Scientific literature comprises scholarly publications that report original empirical and theoretical work in the natural and social sciences, and within an academic field, often abbreviated as the literature. Academic publishing is the process of contributing the results of one's research into the literature, which often requires a peer-review process. Original scientific research published for the first time in scientific journals is called the primary literature. Patents and technical reports, for minor research results and engineering and design work (including computer software), can also be considered primary literature. Secondary sources include review articles (which summarize the findings of published studies to highlight advances and new lines of research) and books (for large projects or broad arguments, including compilations of articles). Tertiary sources might include encyclopedias and similar works intended for broad public consumption.
Scientific literature can include the following kinds of publications:
Literature may also be published in areas considered to be "grey", as they are published outside of traditional channels. This material is traditionally not indexed by major databases and can include manuals, theses and dissertations, or newsletters and bulletins.
The significance of different types of the scientific publications can vary between disciplines and change over time. According to James G. Speight and Russell Foote, peer-reviewed journals are the most prominent and prestigious form of publication. Generally books published by university presses are usually considered more prestigious than those published by commercial presses. The status of working papers and conference proceedings depends on the discipline; they are typically more important in the applied sciences. The value of publication as a preprint or scientific report on the web has in the past been low, but in some subjects, such as mathematics or high energy physics, it is now an accepted alternative.
There are ten different types of scientific papers. Eight of these carry specific objectives, while the other two can vary depending on the style and the intended goal.
Papers that carry specific objectives are:
These two have varying types of scientific classifications and can range from historical articles to speeches:
The actual day-to-day records of scientific information are kept in research notebooks or logbooks. These are usually kept indefinitely as the basic evidence of the work, and are often kept in duplicate, signed, notarized, and archived. The purpose is to preserve the evidence for scientific priority, and in particular for priority for obtaining patents. They have also been used in scientific disputes. Since the availability of computers, the notebooks in some data-intensive fields have been kept as database records, and appropriate software is commercially available.
The work on a project is typically published as one or more technical reports, or articles. In some fields both are used, with preliminary reports, working papers, or preprints followed by a formal article. Articles are usually prepared at the end of a project, or at the end of components of a particularly large one. In preparing such an article vigorous rules for scientific writing have to be followed.
Often, career advancement depends upon publishing in high-impact journals, which, especially in hard and applied sciences, are usually published in English. Consequently, scientists with poor English writing skills are at a disadvantage when trying to publish in these journals, regardless of the quality of the scientific study itself. Yet many international universities require publication in these high-impact journals by both their students and faculty. One way that some international authors are beginning to overcome this problem is by contracting with freelance medical copy editors who are native speakers of English and specialize in ESL (English as a second language) editing to polish their manuscripts' English to a level that high-impact journals will accept.
A scientific article has a standardized structure, which varies only slightly in different subjects. Although the IMRAD structure emphasizes the organization of content and in scientific journal articles, each section (Introduction, Methods, Results, and Discussion) has unique conventions for scientific writing style.
Ultimately, it is not the format that is important, but what lies behind it--the content. However, several key formatting requirements need to be met:
Though peer review and the learned journal format are not themselves an essential part of scientific literature, they are both convenient ways of ensuring that the above fundamental criteria are met. They are essentially a means of quality control, a term which also encompasses other means towards the same goal.
The "quality" being referred to here is the scientific one, which consists of transparency and repeatability of the research for independent verification, the validity of the conclusions and interpretations drawn from the reported data, overall importance for advance within a given field of knowledge, novelty, and in certain fields applicability as well. The lack of peer review is what makes most technical reports and World Wide Web publications unacceptable as contributions to the literature. The relatively weak peer review often applied to books and chapters in edited books means that their status is also second-tier, unless an author's personal standing is so high that prior achievement and a continued stake in one's reputation within the scientific community signals a clear expectation of quality.
The emergence of institutional digital repositories where scholars can post their work as it is submitted to a print-based journal has taken formal peer review into a state of flux. Though publicizing a preprint online does not prevent it from being peer reviewed, it does allow an unreviewed copy to be widely circulated. On the positive side this change has led to faster dissemination of novel work within the scientific community; on the negative it has made it more difficult to discern a valid scientific contribution from the unmeritorious.
Increasing reliance on abstracting services, especially on those available electronically, means that the effective criterion for whether a publication format forms part of the established, trusted literature is whether it is covered by these services; in particular, by the specialised service for the discipline concerned such as Chemical Abstracts Service, and by the major interdisciplinary services such as those marketed by the Institute for Scientific Information.
The transfer of copyright from author to publisher, used by some journals, can be controversial because many authors want to propagate their ideas more widely and re-use their material elsewhere without the need for permission. Usually an author or authors circumvent that problem by rewriting an article and using other pictures. Some publishers may also want publicity for their journal so will approve facsimile reproduction unconditionally; other publishers are more resistant.
In terms of research publications, a number of key issues include and are not restricted to:
BRENDA (The Comprehensive Enzyme Information System) is an information system representing one of the most comprehensive enzyme repositories. It is an electronic resource that comprises molecular and biochemical information on enzymes that have been classified by the IUBMB. Every classified enzyme is characterized with respect to its catalyzed biochemical reaction. Kinetic properties of the corresponding reactants (that is, substrates and products) are described in detail. BRENDA contains enzyme-specific data manually extracted from primary scientific literature and additional data derived from automatic information retrieval methods such as text mining. It provides a web-based user interface that allows a convenient and sophisticated access to the data.Beilstein database
The Beilstein database is the largest database in the field of organic chemistry, in which compounds are uniquely identified by their Beilstein Registry Number. The database covers the scientific literature from 1771 to the present and contains experimentally validated information on millions of chemical reactions and substances from original scientific publications. The electronic database was created from Beilstein's Handbook of Organic Chemistry, founded by Friedrich Konrad Beilstein in 1881, but has appeared online under a number of different names, including Crossfire Beilstein. Since 2009, the content has been maintained and distributed by Elsevier Information Systems in Frankfurt under the product name "Reaxys".The database contains information on reactions, substances, structures and properties. Up to 350 fields containing chemical and physical data (such as melting point, refractive index etc.) are available for each substance. References to the literature in which the reaction or substance data appear are also given.
The Beilstein content made available through Reaxys is complemented by information drawn from Gmelin (which gives access to the Gmelin Database), a very large repository of organometallic and inorganic information, as well as by information drawn from the Patent Chemistry Database. The Reaxys registered trademark and the database itself are owned and protected by Elsevier Properties SA and used under license.CAS Registry Number
A CAS Registry Number, also referred to as CASRN or CAS Number, is a unique numerical identifier assigned by the Chemical Abstracts Service (CAS) to every chemical substance described in the open scientific literature (currently including all substances described from 1957 through the present, plus some substances from the early or mid 1900s), including organic and inorganic compounds, minerals, isotopes, alloys and nonstructurable materials (UVCBs, of unknown, variable composition, or biological origin).The registry maintained by CAS is an authoritative collection of disclosed chemical substance information. It currently identifies more than 144 million unique organic and inorganic substances and 67 million protein and DNA sequences, plus additional information about each substance. It is updated with around 15,000 additional new substances daily.CiteSeerX
CiteSeerx (originally called CiteSeer) is a public search engine and digital library for scientific and academic papers, primarily in the fields of computer and information science. CiteSeer holds a United States patent # 6289342, titled "Autonomous citation indexing and literature browsing using citation context," granted on September 11, 2001. Stephen R. Lawrence, C. Lee Giles, Kurt D. Bollacker are the inventors of this patent assigned to NEC Laboratories America, Inc. This patent was filed on May 20, 1998, which has its roots (Priority) to January 5, 1998. A continuation patent was also granted to the same inventors and also assigned to NEC Labs on this invention i.e. US Patent # 6738780 granted on May 18, 2004 and was filed on May 16, 2001. CiteSeer is considered as a predecessor of academic search tools such as Google Scholar and Microsoft Academic Search. CiteSeer-like engines and archives usually only harvest documents from publicly available websites and do not crawl publisher websites. For this reason, authors whose documents are freely available are more likely to be represented in the index.
CiteSeer's goal is to improve the dissemination and access of academic and scientific literature. As a non-profit service that can be freely used by anyone, it has been considered as part of the open access movement that is attempting to change academic and scientific publishing to allow greater access to scientific literature. CiteSeer freely provided Open Archives Initiative metadata of all indexed documents and links indexed documents when possible to other sources of metadata such as DBLP and the ACM Portal. To promote open data, CiteSeerx shares its data for non-commercial purposes under a Creative Commons license.The name can be construed to have at least two explanations. As a pun, a 'sightseer' is a tourist who looks at the sights, so a 'cite seer' would be a researcher who looks at cited papers. Another is a 'seer' is a prophet and a 'cite seer' is a prophet of citations. CiteSeer changed its name to ResearchIndex at one point and then changed it back.Ei Compendex
Ei Compendex is an engineering bibliographic database published by Elsevier.
It indexes scientific literature pertaining to engineering materials. Beginning in 1884, it was compiled by hand under the original title of Engineering Index.
The name "Compendex" stands for COMPuterized ENgineering inDEX.
As a result of computerization in 1967, the first electronic Engineering Index bulletin was sent to 500 subscribers.
Elsevier purchased the parent company Engineering Information in 1998.Fedorov's catshark
Fedorov's catshark (Apristurus fedorovi) is a catshark of the family Scyliorhinidae. This shark has oviparous reproduction. This is a very poorly known species, with less than 30 specimens reported in the scientific literature. Almost nothing is known of its biology. This species may be endemic to northern Japanese waters, where it is taken in water around 1,200 m deep. However, accurate identification of Apristurus species is particularly difficult, and further research is required to determine its geographical and bathymetrical distribution.Invasive Species Compendium
The Invasive Species Compendium (ISC) is an online, open access reference work covering recognition, biology, distribution, impact, and management of invasive plants and animals produced by CAB International alongside an international consortium. It comprises peer-reviewed datasheets, images, and maps, a bibliographic database, and full text articles. New datasheets, data sets, and scientific literature are added on a weekly basis. The ISC has been resourced by a diverse international consortium of government departments, non-governmental organizations, and private companies.List of miscellaneous designer cannabinoids
Since the first synthetic cannabinoids were discovered in recreational drug products in 2008, new synthetic cannabinoids with no precedent in the scientific literature continue to be identified. These synthetic cannabinoids appear to be rationally designed by clandestine medicinal chemists. These unprecedented synthetic cannabinoids often feature alphanumeric code names intended to mimic the style of chemical nomenclature used by academic laboratories and pharmaceutical companies, and there is generally little, if any, information available regarding their pharmacology and toxicology at the time of first discovery.
5F-AB-PINACA — the terminally fluorinated (5-fluoropentyl) analogue of AB-PINACA.
5F-SDB-006 — the terminally fluorinated (5-fluoropentyl) analogue of SDB-006.
AB-001 — one of the earliest adamantane derivatives discovered as a designer cannabinoid. AB-001 was unknown in the scientific literature at the time of its discovery, and has since been characterized as a CB1 and CB2 agonist with weak cannabimimetic activity in rats.
APICA — also known as 2NE1 and SDB-001, APICA is the carboxamide analogue of AB-001 and was similarly unknown in the scientific literature at the time of its discovery. Like AB-001, APICA is a CB1 and CB2 agonist possessing moderate cannabimimetic potency in rats.
APINACA — also known as AKB-48. APINACA is the indazole analogue of APICA.
BIM-018 — also known as JWH-018 benzimidazole analogue, is a 1,2-disubstituted benzimidazole analogue of JWH-018.
FAB-144 — the indazole analogue of XLR-11.
FUB-144 — the N-(4-fluorobenzyl) analogue of UR-144 and XLR-11.
FUBIMINA — the terminally fluorinated (5-fluoro) analogue of BIM-018.
MN-18 — the indazole analogue of NNE1.
NNE1 — also known as NNEI, MN-24 and AM-6527, is the carboxamide analogue of JWH-018. NNE1 was first described in a paper by Abbott Laboratories in 2011.
SDB-006 — is a benzylic analogue of APICA, and was discovered during research related to AB-001 and APICA.
STS-135 — the terminally fluorinated (5-fluoro) analogue of APICA. STS-135 is believed to be named after the STS-135 jet propulsion system, and functions as an agonist at CB1 and CB2 receptors.
THJ-018 — the indazole analogue of JWH-018.
THJ-2201 — the indazole analogue of AM-2201.
WIN 55,212-2 —
XLR-11 — the terminally fluorinated (5-fluoro) analogue of UR-144.
XLR-12 — the terminally trifluorinated (4,4,4-trifluorobutyl) analogue of UR-144.MetaCyc
The MetaCyc database is one of the largest metabolic pathways and enzymes databases currently available. The data in the database is manually curated from the scientific literature, and covers all domains of life. MetaCyc has extensive information about chemical compounds, reactions, metabolic pathways and enzymes. The data have been curated from more than 58,000 publicationsMetaCyc has been designed for multiple types of uses. It is often used as an extensive online encyclopedia of metabolism. In addition,
MetaCyc is used as a reference data set for computationally predicting the metabolic network of organisms from their sequenced genomes; it has been used to perform pathway predictions for thousands of organisms, including those in the BioCyc Database Collection. MetaCyc is also used in metabolic engineering and metabolomics research.
MetaCyc includes mini reviews for pathways and enzymes that provide background information as well as relevant literature references. It also provides extensive data on individual enzymes, describing their subunit structure, cofactors, activators and inhibitors, substrate specificity, and, when available, kinetic constants. MetaCyc data on metabolites includes chemical structures, predicted Standard energy of formation, and links to external databases. Reactions in MetaCyc are presented in a visual display that includes the structures of all components. The reactions are balanced and include EC numbers, reaction direction, predicted atom mappings that describe the correspondence between atoms in the reactant compounds and the product compounds, and computed Gibbs free energy.
All objects in MetaCyc are clickable and provide easy access to related objects. For example, the page for L-lysine lists all of the reactions in which L-lysine participates, as well as the enzymes that catalyze them and pathways in which these reactions take place.P-process
The term p-process (p is for proton) is used in two ways in the scientific literature concerning the astrophysical origin of the elements (nucleosynthesis). Originally it referred to a proton capture process which is the source of certain, naturally occurring, proton-rich isotopes of the elements from selenium to mercury. These nuclides are called p-nuclei and their origin is still not completely understood. Although it was shown that the originally suggested process cannot produce the p-nuclei, later on the term p-process was sometimes used to generally refer to any nucleosynthesis process supposed to be responsible for the p-nuclei.Often, the two meanings are confused. Recent scientific literature therefore suggests to use the term p-process only for the actual proton capture process, as it is customary with other nucleosynthesis processes in astrophysics.Primary source
In the study of history as an academic discipline, a primary source (also called an original source) is an artifact, document, diary, manuscript, autobiography, recording, or any other source of information that was created at the time under study. It serves as an original source of information about the topic. Similar definitions can be used in library science, and other areas of scholarship, although different fields have somewhat different definitions. In journalism, a primary source can be a person with direct knowledge of a situation, or a document written by such a person.Primary sources are distinguished from secondary sources, which cite, comment on, or build upon primary sources. Generally, accounts written after the fact with the benefit (and possible distortions) of hindsight are secondary. A secondary source may also be a primary source depending on how it is used. For example, a memoir would be considered a primary source in research concerning its author or about his or her friends characterized within it, but the same memoir would be a secondary source if it were used to examine the culture in which its author lived. "Primary" and "secondary" should be understood as relative terms, with sources categorized according to specific historical contexts and what is being studied.Primatomorpha
The Primatomorpha are a mirorder of mammals containing two orders: the Dermoptera or colugos and the Primates (Plesiadapiformes, Strepsirrhini, Haplorhini).
The term "Primatomorpha" first appeared in the general scientific literature in 1991 (K.C. Beard) and 1992 (Kalandadze, Rautian). Major DNA sequence analyses of predominantly nuclear sequences (Murphy et al., 2001) support the Euarchonta hypothesis, while a major study investigating mitochondrial sequences supports a different tree topology (Arnason et al., 2002). A study investigating retrotransposon presence/absence data has claimed strong support for Euarchonta (Kriegs et al., 2007). Some interpretations of the molecular data link Primates and Dermoptera in a clade (mirorder) known as Primatomorpha, which is the sister of Scandentia.
Primates probably split from the Dermoptera sister group 79.6 million years ago during the Cretaceous.Other interpretations link the Dermoptera and Scandentia together in a group called Sundatheria as the sister group of the primates. Some recent studies place Scandentia as sister of the Glires, invalidating Euarchonta.Registry of Toxic Effects of Chemical Substances
Registry of Toxic Effects of Chemical Substances (RTECS) is a database of toxicity information compiled from the open scientific literature without reference to the validity or usefulness of the studies reported. Until 2001 it was maintained by US National Institute for Occupational Safety and Health (NIOSH) as a freely available publication. It is now maintained by the private company BIOVIA or from several value-added resellers and is available only for a fee or by subscription.ResearcherID
ResearcherID is an identifying system for scientific authors. The system was introduced in January 2008 by Thomson Reuters.
This unique identifier aims at solving the problem of author identification. In scientific literature it is common to cite name, surname, and initials of the authors of an article. Sometimes, however, there are authors with the same name, with the same initials, or the journal misspells names, resulting in several spellings for the same authors, and different authors with the same spelling.
On the ResearcherID website, authors are asked to link their ResearcherID to their own articles. In this way, they can also keep their publication list up to date and online. A comprehensive view of an author's total output can thus be given, since not all publications are indexed by Web of Science. This is particularly important for researchers in fields that predominantly use peer-reviewed conference articles (computer science) or in fields that focus on publishing books and chapters in books (humanities and disciplines in the social sciences).
The combined use of the Digital Object Identifier with the ResearcherID allows a unique association of authors and scientific articles. It can be used to link researchers with registered trials or identify colleagues and collaborators in the same field of research.ResearcherID has been criticized for being commercial and proprietary, but also praised as "an initiative addressing the common problem of author misidentification".ResearcherID enables data exchange between its database and ORCID, and vice versa.SeaLifeBase
SeaLifeBase is a global online database of information about marine life. It aims to provide key information on the taxonomy, distribution and ecology of all marine species in the world apart from finfish. SeaLifeBase is in partnership with the WorldFish Center in Malaysia and the UBC Fisheries Centre at the University of British Columbia. Daniel Pauly is the principal investigator and it is coordinated by Maria Lourdes D. Palomares. As of October 2016, it included descriptions of 74,000 species, 47,700 common names, 12,400 pictures, and references to 31,700 works in the scientific literature. SeaLifeBase complements FishBase, which provides parallel information for finfish.Secondary source
In scholarship, a secondary source is a document or recording that relates or discusses information originally presented elsewhere. A secondary source contrasts with a primary source, which is an original source of the information being discussed; a primary source can be a person with direct knowledge of a situation, or a document created by such a person.
A secondary source is one that gives information about a primary source. In this source, the original information is selected, modified and arranged in a suitable format. Secondary sources involve generalization, analysis, interpretation, or evaluation of the original information.
The most accurate classification for any given source is not always obvious. Primary and secondary are relative terms, and some sources may be classified as primary or secondary, depending on how they are used. A third level, the tertiary source, such as an encyclopedia or dictionary, resembles a secondary source in that it contains analysis, but attempts to provide a broad introductory overview of a topic.Tertiary source
A tertiary source is an index or textual consolidation of primary and secondary sources. Some tertiary sources are not to be used for academic research, unless they can also be used as secondary sources, or to find other sources.Text mining
Text mining, also referred to as text data mining, roughly equivalent to text analytics, is the process of deriving high-quality information from text. High-quality information is typically derived through the devising of patterns and trends through means such as statistical pattern learning. Text mining usually involves the process of structuring the input text (usually parsing, along with the addition of some derived linguistic features and the removal of others, and subsequent insertion into a database), deriving patterns within the structured data, and finally evaluation and interpretation of the output. 'High quality' in text mining usually refers to some combination of relevance, novelty, and interest. Typical text mining tasks include text categorization, text clustering, concept/entity extraction, production of granular taxonomies, sentiment analysis, document summarization, and entity relation modeling (i.e., learning relations between named entities).
Text analysis involves information retrieval, lexical analysis to study word frequency distributions, pattern recognition, tagging/annotation, information extraction, data mining techniques including link and association analysis, visualization, and predictive analytics. The overarching goal is, essentially, to turn text into data for analysis, via application of natural language processing (NLP) and analytical methods.
A typical application is to scan a set of documents written in a natural language and either model the document set for predictive classification purposes or populate a database or search index with the information extracted.ZooBank
ZooBank is an open access website intended to be the official International Commission on Zoological Nomenclature (ICZN) registry of zoological nomenclature. Any nomenclatural acts (e.g. publications that create or change a taxonomic name) need to be registered with ZooBank to be "officially" recognized by the ICZN Code of Nomenclature.
Life Science Identifiers (LSIDs) are used as the globally unique identifier for ZooBank registration entries.The ZooBank prototype was seeded with data from Index to Organism Names, which was compiled from the scientific literature in Zoological Record now owned by Thomson Reuters.
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