Effectopedia Files

Download and use effectopedia.jar without need of installation on Windows, Mac OS, Linux and other operating systems supporting Java SE 8. You can use the windows setup file available in Windows_Installer folder if you prefer to run Effectopedia as a native windows application. Effectopedia could be also used offline by loading the last official release of the centralized database file available in OfflineDB folder. 

        ***** Effectopedia 0.9.62 (r411) Alpha Update Log ***** 27 Jan 2016
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Multiple changes and additions were made since last public release of version 0.9.46 the most significant of which are described below. Details can be obtained from the SVN release 338-411

              *************** User interface changes ***************
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    -------- Harmonisation with the OECD Guidance and terminology -------------   
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The basic building block of AOPs: effects and links are now referred as (key) events and (key) event relationships, respectively. Since Link is broader concept it is still used to connect chemical structures with Molecular Initiating Events (MIE)s and two chemicals when representing absorption, distribution, metabolism, and excretion (ADME) processes. Effectopedia encourages linking of existing and creation of new and description of non-key events (e.g. biomarkers) as part of the AOP description. Since events can be key in some pathways and non-key in others the key term is shown in brackets. 
Below are listed some of the harmonisation related changes 
 - Introduction of  LinkType  which could have one of three possible values Unknown, Direct and Indirect. The quantitative nature of relationship is now represented in the field Link Nature
 - (Key) event Relationship Weight of Evidences is a structured description section which provides a field with four possible values – undefined, weak, moderate and strong to summarise the weight of available evidences. The evidences can be further described in the body of the section by describing the biological plausibility, empirical support of linkage and uncertainties or inconsistencies. More details of the empirical support and uncertainties can be provided in the explicit elements (tests, transformation functions (test response mappings), measured data with statistical errors from multiple sources)
 - Support of Essentiality of (Key) Events is now introduced as structured description section of an AOP element. Each event included in the pathway is listed as expandable structured description section.  The essentiality of the key events can be categorised as undefined, weak, moderate and strong. A separate key word will be proposed for non-key events e.g. non-essential. 
 - AOP status free text field was introduced as part of AOP properties
 - A comma separated list of pathway identifiers was also introduced as part of AOP properties. The OECD Project Number can be listed in this field. 
 - Several default description sections were added to different elements. E.g. Quantitative considerations, Applicability of the AOP, Considerations for Potential Application in the pathway description,  Measurement and Detection section in the (key) events, etc. 


    ---------------  Response – response editing interface --------------------
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Response-response editing interface is now available in the (Key) Event Relationship (the link between two events). The interface allows the editing of Proportional, Threshold and data based Response-Response curves. New more universal Analytic function interface is under development which will allow the definition of wide variety of analytic functions. Also categorical response – response curve will be also added for the cases where no continuous information is available. All data interfaces allow definition statistical errors (available by default are: standard deviation, standard error and 95% confidence interval).  In case of analytic function the statistical error need to be provided using the same function type as the relationship. 


    -------------------  Dose – Response editing interface --------------------   
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Dose – response editing interface is now available in the Link between Chemical Structure and MIE, as well as part of summary information on tested substances in Test definition. Dose response in the Test definition can also include the data measured for a reference substance. All dependencies are shown in the embedded chart component along with error bars and areas. Appearance of the charts can be customized and saved as part of the description. 


    --------------------  Chemical substance interface  ----------------------
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Major changes of the chemical structure interface were made with the introduction of substances. While the chemical structure elements represent an abstract notion of chemical a substance represents a physical entity which can be associated with specific supplier or manufacturer. Therefore a single chemical structure can correspond to one or more physical substances. The substances themselves can consist of constituents. Each constituent refers to a specific structure and its typical and actual percent of the mix mass. Each element of the physical mix can be marked as constituent or impurity. Substances can have their own list of identifiers and properties. The new substance interface is embedded in Chemical Structure interface in a collapsible panel


    ------------  Element editor in the Pathway View  ------------------------
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New element editor is now available in the main pathway viewer available under View tab from the main interface. The new element editor allows users when in edit mode to click on any element of a pathway and load its dedicated editor. When clicking outside of any element the AOP editor is loaded providing overview of the whole pathway. Normal full screen editor is still available with double clicking on the representing visual element (or its title in any editor interface)


    ---------------------  Remote description sections  ----------------------
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Description sections now can display remote web content not managed in Effectopedia. Two initial sources for remote content were allowed (white listed) Wikipedia and AOP-Wiki. The Wikipedia based description section allows embedding a related Wikipedia pages in the document description. Similarly information from AOP-Wiki can be embedded in Effectopedia. The pages AOP-Wiki content can be directly edited from Effectopedia interface using the normal editing capabilities of AOP-Wiki. 


    ----------------------  Global in-silico models  -------------------------
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Similarly to Studies which can consist of several lab based experimental assays and tests, several in-silico models can refer to a single global model. A Global in-silico model can be defined and used across several key events and respective (local) in-silico models. The global in-silico model interface is accessible in the in-silico test description can contain mathematical description of the methods used (including MathML formulas) and also a list of parameters describing the model. The parameter list allows users to specify the normal ranged of parameters, mean values, additional descriptors as well as descriptions and references. Each parameter can have more than one value based on different assumptions, references and so on. 

              ***************** File format changes ****************
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- Current file format is version 0.9.61 and is not backward compatible with older versions of Effectopedia (current versions of Effectopedia can still open old versions of the file format but old versions of the program cannot read the current format). The change that produced this lack of backward compatibility is so called DefaultID Negative Revolution. All default objects have negative IDs which are incrementally decreased with the introduction of each new default object. This allows generation of XML files from Java source code which will be used in the future as a backup mechanism. There were several changes in the format related to naming of individual XML elements which also causes lack of backward compatibility. 
 - All experimental and model data are represented in a universal structure called ObjectProperties. This structure is currently used to represent: dose responses and response responses curves, model parameters, analytic function specification, etc. ObjectProperties is a list of ObjectProperty objects each of which has his own type defining its data format. Each object is also array of objects which contain a list of specified values e.g. mean, min, max value, description, reference as well as user defined list of descriptors for example chemical concentration, temperature in which the measurement was taken. Object properties can be also hierarchical and contain a list of sub properties. In summary the structure can represent a table with arbitrary number of columns and rows each cell of which is either simple value or can be another table. 

              *************** Architectural changes ****************
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Major internal source code restructuring was performed to allow cleaner separation of individual modules in line with the adopted OSGI architecture. The essential Effectopedia classes are defined in the kernel bundle of packages which include core, base, data, history, search and other system packages. The kernel does not refer to any external libraries nor depend on any other bundle and can be compiled in a standalone jar with approximate size of 1.5Mb. As part of this package is BaseIO interface which separates the data structure from different format implementations. Multiple implementations can be registered allowing Effectopedia to load and save information from different file formats and systems. Currently two XML format implementations are available one based on JDOM library (originally used in Effectopedia) and one based on Jackson library which is also used for the JSON implementation of BaseIO. All Effectopedia specific graphic representations of objects and their layout is implemented in “go” bundle. This bundle is used as a dependency from the base “gui” bundle which along with “gui.swing” implements the graphic user interface of Effectopedia.  “gui.javafx” library provides rendering of webpages based on java webkit but is currently not available as bundle and prevent the full transition of Effectopedia toward OSGI. 

                ***** Effectopedia < 0.9.62 Alpha Update Log ***** 
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Changes log for earlier versions is available in the respective folders under Archive.