ORIGINAL LICENSE: The Make2D-DB II tool is (c) Copyright 2002 Swiss Institute of Bioinformatics All Rights Reserved. Author : Khaled Mostaguir Co-author : Christine Hoogland Contact : world-2dpage@isb-sib.ch URL : http://world-2dpage.expasy.org/make2ddb/ http://www.isb-sib.ch ========================================================================================================== ================================ version: 3.10.2 December 2011 version: 3.10.1 November 2011 version: 3.01.1 Septembre 2011 ================================ Core schema revision (reference table constraints replaced by triggers to allow database restore) Extension of the '-m update' process for already existing databases built with previous Make2D-DB versions Handling several co-existing MS files document types related to the same spot Web-interface full revision for data exchange / export (with new formats) Web-interface extraction of statistics for data integration Web-interface better cosmetics Compatibility with postgreSQL 9.1 Mapping of non-UniProtKB entry accessions to UniProtKB accession numbers (e.g. RefSeq or NCBI gi numbers) More flexibility in defining remote 2D-PAGE resources More flexibility in parameterizing Web interface behaviour (e.g. viewer zooming) Automatic updating of the remote interfaces configuration file (to query and exchange remote data with remote servers) Extension and improvement of the data exchange process via the ExPASy based mediator Backup of existing databases within the postgreSQL server prior to major modifications (update, transform and create methods) Checking data input encoding Removing meta-data columns from *Parent Tables to allow database export and reload of inheriting tables Extractable statistics per project List of project statistics from the the server home page Correction of a major bug preventing *local* postgreSQL from reading command files during database installation Correction of minor bugs from version 3.00.1 ==================================================== version: 3.00.1 Beta / June 2011 (Major New Version) ==================================================== Update of mediators regarding external resources data format changes and addresses Adaptation to the recent versions of postgreSQL (8.4 and 9.0) Linking to remote/distant postgreSQL servers using ssh Higher granularity in configuring repositories workflows, semi-automatisation of the repository configuration process Automatic creation of symbolic links to share common files between repositories databases Automatic adds and commits into a CVS repository for new and modified Web Servers directories and files Generation of symbolic links lists to keep file structure when working with CVS projects Semi-integration of "The proteomics database of the UMR of Génétique Végétale du Moulon" and similar compliant databases External data: more control in integrating UniProtKB demerged entries, considering recent UniProt entry splitting based on genes Extending GET queries via the search interface, including a '&hits=query' argument e.g. ?&hits=full:methylation -- ?&hits=ac:P11111+xref:P11111+count&format=raw&extract ================================ version: 2.60.1 / March 2007 ================================ Non public version ================================ version: 2.50.2 / September 2006 ================================ Non public version ================================ version: 2.50.1 / September 2006 ================================ Full compatibility with postgreSQL 8.1 and higher, with alternative PGPORT setting. Activation of the '-m update' switch to update both database structure and/or data content. Easy addition of new databases/projects to an already running server. A collection of new functionalities on both the administration and the query interface. An easier way to configure and set up personal interfaces/portals to link to other remote resources, even without having any personal local data. Automatic linking to the World-2DPAGE portal for an up-to-date integration of remote 2D-PAGE resources. Displaying lists of external remote maps and species for dynamic search. For public databases, the possibility to be automatically cross-linked from Swiss-Prot/UniProtKB if desired. Annotation of mapping (identification) methods for a whole map as well as for individual spots. New pre-defined annotation fields for the CSV reports (bibliographic references & cross-references). Free annotations either for a single spot or for all spots together (spots belonging to the same entry). MS peak list integration: adaptation of a more recent version of the Phenyx InSilicoSpectro module (ver.0.9.24). Adoption and management of protein entries' history based on entry versions rather than on database releases. Security enhancement regarding the administration interface. Addition of new types of data extractable by the query interface. Extending and displaying the experimental information of the maps. An additional new MS spectra (peak list) viewer/navigator. HTML 4.01 and CSS full validation of the Web interfaces. More detailed documentation, covering in particular the various server functionalitites. FAQ (frequently asked question) document on line. And many more additions... (refer to the documentation) Major Corrected Bugs: -- Correcting an error in the assignment of new demerged Swiss-Prot accession numbers -- Correcting inconsistencies when some spots contain in their name another spots names (a problem frequently encountered with spots' names of 1 character long, e.g. 1,2,..,11,12,..) -- CSV reports: handling correctly bibliographic references when their list is different between several maps' files -- Database release numbers read from flat files are no more truncated to 1 digit -- The MS/MS parent m/Z value is no more replaced by the highest m/Z value of the whole peak list ================================ version: 2.00.1 / 5-Dec.2005 ================================ Major New Release Rich annotated CSV reports for data input. Integration of data and annotation documents (e.g.PSI documents, MS data, etc..) Automatic assignment of UniProtKB/Swiss-Prot new demerged entries Many new functionalities. Many improvements and fixed bugs. Changes to be listed soon on the Make2D-DB II server. ================================ version: 1.00.c / 25-Apr.2005 ================================ - Some fixed bugs ================================ version: 1.00.a / 15-Apr.2005 ================================ - Generation of flat files directly from excel reports (tabulated exports) or from simple text reports (no explicit need to provide a flat file) (in preparation: flat file generation from Melanie XML exports - please, contact us for the new batch..) - The possibility to interconnect automatically to any other database constructed by the same tool that shares a common entry. (a dynamic list of available databases for the tool to look automatically on, as well as a batch to be distributed, will be available soon on ExPASy) - Queries can be addressed simultaneously to any number of remote databases, and results can be displayed dynamically in various formats - Exports from the database can be made in different formats, and can be extracted to be included (dynamically) in other resources - New interactive batch commands: update views and public schema from changes made on core schema via the core interface (cf. readme for details), export of flat file, Update UniProt external data, purge log schema and so on.. (via a secure cloned interface that accesses, queries and updates the core schema: e.g. http://...../2d.core.cgi) - An new intuitive way to address any object from the database (entries, maps, spots) in different formats, as well as to write search queries in a very natural manner (automatic generation of rules to be used by the Apache mod_rewrite module) - The '-m create' option for void databases also construct all the auxiliary tables' structure (the tmp_* tables) - For an entry: when different species names are related to the same taxonomy code, each species will be interpreted as a strain name (not displayed) - Melanie XML extraction: MelanieIV/ ImageMaster5 XML exports (the tool looks for any *.xml file(s) in the 'data' dir for parsing) - configuration files simplified and restructured (an additional file 'basic_include.pl' contains special definitions that do need not to be modified in most circumstances) - More interactive/visual way for map selection - New search engines, including search by identification methods - ... fixed bugs: - a bug preventing two different species to share the same organism classification has been fixed - when one spot corresponds to several entries, all the entries are now displayed (not only 1 of them), the entries are all simultaneously accessed by clicking on the spot - when viewing a single spot, identification techniques are displayed more precisely - fixing the incorrect masses that were displayed on the small viewer remarks: - Some few recent versions of the perl module DBI (1.43) caused problems of connection at the interface level due to a data type problem. Whenever such a problem is encountered, use the most recent version of DBI (1.48) which has corrected this problem. internal changes: - the default path to data on the server (html files, images, etc..) has changed from <2d_path>/ to <2d_path>/data to avoid confusion and writing extra rules when using the Apache mod_rewrite module ================= version: 0.95.a : ================= postgreSQL 7.4 (or higher) is now required! - Use of internal Schema within the database structure - 4 integrated schema: * core (inner data, constraints and update procedures / accessed only by the database owner), * public (public releases / accessed by the select2d/public user) * common (common functions and procedures / accessed by both the database owner and the select2d user) * log (storing modified and deleted data) To access the core schema from the WEB server, use the script '2d.core.cgi' instead of '2d.cgi', enter login information (login information will be encrypted and will expire after 10 minutes of inactivity) Any operation can be directly performed from this 'core' script (including updates and free-text select commands) - Heavy changes on the schema structure and the class names - More detailed description of the Biological Source - The possibility to include PSI mzData and mzIdent XML files into the appropriate identification tables (no validation/verification methods are included yet) - Addition of a 'backbone' structure to describe a whole project flow schematized by: project -> studies -> study groups -> biosources -> samples, and so on.. - Accession numbers (AC) can now be of any format, and up to 32 characters length (white spaces and ';' are discarded) - Bibliographic references have been extended to cover each appropriate class (projects, samples, maps and identified proteins/spots) - RX line can now be extended to several lines - RG lines (reference group) are recognized and integrated as a 'group' of authors, following the announcement of Swiss-Prot - GN lines (gene names) are now automatically converted to the new Swiss-Prot format (name, synonyms, OLN, ORF) - Identification analysis are now conceptually separated from the identification experiments Interface: - Map display interface improved - Search engine includes, in addition, the parsing of the external data (e.g. Uniprot description, ID, gene names,...) fixed bugs: - fixing a main installation problem related to 'psql' program calls - fixing a display problem (style and borders) within the WEB interface - use of the initial tissue list in case the new extracted tissue list causes any problem - fixing a bug related to the database automatic default selection when no database has been specifically chosen ================== version: 0.89.z+ : ================== - peptide Masses can read pic intensities from the form: mass1 (intensity1); mass2 (intensity2);... - EC (enzyme codes) are automatically updated from Swiss-Prot (original ones kept in the 'DE' line and updated ones displayed) - added Mixed-Case on free-text topics - cross-Refernces for source displayers are now read from the database core itself if not found in the links.txt file - the 'External Index' is now extended to both Swiss-Prot & TrEMBL (UniProt), automatically assigned references (based on the accession number pattern) are verified to correspond to a Swiss-Prot or a TrEMBL entry; - the database reference code for Swiss-Prot remains 1, TrEMBL is assigned the code 2, Swiss-2DPAGE and Swiss-Prot SRS are respectively assigned the codes 3 and 4, GO has the code 5 - new global Cross-reference to UniProt for both Swiss-Prot and TrEMBL - adoption of both the old DT lines syntax and the newly announced syntax in Swiss-Prot - for debugging purpose, a copy of the last converted ASCII tables is kept in the 'temp' sub-directory - DOI (digital object identifiers) are recognized, following the announcement of Swiss-Prot - *internal: D_results tables restructured with inheritance fixed bugs: - automatically assigned references to Swiss-Prot (based on the accession number pattern) are checked if really existent as a Swiss-Prot or a TrEMBL entry (in version 0.89.x inexistant entries caused the installation process to fail) - a bug detected with a recent version of PostgreSQL 7.4 caused the full entry display within the WEB interface to fail, this has been dealt with in the new version ================== version: 0.89.x : ================== - Pg module (used to connect the interface to the postgreSQL server and no more supported by Perl 5.8) replaced by the DBI::Pg module - display improvements in the query interface and the viewer - when replacing an already existing database, the whole old database content is dumped and restored back if the process fails, a copy of the dump is also kept - storing a local copy of the "main configuration file" for each new created database - auto recognition of Swiss-Prot AC patterns / adding of a DR line pointing to the Swiss-Prot database - integration of the auto-assigned Melanie map ID whenever available - search by accession numbers with partial patterns / full list of available ACs - species names attached to the map names in the scrolling lists - %volume and %od values are now displayed in the viewer spot cards - possibility to include a personnel HTML file at the top off the servers's pages and to adjust map positions - cross-reference database names are checked (case-insensitively) during the conversion process v Swiss-Prot common DR links - automatic update of the tissue list from the ExPASy server (from TISSLIST.TXT) - dynamic download of all Swiss-Prot database cross-reference URLs and displayers addresses from the ExPASy server - automatic integration of more external data (from Swiss-Prot) inside the database core itself (e.g. keywords / functions) - gene names are automatically updated from Swiss-Prot - taxonomy data: NCBI_TaxID, OS and OC lines are automatically updated from the Newt database - a new 'DT' line is automatically added to show the "Last map annotation" updates - tracking of all created/modified entries within a date range - more control over the queries constructed by the user ('combined' queries) to reject (and signal) the heavily time-consuming ones fixed bugs: - experimental results display within the viewer spot cards - fixed data output in text format to be saved as text files ============== version: 0.40: ============== - As published in October 2003 (an extended list of specifications will be added later) - species for a specific entry (entry annotated species) may be different from the species referenced map