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  GCube system

  gCube is an open source software system specifically designed and developed to enact the building and operation of a Data Infrastructure providing their users with a rich array of services suitable for supporting the co-creation of Virtual Research Environments and promoting the implementation of open science workflows and practices. It is at the heart of the D4Science Data Infrastructure. == Overview == It is primarily organised in a number of web service called to offer functionality supporting the phases of knowledge production and sharing. In addition, it consists of a set of software libraries supporting service development, service-to-service integration, and service capabilities extension, and a set of portlets dedicated to realise user interface constituents facilitating the exploitation of one or more services. It is designed and conceived to enact system of systems. In fact, its gCube services rely on standards and mediators to interact with other services as well as are made available by standard and APIs to make it possible for clients to use them. For instance, the DataMiner service implements the Web Processing Service protocol to facilitate clients to execute processes. The set of components dealing with Identity and Access Management rely on Keycloak and federates other IDMs thus making the overall Authentication and the Authorization management compliant with open standards such as OAuth2, User-Managed Access (UMA), and OpenID Connect (OIDC)protocols. The Catalogue relies on DCAT, OAI-PMH, and Catalogue Service for the Web to collect contents from other catalogues and data sources and offers its content by DCAT, OAI-PMH, and a proprietary REST API (gCat REST API). Its Continuous Integration/Continuous Delivery pipeline implemented by Jenkins represents an innovative approach to software delivering conceived to be scalable and easy to maintain and upgrade at a minimal cost. == History == gCube has been developed in the context of the D4Science initiative with the support of several EU projects.

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  Behavior selection algorithm

  In artificial intelligence, a behavior selection algorithm, or action selection algorithm, is an algorithm that selects appropriate behaviors or actions for one or more intelligent agents. In game artificial intelligence, it selects behaviors or actions for one or more non-player characters. Common behavior selection algorithms include: Finite-state machines Hierarchical finite-state machines Decision trees Behavior trees Hierarchical task networks Hierarchical control systems Utility systems Dialogue tree (for selecting what to say) == Related concepts == In application programming, run-time selection of the behavior of a specific method is referred to as the strategy design pattern.

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  Car–Parrinello molecular dynamics

  Car–Parrinello molecular dynamics (CPMD) refers to either a method used in molecular dynamics (also known as the Car–Parrinello method) or the computational chemistry software package used to implement this method. The CPMD method is one of the major methods for calculating ab initio molecular dynamics (ab initio MD or AIMD). Ab initio molecular dynamics (AIMD) is a computational method that uses first principles through quantum mechanics to simulate the motion of atoms in a system. It is a type of molecular dynamics (MD) simulation that does not rely on empirical potentials or force fields to describe the interactions between atoms, but rather calculates these interactions entirely from the electronic structure of the system using quantum mechanics. In an ab initio MD simulation, the total energy of the system is calculated at each time step using density functional theory (DFT), Hartree-Fock (HF), or other electronic structure calculation methods. The forces acting on each atom are then determined from the gradient of the energy with respect to the atomic coordinates, and the equations of motion are solved to predict the trajectory of the atoms. AIMD permits chemical bond breaking and forming events to occur and accounts for electronic polarization effect. Therefore, Ab initio MD simulations can be used to study a wide range of phenomena, including the structural, thermodynamic, and dynamic properties of materials and chemical reactions. They are particularly useful for systems that are not well described by empirical potentials or force fields, such as systems with strong electronic correlation or systems with many degrees of freedom. However, ab initio MD simulations are computationally demanding and require significant computational resources. The CPMD method is related to the more common Born–Oppenheimer molecular dynamics (BOMD) method in that the quantum mechanical effect of the electrons is included in the calculation of energy and forces for the classical motion of the nuclei. CPMD and BOMD are different types of AIMD. However, whereas BOMD treats the electronic structure problem within the time-independent Schrödinger equation, CPMD explicitly includes the electrons as active degrees of freedom, via (fictitious) dynamical variables. The software is a parallelized plane wave / pseudopotential implementation of density functional theory, particularly designed for ab initio molecular dynamics. == Car–Parrinello method == The Car–Parrinello method is a type of molecular dynamics, usually employing periodic boundary conditions, planewave basis sets, and density functional theory, proposed by Roberto Car and Michele Parrinello in 1985 while working at SISSA, who were subsequently awarded the Dirac Medal by ICTP in 2009. In contrast to Born–Oppenheimer molecular dynamics wherein the nuclear (ions) degree of freedom are propagated using ionic forces which are calculated at each iteration by approximately solving the electronic problem with conventional matrix diagonalization methods, the Car–Parrinello method explicitly introduces the electronic degrees of freedom as (fictitious) dynamical variables, writing an extended Lagrangian for the system which leads to a system of coupled equations of motion for both ions and electrons. In this way, an explicit electronic minimization at each time step, as done in Born–Oppenheimer MD, is not needed: after an initial standard electronic minimization, the fictitious dynamics of the electrons keeps them on the electronic ground state corresponding to each new ionic configuration visited along the dynamics, thus yielding accurate ionic forces. In order to maintain this adiabaticity condition, it is necessary that the fictitious mass of the electrons is chosen small enough to avoid a significant energy transfer from the ionic to the electronic degrees of freedom. This small fictitious mass in turn requires that the equations of motion are integrated using a smaller time step than the one (1–10 fs) commonly used in Born–Oppenheimer molecular dynamics. Currently, the CPMD method can be applied to systems that consist of a few tens or hundreds of atoms and access timescales on the order of tens of picoseconds. == General approach == In CPMD the core electrons are usually described by a pseudopotential and the wavefunction of the valence electrons are approximated by a plane wave basis set. The ground state electronic density (for fixed nuclei) is calculated self-consistently, usually using the density functional theory method. Kohn-Sham equations are often used to calculate the electronic structure, where electronic orbitals are expanded in a plane-wave basis set. Then, using that density, forces on the nuclei can be computed, to update the trajectories (using, e.g. the Verlet integration algorithm). In addition, however, the coefficients used to obtain the electronic orbital functions can be treated as a set of extra spatial dimensions, and trajectories for the orbitals can be calculated in this context. == Fictitious dynamics == CPMD is an approximation of the Born–Oppenheimer MD (BOMD) method. In BOMD, the electrons' wave function must be minimized via matrix diagonalization at every step in the trajectory. CPMD uses fictitious dynamics to keep the electrons close to the ground state, preventing the need for a costly self-consistent iterative minimization at each time step. The fictitious dynamics relies on the use of a fictitious electron mass (usually in the range of 400 – 800 a.u.) to ensure that there is very little energy transfer from nuclei to electrons, i.e. to ensure adiabaticity. Any increase in the fictitious electron mass resulting in energy transfer would cause the system to leave the ground-state BOMD surface. === Lagrangian === L = 1 2 ( ∑ I n u c l e i M I R ˙ I 2 + μ ∑ i o r b i t a l s ∫ d r | ψ ˙ i ( r , t ) | 2 ) − E [ { ψ i } , { R I } ] + ∑ i j Λ i j ( ∫ d r ψ i ψ j − δ i j ) , {\displaystyle {\mathcal {L}}={\frac {1}{2}}\left(\sum _{I}^{\mathrm {nuclei} }\ M_{I}{\dot {\mathbf {R} }}_{I}^{2}+\mu \sum _{i}^{\mathrm {orbitals} }\int d\mathbf {r} \ |{\dot {\psi }}_{i}(\mathbf {r} ,t)|^{2}\right)-E\left[\{\psi _{i}\},\{\mathbf {R} _{I}\}\right]+\sum _{ij}\Lambda _{ij}\left(\int d\mathbf {r} \ \psi _{i}\psi _{j}-\delta _{ij}\right),} where μ {\displaystyle \mu } is the fictitious mass parameter; E[{ψi},{RI}] is the Kohn–Sham energy density functional, which outputs energy values when given Kohn–Sham orbitals and nuclear positions. === Orthogonality constraint === ∫ d r ψ i ∗ ( r , t ) ψ j ( r , t ) = δ i j , {\displaystyle \int d\mathbf {r} \ \psi _{i}^{}(\mathbf {r} ,t)\psi _{j}(\mathbf {r} ,t)=\delta _{ij},} where δij is the Kronecker delta. === Equations of motion === The equations of motion are obtained by finding the stationary point of the Lagrangian under variations of ψi and RI, with the orthogonality constraint. M I R ¨ I = − ∇ I E [ { ψ i } , { R I } ] {\displaystyle M_{I}{\ddot {\mathbf {R} }}_{I}=-\nabla _{I}\,E\left[\{\psi _{i}\},\{\mathbf {R} _{I}\}\right]} μ ψ ¨ i ( r , t ) = − δ E δ ψ i ∗ ( r , t ) + ∑ j Λ i j ψ j ( r , t ) , {\displaystyle \mu {\ddot {\psi }}_{i}(\mathbf {r} ,t)=-{\frac {\delta E}{\delta \psi _{i}^{}(\mathbf {r} ,t)}}+\sum _{j}\Lambda _{ij}\psi _{j}(\mathbf {r} ,t),} where Λij is a Lagrangian multiplier matrix to comply with the orthonormality constraint. === Born–Oppenheimer limit === In the formal limit where μ → 0, the equations of motion approach Born–Oppenheimer molecular dynamics. == Software packages == There are a number of software packages available for performing AIMD simulations. Some of the most widely used packages include: CP2K: an open-source software package for AIMD. Quantum Espresso: an open-source package for performing DFT calculations. It includes a module for AIMD. VASP: a commercial software package for performing DFT calculations. It includes a module for AIMD. Gaussian: a commercial software package that can perform AIMD. NWChem: an open-source software package for AIMD. LAMMPS: an open-source software package for performing classical and ab initio MD simulations. SIESTA: an open-source software package for AIMD. ORCA: a general-purpose quantum chemistry package. == Applications == Studying the behavior of water across different environments, such as near a hydrophobic graphene sheet. Investigating the structure and dynamics of liquid water at ambient temperature. Solving the heat transfer problems (heat conduction and thermal radiation), such as in Si/Ge superlattices. Probing the proton transfer along hydrogen-bonds in different environments, such as in 1D water chains inside carbon nanotubes. Evaluating the critical point of crystals, composites, and solid-state materials, such as aluminum. Predicting and modelling different phases and phase transitions, such as in the amorphous phase of the phase-change memory material GeSbTe. Studying the combustion of combustibles, such as lignite-water systems. Measuring th

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  Data quality

  Data quality refers to the state of qualitative or quantitative pieces of information. There are many definitions of data quality, but data is generally considered high quality if it is "fit for [its] intended uses in operations, decision making and planning". Data is deemed of high quality if it correctly represents the real-world construct to which it refers. Apart from these definitions, as the number of data sources increases, the question of internal data consistency becomes significant, regardless of fitness for use for any particular external purpose. People's views on data quality can often be in disagreement, even when discussing the same set of data used for the same purpose. When this is the case, businesses may adopt recognised international standards for data quality (See #International Standards for Data Quality below). Data governance can also be used to form agreed upon definitions and standards, including international standards, for data quality. In such cases, data cleansing, including standardization, may be required in order to ensure data quality. == Definitions == Defining data quality is difficult due to the many contexts data are used in, as well as the varying perspectives among end users, producers, and custodians of data. From a consumer perspective, data quality is: "data that are fit for use by data consumers" data "meeting or exceeding consumer expectations" data that "satisfies the requirements of its intended use" From a business perspective, data quality is: data that are "'fit for use' in their intended operational, decision-making and other roles" or that exhibits "'conformance to standards' that have been set, so that fitness for use is achieved" data that "are fit for their intended uses in operations, decision making and planning" "the capability of data to satisfy the stated business, system, and technical requirements of an enterprise" From a standards-based perspective, data quality is: the "degree to which a set of inherent characteristics (quality dimensions) of an object (data) fulfills requirements" "the usefulness, accuracy, and correctness of data for its application" Arguably, in all these cases, "data quality" is a comparison of the actual state of a particular set of data to a desired state, with the desired state being typically referred to as "fit for use," "to specification," "meeting consumer expectations," "free of defect," or "meeting requirements." These expectations, specifications, and requirements are usually defined by one or more individuals or groups, standards organizations, laws and regulations, business policies, or software development policies. == Dimensions of data quality == Drilling down further, those expectations, specifications, and requirements are stated in terms of characteristics or dimensions of the data, such as: accessibility or availability accuracy or correctness comparability completeness or comprehensiveness consistency, coherence, or clarity credibility, reliability, or reputation flexibility plausibility relevance, pertinence, or usefulness timeliness or latency uniqueness validity or reasonableness A systematic scoping review of the literature suggests that data quality dimensions and methods with real world data are not consistent in the literature, and as a result quality assessments are challenging due to the complex and heterogeneous nature of these data. == International standards for data quality == ISO 8000 is an international standard for data quality. Managed by the International Organization for Standardization, the ISO 8000 standards address and describe general aspects of data quality including principles, vocabulary and measurement data governance data quality management data quality assessment quality of master data, including exchange of characteristic data and identifiers quality of industrial data == History == Before the rise of the inexpensive computer data storage, massive mainframe computers were used to maintain name and address data for delivery services. This was so that mail could be properly routed to its destination. The mainframes used business rules to correct common misspellings and typographical errors in name and address data, as well as to track customers who had moved, died, gone to prison, married, divorced, or experienced other life-changing events. Government agencies began to make postal data available to a few service companies to cross-reference customer data with the National Change of Address registry (NCOA). This technology saved large companies millions of dollars in comparison to manual correction of customer data. Large companies saved on postage, as bills and direct marketing materials made their way to the intended customer more accurately. Initially sold as a service, data quality moved inside the walls of corporations, as low-cost and powerful server technology became available. Companies with an emphasis on marketing often focused their quality efforts on name and address information, but data quality is recognized as an important property of all types of data. Principles of data quality can be applied to supply chain data, transactional data, and nearly every other category of data found. For example, making supply chain data conform to a certain standard has value to an organization by: 1) avoiding overstocking of similar but slightly different stock; 2) avoiding false stock-out; 3) improving the understanding of vendor purchases to negotiate volume discounts; and 4) avoiding logistics costs in stocking and shipping parts across a large organization. For companies with significant research efforts, data quality can include developing protocols for research methods, reducing measurement error, bounds checking of data, cross tabulation, modeling and outlier detection, verifying data integrity, etc. == Overview == There are a number of theoretical frameworks for understanding data quality. A systems-theoretical approach influenced by American pragmatism expands the definition of data quality to include information quality, and emphasizes the inclusiveness of the fundamental dimensions of accuracy and precision on the basis of the theory of science (Ivanov, 1972). One framework, dubbed "Zero Defect Data" (Hansen, 1991) adapts the principles of statistical process control to data quality. Another framework seeks to integrate the product perspective (conformance to specifications) and the service perspective (meeting consumers' expectations) (Kahn et al. 2002). Another framework is based in semiotics to evaluate the quality of the form, meaning and use of the data (Price and Shanks, 2004). One highly theoretical approach analyzes the ontological nature of information systems to define data quality rigorously (Wand and Wang, 1996). A considerable amount of data quality research involves investigating and describing various categories of desirable attributes (or dimensions) of data. Nearly 200 such terms have been identified and there is little agreement in their nature (are these concepts, goals or criteria?), their definitions or measures (Wang et al., 1993). Software engineers may recognize this as a similar problem to "ilities". MIT has an Information Quality (MITIQ) Program, led by Professor Richard Wang, which produces a large number of publications and hosts a significant international conference in this field (International Conference on Information Quality, ICIQ). This program grew out of the work done by Hansen on the "Zero Defect Data" framework (Hansen, 1991). In practice, data quality is a concern for professionals involved with a wide range of information systems, ranging from data warehousing and business intelligence to customer relationship management and supply chain management. One industry study estimated the total cost to the U.S. economy of data quality problems at over U.S. $600 billion per annum (Eckerson, 2002). Incorrect data – which includes invalid and outdated information – can originate from different data sources – through data entry, or data migration and conversion projects. In 2002, the USPS and PricewaterhouseCoopers released a report stating that 23.6 percent of all U.S. mail sent is incorrectly addressed. One reason contact data becomes stale very quickly in the average database – more than 45 million Americans change their address every year. In fact, the problem is such a concern that companies are beginning to set up a data governance team whose sole role in the corporation is to be responsible for data quality. In some organizations, this data governance function has been established as part of a larger Regulatory Compliance function - a recognition of the importance of Data/Information Quality to organizations. Problems with data quality don't only arise from incorrect data; inconsistent data is a problem as well. Eliminating data shadow systems and centralizing data in a warehouse is one of the initiatives a company can take to ensure data consistency. En

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  Quack.com

  Quack.com was an early voice portal company. The domain name later was used for Quack, an iPad search application from AOL. == History == It was founded in 1998 by Steven Woods, Jeromy Carriere and Alex Quilici as a Pittsburgh, Pennsylvania, USA, based voice portal infrastructure company named Quackware. Quack was the first company to try to create a voice portal: a consumer-based destination "site" in which consumers could not only access information by voice alone, but also complete transactions. Quackware launched a beta phone service in 1999 that allowed consumers to purchase books from sites such as Amazon and CDs from sites such as CDNow by answering a short set of questions. Quack followed with a set of information services from movie listings (inspired by, but expanding upon, Moviefone) to news, weather and stock quotes. This concept introduced a series of lookalike startups including Tellme Networks which raised more money than any Internet startup in history on a similar concept. Quack received its first venture funding from HDL Capital in 1999 and moved operations to Mountain View in Silicon Valley, California in 1999. A deal with Lycos was announced in May 2000. In September 2000 Quack was acquired for $200 million by America Online (AOL) and moved onto the Netscape campus with what was left of the Netscape team. Quack was attacked in the Canadian press for being representative of the Canadian "brain drain" to the US during the Internet bubble, focusing its recruiting efforts on the University of Waterloo, hiring more than 50 engineers from Waterloo in less than 10 months. Quack competitor Tellme Networks raised enormous funds in what became a highly competitive market in 2000, with the emergence of more than a dozen additional competitors in a 12-month period. Following its acquisition by America Online in an effort led by Ted Leonsis to bring Quack into AOL Interactive, the Quack voice service became AOLbyPhone as one of AOL's "web properties" along with MapQuest, Moviefone and others. Quack secured several patents that underlie the technical challenges of delivering interactive voice services. Constructing a voice portal required integrations and innovations not only in speech recognition and speech generation, but also in databases, application specification, constraint-based reasoning and artificial intelligence and computational linguistics. "Quack"'s name derived from the company goal of providing not only voice-based services, but more broadly "Quick Ubiquitous Access to Consumer Knowledge". The patents assigned to Quack.com include: System and method for voice access to Internet-based information, System and method for advertising with an Internet Voice Portal and recognizing the axiom that in interactive voice systems one must "know the set of possible answers to a question before asking it". System and method for determining if one web site has the same information as another web site. Quack.com was spoofed in The Simpsons in March 2002 in the episode "Blame It on Lisa" in which a "ComQuaak" sign is replaced by another equally crazy telecom company name. == 2010 onwards == In July 2010, quack.com became the focus of a new AOL iPad application, that was a web search experience. The product delivers web results and blends in picture, video and Twitter results. It enables you to preview the web results before you go to the site, search within each result, and flip through the results pages, making full use of the iPad's touch screen features. The iPad app was free via iTunes, but support discontinued in 2012.

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  Systematic review

  A systematic review is a scholarly synthesis of the evidence on a clearly presented topic using critical methods to identify, define and assess research on the topic. A systematic review extracts and interprets data from published studies on the topic (in the scientific literature), then analyzes, describes, critically appraises and summarizes interpretations into a refined evidence-based conclusion. For example, a systematic review of randomized controlled trials is a way of summarizing and implementing evidence-based medicine. Systematic reviews, sometimes along with meta-analyses, are generally considered the highest level of evidence in medical research. While a systematic review may be applied in the biomedical or health care context, it may also be used where an assessment of a precisely defined subject can advance understanding in a field of research. A systematic review may examine clinical tests, public health interventions, environmental interventions, social interventions, adverse effects, qualitative evidence syntheses, methodological reviews, policy reviews, and economic evaluations. Systematic reviews are closely related to meta-analyses, and often the same instance will combine both (being published with a subtitle of "a systematic review and meta-analysis"). The distinction between the two is that a meta-analysis uses statistical methods to induce a single number from the pooled data set (such as an effect size), whereas the strict definition of a systematic review excludes that step. However, in practice, when one is mentioned, the other may often be involved, as it takes a systematic review to assemble the information that a meta-analysis analyzes, and people sometimes refer to an instance as a systematic review, even if it includes the meta-analytical component. An understanding of systematic reviews and how to implement them in practice is common for professionals in health care, public health, and public policy. Systematic reviews contrast with a type of review often called a narrative review. Systematic reviews and narrative reviews both review the literature (the scientific literature), but the term literature review without further specification refers to a narrative review. == Characteristics == A systematic review can be designed to provide a thorough summary of current literature relevant to a research question. A systematic review uses a rigorous and transparent approach for research synthesis, with the aim of assessing and, where possible, minimizing bias in the findings. While many systematic reviews are based on an explicit quantitative meta-analysis of available data, there are also qualitative reviews and other types of mixed-methods reviews that adhere to standards for gathering, analyzing, and reporting evidence. Systematic reviews of quantitative data or mixed-method reviews sometimes use statistical techniques (meta-analysis) to combine results of eligible studies. Scoring levels are sometimes used to rate the quality of the evidence depending on the methodology used, although this is discouraged by the Cochrane Library. As evidence rating can be subjective, multiple people may be consulted to resolve any scoring differences between how evidence is rated. The EPPI-Centre, Cochrane, and the Joanna Briggs Institute have been influential in developing methods for combining both qualitative and quantitative research in systematic reviews. Several reporting guidelines exist to standardise reporting about how systematic reviews are conducted. Such reporting guidelines are not quality assessment or appraisal tools. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement suggests a standardized way to ensure a transparent and complete reporting of systematic reviews, and is now required for this kind of research by more than 170 medical journals worldwide. The latest version of this commonly used statement corresponds to PRISMA 2020 (the respective article was published in 2021). Several specialized PRISMA guideline extensions have been developed to support particular types of studies or aspects of the review process, including PRISMA-P for review protocols and PRISMA-ScR for scoping reviews. A list of PRISMA guideline extensions is hosted by the EQUATOR (Enhancing the QUAlity and Transparency Of health Research) Network. However, the PRISMA guidelines have been found to be limited to intervention research and the guidelines have to be changed in order to fit non-intervention research. As a result, Non-Interventional, Reproducible, and Open (NIRO) Systematic Reviews was created to counter this limitation. For qualitative reviews, reporting guidelines include ENTREQ (Enhancing transparency in reporting the synthesis of qualitative research) for qualitative evidence syntheses; RAMESES (Realist And MEta-narrative Evidence Syntheses: Evolving Standards) for meta-narrative and realist reviews; and eMERGe (Improving reporting of Meta-Ethnography) for meta-ethnograph. Developments in systematic reviews during the 21st century included realist reviews and the meta-narrative approach, both of which addressed problems of variation in methods and heterogeneity existing on some subjects. == Types == There are over 30 types of systematic review and Table 1 below non-exhaustingly summarises some of these. There is not always consensus on the boundaries and distinctions between the approaches described below. === Scoping reviews === Scoping reviews are distinct from systematic reviews in several ways. A scoping review is an attempt to search for concepts by mapping the language and data which surrounds those concepts and adjusting the search method iteratively to synthesize evidence and assess the scope of an area of inquiry. This can mean that the concept search and method (including data extraction, organisation and analysis) are refined throughout the process, sometimes requiring deviations from any protocol or original research plan. A scoping review may often be a preliminary stage before a systematic review, which 'scopes' out an area of inquiry and maps the language and key concepts to determine if a systematic review is possible or appropriate, or to lay the groundwork for a full systematic review. The goal can be to assess how much data or evidence is available regarding a certain area of interest. This process is further complicated if it is mapping concepts across multiple languages or cultures. As a scoping review should be systematically conducted and reported (with a transparent and repeatable method), some academic publishers categorize them as a kind of 'systematic review', which may cause confusion. Scoping reviews are helpful when it is not possible to carry out a systematic synthesis of research findings, for example, when there are no published clinical trials in the area of inquiry. Scoping reviews are helpful when determining if it is possible or appropriate to carry out a systematic review, and are a useful method when an area of inquiry is very broad, for example, exploring how the public are involved in all stages systematic reviews. There is still a lack of clarity when defining the exact method of a scoping review as it is both an iterative process and is still relatively new. There have been several attempts to improve the standardisation of the method, for example via a Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline extension for scoping reviews (PRISMA-ScR). PROSPERO (the International Prospective Register of Systematic Reviews) does not permit the submission of protocols of scoping reviews, although some journals will publish protocols for scoping reviews. == Stages == While there are multiple kinds of systematic review methods, the main stages of a review can be summarised as follows: === Defining the research question === Some reported that the 'best practices' involve 'defining an answerable question' and publishing the protocol of the review before initiating it to reduce the risk of unplanned research duplication and to enable transparency and consistency between methodology and protocol. Clinical reviews of quantitative data are often structured using the mnemonic PICO, which stands for 'Population or Problem', 'Intervention or Exposure', 'Comparison', and 'Outcome', with other variations existing for other kinds of research. For qualitative reviews, PICo is 'Population or Problem', 'Interest', and 'Context'. === Searching for sources === Relevant criteria can include selecting research that is of good quality and answers the defined question. The search strategy should be designed to retrieve literature that matches the protocol's specified inclusion and exclusion criteria. The methodology section of a systematic review should list all of the databases and citation indices that were searched. The titles and abstracts of identified articles can be checked against predetermined criteria for eligibility and r

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  Weak stability boundary

  Weak stability boundary (WSB), including low-energy transfer, is a concept introduced by Edward Belbruno in 1987. The concept explained how a spacecraft could change orbits using very little fuel. Weak stability boundary is defined for the three-body problem. This problem considers the motion of a particle P of negligible mass moving with respect to two larger bodies, P1, P2, modeled as point masses, where these bodies move in circular or elliptical orbits with respect to each other, and P2 is smaller than P1. The force between the three bodies is the classical Newtonian gravitational force. For example, P1 is the Earth, P2 is the Moon and P is a spacecraft; or P1 is the Sun, P2 is Jupiter and P is a comet, etc. This model is called the restricted three-body problem. The weak stability boundary defines a region about P2 where P is temporarily captured. This region is in position-velocity space. Capture means that the Kepler energy between P and P2 is negative. This is also called weak capture. == Background == This boundary was defined for the first time by Edward Belbruno of Princeton University in 1987. He described a Low-energy transfer which would allow a spacecraft to change orbits using very little fuel. It was for motion about Moon (P2) with P1 = Earth. It is defined algorithmically by monitoring cycling motion of P about the Moon and finding the region where cycling motion transitions between stable and unstable after one cycle. Stable motion means P can completely cycle about the Moon for one cycle relative to a reference section, starting in weak capture. P needs to return to the reference section with negative Kepler energy. Otherwise, the motion is called unstable, where P does not return to the reference section within one cycle or if it returns, it has non-negative Kepler energy. The set of all transition points about the Moon comprises the weak stability boundary, W. The motion of P is sensitive or chaotic as it moves about the Moon within W. A mathematical proof that the motion within W is chaotic was given in 2004. This is accomplished by showing that the set W about an arbitrary body P2 in the restricted three-body problem contains a hyperbolic invariant set of fractional dimension consisting of the infinitely many intersections Hyperbolic manifolds. The weak stability boundary was originally referred to as the fuzzy boundary. This term was used since the transition between capture and escape defined in the algorithm is not well defined and limited by the numerical accuracy. This defines a "fuzzy" location for the transition points. It is also due the inherent chaos in the motion of P near the transition points. It can be thought of as a fuzzy chaos region. As is described in an article in Discover magazine, the WSB can be roughly viewed as the fuzzy edge of a region, referred to as a gravity well, about a body (the Moon), where its force of gravity becomes small enough to be dominated by force of gravity of another body (the Earth) and the motion there is chaotic. A much more general algorithm defining W was given in 2007. It defines W relative to n-cycles, where n = 1,2,3,..., yielding boundaries of order n. This gives a much more complex region consisting of the union of all the weak stability boundaries of order n. This definition was explored further in 2010. The results suggested that W consists, in part, of the hyperbolic network of invariant manifolds associated to the Lyapunov orbits about the L1, L2 Lagrange points near P2. The explicit determination of the set W about P2 = Jupiter, where P1 is the Sun, is described in "Computation of Weak Stability Boundaries: Sun-Jupiter Case". It turns out that a weak stability region can also be defined relative to the larger mass point, P1. A proof of the existence of the weak stability boundary about P1 was given in 2012, but a different definition is used. The chaos of the motion is analytically proven in "Geometry of Weak Stability Boundaries". The boundary is studied in "Applicability and Dynamical Characterization of the Associated Sets of the Algorithmic Weak Stability Boundary in the Lunar Sphere of Influence". == Applications == There are a number of important applications for the weak stability boundary (WSB). Since the WSB defines a region of temporary capture, it can be used, for example, to find transfer trajectories from the Earth to the Moon that arrive at the Moon within the WSB region in weak capture, which is called ballistic capture for a spacecraft. No fuel is required for capture in this case. This was numerically demonstrated in 1987. This is the first reference for ballistic capture for spacecraft and definition of the weak stability boundary. The boundary was operationally demonstrated to exist in 1991 when it was used to find a ballistic capture transfer to the Moon for Japan's Hiten spacecraft. Other missions have used the same transfer type as Hiten, including Grail, Capstone, Danuri, Hakuto-R Mission 1 and SLIM. The WSB for Mars is studied in "Earth-Mars Transfers with Ballistic Capture" and ballistic capture transfers to Mars are computed. The BepiColombo mission of ESA should achieve ballistic capture at the WSB of Mercury in November 2026. The WSB region can be used in the field of Astrophysics. It can be defined for stars within open star clusters. This is done in "Chaotic Exchange of Solid Material Between Planetary Systems: Implications for the Lithopanspermia Hypothesis" to analyze the capture of solid material that may have arrived on the Earth early in the age of the Solar System to study the validity of the lithopanspermia hypothesis. Numerical explorations of trajectories for P starting in the WSB region about P2 show that after the particle P escapes P2 at the end of weak capture, it moves about the primary body, P1, in a near resonant orbit, in resonance with P2 about P1. This property was used to study comets that move in orbits about the Sun in orbital resonance with Jupiter, which change resonance orbits by becoming weakly captured by Jupiter. An example of such a comet is 39P/Oterma. This property of change of resonance of orbits about P1 when P is weakly captured by the WSB of P2 has an interesting application to the field of quantum mechanics to the motion of an electron about the proton in a hydrogen atom. The transition motion of an electron about the proton between different energy states described by the Schrödinger equation is shown to be equivalent to the change of resonance of P about P1 via weak capture by P2 for a family of transitioning resonance orbits. This gives a classical model using chaotic dynamics with Newtonian gravity for the motion of an electron.

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  Overcategorization

  Overcategorization or category clutter is a phenomenon during classification where too many categories or classes are assigned to a document, record, or item. Overcategorization is related to the library and information science (LIS) concepts of document classification and subject indexing. It is also related to online shopping where excessive product categories can overwhelm users with too many choices or make it more difficult for customers to find the products they need. Although these categories are intended to improve organization and ease of navigation when shipping online, too many categories can lower customer satisfaction, increase difficulty navigating the online store, and reduce future shopping intentions. In LIS, the ideal number of terms that should be assigned to classify an item are measured by the variables precision and recall. Assigning few category labels that are most closely related to the content of the item being classified will result in searches that have high precision, I.e., where a high proportion of the results are closely related to the query. Assigning more category labels to each item will reduce the precision of each search, but increase the recall, retrieving more relevant results. Related LIS concepts include exhaustivity of indexing and information overload. == Basic principles == If too many categories are assigned to a given document, the implications for users depend on how informative the links are. If the user is able to distinguish between useful and not useful links, the damage is limited: The user only wastes time selecting links. In many cases, however, the user cannot judge whether or not a given link will turn out to be fruitful. In that case he or she has to follow the link and to read or skim another document. The worst case scenario is, of course, that even after reading the new document the user is unable to decide whether or not it might be useful if its subject matter is not thoroughly investigated. Overcategorization also has another unpleasant implication: It makes the system (for example in Wikipedia) difficult to maintain in a consistent way. If the system is inconsistent, it means that when the user considers the links in a given category, he or she will not find all documents relevant to that category. Basically, the problem of overcategorization should be understood from the perspective of relevance and the traditional measures of recall and precision. If too few relevant categories are assigned to a document, recall may decrease. If too many non-relevant categories are assigned, precision becomes lower. The hard job is to say which categories are fruitful or relevant for future use of the document.

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  Learning to rank

  Learning to rank (LTR) or machine-learned ranking (MLR) is the application of machine learning, often supervised, semi-supervised or reinforcement learning, in the construction of ranking models for information retrieval and recommender systems. Training data may, for example, consist of lists of items with some partial order specified between items in each list. This order is typically induced by giving a numerical or ordinal score or a binary judgment (e.g. "relevant" or "not relevant") for each item. The goal of constructing the ranking model is to rank new, unseen lists in a similar way to rankings in the training data. == Applications == === In information retrieval === Ranking is a central part of many information retrieval problems, such as document retrieval, collaborative filtering, sentiment analysis, and online advertising. A possible architecture of a machine-learned search engine is shown in the accompanying figure. Training data consists of queries and documents matching them together with the relevance degree of each match. It may be prepared manually by human assessors (or raters, as Google calls them), who check results for some queries and determine relevance of each result. It is not feasible to check the relevance of all documents, and so typically a technique called pooling is used — only the top few documents, retrieved by some existing ranking models are checked. This technique may introduce selection bias. Alternatively, training data may be derived automatically by analyzing clickthrough logs (i.e. search results which got clicks from users), query chains, or such search engines' features as Google's (since-replaced) SearchWiki. Clickthrough logs can be biased by the tendency of users to click on the top search results on the assumption that they are already well-ranked. Training data is used by a learning algorithm to produce a ranking model which computes the relevance of documents for actual queries. Typically, users expect a search query to complete in a short time (such as a few hundred milliseconds for web search), which makes it impossible to evaluate a complex ranking model on each document in the corpus, and so a two-phase scheme is used. First, a small number of potentially relevant documents are identified using simpler retrieval models which permit fast query evaluation, such as the vector space model, Boolean model, weighted AND, or BM25. This phase is called top- k {\displaystyle k} document retrieval and many heuristics were proposed in the literature to accelerate it, such as using a document's static quality score and tiered indexes. In the second phase, a more accurate but computationally expensive machine-learned model is used to re-rank these documents. === In other areas === Learning to rank algorithms have been applied in areas other than information retrieval: In machine translation for ranking a set of hypothesized translations; In computational biology for ranking candidate 3-D structures in protein structure prediction problems; In recommender systems for identifying a ranked list of related news articles to recommend to a user after he or she has read a current news article. == Feature vectors == For the convenience of MLR algorithms, query-document pairs are usually represented by numerical vectors, which are called feature vectors. Such an approach is sometimes called bag of features and is analogous to the bag of words model and vector space model used in information retrieval for representation of documents. Components of such vectors are called features, factors or ranking signals. They may be divided into three groups (features from document retrieval are shown as examples): Query-independent or static features — those features, which depend only on the document, but not on the query. For example, PageRank or document's length. Such features can be precomputed in off-line mode during indexing. They may be used to compute document's static quality score (or static rank), which is often used to speed up search query evaluation. Query-dependent or dynamic features — those features, which depend both on the contents of the document and the query, such as TF-IDF score or other non-machine-learned ranking functions. Query-level features or query features, which depend only on the query. For example, the number of words in a query. Some examples of features, which were used in the well-known LETOR dataset: TF, TF-IDF, BM25, and language modeling scores of document's zones (title, body, anchors text, URL) for a given query; Lengths and IDF sums of document's zones; Document's PageRank, HITS ranks and their variants. Selecting and designing good features is an important area in machine learning, which is called feature engineering. == Evaluation measures == There are several measures (metrics) which are commonly used to judge how well an algorithm is doing on training data and to compare the performance of different MLR algorithms. Often a learning-to-rank problem is reformulated as an optimization problem with respect to one of these metrics. Examples of ranking quality measures: Mean average precision (MAP); DCG and NDCG; Precision@n, NDCG@n, where "@n" denotes that the metrics are evaluated only on top n documents; Mean reciprocal rank; Kendall's tau; Spearman's rho. DCG and its normalized variant NDCG are usually preferred in academic research when multiple levels of relevance are used. Other metrics such as MAP, MRR and precision, are defined only for binary judgments. Recently, there have been proposed several new evaluation metrics which claim to model user's satisfaction with search results better than the DCG metric: Expected reciprocal rank (ERR); Yandex's pfound. Both of these metrics are based on the assumption that the user is more likely to stop looking at search results after examining a more relevant document, than after a less relevant document. == Approaches == Learning to Rank approaches are often categorized using one of three approaches: pointwise (where individual documents are ranked), pairwise (where pairs of documents are ranked into a relative order), and listwise (where an entire list of documents are ordered). Tie-Yan Liu of Microsoft Research Asia has analyzed existing algorithms for learning to rank problems in his book Learning to Rank for Information Retrieval. He categorized them into three groups by their input spaces, output spaces, hypothesis spaces (the core function of the model) and loss functions: the pointwise, pairwise, and listwise approach. In practice, listwise approaches often outperform pairwise approaches and pointwise approaches. This statement was further supported by a large scale experiment on the performance of different learning-to-rank methods on a large collection of benchmark data sets. In this section, without further notice, x {\displaystyle x} denotes an object to be evaluated, for example, a document or an image, f ( x ) {\displaystyle f(x)} denotes a single-value hypothesis, h ( ⋅ ) {\displaystyle h(\cdot )} denotes a bi-variate or multi-variate function and L ( ⋅ ) {\displaystyle L(\cdot )} denotes the loss function. === Pointwise approach === In this case, it is assumed that each query-document pair in the training data has a numerical or ordinal score. Then the learning-to-rank problem can be approximated by a regression problem — given a single query-document pair, predict its score. Formally speaking, the pointwise approach aims at learning a function f ( x ) {\displaystyle f(x)} predicting the real-value or ordinal score of a document x {\displaystyle x} using the loss function L ( f ; x j , y j ) {\displaystyle L(f;x_{j},y_{j})} . A number of existing supervised machine learning algorithms can be readily used for this purpose. Ordinal regression and classification algorithms can also be used in pointwise approach when they are used to predict the score of a single query-document pair, and it takes a small, finite number of values. === Pairwise approach === In this case, the learning-to-rank problem is approximated by a classification problem — learning a binary classifier h ( x u , x v ) {\displaystyle h(x_{u},x_{v})} that can tell which document is better in a given pair of documents. The classifier shall take two documents as its input and the goal is to minimize a loss function L ( h ; x u , x v , y u , v ) {\displaystyle L(h;x_{u},x_{v},y_{u,v})} . The loss function typically reflects the number and magnitude of inversions in the induced ranking. In many cases, the binary classifier h ( x u , x v ) {\displaystyle h(x_{u},x_{v})} is implemented with a scoring function f ( x ) {\displaystyle f(x)} . As an example, RankNet adapts a probability model and defines h ( x u , x v ) {\displaystyle h(x_{u},x_{v})} as the estimated probability of the document x u {\displaystyle x_{u}} has higher quality than x v {\displaystyle x_{v}} : P u , v ( f ) = CDF ( f ( x u ) − f ( x v ) ) , {\displaystyle P_{u,v}(f)={\text{CDF}

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  Pointer jumping

  Pointer jumping or path doubling is a design technique for parallel algorithms that operate on pointer structures, such as linked lists and directed graphs. Pointer jumping allows an algorithm to follow paths with a time complexity that is logarithmic with respect to the length of the longest path. It does this by "jumping" to the end of the path computed by neighbors. The basic operation of pointer jumping is to replace each neighbor in a pointer structure with its neighbor's neighbor. In each step of the algorithm, this replacement is done for all nodes in the data structure, which can be done independently in parallel. In the next step when a neighbor's neighbor is followed, the neighbor's path already followed in the previous step is added to the node's followed path in a single step. Thus, each step effectively doubles the distance traversed by the explored paths. Pointer jumping is best understood by looking at simple examples such as list ranking and root finding. == List ranking == One of the simpler tasks that can be solved by a pointer jumping algorithm is the list ranking problem. This problem is defined as follows: given a linked list of N nodes, find the distance (measured in the number of nodes) of each node to the end of the list. The distance d(n) is defined as follows, for nodes n that point to their successor by a pointer called next: If n.next is nil, then d(n) = 0. For any other node, d(n) = d(n.next) + 1. This problem can easily be solved in linear time on a sequential machine, but a parallel algorithm can do better: given n processors, the problem can be solved in logarithmic time, O(log N), by the following pointer jumping algorithm: The pointer jumping occurs in the last line of the algorithm, where each node's next pointer is reset to skip the node's direct successor. It is assumed, as in common in the PRAM model of computation, that memory access are performed in lock-step, so that each n.next.next memory fetch is performed before each n.next memory store; otherwise, processors may clobber each other's data, producing inconsistencies. The following diagram follows how the parallel list ranking algorithm uses pointer jumping for a linked list with 11 elements. As the algorithm describes, the first iteration starts initialized with all ranks set to 1 except those with a null pointer for next. The first iteration looks at immediate neighbors. Each subsequent iteration jumps twice as far as the previous. Analyzing the algorithm yields a logarithmic running time. The initialization loop takes constant time, because each of the N processors performs a constant amount of work, all in parallel. The inner loop of the main loop also takes constant time, as does (by assumption) the termination check for the loop, so the running time is determined by how often this inner loop is executed. Since the pointer jumping in each iteration splits the list into two parts, one consisting of the "odd" elements and one of the "even" elements, the length of the list pointed to by each processor's n is halved in each iteration, which can be done at most O(log N) time before each list has a length of at most one. == Root finding == Following a path in a graph is an inherently serial operation, but pointer jumping reduces the total amount of work by following all paths simultaneously and sharing results among dependent operations. Pointer jumping iterates and finds a successor — a vertex closer to the tree root — each time. By following successors computed for other vertices, the traversal down each path can be doubled every iteration, which means that the tree roots can be found in logarithmic time. Pointer doubling operates on an array successor with an entry for every vertex in the graph. Each successor[i] is initialized with the parent index of vertex i if that vertex is not a root or to i itself if that vertex is a root. At each iteration, each successor is updated to its successor's successor. The root is found when the successor's successor points to itself. The following pseudocode demonstrates the algorithm. algorithm Input: An array parent representing a forest of trees. parent[i] is the parent of vertex i or itself for a root Output: An array containing the root ancestor for every vertex for i ← 1 to length(parent) do in parallel successor[i] ← parent[i] while true for i ← 1 to length(successor) do in parallel successor_next[i] ← successor[successor[i]] if successor_next = successor then break for i ← 1 to length(successor) do in parallel successor[i] ← successor_next[i] return successor The following image provides an example of using pointer jumping on a small forest. On each iteration the successor points to the vertex following one more successor. After two iterations, every vertex points to its root node. == History and examples == Although the name pointer jumping would come later, JáJá attributes the first uses of the technique in early parallel graph algorithms and list ranking. The technique has been described with other names such as shortcutting, but by the 1990s textbooks on parallel algorithms consistently used the term pointer jumping. Today, pointer jumping is considered a software design pattern for operating on recursive data types in parallel. As a technique for following linked paths, graph algorithms are a natural fit for pointer jumping. Consequently, several parallel graph algorithms utilizing pointer jumping have been designed. These include algorithms for finding the roots of a forest of rooted trees, connected components, minimum spanning trees, and biconnected components. However, pointer jumping has also shown to be useful in a variety of other problems including computer vision, image compression, and Bayesian inference.

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  Information strategist

  An information strategist analyses the information flow within an organisation and directs its information resources to better serve the organisation's strategic goals. They work with information technology or within a corporate library to direct high quality information from a variety of sources to users, based upon their profiles and needs. In warfare, information strategists not only seek to improve information flows for their own side but also try to disrupt the information flows of the enemy in order to demoralize and deceive them.

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  Algorithmic paradigm

  An algorithmic paradigm or algorithm design paradigm is a generic model or framework which underlies the design of a class of algorithms. An algorithmic paradigm is an abstraction higher than the notion of an algorithm, just as an algorithm is an abstraction higher than a computer program. == List of well-known paradigms == === General === Backtracking Branch and bound Brute-force search Divide and conquer Dynamic programming Greedy algorithm Recursion Prune and search === Parameterized complexity === Kernelization Iterative compression === Computational geometry === Sweep line algorithms Rotating calipers Randomized incremental construction

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  Iterative reconstruction

  Iterative reconstruction refers to iterative algorithms used to reconstruct 2D and 3D images in certain imaging techniques. For example, in computed tomography an image must be reconstructed from projections of an object. Here, iterative reconstruction techniques are usually a better, but computationally more expensive alternative to the common filtered back projection (FBP) method, which directly calculates the image in a single reconstruction step. In recent research works, scientists have shown that extremely fast computations and massive parallelism is possible for iterative reconstruction, which makes iterative reconstruction practical for commercialization. == Basic concepts == The reconstruction of an image from the acquired data is an inverse problem. Often, it is not possible to exactly solve the inverse problem directly. In this case, a direct algorithm has to approximate the solution, which might cause visible reconstruction artifacts in the image. Iterative algorithms approach the correct solution using multiple iteration steps, which allows to obtain a better reconstruction at the cost of a higher computation time. There are a large variety of algorithms, but each starts with an assumed image, computes projections from the image, compares the original projection data and updates the image based upon the difference between the calculated and the actual projections. === Algebraic reconstruction === The Algebraic Reconstruction Technique (ART) was the first iterative reconstruction technique used for computed tomography by Hounsfield. === Iterative Sparse Asymptotic Minimum Variance === The iterative sparse asymptotic minimum variance algorithm is an iterative, parameter-free superresolution tomographic reconstruction method inspired by compressed sensing, with applications in synthetic-aperture radar, computed tomography scan, and magnetic resonance imaging (MRI). === Statistical reconstruction === There are typically five components to statistical iterative image reconstruction algorithms, e.g. An object model that expresses the unknown continuous-space function f ( r ) {\displaystyle f(r)} that is to be reconstructed in terms of a finite series with unknown coefficients that must be estimated from the data. A system model that relates the unknown object to the "ideal" measurements that would be recorded in the absence of measurement noise. Often this is a linear model of the form A x + ϵ {\displaystyle \mathbf {A} x+\epsilon } , where ϵ {\displaystyle \epsilon } represents the noise. A statistical model that describes how the noisy measurements vary around their ideal values. Often Gaussian noise or Poisson statistics are assumed. Because Poisson statistics are closer to reality, it is more widely used. A cost function that is to be minimized to estimate the image coefficient vector. Often this cost function includes some form of regularization. Sometimes the regularization is based on Markov random fields. An algorithm, usually iterative, for minimizing the cost function, including some initial estimate of the image and some stopping criterion for terminating the iterations. === Learned Iterative Reconstruction === In learned iterative reconstruction, the updating algorithm is learned from training data using techniques from machine learning such as convolutional neural networks, while still incorporating the image formation model. This typically gives faster and higher quality reconstructions and has been applied to CT and MRI reconstruction. == Advantages == The advantages of the iterative approach include improved insensitivity to noise and capability of reconstructing an optimal image in the case of incomplete data. The method has been applied in emission tomography modalities like SPECT and PET, where there is significant attenuation along ray paths and noise statistics are relatively poor. Statistical, likelihood-based approaches: Statistical, likelihood-based iterative expectation-maximization algorithms are now the preferred method of reconstruction. Such algorithms compute estimates of the likely distribution of annihilation events that led to the measured data, based on statistical principle, often providing better noise profiles and resistance to the streak artifacts common with FBP. Since the density of radioactive tracer is a function in a function space, therefore of extremely high-dimensions, methods which regularize the maximum-likelihood solution turning it towards penalized or maximum a-posteriori methods can have significant advantages for low counts. Examples such as Ulf Grenander's Sieve estimator or Bayes penalty methods, or via I.J. Good's roughness method may yield superior performance to expectation-maximization-based methods which involve a Poisson likelihood function only. As another example, it is considered superior when one does not have a large set of projections available, when the projections are not distributed uniformly in angle, or when the projections are sparse or missing at certain orientations. These scenarios may occur in intraoperative CT, in cardiac CT, or when metal artifacts require the exclusion of some portions of the projection data. In Magnetic Resonance Imaging it can be used to reconstruct images from data acquired with multiple receive coils and with sampling patterns different from the conventional Cartesian grid and allows the use of improved regularization techniques (e.g. total variation) or an extended modeling of physical processes to improve the reconstruction. For example, with iterative algorithms it is possible to reconstruct images from data acquired in a very short time as required for real-time MRI (rt-MRI). In Cryo Electron Tomography, where the limited number of projections are acquired due to the hardware limitations and to avoid the biological specimen damage, it can be used along with compressive sensing techniques or regularization functions (e.g. Huber function) to improve the reconstruction for better interpretation. Here is an example that illustrates the benefits of iterative image reconstruction for cardiac MRI.

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  Physical schema

  A physical data model (or database design) is a representation of a data design as implemented, or intended to be implemented, in a database management system. In the lifecycle of a project it typically derives from a logical data model, though it may be reverse-engineered from a given database implementation. A complete physical data model will include all the database artifacts required to create relationships between tables or to achieve performance goals, such as indexes, constraint definitions, linking tables, partitioned tables or clusters. Analysts can usually use a physical data model to calculate storage estimates; it may include specific storage allocation details for a given database system. As of 2012 seven main databases dominate the commercial marketplace: Informix, Oracle, Postgres, SQL Server, Sybase, IBM Db2 and MySQL. Other RDBMS systems tend either to be legacy databases or used within academia such as universities or further education colleges. Physical data models for each implementation would differ significantly, not least due to underlying operating-system requirements that may sit underneath them. For example: SQL Server runs only on Microsoft Windows operating-systems (Starting with SQL Server 2017, SQL Server runs on Linux. It's the same SQL Server database engine, with many similar features and services regardless of your operating system), while Oracle and MySQL can run on Solaris, Linux and other UNIX-based operating-systems as well as on Windows. This means that the disk requirements, security requirements and many other aspects of a physical data model will be influenced by the RDBMS that a database administrator (or an organization) chooses to use. == Physical schema == Physical schema is a term used in data management to describe how data is to be represented and stored (files, indices, etc.) in secondary storage using a particular database management system (DBMS) (e.g., Oracle RDBMS, Sybase SQL Server, etc.). In the ANSI/SPARC Architecture three schema approach, the internal schema is the view of data that involved data management technology. This is as opposed to an external schema that reflects an individual's view of the data, or the conceptual schema that is the integration of a set of external schemas. The logical schema was the way data were represented to conform to the constraints of a particular approach to database management. At that time the choices were hierarchical and network. Describing the logical schema, however, still did not describe how physically data would be stored on disk drives. That is the domain of the physical schema. Now logical schemas describe data in terms of relational tables and columns, object-oriented classes, and XML tags. A single set of tables, for example, can be implemented in numerous ways, up to and including an architecture where table rows are maintained on computers in different countries.

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  BioCreative

  BioCreAtIvE (A critical assessment of text mining methods in molecular biology) consists in a community-wide effort for evaluating information extraction and text mining developments in the biological domain. It was preceded by the Knowledge Discovery and Data Mining (KDD) Challenge Cup for detection of gene mentions. == Community Challenges == === First edition (2004-2005) === Three main tasks were posed at the first BioCreAtIvE challenge: the entity extraction task, the gene name normalization task, and the functional annotation of gene products task. The data sets produced by this contest serve as a Gold Standard training and test set to evaluate and train Bio-NER tools and annotation extraction tools. === Second edition (2006-2007) === The second BioCreAtIvE challenge (2006-2007) had also 3 tasks: detection of gene mentions, extraction of unique idenfiers for genes and extraction information related to physical protein-protein interactions. It counted with participation of 44 teams from 13 countries. === Third edition (2011-2012) === The third edition of BioCreative included for the first time the InterActive Task (IAT), designed to evaluate the practical usability of text mining tools in real-world biocuration tasks. === Fifth edition (2016) === BioCreative V had 5 different tracks, including an interactive task (IAT) for usability of text mining systems and a track using the BioC format for curating information for BioGRID.

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