obi-bot
commented
15 years ago merge with old tracker item https://sourceforge.net/tracker/index.php?func=detail&aid=1917039&group\_id=177891&atid=886178 which I have now closed
MathML, SMILES, FieldML, SBML, and CellML formats
MathML proposed def: MathML 2.0, a W3C Recommendation was released on 21 Feb 2001. A product of the W3C Math working group, MathML is a low-level specification for describing mathematics as a basis for machine to machine communication. It provides a much needed foundation for the inclusion of mathematical expressions in Web pages def src: http://www.w3.org/Math/
FieldML proposed def: FieldML is an XML-based language for describing time-varying and spatially-varying fields. The aims of the language design process are to keep the language concise, consistent, intuitive and flexible. def src: http://www.physiomeproject.org/xml\_languages/fieldml
SMILES proposed def: SMILES™ (Simplified Molecular Input Line Entry System) as a simple yet comprehensive chemical language in which molecules and reactions can be specified using ASCII characters representing atom and bond symbols. SMILES™ contains the same information as is found in an extended connection table but with several advantages. A SMILES™ string is human understandable, very compact, and if canonicalized represents a unique string that can be used as a universal identifier for a specific chemical structure. In addition, a chemically correct and comprehensible depiction can be made from any SMILES™ string symbolizing either a molecule or reaction. SMILES™ development was initiated by David Weininger in the late 1980s using the concept of a graph with nodes as atoms and edges as bonds to represent a molecule. Parentheses are used to indicate branching points and numeric labels designate ring connection points. The basic SMILES™ grammar also includes as well as isotopic information, configuration about double bonds, and chirality leading to what is known as isomeric SMILES™. Since its inception, SMILES™ has been modified and expanded by Daylight to include not only new features but two additional chemical languages: SMARTS®, an expansion of SMILES™ allowing specification of molecular patterns and properties for substructure searching with varying levels of specificity, and SMIRKS®, a restricted version of reaction SMARTS® involving changes in atom-bond patterns that define generic reactions. def src: http://www.daylight.com/smiles/
SBML proposed def: The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biochemical reaction networks in software. It's applicable to models of metabolism, cell-signaling, and many others. def src: http://sbml.org/
CellML proposed def: The purpose of CellML is to store and exchange computer-based mathematical models. CellML allows scientists to share models even if they are using different model-building software. It also enables them to reuse components from one model in another, thus accelerating model building. Although CellML was originally intended for the description of biological models, it has a broader application (for an example, see the classical Mooney-Rivlin Constitutive Material Law). CellML includes information about model structure (how the parts of a model are organizationally related to one another), mathematics (equations describing the underlying processes) and metadata (additional information about the model that allows scientists to search for specific models or model components in a database or other repository). CellML includes mathematics and metadata by leveraging existing languages, including MathML and RDF. In the future, CellML may also use other existing languages to specify data and define simulation and rendering information. def src: http://www.cellml.org/
Original comment by: mcourtot
Generated during and then after the workshop this summer for addition to OBI (or IO):
wk? is a data matrix file format specific for the 1-2-3 software wb? is a data matrix file format specific for the 1-2-3 software stsd is a data matrix file format encoded in the ASCII - Delimited with Schema format stsf is a data matrix file format encoded in the ASCII - Fixed with Schema format txt,csv is a data matrix file format encoded in the ASCII - Delimited format fix is a data matrix file format encoded in the ASCII - Fixed Format - all programs format sts is a data matrix file format encoded in the ASCII - With Schema - Input format rdata is a data matrix file format for the R language, encoded in ASCII format ssd04 is a data matrix file format specific for the SAS V6 for Unix - DEC software ssd01 is a data matrix file format specific for the SAS V6 for Mac, Unix - HP, Sun, IBM software stc is a data matrix file format specific for the SAS CPORT software tpt is a data matrix file format specific for the SAS Transport Files software xpt is a data matrix file format specific for the SAS Transport Files software xls is a data matrix file format specific for the Excel Version 2 software wq? is a data matrix file format specific for the Quattro Pro software wb? is a data matrix file format specific for the Quattro Pro software sd2 is a data matrix file format specific for the SAS V6 for Windows and OS/2 software sas7bdat is a data matrix file format specific for the SAS V7, V8 and V9 for Windows software sys is a data matrix file format specific for the SYSTAT software dta is a data matrix file format specific for the Stata (Standard) software sps is a data matrix file format specific for the SPSS 'Syntax' & Data File software do is a data matrix file format specific for the Stata Program & Data File software dta is a data matrix file format specific for the Stata/SE software sav is a data matrix file format specific for the SPSS Data for Windows, OS/2, DEC Unix software . is a data matrix file format specific for the S-PLUS for Windows, OS/2, DEC Unix software por is a data matrix file format specific for the SPSS Portable software sav is a data matrix file format specific for the SPSS Data for Unix - HP, Sun, IBM software dbf is a data matrix file format specific for the FoxPro software dat is a data matrix file format specific for the Gauss software dat is a data matrix file format specific for the Gauss '96 software dbf is a data matrix file format specific for the dBASE and compatibles software epi is a data matrix file format specific for the Epi Info software xlsx is a data matrix file format specific for the Excel 2007 software xls is a data matrix file format specific for the Excel 97+ software jmp is a data matrix file format specific for the JMP software dbf is a data matrix file format specific for the Paradox software mtw is a data matrix file format specific for the Minitab software jmp is a data matrix file format specific for the JMP Version 3 software dct is a data matrix file format specific for the OSIRIS software dict is a data matrix file format specific for the OSIRIS software lpj is a data matrix file format specific for the NLOGIT software lpj is a data matrix file format specific for the LIMDEP software schema is a data matrix file format specific for the Mineset software mat is a data matrix file format specific for the Matlab software html is a data matrix file format for the HTML standard
Reported by: jamesmalone
Original Ticket: "obi/obi-terms/111":https://sourceforge.net/p/obi/obi-terms/111