Shapiro–Senapathy algorithm

The Shapiro—Senapathy algorithm (S&S) is a computational method for identifying splice sites in eukaryotic genes. The algorithm employs a Position Weight Matrix (PWM) scoring formula to predict donor and acceptor splice sites in any given gene. This methodology has been used to discover splice sites and disease-causing splice site mutations in the human genome, and has become a standard tool in clinical genomics. The S&S algorithm has been cited in thousands of clinical studies, according to Google Scholar. It has also formed the basis of widely used software, including Human Splicing Finder, SROOGLE, and Alamut, which identify splice sites and splice site mutations that cause disease. The algorithm has uncovered splicing mutations in diseases ranging from cancers to inherited disorders, and predicted the deleterious effects of these mutations including exon skipping, intron retention, and cryptic splice site activation. == The algorithm == A splice site defines the boundary between a coding exon and a non-coding intron in eukaryotic genes. The S&S algorithm employs a sliding window, corresponding to the length of the splice site motif, to scan a gene sequence and detect potential splice sites. For each sliding window, the algorithm calculates a score by comparing the nucleotide sequence to a Position Weight Matrix (PWM) derived from known splice sites. This formula generates a percentile score, indicating the likelihood that a given sequence functions as a donor or acceptor splice site. The majority of disease-causing mutations in the human genome are located in splice sites. Clinical genomics studies analyze the splice site scores generated by the S&S algorithm to predict the consequences of splice site mutations including exon skipping and intron retention. The algorithm's sensitivity to single-nucleotide changes allows it to determine mutations that may impact RNA splicing and contribute to disease. In addition to identifying real splice sites, the S&S algorithm has been used to discover cryptic splice sites — alternative splice sites activated by mutations — which may disrupt normal splicing. The algorithm detects mutations that lead to the activation of cryptic splice sites, which may be located proximal to real splice sites or deep within non-coding introns. It has thus been used to determine the causes of numerous diseases that are due to cryptic splicing. == Cancer gene discovery using S&S == The S&S algorithm has been used to identify splice-site mutations in genes associated with several cancers. For example, genes causing commonly occurring cancers including breast cancer, ovarian cancer, colorectal cancer, leukemia, head and neck cancers, prostate cancer, retinoblastoma, squamous cell carcinoma, gastrointestinal cancer, melanoma, liver cancer, Lynch syndrome, skin cancer, and neurofibromatosis have been found. In addition, splicing mutations in genes causing less commonly known cancers including gastric cancer, gangliogliomas, Li-Fraumeni syndrome, Loeys–Dietz syndrome, Osteochondromas (bone tumor), Nevoid basal cell carcinoma syndrome, and Pheochromocytomas have been identified. Specific mutations in different splice sites in various genes causing breast cancer (e.g., BRCA1, PALB2), ovarian cancer (e.g., SLC9A3R1, COL7A1, HSD17B7), colon cancer (e.g., APC, MLH1, DPYD), colorectal cancer (e.g., COL3A1, APC, HLA-A), skin cancer (e.g., COL17A1, XPA, POLH), and Fanconi anemia (e.g., FANC, FANA) have been uncovered. The mutations in the donor and acceptor splice sites in different genes causing a variety of cancers that have been identified by S&S are shown in Table 1. == Discovery of genes causing inherited disorders using S&S == Specific mutations in different splice sites in various genes that cause inherited disorders, including, for example, Type 1 diabetes (e.g., PTPN22, TCF1 (HCF-1A)), hypertension (e.g., LDL, LDLR, LPL), Marfan syndrome (e.g., FBN1, TGFBR2, FBN2), cardiac diseases (e.g., COL1A2, MYBPC3, ACTC1), eye disorders (e.g., EVC, VSX1) have been uncovered. A few example mutations in the donor and acceptor splice sites in different genes causing a variety of inherited disorders identified using S&S are shown in Table 2. == Genes causing immune system disorders == More than 100 immune system disorders affect humans, including inflammatory bowel diseases, multiple sclerosis, systemic lupus erythematosus, bloom syndrome, familial cold autoinflammatory syndrome, and dyskeratosis congenita. The Shapiro–Senapathy algorithm has been used to discover genes and mutations involved in many immune disorder diseases, including Ataxia telangiectasia, B-cell defects, epidermolysis bullosa, and X-linked agammaglobulinemia. Xeroderma pigmentosum, an autosomal recessive disorder is caused by faulty proteins formed due to new preferred splice donor site identified using S&S algorithm and resulted in defective nucleotide excision repair. Type I Bartter syndrome (BS) is caused by mutations in the gene SLC12A1. S&S algorithm helped in disclosing the presence of two novel heterozygous mutations c.724 + 4A > G in intron 5 and c.2095delG in intron 16 leading to complete exon 5 skipping. Mutations in the MYH gene, which is responsible for removing the oxidatively damaged DNA lesion are cancer-susceptible in the individuals. The IVS1+5C plays a causative role in the activation of a cryptic splice donor site and the alternative splicing in intron 1, S&S algorithm shows, guanine (G) at the position of IVS+5 is well conserved (at the frequency of 84%) among primates. This also supported the fact that the G/C SNP in the conserved splice junction of the MYH gene causes the alternative splicing of intron 1 of the β type transcript. Splice site scores were calculated according to S&S to find EBV infection in X-linked lymphoproliferative disease. Identification of Familial tumoral calcinosis (FTC) is an autosomal recessive disorder characterized by ectopic calcifications and elevated serum phosphate levels and it is because of aberrant splicing. == Application of S&S in hospitals for clinical practice and research == The Shapiro–Senapathy (S&S) algorithm has played a significant role in advancing the diagnosis and treatment of human diseases through its application in modern clinical genomics. With the widespread adoption of next-generation sequencing (NGS) technologies, the S&S algorithm is now routinely integrated into clinical practice by geneticists and diagnostic laboratories. It is implemented in various computational tools such as Human Splicing Finder (HSF), Splice Site Finder (SSF), and Alamut Visual, which assist in interpreting the functional impact of genetic variants on RNA splicing. The algorithm is particularly useful in identifying pathogenic splice site mutations in cases where the clinical presentation is unclear or where conventional diagnostic methods have failed to identify a causative gene. Its utility has been demonstrated across diverse patient cohorts, including individuals from different ethnic backgrounds with various cancers and inherited genetic disorders. The following are selected examples illustrating its application in clinical research. === Cancers === === Inherited disorders === == S&S - Algorithm for identifying splice sites, exons and split genes == The Shapiro–Senapathy algorithm (SSA) was developed to identify splice sites in uncharacterized genomic sequences, with early applications in the Human Genome Project. The method introduced a Position Weight Matrix (PWM)-based approach to analyze splicing sequences across eukaryotic organisms, marking the first computational framework to systematically define splice sites using probabilistic scoring. Key innovations of the algorithm included: Exon Detection – Exons were defined as sequences bounded by acceptor and donor splice sites with S&S scores above a threshold, requiring an open reading frame (ORF) for validation. Gene Prediction – The method enabled the identification of complete genes by assembling predicted exons, forming a basis for later gene-finding tools. Mutation Analysis – The algorithm distinguishes deleterious splice-site mutations (which disrupt protein function by lowering S&S scores) from neutral variations. This capability allowed researchers to study disease-linked cryptic splice sites in humans, animals, and plants. SSA's PWM-based framework influenced subsequent computational methods, including machine learning and neural network approaches, for splice-site prediction and alternative splicing research. It remains a foundational tool in genomics and disease studies. == Discovering the mechanisms of aberrant splicing in diseases == The Shapiro–Senapathy algorithm has been used to determine the various aberrant splicing mechanisms in genes due to deleterious mutations in the splice sites, which cause numerous diseases. Deleterious splice site mutations impair the normal splicing of the gene transcripts, and thereby make the encoded protei

Glossary of machine vision

The following are common definitions related to the machine vision field. General related fields Machine vision Computer vision Image processing Signal processing == 0-9 == 1394. FireWire is Apple Inc.'s brand name for the IEEE 1394 interface. It is also known as i.Link (Sony's name) or IEEE 1394 (although the 1394 standard also defines a backplane interface). It is a personal computer (and digital audio/digital video) serial bus interface standard, offering high-speed communications and isochronous real-time data services. 1D. One-dimensional. 2D computer graphics. The computer-based generation of digital images—mostly from two-dimensional models (such as 2D geometric models, text, and digital images) and by techniques specific to them. 3D computer graphics. 3D computer graphics are different from 2D computer graphics in that a three-dimensional representation of geometric data is stored in the computer for the purposes of performing calculations and rendering 2D images. Such images may be for later display or for real-time viewing. Despite these differences, 3D computer graphics rely on many of the same algorithms as 2D computer vector graphics in the wire frame model and 2D computer raster graphics in the final rendered display. In computer graphics software, the distinction between 2D and 3D is occasionally blurred; 2D applications may use 3D techniques to achieve effects such as lighting, and primarily 3D may use 2D rendering techniques. 3D scanner. This is a device that analyzes a real-world object or environment to collect data on its shape and possibly color. The collected data can then be used to construct digital, three dimensional models useful for a wide variety of applications. == A == Aberration. Optically, defocus refers to a translation along the optical axis away from the plane or surface of best focus. In general, defocus reduces the sharpness and contrast of the image. What should be sharp, high-contrast edges in a scene become gradual transitions. Algebraic distance or algebraic error. The algebraic distance from a point xi to a curve or surface defined by f ( x , β ) = 0 {\displaystyle f(x,\beta )=0} is the value of f ( x i , β ) {\displaystyle f(x_{i},\beta )} , i.e. the residual in the least squares problem with data point (xi, 0) and model function f. This term is mainly used in computer vision.[1][2] Aperture. In context of photography or machine vision, aperture refers to the diameter of the aperture stop of a photographic lens. The aperture stop can be adjusted to control the amount of light reaching the film or image sensor. aspect ratio (image). The aspect ratio of an image is its displayed width divided by its height (usually expressed as "x:y"). Angular resolution. Describes the resolving power of any image forming device such as an optical or radio telescope, a microscope, a camera, or an eye. Automated optical inspection. == B == Barcode. A barcode (also bar code) is a machine-readable representation of information in a visual format on a surface. Blob discovery. Inspecting an image for discrete blobs of connected pixels (e.g. a black hole in a grey object) as image landmarks. These blobs frequently represent optical targets for machining, robotic capture, or manufacturing failure. Bitmap. A raster graphics image, digital image, or bitmap, is a data file or structure representing a generally rectangular grid of pixels, or points of color, on a computer monitor, paper, or other display device. == C == Camera. A camera is a device used to take pictures, either singly or in sequence. A camera that takes pictures singly is sometimes called a photo camera to distinguish it from a video camera. Camera Link. Camera Link is a serial communication protocol designed for computer vision applications based on the National Semiconductor interface Channel-link. It was designed for the purpose of standardizing scientific and industrial video products including cameras, cables and frame grabbers. The standard is maintained and administered by the Automated Imaging Association, or AIA, the global machine vision industry's trade group. Charge-coupled device. A charge-coupled device (CCD) is a sensor for recording images, consisting of an integrated circuit containing an array of linked, or coupled, capacitors. CCD sensors and cameras tend to be more sensitive, less noisy, and more expensive than CMOS sensors and cameras. CIE 1931 Color Space. In the study of the perception of color, one of the first mathematically defined color spaces was the CIE XYZ color space (also known as CIE 1931 color space), created by the International Commission on Illumination (CIE) in 1931. CMOS. CMOS ("see-moss")stands for complementary metal-oxide semiconductor, is a major class of integrated circuits. CMOS imaging sensors for machine vision are cheaper than CCD sensors but more noisy. CoaXPress. CoaXPress (CXP) is an asymmetric high speed serial communication standard over coaxial cable. CoaXPress combines high speed image data, low speed camera control and power over a single coaxial cable. The standard is maintained by JIIA, the Japan Industrial Imaging Association. Color. The perception of the frequency (or wavelength) of light, and can be compared to how pitch (or a musical note) is the perception of the frequency or wavelength of sound. Color blindness. Also known as color vision deficiency, in humans is the inability to perceive differences between some or all colors that other people can distinguish Color temperature. "White light" is commonly described by its color temperature. A traditional incandescent light source's color temperature is determined by comparing its hue with a theoretical, heated black-body radiator. The lamp's color temperature is the temperature in kelvins at which the heated black-body radiator matches the hue of the lamp. Color vision. CV is the capacity of an organism or machine to distinguish objects based on the wavelengths (or frequencies) of the light they reflect or emit. computer vision. The study and application of methods which allow computers to "understand" image content. Contrast. In visual perception, contrast is the difference in visual properties that makes an object (or its representation in an image) distinguishable from other objects and the background. C-Mount. Standardized adapter for optical lenses on CCD - cameras. C-Mount lenses have a back focal distance 17.5 mm vs. 12.5 mm for "CS-mount" lenses. A C-Mount lens can be used on a CS-Mount camera through the use of a 5 mm extension adapter. C-mount is a 1" diameter, 32 threads per inch mounting thread (1"-32UN-2A.) CS-Mount. Same as C-Mount but the focal point is 5 mm shorter. A CS-Mount lens will not work on a C-Mount camera. CS-mount is a 1" diameter, 32 threads per inch mounting thread. == D == Data matrix. A two dimensional Barcode. Depth of field. In optics, particularly photography and machine vision, the depth of field (DOF) is the distance in front of and behind the subject which appears to be in focus. Depth perception. DP is the visual ability to perceive the world in three dimensions. It is a trait common to many higher animals. Depth perception allows the beholder to accurately gauge the distance to an object. Diaphragm. In optics, a diaphragm is a thin opaque structure with an opening (aperture) at its centre. The role of the diaphragm is to stop the passage of light, except for the light passing through the aperture. == E == Edge detection. ED marks the points in a digital image at which the luminous intensity changes sharply. It also marks the points of luminous intensity changes of an object or spatial-taxon silhouette. Electromagnetic interference. Radio Frequency Interference (RFI) is electromagnetic radiation which is emitted by electrical circuits carrying rapidly changing signals, as a by-product of their normal operation, and which causes unwanted signals (interference or noise) to be induced in other circuits. == F == FireWire. FireWire (also known as i. Link or IEEE 1394) is a personal computer (and digital audio/video) serial bus interface standard, offering high-speed communications. It is often used as an interface for industrial cameras. Fixed-pattern noise. Flat-field correction. Frame grabber. An electronic device that captures individual, digital still frames from an analog video signal or a digital video stream. Fringe Projection Technique. 3D data acquisition technique employing projector displaying fringe pattern on a surface of measured piece, and one or more cameras recording image(s). Field of view. The field of view (FOV) is the part which can be seen by the machine vision system at one moment. The field of view depends from the lens of the system and from the working distance between object and camera. Focus. An image, or image point or region, is said to be in focus if light from object points is converged about as well as possible in the image; conversely, it is out of focus if light is not w

Record linkage

Record linkage (also known as data matching, data linkage, entity resolution, and many other terms) is the task of finding records in a data set that refer to the same entity across different data sources (e.g., data files, books, websites, and databases). Record linkage is necessary when joining different data sets based on entities that may or may not share a common identifier (e.g., database key, URI, National identification number), which may be due to differences in record shape, storage location, or curator style or preference. A data set that has undergone RL-oriented reconciliation may be referred to as being cross-linked. == Naming conventions == "Record linkage" is the term used by statisticians, epidemiologists, and historians, among others, to describe the process of joining records from one data source with another that describe the same entity. However, many other terms are used for this process. Unfortunately, this profusion of terminology has led to few cross-references between these research communities. Computer scientists often refer to it as "data matching" or as the "object identity problem". Commercial mail and database applications refer to it as "merge/purge processing" or "list washing". Other names used to describe the same concept include: "coreference/entity/identity/name/record resolution", "entity disambiguation/linking", "fuzzy matching", "duplicate detection", "deduplication", "record matching", "(reference) reconciliation", "object identification", "data/information integration" and "conflation". While they share similar names, record linkage and linked data are two separate approaches to processing and structuring data. Although both involve identifying matching entities across different data sets, record linkage standardly equates "entities" with human individuals; by contrast, Linked Data is based on the possibility of interlinking any web resource across data sets, using a correspondingly broader concept of identifier, namely a URI. == History == The initial idea of record linkage goes back to Halbert L. Dunn in his 1946 article titled "Record Linkage" published in the American Journal of Public Health. Howard Borden Newcombe then laid the probabilistic foundations of modern record linkage theory in a 1959 article in Science. These were formalized in 1969 by Ivan Fellegi and Alan Sunter, in their pioneering work "A Theory For Record Linkage", where they proved that the probabilistic decision rule they described was optimal when the comparison attributes were conditionally independent. In their work they recognized the growing interest in applying advances in computing and automation to large collections of administrative data, and the Fellegi-Sunter theory remains the mathematical foundation for many record linkage applications. Since the late 1990s, various machine learning techniques have been developed that can, under favorable conditions, be used to estimate the conditional probabilities required by the Fellegi-Sunter theory. Several researchers have reported that the conditional independence assumption of the Fellegi-Sunter algorithm is often violated in practice; however, published efforts to explicitly model the conditional dependencies among the comparison attributes have not resulted in an improvement in record linkage quality. On the other hand, machine learning or neural network algorithms that do not rely on these assumptions often provide far higher accuracy, when sufficient labeled training data is available. Record linkage can be done entirely without the aid of a computer, but the primary reasons computers are often used to complete record linkages are to reduce or eliminate manual review and to make results more easily reproducible. Computer matching has the advantages of allowing central supervision of processing, better quality control, speed, consistency, and better reproducibility of results. == Methods == === Data preprocessing === Record linkage is highly sensitive to the quality of the data being linked, so all data sets under consideration (particularly their key identifier fields) should ideally undergo a data quality assessment before record linkage. Many key identifiers for the same entity can be presented quite differently between (and even within) data sets, which can greatly complicate record linkage unless understood ahead of time. For example, key identifiers for a man named William J. Smith might appear in three different data sets as follows: In this example, the different formatting styles lead to records that look different but in fact all refer to the same entity with the same logical identifier values. Most, if not all, record linkage strategies would result in more accurate linkage if these values were first normalized or standardized into a consistent format (e.g., all names are "Surname, Given name", and all dates are "YYYY/MM/DD"). Standardization can be accomplished through simple rule-based data transformations or more complex procedures such as lexicon-based tokenization and probabilistic hidden Markov models. Several of the packages listed in the Software Implementations section provide some of these features to simplify the process of data standardization. === Entity resolution === Entity resolution is an operational intelligence process, typically powered by an entity resolution engine or middleware, whereby organizations can connect disparate data sources with a view to understand possible entity matches and non-obvious relationships across multiple data silos. It analyzes all of the information relating to individuals and/or entities from multiple sources of data, and then applies likelihood and probability scoring to determine which identities are a match and what, if any, non-obvious relationships exist between those identities. Entity resolution engines are typically used to uncover risk, fraud, and conflicts of interest, but are also useful tools for use within customer data integration (CDI) and master data management (MDM) requirements. Typical uses for entity resolution engines include terrorist screening, insurance fraud detection, USA Patriot Act compliance, organized retail crime ring detection and applicant screening. For example, across different data silos – employee records, vendor data, watch lists, etc. – an organization may have several variations of an entity named ABC, which may or may not be the same individual. These entries may, in fact, appear as ABC1, ABC2, or ABC3 within those data sources. By comparing similarities between underlying attributes such as address, date of birth, or social security number, the user can eliminate some possible matches and confirm others as very likely matches. Entity resolution engines then apply rules, based on common sense logic, to identify hidden relationships across the data. In the example above, perhaps ABC1 and ABC2 are not the same individual, but rather two distinct people who share common attributes such as address or phone number. ==== Data matching ==== While entity resolution solutions include data matching technology, many data matching offerings do not fit the definition of entity resolution. Here are four factors that distinguish entity resolution from data matching, according to John Talburt, director of the UALR Center for Advanced Research in Entity Resolution and Information Quality: Works with both structured and unstructured records, and it entails the process of extracting references when the sources are unstructured or semi-structured Uses elaborate business rules and concept models to deal with missing, conflicting, and corrupted information Utilizes non-matching, asserted linking (associate) information in addition to direct matching Uncovers non-obvious relationships and association networks (i.e. who's associated with whom) In contrast to data quality products, more powerful identity resolution engines also include a rules engine and workflow process, which apply business intelligence to the resolved identities and their relationships. These advanced technologies make automated decisions and impact business processes in real time, limiting the need for human intervention. === Deterministic record linkage === The simplest kind of record linkage, called deterministic or rules-based record linkage, generates links based on the number of individual identifiers that match among the available data sets. Two records are said to match via a deterministic record linkage procedure if all or some identifiers (above a certain threshold) are identical. Deterministic record linkage is a good option when the entities in the data sets are identified by a common identifier, or when there are several representative identifiers (e.g., name, date of birth, and sex when identifying a person) whose quality of data is relatively high. As an example, consider two standardized data sets, Set A and Set B, that contain different bits of information about patients in a hospital system. T

Information explosion

Information explosion is the rapid increase in the amount of published information or data and the effects of this abundance. As the amount of available data grows, the problem of managing the information becomes more difficult, which can lead to information overload. The Online Oxford English Dictionary indicates use of the phrase in a March 1964 New Statesman article. The New York Times first used the phrase in its editorial content in an article by Walter Sullivan on June 7, 1964, in which he described the phrase as "much discussed". The earliest known use of the phrase was in a speech about television by NBC president Pat Weaver at the Institute of Practitioners of Advertising in London on September 27, 1955. The speech was rebroadcast on radio station WSUI in Iowa City and excerpted in the Daily Iowan newspaper two months later. Many sectors are seeing this rapid increase in the amount of information available such as healthcare, supermarkets, and governments. Another sector that is being affected by this phenomenon is journalism. Such a profession, which in the past was responsible for the dissemination of information, may be suppressed by the overabundance of information today. Techniques to gather knowledge from an overabundance of electronic information (e.g., data fusion may help in data mining) have existed since the 1970s. Another common technique to deal with such amount of information is qualitative research. Such approaches aim to organize the information, synthesizing, categorizing and systematizing in order to be more usable and easier to search. == Growth patterns == The world's technological capacity to store information grew from, optimally compressed, 2.6 exabytes in 1986 to 15.7 in 1993, over 54.5 in 2000, and to 295 exabytes in 2007. The world's technological capacity to receive information through one-way broadcast networks was 432 exabytes of (optimally compressed) information in 1986, 715 (optimally compressed) exabytes in 1993, 1,200 (optimally compressed) exabytes in 2000, and 1,900 in 2007. The world's effective capacity to exchange information through two-way telecommunications networks was 0.281 exabytes of (optimally compressed) information in 1986, 0.471 in 1993, 2.2 in 2000, and 65 (optimally compressed) exabytes in 2007. A new metric that is being used in an attempt to characterize the growth in person-specific information, is the disk storage per person (DSP), which is measured in megabytes/person (where megabytes is 106 bytes and is abbreviated MB). Global DSP (GDSP) is the total rigid disk drive space (in MB) of new units sold in a year divided by the world population in that year. The GDSP metric is a crude measure of how much disk storage could possibly be used to collect person-specific data on the world population. In 1983, one million fixed drives with an estimated total of 90 terabytes were sold worldwide; 30MB drives had the largest market segment. In 1996, 105 million drives, totaling 160,623 terabytes were sold with 1 and 2 gigabyte drives leading the industry. By the year 2000, with 20GB drive leading the industry, rigid drives sold for the year are projected to total 2,829,288 terabytes Rigid disk drive sales to top $34 billion in 1997. According to Latanya Sweeney, there are three trends in data gathering today: Type 1. Expansion of the number of fields being collected, known as the “collect more” trend. Type 2. Replace an existing aggregate data collection with a person-specific one, known as the “collect specifically” trend. Type 3. Gather information by starting a new person-specific data collection, known as the “collect it if you can” trend. == Related terms == Since "information" in electronic media is often used synonymously with "data", the term information explosion is closely related to the concept of data flood (also dubbed data deluge). Sometimes the term information flood is used as well. All of those basically boil down to the ever-increasing amount of electronic data exchanged per time unit. A term that covers the potential negative effects of information explosion is information inflation. The awareness about non-manageable amounts of data grew along with the advent of ever more powerful data processing since the mid-1960s. == Challenges == Even though the abundance of information can be beneficial in several levels, some problems may be of concern such as privacy, legal and ethical guidelines, filtering and data accuracy. Filtering refers to finding useful information in the middle of so much data, which relates to the job of data scientists. A typical example of a necessity of data filtering (data mining) is in healthcare since in the next years is due to have EHRs (Electronic Health Records) of patients available. With so much information available, the doctors will need to be able to identify patterns and select important data for the diagnosis of the patient. On the other hand, according to some experts, having so much public data available makes it difficult to provide data that is actually anonymous. Another point to take into account is the legal and ethical guidelines, which relates to who will be the owner of the data and how frequently he/she is obliged to the release this and for how long. With so many sources of data, another problem will be accuracy of such. An untrusted source may be challenged by others, by ordering a new set of data, causing a repetition in the information. According to Edward Huth, another concern is the accessibility and cost of such information. The accessibility rate could be improved by either reducing the costs or increasing the utility of the information. The reduction of costs according to the author, could be done by associations, which should assess which information was relevant and gather it in a more organized fashion. == Web servers == As of August 2005, there were over 70 million web servers. As of September 2007 there were over 135 million web servers. == Blogs == According to Technorati, the number of blogs doubles about every 6 months with a total of 35.3 million blogs as of April 2006. This is an example of the early stages of logistic growth, where growth is approximately exponential, since blogs are a recent innovation. As the number of blogs approaches the number of possible producers (humans), saturation occurs, growth declines, and the number of blogs eventually stabilizes.

Documentation science

Documentation science is the study of the recording and retrieval of information. It includes methods for storing, retrieving, and sharing of information captured on physical as well as digital documents. This field is closely linked to the fields of library science and information science but has its own theories and practices. The term documentation science was coined by Belgian lawyer and peace activist Paul Otlet. He is considered to be the forefather of information science. He along with Henri La Fontaine laid the foundations of documentation science as a field of study. Professionals in this field are called documentalists. Over the years, documentation science has grown to become a large and important field of study. Evolving from traditional practices like archiving and retrieval to modern theories about the nature of documents, novel methods for organizing digital information, and applications in libraries, research, healthcare, business, and technology and more. This field continues to evolve in the digital age. == Developments in documentation science == 1895: The International Institute of Bibliography (originally Institut International de Bibliographie, IIB) was established on 12 September 1895, in Brussels, Belgium by Paul Otlet and Henri La Fontaine. It aimed to catalog all recorded knowledge using a universal classification system now known as the Universal Decimal Classification (UDC). 1931: International Institute of Bibliography (originally Institut International de Bibliographie, IIB) was renamed The International Institute for Documentation, (Institut International de Documentation, IID). 1934: Paul Otlet envisioned a “radiated library,” a global network of interconnected documents accessible from anywhere via telecommunication. This early idea is now seen as a forerunner of the internet. 1937: American Documentation Institute was founded (1968 nameshift to American Society for Information Science). 1951: Suzanne Briet published Qu'est-ce que la documentation? where she proposed that “a document is evidence in support of a fact,” expanding the definition to include objects such as animals in zoos when they are part of a scientific study. This was a significant theoretical shift in defining documents. 1965-1990: Documentation departments were established, for example, large research libraries, online computer retrieval systems and more. The persons doing the searches were called documentalists. But with the appearance of first CD-ROM databases in the mid-1980s and later the internet in 1990s, these intermediary searches decreased and most such departments closed or merged with other departments. 1996: "Dokvit", Documentation Studies, was established in 1996 at the University of Tromsø in Norway. 2001: The Document Academy was established. It is an international network that celebrates documentation. It was conducted by The Program of Documentation Studies, University of Tromsø, Norway and The School of Information Management and Systems, UC Berkeley. 2003: The first Document Research Conference (DOCAM), a series of conferences made by the Document Academy. DOCAM '03 (2003) was held 13–15 August 2003 at The School of Information Management and Systems (SIMS) at the University of California, Berkeley. 2007: Michael Buckland, Ronald Day, and Birger Hjørland expanded the theoretical foundations of documentation science. They researched and explored documents to be social artifacts, the role of ideology in classification, and how documents influenced knowledge systems. 2010s: The concept of post-documentation or “documentality” began in the 2010s, which focused on how digital traces (e.g., tweets, logs) function as documents without traditional physical form. This led to new thinking in document theory. 2016–present: The Document Academy's DOCAM conferences have continued, offering ongoing developments in the theory and practice of documentation. Themes include affect, memory, activism, and born-digital records. 2017: The journal Information Research published special issues addressing “document theory,” including views on documentation in virtual environments and digital archives. 2020–present: The growth of research data management (RDM) and open science has made documentation practices central to data sharing, metadata standards, and reproducibility in scientific work. == Theoretical foundations == Documentation science has some deep theories that explain what a document is, how people use documents, and how they are organized. These concepts were introduced by scholars who have not only studied libraries, but also philosophy, language, and social sciences. Suzanne Briet described a document as “any material form of evidence” that is made to be used as proof or to share information. An antelope in a zoo, for example, can be a document because it is being studied, classified, and described. Documents are not just things or materials but are also shaped by society. Michael Buckland noted that documents have meaning only when people agree they are useful or valid as information. He explained a document becomes a document when someone decides to use it as evidence. Ronald Day wrote about how documentation is not neutral, it can be influenced by power, ideology, and politics. He claimed that classification systems, like how libraries organize books, are not just technical tools. They also show what kinds of knowledge are seen as more important than others. In recent years, new theories have been introduced, like “documentality” by Maurizio Ferraris. He proposed that a document does not have to be a paper or file, it can also be something digital like a tweet, a database entry, or a log file, as long as it leaves a trace that can be looked at later. This theory helps explain modern digital documents. == Methodologies and practice == Documentation science includes many methods that help people collect, organize, store, and find information. These practices are used in libraries, archives, research labs, companies, and now also in online systems. === Collecting and creating documents === In the past, documentation work included gathering books, articles, reports, and other printed materials. People created records of these materials manually, using catalog cards, indexes, or bibliographies. Paul Otlet’s work with the Universal Bibliographic Repertory is one example. He created millions of card entries to organize knowledge from around the world. Today, documents are not only created by humans. Computers and machines also generate documents, like log files, metadata, and sensor data. These need new tools and methods for collection and management. === Organizing information === Organizing documents has always been a foundational element of documentation science. Methods like classification (dividing things into groups) and indexing (making lists of topics or keywords) help individuals find what they need. A widely used system is the Universal Decimal Classification (UDC) developed by Otlet and La Fontaine. Another is the Library of Congress Classification (LCC) used in the majority of U.S. libraries. Indexing can be performed by humans or by software programs that read the text and add tags to documents. Metadata is also used to describe documents. Metadata is “data about data” like the title, author, date, and subject of a document. Standards like Dublin Core are used in digital libraries to keep metadata consistent. === Retrieval and access === One of the main objectives of documentation is helping users find the right document. This is called information retrieval. In the past, this meant using catalog drawers or printed indexes. Today, people use search engines, databases, and digital libraries. Modern retrieval tools use Boolean logic, ranking algorithms, and sometimes machine learning to show the most useful results first. This is part of what is studied in both documentation science and information retrieval. === Preservation and archiving === Documents require long-term storage. This is called preservation of documents. Printed documents can be damaged by light, pests, or even time on the other hand digital documents can be deemed worthless if formats become outdated or storage facilities fail. Archivists use methods like migration, which includes moving files to new formats, and emulation, which replicates obsolete systems, to preserve materials. These methods and tools are ever changing as new technologies develop. But the main objective of documentation has remained the same, which is to keep information safe, organized, and easy to find. == Documentation in the digital age == With the expansion of the internet, computers, and cloud storage, documents are no longer just books, papers, or reports. They can now be emails, tweets, videos, websites, databases, or even log files created by machines. === Born-digital documents === Many documents today are created directly in digital form. These are called born-digit

Datasource

A datasource or DataSource is a name given to the connection set up to a database from a server. The name is commonly used when creating a query to the database. The data source name (DSN) need not be the same as the filename for the database. For example, a database file named friends.mdb could be set up with a DSN of school. Then DSN school would be used to refer to the database when performing a query. == Sun's version of DataSource [1] == A factory for connections to the physical data source that this DataSource object represents. An alternative to the DriverManager facility, a DataSource object is the preferred means of getting a connection. An object that implements the DataSource interface will typically be registered with a naming service based on the Java Naming and Directory Interface (JNDI) API. The DataSource interface is implemented by a driver vendor. There are three types of implementations: Basic implementation — produces a standard Connection object Connection pooling implementation — produces a Connection object that will automatically participate in connection pooling. This implementation works with a middle-tier connection pooling manager. Distributed transaction implementation — produces a Connection object that may be used for distributed transactions and almost always participates in connection pooling. This implementation works with a middle-tier transaction manager and almost always with a connection pooling manager. A DataSource object has properties that can be modified when necessary. For example, if the data source is moved to a different server, the property for the server can be changed. The benefit is that because the data source's properties can be changed, any code accessing that data source does not need to be changed. A driver that is accessed via a DataSource object does not register itself with the DriverManager. Rather, a DataSource object is retrieved through a lookup operation and then used to create a Connection object. With a basic implementation, the connection obtained through a DataSource object is identical to a connection obtained through the DriverManager facility. == Sun's DataSource Overview [2] == A DataSource object is the representation of a data source in the Java programming language. In basic terms, a data source is a facility for storing data. It can be as sophisticated as a complex database for a large corporation or as simple as a file with rows and columns. A data source can reside on a remote server, or it can be on a local desktop machine. Applications access a data source using a connection, and a DataSource object can be thought of as a factory for connections to the particular data source that the DataSource instance represents. The DataSource interface provides two methods for establishing a connection with a data source. Using a DataSource object is the preferred alternative to using the DriverManager for establishing a connection to a data source. They are similar to the extent that the DriverManager class and DataSource interface both have methods for creating a connection, methods for getting and setting a timeout limit for making a connection, and methods for getting and setting a stream for logging. Their differences are more significant than their similarities, however. Unlike the DriverManager, a DataSource object has properties that identify and describe the data source it represents. Also, a DataSource object works with a Java Naming and Directory Interface (JNDI) naming service and can be created, deployed, and managed separately from the applications that use it. A driver vendor will provide a class that is a basic implementation of the DataSource interface as part of its Java Database Connectivity (JDBC) 2.0 or 3.0 driver product. What a system administrator does to register a DataSource object with a JNDI naming service and what an application does to get a connection to a data source using a DataSource object registered with a JNDI naming service are described later in this chapter. Being registered with a JNDI naming service gives a DataSource object two major advantages over the DriverManager. First, an application does not need to hardcode driver information, as it does with the DriverManager. A programmer can choose a logical name for the data source and register the logical name with a JNDI naming service. The application uses the logical name, and the JNDI naming service will supply the DataSource object associated with the logical name. The DataSource object can then be used to create a connection to the data source it represents. The second major advantage is that the DataSource facility allows developers to implement a DataSource class to take advantage of features like connection pooling and distributed transactions. Connection pooling can increase performance dramatically by reusing connections rather than creating a new physical connection each time a connection is requested. The ability to use distributed transactions enables an application to do the heavy duty database work of large enterprises. Although an application may use either the DriverManager or a DataSource object to get a connection, using a DataSource object offers significant advantages and is the recommended way to establish a connection. Since 1.4 Since Java EE 6 a JNDI-bound DataSource can alternatively be configured in a declarative way directly from within the application. This alternative is particularly useful for self-sufficient applications or for transparently using an embedded database. == Yahoo's version of DataSource [3] == A DataSource is an abstract representation of a live set of data that presents a common predictable API for other objects to interact with. The nature of your data, its quantity, its complexity, and the logic for returning query results all play a role in determining your type of DataSource. For small amounts of simple textual data, a JavaScript array is a good choice. If your data has a small footprint but requires a simple computational or transformational filter before being displayed, a JavaScript function may be the right approach. For very large datasets—for example, a robust relational database—or to access a third-party webservice you'll certainly need to leverage the power of a Script Node or XHR DataSource.

Metadata

Metadata (or metainformation) is data (or information) that defines and describes the characteristics of other data. It often helps to describe, explain, locate, or otherwise make data easier to retrieve, use, or manage. For example, the title, author, and publication date of a book are metadata about the book. But, while a data asset is finite, its metadata is infinite. As such, efforts to define, classify types, or structure metadata are expressed as examples in the context of its use. The term "metadata" has a history dating to the 1960s where it occurred in computer science and in popular culture. Different types of metadata serve different functions. For example, descriptive metadata for a document might include the author, creation date, file size and keywords. Metadata has various purposes. It can help users find relevant information and discover resources. It can also help organize electronic resources, provide digital identification, and archive and preserve resources. Metadata allows users to access resources by "allowing resources to be found by relevant criteria, identifying resources, bringing similar resources together, distinguishing dissimilar resources, and giving location information". Metadata of telecommunication activities including Internet traffic is very widely collected by various national governmental organizations. This data is used for the purposes of traffic analysis and can be used for mass surveillance. Unique metadata standards exist for different disciplines (e.g., museum collections, digital audio files, websites, etc.). Describing the contents and context of data or data files increases its usefulness. For example, a web page may include metadata specifying what software language the page is written in (e.g., HTML), what tools were used to create it, what subjects the page is about, and where to find more information about the subject. This metadata can automatically improve the reader's experience and make it easier for users to find the web page online. A CD may include metadata providing information about the musicians, singers, and songwriters whose work appears on the disc. In many countries, government organizations routinely store metadata about emails, telephone calls, web pages, video traffic, IP connections, and cell phone locations. == Types == There are many distinct types of metadata, including: Descriptive metadata – the descriptive information about a resource. It is used for discovery and identification. It includes elements such as title, abstract, author, and keywords. Structural metadata – metadata about containers of data and indicates how compound objects are put together, for example, how pages are ordered to form chapters. It describes the types, versions, relationships, and other characteristics of digital materials. Administrative metadata – the information to help manage a resource, like resource type, and permissions, and when and how it was created. Reference metadata – the information about the contents and quality of statistical data. Statistical metadata – also called process data, may describe processes that collect, process, or produce statistical data. Legal metadata – provides information about the creator, copyright holder, and public licensing, if provided. Metadata is not strictly bound to one of these categories, as it can describe a piece of data in many other ways. While the metadata application is manifold, covering a large variety of fields, there are specialized and well-accepted models to specify types of metadata. Bretherton & Singley (1994) distinguish between two distinct classes: structural/control metadata and guide metadata. Structural metadata describes the structure of database objects such as tables, columns, keys and indexes. Guide metadata helps humans find specific items and is usually expressed as a set of keywords in a natural language. According to Ralph Kimball, metadata can be divided into three categories: technical metadata (or internal metadata), business metadata (or external metadata), and process metadata. Dan Linstedt, creator of the data vault methodology, says business metadata "...provide[s] definition of the functionality, definition of the data, definition of the elements, and definition of how the data is used within business...business metadata includes business requirements, time-lines, business metrics, business process flows, and business terminology." Business metadata is important because it can greatly facilitate the usefulness of the data to business people. A simple example of business metadata is a glossary entry. Hover functionality in an application or web form can enable a glossary definition to be shown when cursor is on a field or term. Other examples of business metadata include annotation ability within applications. For example, a business user may be viewing a business intelligence (BI) report and notice a trend in the data. The user may have background knowledge as to why this trend occurs. Some business intelligence tools enable the user to create an annotation within the report that explains the trend. Such an annotation can enhance other users' understanding of the data. This example is especially powerful because it is created by a business user for the use of other business people. NISO distinguishes three types of metadata: descriptive, structural, and administrative. Descriptive metadata is typically used for discovery and identification, as information to search and locate an object, such as title, authors, subjects, keywords, and publisher. Structural metadata describes how the components of an object are organized. An example of structural metadata would be how pages are ordered to form chapters of a book. Finally, administrative metadata gives information to help manage the source. Administrative metadata refers to the technical information, such as file type, or when and how the file was created. Two sub-types of administrative metadata are rights management metadata and preservation metadata. Rights management metadata explains intellectual property rights, while preservation metadata contains information to preserve and save a resource. Statistical data repositories have their own requirements for metadata in order to describe not only the source and quality of the data but also what statistical processes were used to create the data, which is of particular importance to the statistical community in order to both validate and improve the process of statistical data production. An additional type of metadata beginning to be more developed is accessibility metadata. Accessibility metadata is not a new concept to libraries; however, advances in universal design have raised its profile. Projects like Cloud4All and GPII identified the lack of common terminologies and models to describe the needs and preferences of users and information that fits those needs as a major gap in providing universal access solutions. Those types of information are accessibility metadata. The Schema.org website has incorporated several accessibility properties based on IMS Global Access for All Information Model Data Element Specification. While the efforts to describe and standardize the varied accessibility needs of information seekers are beginning to become more robust, their adoption into established metadata schemas has not been as developed. For example, while Dublin Core (DC)'s "audience" and MARC 21's "reading level" could be used to identify resources suitable for users with dyslexia and DC's "format" could be used to identify resources available in braille, audio, or large print formats, there is more work to be done. == History == Metadata was traditionally used in the card catalogs of libraries until the 1980s when libraries converted their catalog data to digital databases. In the 2000s, as data and information were increasingly stored digitally, this digital data was described using metadata standards. An early description of "meta data" for computer systems was written by David Griffel and Stuart McIntosh at the MIT Center for International Studies in 1967: "In summary then, we have statements in an object language about subject descriptions of data and token codes for the data. We also have statements in a meta language describing the data relationships and transformations, and ought/is relations between norm and data." == Definition == Metadata means "data about data". Metadata is defined as the data providing information about one or more aspects of the data; it is used to summarize basic information about data that can make tracking and working with specific data easier. Some examples include: Means of creation of the data Source of the data Time and date of creation Creator or author of the data Location on a computer network where the data was created Standards used Data quality For example, a digital image may include metadata that describes the size of the image, its color depth, resolution,