN Counsil
Each name is assigned by the USAN Council, which is co-sponsored by the American Medical Association (AMA), the United States Pharmacopeial Convention (USP), and the American Pharmacists Association (APhA).


Thoughts on scientific visualizations.
  1. Themescape — topgraphical maps of subject matter.
  2. Timelines — Used for ordering scientific articles and citation data by age. Important for figuring out the age of research or if there are issues with patenting new drugs due to prior disclosure of an invention via research. Patent Scientists need to see the timeline so they can write drug applications and patent applications around prior art.


Web of Science
Web of Science is a Thompson Reuters product for finding abstracts of articles.
Used extensively for finding and capturing abstracts on scientific articles before researchers/scientists actually "buy" the articles either through subscription products with counts of article access or straight out pay for download.
Global Map of Science maps 224 Web of Science Categories.



Yale University Open Data Access (YODA)


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