diff --git a/productMods/WEB-INF/filegraph/tbox/agent.owl b/productMods/WEB-INF/filegraph/tbox/agent.owl index fea2366e..f8a451a8 100644 --- a/productMods/WEB-INF/filegraph/tbox/agent.owl +++ b/productMods/WEB-INF/filegraph/tbox/agent.owl @@ -150,34 +150,6 @@ - - - - - hospital units - - - - - - - - - hospitals - - - - - - - - - laboratories - - - - - diff --git a/productMods/WEB-INF/filegraph/tbox/contact-vcard.owl b/productMods/WEB-INF/filegraph/tbox/contact-vcard.owl index c719bdf7..23401744 100644 --- a/productMods/WEB-INF/filegraph/tbox/contact-vcard.owl +++ b/productMods/WEB-INF/filegraph/tbox/contact-vcard.owl @@ -150,11 +150,6 @@ - - - - - @@ -1115,9 +1110,6 @@ Was called CALADRURI in vCard - - - Defines all the properties required to be a Group of Individuals or Organizations @@ -1255,8 +1247,6 @@ Was called CALADRURI in vCard - - Defines all the properties required to be an Individual @@ -1330,7 +1320,7 @@ Was called IMPP in vCard. - + @@ -1338,59 +1328,11 @@ Was called IMPP in vCard. - - - - - - - - - 0 - - - - - - - - - - - - 0 - - - - - - - - - - - - 0 - - - - - - - - - - - - 0 - - - - + @@ -1402,7 +1344,7 @@ Was called IMPP in vCard. - + @@ -1410,71 +1352,11 @@ Was called IMPP in vCard. - - - - - - - - - 0 - - - - - - - - - - - - 0 - - - - - - - - - - - - 0 - - - - - - - - - - - - 0 - - - - - - - - - - - - 0 - - - - + @@ -1482,71 +1364,11 @@ Was called IMPP in vCard. - - - - - - - - - 0 - - - - - - - - - - - - 0 - - - - - - - - - - - - 0 - - - - - - - - - - - - 0 - - - - - - - - - - - - 0 - - - - + @@ -1554,23 +1376,11 @@ Was called IMPP in vCard. - - - - - - - - - 0 - - - - + @@ -1582,7 +1392,7 @@ Was called IMPP in vCard. - + @@ -1590,42 +1400,6 @@ Was called IMPP in vCard. - - - - - - - - - 0 - - - - - - - - - - - - 0 - - - - - - - - - - - - 0 - - - @@ -1664,7 +1438,6 @@ Was called IMPP in vCard. location (vcard c) - Defines all the properties required to be a Location @@ -2076,28 +1849,6 @@ Was called IMPP in vCard. - - - - role (vcard c) - - - - - - - - - - 1 - - - - - - To specify the function or part played in a particular situation by the object the vCard represents - - diff --git a/productMods/WEB-INF/filegraph/tbox/research-resource-iao.owl b/productMods/WEB-INF/filegraph/tbox/research-resource-iao.owl index 43b37ea3..2b748398 100644 --- a/productMods/WEB-INF/filegraph/tbox/research-resource-iao.owl +++ b/productMods/WEB-INF/filegraph/tbox/research-resource-iao.owl @@ -70,13 +70,6 @@ - - - - - - - diff --git a/productMods/WEB-INF/filegraph/tbox/research-resource.owl b/productMods/WEB-INF/filegraph/tbox/research-resource.owl index c3e0dfd5..796fdf84 100644 --- a/productMods/WEB-INF/filegraph/tbox/research-resource.owl +++ b/productMods/WEB-INF/filegraph/tbox/research-resource.owl @@ -113,6 +113,7 @@ http://www.yourdictionary.com/reagent reagent + @@ -298,25 +299,6 @@ - - - - data storage - - A data transformation technique that involves the process of recording or retrieving information or data. - Information storage - PERSON: Karen Corday - Storing data on a server. - bulk data storage - data storage - http://en.wikipedia.org/wiki/Data_storage - research data storage - - - - - - @@ -331,35 +313,6 @@ - - - - - - - data entry - - A data transformation technique that involves transcribing some form of data into another form, usually a computer program. - Entry of data about research resources into eagle-i. - PERSON: Nicole Vasilevsky - http://www.wisegeek.com/what-is-data-entry.htm - - - - - - - - - bioinformatics analysis - - A data transformation technique that involves the analysis of bioinformatics data, which is the application of statistics and computer science to the field of molecular biology. - Analysis of DNA sequence data. - PERSON: Nicole Vasilevsky - http://en.wikipedia.org/wiki/Bioinformatics - - - @@ -556,768 +509,4 @@ - - - - academic software license - - - - - - - software license - - - - - - - - - - - spreadsheet - - A spreadsheet data format is one in which data is organised into a matrix (or matrices) of columns and rows to form cells in which values are entered. - - - - - - - - - xls spreadsheet - - A spreadsheet data format designed for Microsoft Excel. - - - - - - - - - xml spreadsheet - - A spreadsheet data format in which the structure of the data is described using XML, such as column and row headers and cell identity. - - - - - - - - - matlab m file - - - - - - - - - - xml - - Extensible Markup Language (XML) is a standard set of rules for encoding documents in a machine-readable form defined by the W3C. - - - - - - - - - rdf - - http://www.w3.org/TR/REC-rdf-syntax/ - The Resource Description Framework (RDF) is a general-purpose language for representing information in the Web. - - - - - - - - - rdf-xml - - - A serialisation of RDF into an XML format. - - - - - - - - - image format - - - - - - - - - - dwg - - http://en.wikipedia.org/wiki/.dwg - DWG ("drawing") is a binary file format used for storing two and three dimensional design data and metadata - - - - - - - - - dxf - - http://en.wikipedia.org/wiki/AutoCAD_DXF - DXF (Drawing Interchange Format, or Drawing Exchange Format) is a CAD data file format developed by Autodesk for enabling data interoperability between AutoCAD and other programs. - - - - - - - - - bmp - - http://www.fileformat.info/format/bmp/egff.htm - The BMP File Format is a Raster graphics image file format used to store bitmap digital images, independently of the display device (such as a graphics adapter). - - - - - - - - - cgm - - Computer Graphics Metafile (CGM) is a free and open international standard file format for 2D vector graphics, raster graphics, and text, and is defined by ISO/IEC 8632. - http://en.wikipedia.org/wiki/Computer_Graphics_Metafile - - - - - - - - - web page specification - - - - - - - - - - document exchange format - - - - - - - - - - pdf - - Portable Document Format - PDF is an open standard for document exchange. - - - - - - - - - tiff - - Tagged Image File Format - TIFF is a flexible, adaptable file format for handling images and data within a single file, by including the header tags (size, definition, image-data arrangement, applied image compression) defining the image's geometry. - - - - - - - - - jpeg - - JPEG is a lossy file format for storing images - JPG - - - - - - - - - png - - Portable Network Graphics - PNG is a bitmapped image format and video codec that employs lossless data compression. - - - - - - - - - gif - - The Graphics Interchange Format (GIF) is a bitmap image format. The format supports up to 8 bits per pixel thus allowing a single image to reference a palette of up to 256 distinct colors. The colors are chosen from the 24-bit RGB color space. It also supports animations and allows a separate palette of 256 colors for each frame. The color limitation makes the GIF format unsuitable for reproducing color photographs and other images with continuous color, but it is well-suited for simpler images such as graphics or logos with solid areas of color. [wikipedia] - Graphics Interchange Format - - - - - - - - - raster image format - - A raster image is a format for representing a rectangular grid of dots (pixels) which contains information on the specific colour of each pixel. - - - - - - - - - vector image format - - A vector image is a collection of connected lines and curves that produce objects. This geometric description enables the image to be displayed without loss at any size rendering. - - - - - - - - - svg - - Scalable Vector Graphics - - - - - - - - - ai - - Adobe Illustrator format - - - - - - - - - postscript - - PostScript is a format used for describing documents. - - - - - - - - - tex - - LaTeX format - tex is a format for documents written in the document markup language and document preparation system LaTeX. - - - - - - - - - outline document format - - A format specification for data used or produced by outliner software - - - - - - - - - omnioutline format - - A proprietary format for documents created and edited using OmniOutliner outliner software, - - - - - - - - - opml - - OPML (Outline Processor Markup Language) is an XML format for outlines - Outline Processor Markup Language - - - - - - - - - jpeg 2000 - - JPEG 2000 is a compression standard enabling both lossless and lossy storage. The compression methods used are different from the ones in standard JFIF/JPEG; they improve quality and compression ratios, but also require more computational power to process. [wikipedia] - - - - - - - - - word processing document format - - - - - - - - - - wordstar format - - - - - - - - - - microsoft word doc - - A file format for word processing documents for Microsoft Word. - - - - - - - - - programming language format - - - - - - - - - - .java file - - James Malone - A source code file format which is specified to be used with the Java programming language. - - - - - - - - - .class file - - A format in which a .java file has been compiled into bytecode using a Java compiler and which is specified to be executed using the Java virtual machine. - James Malone - - - - - - - - - copasiml - - .cps - An XML-based file format for use with the COPASI software. - - - - - - - - - sbml - - Systems Biology Markup Language - Systems Biology Markup Language (SBML) is a machine-readable format for representing models. It's oriented towards describing systems where biological entities are involved in, and modified by, processes that occur over time. - http://sbml.org - - - - - - - - - owl-xml - - The Web Ontology Language (OWL) in XML serialization - - - - - - - - - owl2-xml - - Web Ontology Language version 2 in XML Serialization - - - - - - - - - obo flat file format - - OBO format is the text file format used by OBO-Edit, the open source, platform-independent application for viewing and editing ontologies. - - - - - - - - - text file format - - - - - - - - - - ascii format - - - - - - - - - - plain text file format - - - - - - - - - - mage tab format - - MAGE-TAB is a tab delimited data format comprimising of ADF file for array design, IDFfor experimental design, SDRF for sample data relationships and associated data files. - http://www.mged.org/mage-tab/ - A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. - - - - - - - - - tab delimited file format - - - - - - - - - - psi-mi format - - Modified from http://wiki.cytoscape.org/GettingStarted, accessed 20 June 2012. - The PSI-MI format is an acronym for the Proteomics Standards Initiative - Molecular Interaction format. It provides an XML standard for molecular interactions and is supported by many molecular interaction databases and tools. - PSI-MIF - - - - - - - - - sif - - http://wiki.cytoscape.org/GettingStarted and http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats, accessed 20 June 2012 - SIF stands for Simple Interaction Format, and is a text format invented for Cytoscape. If the file contains any tab characters, then tabs are used to delimit the fields and spaces are considered part of the name. If the file contains no tabs, then any spaces are delimiters that separate names (and names cannot contain spaces). - - - - - - - - - gml - - GML stands for Graph Markup Language, and is a standard network file format; supported by multiple generic network software packages - http://wiki.cytoscape.org/GettingStarted, accessed 20 June 2012 - - - - - - - - - xgmml - - XGMML stands for eXtensible Graph Markup and Modelling Language, and it is a XML standard; similar to but preferred over GML. - http://wiki.cytoscape.org/GettingStarted, accessed 20 June 2012 - - - - - - - - - biopax rdf/xml format - - - - - - - - - - biopax manchester owl syntax format - - - - - - - - - - creative commons - - - - - - - - - - proprietary commercial software license - - - - - - - - - - mozilla public license version 1.1 - - - - - - - - - - gnu general public license - - - - - - - - - - apache license v2 - - - - - - - - - - academic license version 3 - - - - - - - - - - freebsd license - - 2 clause BSD License - - - - - - - - - open source software license - - - - - - - - - - license without restrictions on derivatives - - - - - - - - - - mit license - - - - - - - - - - lesser gnu public license - - - - - - - - - - the artistic license 1.0 - - - - - - - - - - eclipse public license - - - - - - - - - - modified bsd license - - 3 clause BSD License - - - - - - - - - latex project public license - - - - - - - - - - open public license - - http://wyatterp.com/opl.html - - - - - - - - - mozilla public license - - - - - - diff --git a/productMods/WEB-INF/filegraph/tbox/research.owl b/productMods/WEB-INF/filegraph/tbox/research.owl index cb31ce2c..104e0be3 100644 --- a/productMods/WEB-INF/filegraph/tbox/research.owl +++ b/productMods/WEB-INF/filegraph/tbox/research.owl @@ -65,422 +65,6 @@ - - - - gene knockdown function - - A perturb function that results in decreased expression levels of a target gene. This can be achieved through targeting a gene directly through gene knockout or modification of the its DNA sequence, or targeting of the mRNA product of a gene using technologies such as RNAi. - Gene repression function - Gene silencing function - Knockdown the function of a gene, to study the function of that gene. - PERSON: Matthew Brush - PERSON: Matthew Brush - - - - - - - - - rna interference function - - A gene knockdown function that targets genes for post-transcriptional silencing through the RNA interference pathway. - PERSON: Matthew Brush - PERSON: Matthew Brush - RNAi function - - - - - - - - - - - - - - - record function - - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - A record function is a function that registers or collects information in a particular format on a particular recording medium. For example on paper or a digital representation - record function - - - - - - - - - - magnify function - - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path. - magnify function - - - - - - - - - - contain function - - A syringe, a beaker - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - A contain function is a function to constrain a material entities location in space - contain function - - - - - - - - - - heat function - - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - A heat function is a function that increases the internal kinetic energy of a material - heat function - - - - - - - - - - material separation function - - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality. - material separation function - - - - - - - - - - excitation function - - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons. - excitation function - - - - - - - - - - freeze function - - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material. - freeze function - - - - - - - - - - synthesizing function - - A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - synthesizing function - - - - - - - - - - perturb function - - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - A perturb function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function. - http://en.wikipedia.org/wiki/Perturbation_biology - perturb function - - - - - - - - - - mechanical function - - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force). - http://en.wikipedia.org/wiki/Mechanical_work - mechanical function - - - - - - - - - - transfer function - - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - A transfer function is a function to displace a material from one location to another. - transfer function - - - - - - - - - - cool function - - Daniel Schober - Frank Gibson - Melanie Courtot - A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material. - cool function - - - - - - - - - - information processor function - - Frank Gibson - An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process. - data processor function - information processor function - - - - - - - - - - signal conversion function - - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - transduction function - A signal conversion function is an information processor function which transforms a signal into another type of signal. For example an analog-to-digital_converter, Ac/Ac converter, a synapse converts electrical action potentials into an intermediate chemical signal. The post synapse converts it back into an electric one passed on to the axon. - signal conversion function - - - - - - - - - - signal amplification function - - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - A signal amplification function is a signal conversion function to inject energy into an input signal so as to produce an output signal with increased differential magnitude while also seeking to minimize increases in the signal to noise ratio. For example, to produce a 0.1 KW output signal from a 1 mW RMS input signal. - signal amplification function - - - - - - - - - - image acquisition function - - Frank Gibson - An image acquisition function is a function to acquire an image of a material - image acquisition function - - - - - - - - - - environment control function - - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature. - environment control function - - - - - - - - - - measure function - - A glucometer measures blood glucose concentration, the glucometer has a measure function. - PERSON: Daniel Schober - PERSON: Helen Parkinson - PERSON: Melanie Courtot - PERSON:Frank Gibson - Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference. - measure function - - - - - - - - - - sterilization function - - a function to remove viable organisms from an input material - sterilization function - - - - - - - - - - reagent application function - - reagent application function - An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations. - A function that is realized when a reagent is automatically added to some research material. - PERSON: Nicole Vasilevsky, Matthew Brush - PERSON: Nicole Vasilevsky, Matthew Brush - - - - - - - - - - addition of molecular tracer function - - addition of molecular tracer function - PERSON: Nicole Vasilevsky, Matthew Brush - A reagent application function that is realized when a molecular tracer, such as an antibody or probe is automatically transferred to a biological specimen. - PERSON: Nicole Vasilevsky, Matthew Brush - Immunohistochemical labeling of tissue sections by an autostainer staining system. - - - - - - - - - - specimen fixation function - - EAGLE-I - a function that allows specific identification of individual speciment from one another. - e.g the function of a bar code reader used to read slide bar codes - specimen fixation function - - - - - - - - - - cell transfer function - - A cell harvester has a cell transfer function. - EAGLE-I - cell transfer function - is a transfer function that displaces cells from one place to another - - - - - -