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24-519: Members of the FGED Society worked with other organizations to support the effective sharing and reproducibility of functional genomics data; facilitate the creation of standards and software tools that leverage the standards; and promote the sharing of high quality, well annotated data within the life sciences and biomedical communities. Founded in 1999 as the "Microarray Gene Expression Data (MGED) Society", this organization changed its name to

48-582: A non-profit public benefit organization with the title Microarray Gene Expression Data Society and obtained permanent charity status in 2007. The MGED name was legally changed in 2007 to Microarray and Gene Expression Data Society to emphasize a broader scope. In September 2008, the Society decided to promote itself simply as the MGED Society to broaden the Society's scope beyond microarray technology and gene expression applications, yet still retain

72-532: A cross-section of those generating, analyzing, archiving, and publishing in the functional genomics area. Although there is no formal membership, the attendees of the annual FGED meetings are considered to be part of the FGED community. To date, FGED has produced a variety of standards specifications pertaining to DNA microarray experiments. These standards are designed to improve the annotation, communication, and sharing of data and findings from such experiments within

96-492: A standard terminology for describing components of a DNA microarray experiment. The Ontology for Biomedical Investigations (OBI) is being developed as a replacement for the MO. A mapping of ontology terms from MO to OBI is available. A major component of the FGED Society effort has been the annual FGED meeting to showcase cutting-edge scientific work and promote standards. The FGED Society has held its annual meeting at venues around

120-505: A way to " escape " the field wrapper itself, in this case the double quote; it is customary to double the double quotes actually contained in a field as with those surrounding "Hank". In this way, any ASCII text including newlines can be contained in a field. ASCII and Unicode include several control characters that are intended to be used as delimiters. They are: 28 for File Separator , 29 for Group Separator , 30 for Record Separator , and 31 for Unit Separator . Example of such use

144-412: Is MARC 21 bibliographic data format. Use of these characters has not achieved widespread adoption; some systems have replaced their control properties with more accepted controls such as CR/LF and TAB. Due to their widespread use, comma- and tab-delimited text files can be opened by several kinds of applications, including most spreadsheet programs and statistical packages , sometimes even without

168-454: Is a data content standard that describes the essential information needed to adequately document a DNA microarray experiment for the purpose of interpretation and replication of the results. It was the first published example of a minimum information standard for high-throughput experiments in the life sciences, and as such, laid the groundwork for similar standards in other bioscience domains. MAGE-OM (MicroArray Gene Expression Object Model)

192-621: Is a data exchange and data modeling standard for use in encoding data from microarray experiments for the purpose of export and import into software tools and databases via XML files. MAGE-OM is a platform-independent model implemented in the XML-based MAGE-ML format. A new version, MAGE-TAB , has been developed to be easier to understand and generate by data producers as it is in a format ( tab-delimited ) that can be viewed and edited using widely available spreadsheet software, such as Microsoft Excel . The MGED Ontology (MO) provides

216-409: Is a problem that occurs when a character that is intended as part of the data gets interpreted as a delimiter instead. Comma- and space-separated formats often suffer from this problem, since in many contexts those characters are legitimate parts of a data field. Most such files avoid delimiter collision either by surrounding all data fields in double quotes, or only quoting those data fields that contain

240-484: Is the study of animals, while botany is the study of plants. Other life sciences focus on aspects common to all or many life forms, such as anatomy and genetics . Some focus on the micro-scale (e.g. molecular biology , biochemistry ) other on larger scales (e.g. cytology , immunology , ethology , pharmacy, ecology). Another major branch of life sciences involves understanding the mind  – neuroscience . Life sciences discoveries are helpful in improving

264-462: The "Functional Genomics Data Society" in 2010 to reflect the fact that it has broadened its focus beyond the application of DNA microarrays for gene expression analysis to include technologies such as high-throughput sequencing . The scope of the FGED Society includes data generated using any functional genomics technology when applied to genome-scale studies of gene expression, binding, modification and other related applications. In September 2021,

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288-412: The FGED Society ceased operations. The FGED Society was formed in 1999 at a meeting on Microarray Gene Expression Databases in recognition of the need to establish standards for sharing and storing data from DNA microarray experiments. Originally named the "MGED Society," the society began with a focus on DNA microarrays and gene expression data. The original MGED Society was incorporated in 2002 as

312-459: The data itself, it may be beneficial to use non-standard characters such as the tilde (~) as delimiters. With rising prevalence of web sites and other applications that store snippets of code in databases, simply using a " which occurs in every hyperlink and image source tag simply is not sufficient to avoid this type of collision. Since colons (:), semi-colons (;), pipes (|), and many other characters are also used, it can be quite challenging to find

336-432: The delimiter character. One problem with tab-delimited text files is that tabs are difficult to distinguish from spaces; therefore, there are sometimes problems with the files being corrupted when people try to edit them by hand. Another set of problems occur due to errors in the file structure, usually during import of file into a database (in the example above, such error may be a pupil's first name missing). Depending on

360-438: The delimiter. Compared to the kind of flat file that uses spaces to force every field to the same width, a delimited file has the advantage of allowing field values of any length. Any character may be used to separate the values, but the most common delimiters are the comma , tab , and colon . The vertical bar (also referred to as pipe ) and space are also sometimes used. Column headers are sometimes included as

384-409: The first line, and each subsequent line is a row of data. The lines are separated by newlines . For example, the following fields in each record are delimited by commas, and each record by newlines: Note the use of the double quote to enclose each field. This prevents the comma in the actual field value (Bloggs, Fred; Doe, Jane; etc.) from being interpreted as a field separator. This necessitates

408-404: The life science research community. Minimal Information about a high-throughput SEQuencing Experiment (MINSEQE) is a data content minimum information standard that describes the essential information needed to adequately document a high-throughput sequencing experiment for the purpose of interpretation and replication of the results. MIAME (Minimal Information About a Microarray Experiment)

432-414: The quality and standard of life and have applications in health, agriculture, medicine, and the pharmaceutical and food science industries. For example, it has provided information on certain diseases which has overall aided in the understanding of human health. Delimiter-separated values Formats that use delimiter-separated values (also DSV ) store two-dimensional arrays of data by separating

456-510: The recognized value of the MGED name within the community. In July 2010, the society voted to change its name to the "Functional Genomics Data (FGED) Society" to reflect its current mission which goes beyond microarrays and gene expression to encompass data generated using any functional genomics technology applied to genomic -scale studies of gene expression, binding , modification (such as DNA methylation ), and other related applications. This

480-445: The scientific study of life – such as microorganisms , plants, and animals including human beings . This science is one of the two major branches of natural science , the other being physical science , which is concerned with non-living matter. Biology is the overall natural science that studies life, with the other life sciences as its sub-disciplines. Some life sciences focus on a specific type of organism. For example, zoology

504-440: The user designating which delimiter has been used. Despite that each of those applications has its own database design and its own file format (for example, accdb or xlsx), they can all map the fields in a DSV file to their own data model and format. Typically a delimited file format is indicated by a specification. Some specifications provide conventions for avoiding delimiter collision , others do not. Delimiter collision

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528-422: The values in each row with specific delimiter characters . Most database and spreadsheet programs are able to read or save data in a delimited format. Due to their wide support, DSV files can be used in data exchange among many applications. A delimited text file is a text file used to store data, in which each line represents a single book, company, or other thing, and each line has fields separated by

552-433: The world since 1999, coordinating with a local scientific organization that provides space for talks, poster sessions, workshops, and tutorials. Here is a list of the annual meeting dates and locations for past meetings of the FGED Society. All meetings from 2010 and prior were held under the name "MGED Society". Life sciences This list of life sciences comprises the branches of science that involve

576-451: Was formally announced on 14 July 2010 at the society's "MGED13" annual meeting. Board members and officers of the FGED Society are elected annually each May and start serving in June. Presidents of the FGED Society along with their terms in office are as follows: The FGED Board of Directors and Advisory Board consist of volunteers from academia, industry, government, and journals representing

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