Portable Document Format (PDF), standardized as ISO 32000, is a file format developed by Adobe in 1992 to present documents, including text formatting and images, in a manner independent of application software, hardware, and operating systems. Based on the PostScript language, each PDF file encapsulates a complete description of a fixed-layout flat document, including the text, fonts, vector graphics, raster images and other information needed to display it. PDF has its roots in "The Camelot Project" initiated by Adobe co-founder John Warnock in 1991.
The Semantic Web, sometimes known as Web 3.0, is an extension of the World Wide Web through standards set by the World Wide Web Consortium (W3C). The goal of the Semantic Web is to make Internet data machine-readable.
Waveform Audio File Format is an audio file format standard, developed by IBM and Microsoft, for storing an audio bitstream on PCs. It is the main format used on Microsoft Windows systems for uncompressed audio. The usual bitstream encoding is the linear pulse-code modulation (LPCM) format.
The JPEG File Interchange Format (JFIF) is an image file format standard published as ITU-T Recommendation T.871 and ISO/IEC 10918-5. It defines supplementary specifications for the container format that contains the image data encoded with the JPEG algorithm. The base specifications for a JPEG container format are defined in Annex B of the JPEG standard, known as JPEG Interchange Format (JIF). JFIF builds over JIF to solve some of JIF's limitations, including unnecessary complexity, component sample registration, resolution, aspect ratio, and color space. Because JFIF is not the original JPG standard, one might expect another mime-type. However, it is still registered as "image/jpeg".
A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Each DNA spot contains picomoles of a specific DNA sequence, known as probes. These can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA sample under high-stringency conditions. Probe-target hybridization is usually detected and quantified by detection of fluorophore-, silver-, or chemiluminescence-labeled targets to determine relative abundance of nucleic acid sequences in the target. The original nucleic acid arrays were macro arrays approximately 9 cm × 12 cm and the first computerized image based analysis was published in 1981. It was invented by Patrick O. Brown. An example of its application is in SNPs arrays for polymorphisms in cardiovascular diseases, cancer, pathogens and GWAS analysis. It is also used for the identification of structural variations and the measurement of gene expression.
Job Definition Format (JDF) is a technical standard being developed by the graphic arts industry to facilitate cross-vendor workflow implementations of the application domain. It is an XML format about job ticket, message description, and message interchange. JDF is managed by CIP4, the International Cooperation for the Integration of Processes in Prepress, Press and Postpress Organization. JDF was initiated by Adobe Systems, Agfa, Heidelberg and MAN Roland in 1999 but handed over to CIP3 at Drupa 2000. CIP3 then renamed itself CIP4.
Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology.
In the field of molecular biology, gene expression profiling is the measurement of the activity of thousands of genes at once, to create a global picture of cellular function. These profiles can, for example, distinguish between cells that are actively dividing, or show how the cells react to a particular treatment. Many experiments of this sort measure an entire genome simultaneously, that is, every gene present in a particular cell.
PDF/A is an ISO-standardized version of the Portable Document Format (PDF) specialized for use in the archiving and long-term preservation of electronic documents. PDF/A differs from PDF by prohibiting features unsuitable for long-term archiving, such as font linking and encryption. The ISO requirements for PDF/A file viewers include color management guidelines, support for embedded fonts, and a user interface for reading embedded annotations.
RDFa or Resource Description Framework in Attributes is a W3C Recommendation that adds a set of attribute-level extensions to HTML, XHTML and various XML-based document types for embedding rich metadata within Web documents. The Resource Description Framework (RDF) data-model mapping enables its use for embedding RDF subject-predicate-object expressions within XHTML documents. It also enables the extraction of RDF model triples by compliant user agents.
MIRIAM is a community-level effort to standardize the annotation and curation processes of quantitative models of biological systems. It consists of a set of guidelines suitable for use with any structured format, allowing different groups to collaborate and share resulting models. Adherence to these guidelines also facilitates the sharing of software and service infrastructures built upon modeling activities.
Microarray analysis techniques are used in interpreting the data generated from experiments on DNA, RNA, and protein microarrays, which allow researchers to investigate the expression state of a large number of genes - in many cases, an organism's entire genome - in a single experiment. Such experiments can generate very large amounts of data, allowing researchers to assess the overall state of a cell or organism. Data in such large quantities is difficult - if not impossible - to analyze without the help of computer programs.
The Functional GEnomics Data Society (FGED) was a non-profit, volunteer-run international organization of biologists, computer scientists, and data analysts that aims to facilitate biological and biomedical discovery through data integration. The approach of FGED was to promote the sharing of basic research data generated primarily via high-throughput technologies that generate large data sets within the domain of functional genomics.
Gene Expression Omnibus (GEO) is a database for gene expression profiling and RNA methylation profiling managed by the National Center for Biotechnology Information (NCBI). These high-throughput screening genomics data are derived from microarray or RNA-Seq experimental data. These data need to conform to the minimum information about a microarray experiment (MIAME) format.
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 Sample and Data Relationship Format (SDRF) is part of the MAGE-TAB standard for communicating the results of microarray investigations, including all information required for MIAME compliance.
Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves as a transient intermediary molecule in the information network, whilst non-coding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell. Transcriptomics technologies provide a broad account of which cellular processes are active and which are dormant. A major challenge in molecular biology is to understand how a single genome gives rise to a variety of cells. Another is how gene expression is regulated.
The Minimum Information Required About a Glycomics Experiment (MIRAGE) initiative is part of the Minimum Information Standards and specifically applies to guidelines for reporting on a glycomics experiment. The initiative is supported by the Beilstein Institute for the Advancement of Chemical Sciences. The MIRAGE project focuses on the development of publication guidelines for interaction and structural glycomics data as well as the development of data exchange formats. The project was launched in 2011 in Seattle and set off with the description of the aims of the MIRAGE project.
Theresa Gaasterland is an American politician and scientist. She is a Professor of Computational Biology and Genomics and Director of the Scripps Genome Center at the University of California, San Diego (UCSD). She was elected a Fellow of the International Society for Computational Biology (ISCB) in 2018 for outstanding contributions to the fields of computational biology and bioinformatics.
Minimum information standards are sets of guidelines and formats for reporting data derived by specific high-throughput methods. Their purpose is to ensure the data generated by these methods can be easily verified, analysed and interpreted by the wider scientific community. Ultimately, they facilitate the transfer of data from journal articles into databases in a form that enables data to be mined across multiple data sets. Minimal information standards are available for a vast variety of experiment types including microarray (MIAME), RNAseq (MINSEQE), metabolomics (MSI) and proteomics (MIAPE).
