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MzML
Mass spectrometry is a scientific technique for measuring the mass-to-charge ratio of ions. It is often coupled to chromatographic techniques such as gas- or liquid chromatography and has found widespread adoption in the fields of analytical chemistry and biochemistry where it can be used to identify and characterize small molecules and proteins (proteomics). The large volume of data produced in a typical mass spectrometry experiment requires that computers be used for data storage and processing. Over the years, different manufacturers of mass spectrometers have developed various proprietary data formats for handling such data which makes it difficult for academic scientists to directly manipulate their data. To address this limitation, several open, XML-based data formats have recently been developed by the Trans-Proteomic Pipeline at the Institute for Systems Biology to facilitate data manipulation and innovation in the public sector. These data formats are described here. O ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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Mass Spectrometry Imaging
Mass spectrometry imaging (MSI) is a technique used in mass spectrometry to visualize the spatial distribution of molecules, as biomarkers, metabolites, peptides or proteins by their molecular masses. After collecting a mass spectrum at one spot, the sample is moved to reach another region, and so on, until the entire sample is scanned. By choosing a peak in the resulting spectra that corresponds to the compound of interest, the MS data is used to map its distribution across the sample. This results in pictures of the spatially resolved distribution of a compound pixel by pixel. Each data set contains a veritable gallery of pictures because any peak in each spectrum can be spatially mapped. Despite the fact that MSI has been generally considered a qualitative method, the signal generated by this technique is proportional to the relative abundance of the analyte. Therefore, quantification is possible, when its challenges are overcome. Although widely used traditional methodologies li ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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Insilicos
Insilicos is a life science software company founded in 2002 by Erik Nilsson, Brian Pratt and Bryan Prazen. Insilicos develops scientific computing software to provide software for disease diagnoses. Technology Insilicos' key technologies includes pattern recognition techniques to interpret proteomics mass spectrometry data. Insilicos products include InsilicosViewer and Insilicos Proteomics Pipeline (IPP). These products support the mzXML, mzDATA and mzML file formats. In 2007, Insilicos received a grant from the National Human Genome Research Institute to further develop software allowing for studies to be conducted more quickly. The open-source software, developed in connection with the Institute for Systems Biology, has been referred to as the Trans Proteomic Pipeline. IPP is commercial version of the Trans-Proteomic Pipeline The Trans-Proteomic Pipeline (TPP) is an open-source data analysis software for proteomics developed at the Institute for Systems Biology (ISB) ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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Proteomics Standards Initiative
The Proteomics Standards Initiative (PSI) is a working group of the Human Proteome Organization. It aims to define data standards for proteomics to facilitate data comparison, exchange and verification. The Proteomics Standards Initiative focuses on the following subjects: minimum information about a proteomics experiment defines the metadata that should be provided along with a proteomics experiment. a data markup language for encoding the data, and metadata ontologies for consistent annotation and representation. Minimum information about a proteomics experiment Minimum information about a proteomics experiment (MIAPE) is a minimum information standard, created by the Proteomics Standards Initiative of the Human Proteome Organization, for reporting proteomics experiments. You can't just introduce the results of an analysis, it is intended to specify all the information necessary to interpret the experiment results unambiguously and to potentially reproduce the experiment. Wh ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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ASTM International
ASTM International, formerly known as American Society for Testing and Materials, is a standards organization that develops and publishes voluntary consensus technical international standards for a wide range of materials, products, systems and services. Some 12,575 apply globally. The headquarters is in West Conshohocken, Pennsylvania, about northwest of Philadelphia. It was founded in 1902 as the American Section of the International Association for Testing Materials. In addition to its traditional standards work, ASTM operates several global initiatives advancing additive manufacturing, advanced manufacturing, and emerging technologies, including the Additive Manufacturing Center of Excellence (AM CoE), the acquisition oWohlers Associatesfor market intelligence and advisory services, and the National Institute of Standards and Technology, NIST-funded Standardization Center of Excellence (SCOE). History In 1898, a group of scientists and engineers, led by chemist, industry ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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JSON
JSON (JavaScript Object Notation, pronounced or ) is an open standard file format and electronic data interchange, data interchange format that uses Human-readable medium and data, human-readable text to store and transmit data objects consisting of name–value pairs and array data type, arrays (or other serialization, serializable values). It is a commonly used data format with diverse uses in electronic data interchange, including that of web applications with server (computing), servers. JSON is a Language-independent specification, language-independent data format. It was derived from JavaScript, but many modern programming languages include code to generate and parse JSON-format data. JSON filenames use the extension .json. Douglas Crockford originally specified the JSON format in the early 2000s. Transcript: He and Chip Morningstar sent the first JSON message in April 2001. Naming and pronunciation The 2017 international standard (ECMA-404 and ISO/IEC 21778:2017) ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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Triplestore
A triplestore or RDF store is a purpose-built database for the storage and retrieval of triples through semantic queries. A triple is a data entity composed of subject– predicate– object, like "Bob is 35" (i.e., Bob's age measured in years is 35) or "Bob knows Fred". Much like a relational database, information in a triplestore is stored and retrieved via a query language. Unlike a relational database, a triplestore is optimized for the storage and retrieval of triples. In addition to queries, triples can usually be imported and exported using the Resource Description Framework (RDF) and other formats. Implementations Some triplestores have been built as database engines from scratch, while others have been built on top of existing commercial relational database engines (such as SQL-based) or NoSQL document-oriented database engines. Like the early development of online analytical processing (OLAP) databases, this intermediate approach allowed large and powerful database ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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Allotrope Foundation
The Allotrope Foundation is a consortium of pharmaceutical companies, instrument vendors and software companies to simplify the exchange of scientific electronic data. It publishes the Allotrope Foundation Ontology (AFO) which is a controlled vocabulary to structure data, the Allotrope Data Models (ADM) and the Allotrope Data Format (ADF) based on HDF5 which incorporates those for use in practice. Standardization aims at the goal of FAIR data.{{cite journal , title=Coming of age of Allotrope: Proceedings from the Fall 2020 Allotrope Connect , journal=Drug Discovery Today , date=1 August 2021 , volume=26 , issue=8 , pages=1922–1928 , doi=10.1016/j.drudis.2021.03.028 , language=en , issn=1359-6446, doi-access=free , last1=Millecam , first1=Todd , last2=Jarrett , first2=Austin J. , last3=Young , first3=Naomi , last4=Vanderwall , first4=Dana E. , last5=Della Corte , first5=Dennis , pmid=33831582 Members Foundation members are Amgen, BASF, Bayer, Boehringer Ingelheim, Dow Chemical ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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Data-independent Acquisition
In mass spectrometry, data-independent acquisition (DIA) is a method of molecular structure determination in which all ions within a selected '' m/z'' range are fragmented and analyzed in a second stage of tandem mass spectrometry. Tandem mass spectra are acquired either by fragmenting all ions that enter the mass spectrometer at a given time (called broadband DIA) or by sequentially isolating and fragmenting ranges of '' m/z''. DIA is an alternative to data-dependent acquisition (DDA) where a fixed number of precursor ions are selected and analyzed by tandem mass spectrometry. Broadband One of the first DIA approaches was a nozzle-skimmer dissociation method called shotgun collision-induced dissociation (CID). Fragmentation can be in the ion source of the mass spectrometer by increasing the nozzle-skimmer voltage in electrospray ionization. MSE is a broadband DIA technique that uses alternating low-energy CID and high-energy CID. The low-energy CID is used to acquire precursor ion ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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Relational Database
A relational database (RDB) is a database based on the relational model of data, as proposed by E. F. Codd in 1970. A Relational Database Management System (RDBMS) is a type of database management system that stores data in a structured format using rows and columns. Many relational database systems are equipped with the option of using SQL (Structured Query Language) for querying and updating the database. History The concept of relational database was defined by E. F. Codd at IBM in 1970. Codd introduced the term ''relational'' in his research paper "A Relational Model of Data for Large Shared Data Banks". In this paper and later papers, he defined what he meant by ''relation''. One well-known definition of what constitutes a relational database system is composed of Codd's 12 rules. However, no commercial implementations of the relational model conform to all of Codd's rules, so the term has gradually come to describe a broader class of database systems, which at a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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SQLite
SQLite ( "S-Q-L-ite", "sequel-ite") is a free and open-source relational database engine written in the C programming language. It is not a standalone app; rather, it is a library that software developers embed in their apps. As such, it belongs to the family of embedded databases. It is the most widely deployed database engine, as it is used by several of the top web browsers, operating systems, mobile phones, and other embedded systems. Many programming languages have bindings to the SQLite library. It generally follows PostgreSQL syntax, but does not enforce type checking by default. This means that one can, for example, insert a string into a column defined as an integer. Although it is a lightweight embedded database, SQLite implements most of the SQL standard and the relational model, including transactions and ACID guarantees. However, it omits many features implemented by other databases, such as materialized views and complete support for triggers and AL ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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Universally Unique Identifier
A Universally Unique Identifier (UUID) is a 128-bit label used to uniquely identify objects in computer systems. The term Globally Unique Identifier (GUID) is also used, mostly in Microsoft systems. When generated according to the standard methods, UUIDs are, for practical purposes, unique. Their uniqueness does not depend on a central registration authority or coordination between the parties generating them, unlike most other numbering schemes. While the probability that a UUID will be duplicated is not zero, it is generally considered close enough to zero to be negligible. Thus, anyone can create a UUID and use it to identify something with near certainty that the identifier does not duplicate one that has already been, or will be, created to identify something else. Information labeled with UUIDs by independent parties can therefore be later combined into a single database or transmitted on the same channel, with a negligible probability of duplication. Adoption of UUIDs is wi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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HDF5
Hierarchical Data Format (HDF) is a set of file formats (HDF4, HDF5) designed to store and organize large amounts of data. Originally developed at the U.S. National Center for Supercomputing Applications, it is supported by The HDF Group, a non-profit corporation whose mission is to ensure continued development of HDF5 technologies and the continued accessibility of data stored in HDF. In keeping with this goal, the HDF libraries and associated tools are available under a liberal, BSD-like license for general use. HDF is supported by many commercial and non-commercial software platforms and programming languages. The freely available HDF distribution consists of the library, command-line utilities, test suite source, Java interface, and the Java-based HDF Viewer (HDFView). The current version, HDF5, differs significantly in design and API from the major legacy version HDF4. Early history The quest for a portable scientific data format, originally dubbed AEHOO (All Encompassin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |