Software and version history

From Species File Help
Jump to: navigation, search

The database behind the website was originally on FileMaker Pro, moved to MS Access, moved again to MS SQL Server. The greater complexity of SQL Server has made the task more difficult, but it has allowed the addition of more complex programming that does a better job of detecting and preventing user errors in updating the data.

Programming for the Orthoptera Species File was initially done with MS Visual Interdev. The web pages are published using HTML 4. The Active Server Pages (ASP) use Visual Basic Script. Client side programming is done using JavaScript. Web pages can be viewed using Microsoft Internet Explorer, version 4 and higher, or Netscape Navigator, version 4 and higher. Current work is done using Visual Studio.NET. The conversion from ASP to ASP.NET and from Visual Basic Script to Visual Basic.NET was completed in November 2003.

Version history

Version 0:  The entire project started with the Orthoptera Species File books prepared by Daniel Otte and published in eight volumes from 1994 to 2000.

Version 1:  The initial Internet version was the Orthoptera Species File Online developed by Piotr Naskrecki and first posted to the web October 20, 1997 with coverage of the family Tettigoniidae (katydids).

Versions 2.0 to 2.8:  Beginning in 1999 David Eades assembled a team to increase the data content (now covering all of Orthoptera), upgrade the database design, and improve the interface for the public and for editing.

Version 3.0:  This version, released in February 2007, marks the transition from software designed to support a single database and website to software supporting multiple independent databases and websites.

Version 3.1:  Development of this version began May 21, 2007 using the Orthoptera Species File for testing.  Other species files advanced to version 3.1 on July 16, 2007.  Features developed in this version include:

  • Web services
  • Additional details for references including links to electronic copies
  • Improved data structure
  • Systematic procedures to facilitate updating software in use for the various species files
  • Improved handling for specimen data including cross linkage with images and sound recordings
  • Added fields for distribution and habitat for taxa
  • Images and sound recordings cross referenced with specimens and with enforced consistency of current identifications.

Version 3.2:  Development of this version began August 31, 2007 using the Plecoptera Species File for testing.  Other species files advanced to version 3.2 by November 26, 2007.  Features developed include:

  • Major restructuring of the manner in which hierarchial relationships are recorded in the taxa table.  The result is simpler programming and more efficient searching with scopes less than the entire species file.
  • Rewritten interface for adding a new type genus
  • Ecological relationships with organisms outside the primary taxonomic scope.  This can be done both at specimen level and at taxon level.

Version 3.3:  Development of this version began November 9, 2007 using a separate development copy of the Orthoptera Species File.  The public version of OSF advanced to 3.3 on February 16, 2008.  Remaining species files advanced March 18, 2008.

  • This is the start of a major effort to use web services and GUIDs (globally unique identifiers) to facilitate exchange of information between species files and other databases.  The step to be included in version 3.3 will provide a table with author data shared across species files.  This is a prerequisite for exchanging data with ZooBank.  Status:  On hold pending resolution of design details with ZooBank.
  • Improve the ease for locating particular entries in the edit log.  Status:  Completed. 
  • Make management of impaired key groups and blocks more user friendly.  Status:  Completed. 
  • Record information about citations sufficient to designate taxon concepts and provide better data about the type of information contained in each citation.  This task must be subdivided, and only some portions are likely to be completed in version 3.3. Status:  Completed. 
  • Added support for alternate names for publication.  Status:  Completed.  This involved:
    • Creating a display publication page (modeled on the display people and display reference pages.
    • Creating an alternate publication name page.
    • Adding the automatic generation of non-diacritic version of publication names as alternate names.

Version 3.4:  Development of this version began February 22, 2008 using a separate development copy of the Orthoptera Species File.  The public version of OSF was advanced to 3.4 on June 23, 2008.

  • Identify the distribution of each taxon by continent and country.  Display in the taxa page a small world map shaded to show where the taxon is found.  Provide links to see maps of continents shaded to show countries.  ("Countries" are defined as the level 2 areas as defined by the TDWG recommended classification.  Correspondence to actual countries varies.)  Status:  Completed, but internal table structure should be revised. 
  • Extend distribution map coverage to level 3 of the TDWG recommended classification.  Status:  Completed. 
  • Enable a block-specific text message to be shown in key drivers.  Status:  Completed. 
  • Taxon names with citations should not be italicized when they are informal names.  Status: Completed. 
  • Reorganization of the edit page (SelectTypeEdit) to give more prominence to frequently-used features.  The use of drop down lists provides easy access to adding and editing data objects.  Status:   Completed.
  • Maintain statistics about website usage.  Status:  Completed for session counts only.  Further development is needed. 
  • Enforce correct date sequence for names, citations and type information.  This included among other things a complete rewrite of type genus pages.  Status:  Completed.

Version 3.5:  Created August 14, 2008 and available only on a private development copy.  January 19, 2009 Orthoptera Species File moved to 3.5.  All species files advanced by Feb. 11, 2009.  Additional features with minimum risk of breaking existing features were added after this date.

  • A logical inconsistancy was recognized in the distribution data implemented for version 3.4.  Fixing this required extensive revision of the data structure.  Status:  Completed. 
  • Enhance handling of distribution information based on data found in references.  Status:  Completed. 
  • Provide tables in SFSdb to share information across species files.  This has no effect on what users will see.  The benefit is to simplify the programming task and not require duplicate tables in each separate species file.  Status:  Completed.
  • When an author's name includes diacritic marks, an alternate non-diacritic version is automatically added to help in searches.  Status:  Completed.
  • Numerous less significant enhancements and error corrections.  Status:  Completed.
  • Provide better website usage counts using Google Analytics.  Status:  Completed.
  • Add rank as an additional criterion in complex search for taxon.  Status:  Completed July 1, 2009.
  • Provide a way to run all 57 data integrity tests without repeated manual interaction.  Status:  Completed May 27, 2009.
  • Develop a web service that will enable other websites to copy species file taxonomic hierarchies Status: Simple test case completed June 19, 2009, but not ready for general usage.
  • Generate maps based on latitude/longitude data for specimens.  Status:  Completed Aug. 7, 2009. 
  • Track the relationship between lapsus calami and the corrected name and prevent changes that separate them in the hierarchy.  Status:  Completed Aug. 19, 2009.
  • Update the statistical capabilities concerning webpage/database usage. This includes the usage of a utility.  Status: Completed except for minor extension. 
  • Merge a private species file back into the public species file when a revision is published.  Status:  Completed May 12, 2010. 
  • Add image comparison feature to allow users to display up to twelve images simultaneously on a single page.  Different orientations and resolutions are available for comparing the current image with one of the selected images by clicking on the symbols below the selected image.  Status:  Completed Feb. 10, 2010 [thanks to HernĂ¡n Pereira].

Version 4.0:  Created May 12, 2010.  All species files were advanced at this time.

  • Upgrade management of key data with new integrity tests and error checking.  Status:  Substantially completed and implemented June 20, 2010. 
  • Add new features in specimen data.  Status:  Completed June 30, 2010 except for hyperlinks and export of results from a specimen search. 
  • Cross check geographic area selections with latitude/longitude data.  Status:  Implementation in progress. 
  • Organize the history of taxon concepts and taxon names.  Status:  Initial generation of data completed January 28, 2011.  Procedures for editing and automatic updating of data are being developed.  Note:  This effort was extended beginning Sept. 1, 2011 to include greatly expanded testing of data integrity for determining which citations justify taxon name LSIDs and inclusion in export of data to the Catalogue of Life and Darwin Core Archives. 
  • New edit page features:  Search for objects (references, taxa, etc.) by object ID; compare two items (e.g., references, publications, etc.) for possible deletion of duplicates.  Status:  Completed August 25, 2010.
  • New image display for taxa: Images are organized by default to first display specimen images by type, but the default order may be overridden.  Status:  Completed September 14, 2010.
  • Editors may run selected test programs; these integrity tests list objects that are not used, are duplicates or nearly similar to others, or have missing information.  Status:  Completed September 21, 2010.
  • Reorganize data about the content in citations including new columns with more specific information.  Status:  Completed November 19, 2010.
  • Italics are now supported in reference titles and notes.  Status:  Completed November 30, 2010
  • Handle relationship between misapplied name usage and correct name usage.  Status:  Completed January 29, 2011
  • Add LifeZone (Marine, Brackish, Freshwater, and/or Terrestrial) as column in taxon table.  Status:  Completed April 15, 2011.
  • Enhanced faunal lists now have taxon hyperlinks.  Status:  Completed May 16, 2011.
  • Issue LSIDs for taxon names.  Status:  In use November 2011 but dependent on running test programs to update for edits since the previous run of test programs and fixes. 
  • Add "Basis of record" to Specimen records.  Status:  Completed August 15, 2011. 
  • Handle text for languages that use characters not found in most European languages.  Status:  Completed July 21, 2011.
  • Add information to specimen records.  Status:  Ongoing.

Version 4.1:  Created March 14, 2012.  All species files advanced soon after.

  • Add identification qualifiers and verbatim identification label as optional additional information about specimen identifications.  Status:  Development completed April 4, 2012.

Features run from this website and thus independent of species file version number:

  • Copy a portion of a species to a new species file.  This can be used to generate a private species file while a revision is in progress or to subdivide one species file into multiple species file.  Status:  Completed June 28, 2009. 

Proposed future development:

  • Create a publication registry shared across all species files.  Each species file will still maintain its separate table of publications, many of which will be reconciled with the registry.  Status:  Substantial development was completed in version 3.5.  However, due to insufficient testing and expansion of the design requirements, this will not be made available until version 3.6. 
  • Provide an alternate format for the taxa page with technical and nomenclatural issues made less prominent.  Synomyms would not be shown, but their citations would be shown with the valid names.  It should be more attractive for non taxonomist users.  Status:  Too big a task to fit in current priorities. 
  • Exchange data among species files and with ZooBank about authors, publications, references, taxon names and taxon concepts and provide LSIDs.  The publication registry listed in Version 3.5 is the first step in this much larger task.  Status:  Initial concept development. 
  • Extend functionality of identifications to preserve progression of names for taxa.  Status:  Design partially developed, currently on hold. 
Personal tools

Species Files