OBO-Edit 2.0 beta release notes

Release notes for OBO-Edit2 betas

Release Name: 2.000-beta25

Notes: Bye, y'all!

Changes:

• Graph DAG Viewer succinct mode is fixed! (SF 1829694)
• Fixed some layout problems in Configuration Manager
• Added a "has multiple roots" search criterion (SF 1833117)
• Modification stamps are now optional (SF 1820650)
• Made a stab at stabilizing progress window size (SF 1816415)
• Fixed bug where Configuration Manager would not save if window close button (as opposed to titlebar close button) was clicked
• Fixed bug where invisible zombie components could be trapped in a layout if an undocked component was closed using the window close button (rather than the titlebar button)
• Fixed minor bug in search configuration
• Rebuilt image plugin

Release Name: 2.000-beta24

Notes:

Changes: * (See beta23 release notes for many other changes) * Fixed bug where menus would not appear (SF 1845378) * Removed option to create a desktop link from installer (SF 1845378)

Release Name: 2.000-beta23

Notes:

Changes: * Added framework to attach help topics to components. If a component has a help topic attached, a little question mark button appears in the title bar. When the button is clicked, help for that component is displayed. * Text edits no longer lost when a new search item is selected (SF 1844991) * Fixed numerous bugs in custom verification checks * Fixed bug where Graph Editor would not properly display explanations for some links (thanks to Chris for fixing this) * Fixed bug where the save dialog would appear when there were fatal errors in the ontology (all the more ironic because it appeared after a message explaining that you will not be allowed to save until these errors are fixed) * Redundant and implied links once again have a distinctive appearance - you will need to delete ~/.oboeditbeta/filter_prefs.xml to get the new default settings (SF 1844745) * Many changes to text editor quickfix system (SF 1844885): * Added quickfix for "no punctuation at end of sentence" error * Added quickfix for "non-url characters in dbxref" error * In text editor panes, errors are highlighted in red. Errors that can be quickfixed are also underlined. * In list editors (like the dbxref editor or the synonym editor), items that contain errors are listed in red. Items that can be quickfixed display a quickfix icon next to them. Quickfixes can be applied by right-clicking an item and selecting a fix from the menu. * Quickfixes are now available in the synonym text text editor.

Release Name: 2.000-beta22

Notes:

Changes: * Global renderers are now used to display search results * Fixed problem where live verification data would not be updated properly when definition dbxref problems have been fixed (SF 1844213) * The big, distracting text editor error message panel has been removed. Now error messages appear in the text editor's title bar. Mousing over the title bar will display a tooltip listing the errors. * Remove redundant links problem (SF 1844193) and associated reasoned link deletion bugs are fixed. * Platform independent launcher bug fixed (SF 1843989) * Log files are being generated correctly again (SF 1844183) * Garbage tabs no longer appear if OBO-Edit is shut down with search results still visible (SF 1844184) * Fixed disappearing global/local selection mode buttons (SF 1838678) * Added new log messages to aid in diagnosis of rogue popup menu problem (SF 1839411) * Fixed problem where list editors (like the synonym editor) could cause unexpected changes if the selection changed while the editor panel was still open (SF 1837056)

Release Name: 2.000-beta21

Notes:

Changes: * Fixed bug where synonym dbxrefs would be lost on synonym edit (SF 1843460) * Added editor for synonym dbxrefs * Dbxref listing is now always the same size in synonym editor (SF 1843405) * Live error highlighting in the text editor now works properly * All TableList editors (like the dbxref editors and the synonym editor) now commit their changes the minute they are unfocused, which should make them easier to use

Release Name: 2.000-beta20

Notes:

Changes: * Added customizable heat maps * Right-clicking a component's title bar allows you to change the title * Search control now remembers last settings * Search results text is now customizable in search control settings * Added new Icons & Colors tab in configuration manager (SF 1838664) * Added icons for OBO-Edit application and installer * The Mac OS "Quit" and "About" menus are now properly handled by OBO-Edit * Text edits now autocommit if another edit occurs (for example, if you have pending text edits and you create a new term, your text edits are no longer lost) * Changed Parent Editor appearance to make things fit on the screen better * Fixed unhandled exceptions when clicking "classes", "properties", etc (SF 1840390) * Fixed undo/redo failures (SF 1839564, SF 1839564) * Fixed shortcut key bugs (SF 1838830, SF 1836524) * Fixed bug where "<new term>" did not appear correctly after new terms were created (SF 1838829) * Made "working" popup look a little better (SF 1838787) * Fixed bug where search results disappeared between layout switches (SF 1838784) * Fixed bug where panels would not update correctly after new ontology load (SF 1838764), and for good measure fixed some other screen update bugs in the graph editor, including bugs that left stray arrows floating around * Fixed graphical artifacts and switched-around button behaviors in term change tracker (SF 1838679) * Fixed problem where a change in the autocommit setting did not cause "commit" and "revert" buttons to immediately appear (SF 1838673) * Fixed parent editor drag and drop button (SF 1838669) * Fixed bug where namespace changes would not be saved (SF 1838656) * Fixed icon browsing problem (SF 1838651) * Fixed bug where OBO-Edit would not display installer-generated memory settings on Mac OS (SF 1838648) * Installer now WILL create a desktop icon if you ask it to (SF 1838648) * If there are unsaved changes to an ontology, a special message appears in the quit confirmation dialog (SF 1838644) (note that this message will appear whether or not you have "confirm on exit" checked, on the theory that anyone would want to know about this potential disaster) * Fixed spurious "unsaved changes" message (SF 1837005) * It is now possible to re-select already selected search results (SF 1836549)

Release Name: 2.000-beta19

Notes:

Changes: * Added Import... to the file menu * Added Fix ids... to the file menu * Added a verification system check for bad ids. The id fix options are all available as quickfixes * Added a new system for installing custom graph decorators

Release Name: 2.000-beta18

Notes:

Changes: * Fixed OBO 1.2 save bug (SF 1827542) * Fixed bugs when saving filtered files with range & domain defined * Changed method of starting load/save operations

Release Name: 2.000-beta17

Notes:

Changes: * Added new rendering system * Added Image Display Component * Added Configurable Message Component * You can now autotype individual words in an autocomplete box using Ctrl+Space (on any platform) or Command+Shift+Space (on macs only) or Ctrl+Shift+Space (on non-mac-platforms only) * Fixed problem where arrowheads would drift around while scrolling the ontology editor panel * Changed wording of "load" menu item to Load Ontologies (SF 1826388) * Changed default ordering of data adapters to something sensible (SF 1826388) * Added clearer error messages when a file of the wrong type is loaded by the serial adapter (SF 1826388) * Fixed broken autocomplete in Cross Products panel (SF 1825311) * Fixed bugs in list editors (SF 1824736 + others) * Fixed "change relationship type" bug (SF 1824731) * Disabled autopanning in the graph editor (SF 1820642) * Fixed "multiple globe icons" problem (SF 1820621 & 1820134) * Fixed graph dag viewer problems (SF 1820621)

Release Name: 2.000-beta16

Notes: To use the new image saving plugin, create the following folder:

~/.oboeditbeta/extensions

and put the jar file in there. When you start OBO-Edit, every component will have a tiny camera icon in the title bar that lets you save an image of the component in a number of different formats. Also, when you right-click in the graph editor, you have the option to save an image of the current graph (unlike the title bar button, the image will contain the entire graph, even if the whole graph doesn't fit on the screen).

Changes: * Added lots o' hotkeys, see release notes on sourceforge * Reworded obsolete warning message (SF 1810837) * Fixed bugs in ancestor & descendant searching (SF 1811624) * Fixed commit keyboard shortcut (SF 1811771) * Fixed save bug (SF 1811658) * Added ability to expand the full path to a term in the Graph Editor (this can be disabled in the configuration screen) (SF 1811581) * When multiple child terms are added, they are assigned to the parent namespace (SF 1814547) * Default id rule is no longer broken (SF 1811685) * Text edit hotkey now works (SF 1811771) * Fixed problem where table lists in the text editor did not autocommit pending edits when their values are requested. This manifested as bugs in the dbxref and synonym editing lists (SF 1814568). * Added add/remove buttons to renderer lists in Global Filter Manager * Load/save error details are once again displayed * Created image saving plugin * No more flickers of movement in graph no-animations mode * Added option to hide "Search results" prefix for search results (SF 1816398)

Release Name: a>

Notes:

Changes: * Added ability to remove consider/replaced-by terms with the right-click "delete" option * Added in-panel "popup-window" that appears when a parent/child expansion control is clicked in the graph editor * Disabled default spell checking when saving * Fixed icon configuration bugs * Fixed text editor bugs * Fixed drag and drop bugs * Fixed autocommit bugs * Fixed right-click editing menu bugs * Fixed expanding children when right-clicking in graph editor

Release Name: 2.000-beta14

Notes:

Changes: * Fixed Save As lockups * Fixed autocomplete bugs * Changed autocomplete box in search control to initiate a search if enter is pressed when the autocomplete popup is hidden * Added lightbulb tooltips in new search controls * Graph editor tooltips are no longer animated in no-animations mode * Fixed bugs in reasoning over intersections with sub-properties * Graph editor now only pans to a newly selected node if it is not currently on the screen * Fixed bug where OBO-Edit would not exit properly if closed from the window controls * Added possible fixes for Windows XP problems - if problems persist, try the command-line switch -J-DuseModalProgressMonitors=false to disable a potentially problematic feature on Windows * Improved animation disabling code * Animations can now be disabled in the graph dag viewer * Added unicode character searching * Progress windows now automatically choose the correct size * Added better progress bar updating for long-running tasks * Added support for plugins

Release Name: 2.000-beta13

Notes:

Changes: * Faster graph relayout * Changed expand/collapse graph editor controls * Graph editor node boxes are now sized to just fit the node label * Link lines in graph editor will no longer appear above term boxes * Changed default font size to 12 point * Fixed bugs in reloading saved renderers * User-added links are no longer trimmed by the reasoner

Release Name: 2.000-beta12

Notes:

Changes: * Fixed bugs where sometimes screen would go blank when showing a new component * Big reasoner speedups * BIG editing speedups * New search interface * Updated filtering interface in most places (old filtering system is still in use for filtered saves) * Graph Editor now supports filtering (but not rendering)

Release Name: 2.000-beta11

Notes:

Changes: * Fixed bugs in obo2obo * Fixed bug in dbxref checking that greatly increases speed of verification checks * Fixed bug where links don't work properly in verification results page * Dbxref verification no longer reports % as a non-dbxref character * Added resizable graph overview panel to the graph editor * Added "Remove redundant links..." menu item * Fixed bug where panning the graph editor would cause view to jump wildly * Dbxref library buttons now work * Fixed bug where dag graph view would be disconnected if there were many is_a links between the selected term and the first non-is_a link in a transitive path * Graph editor now does text wrapping * OBO-Edit no longer applies font changes to menus - instead it uses the system default. This should allow better integration with a given platform's look and feel

Release Name: 2.000-beta10

Notes:

Changes: * Improved Graph DAG Viewer display * Fixed bugs in search panel selection that would make it impossible to select search results if many intersection definitions were loaded * Dangling relationship types are now supported * Fixed bugs in displaying dangling references in the intersection editor * Changed implementation of links in OBO-Edit so that most link objects should use about half the space they used to use (this is significant, particularly when the reasoner is running, because there are *far* more links than terms) * Fixed reasoner bugs that would manifest with certain kinds of redundant links * Improved support for reading in links implied by an external reasoner * Platform independent OBO-Edit launcher now reads memory settings correctly * Font changes update immediately. No need to restart! * Fixed inconsistencies in typeface, background colors and button colors

Release Name: 2.000-beta9

Notes:

Changes: * Added scale bar to graph editor * Changed the way toolbar is added to the graph editor to save space

Release Name: 2.00-beta8

Notes:

Changes: * Fixed bugs in implied link expansion menu * Fixed search bugs * Fixed bug where Configuration Manager settings were lost * Greatly sped up save of Configuration Manager settings * Individual component settings now save properly * Added OWL URL reader adapter

Release Name: 2.000-beta7

Notes:

Changes: * Beta versions now write settings to the .oboeditbeta directory

Release Name: 2.000-beta6

Notes:

Changes: * obomerge now properly merges consider and replaced_by tags * New memory settings screen in installers

Release Name: a>

Notes:

Changes: * Added global selection controls to component title bars * Added filter control button to component title bars * Reinstated autosave; autosave files are now in OBO format * Disabling graph editor animations now disables tooltip popup animations as well * Added ability to right-click highlighted errors in text editor and choose a quick fix from the popup menu

	* obo2obo now supports dangling links in loaded-in files

Release Name: 2.000-beta4

Notes: Known issues:

• Some text edit errors are reported too many times
• Modal progress boxes (like the reasoner progress box) sometimes do not disappear properly on Mac OS
• Autocommit mode is always on

Changes: * Fixed search * Changed to IDW docking framework * Changed the way automatic error reporting works * Changed synonym editor to list-based editor * Enabled basic perspective switching in the text editor * Added quick configuration buttons to docking headers

Release Name: 2.000-beta3

Notes:

Changes:

• Fixed swing-based memory leaks
• Added an option to turn off graph editor animations

Release Name: 2.000-beta2

Notes: Known issues:

  * The text edit tool graph editing tool may have problems
  * Text-edit error checking is disabled
  * Some quick-fixes are not available
  * The automatic error loader will occassionally report a non-existent error, usually one about definitions with no dbxrefs, even though they're there
  * The user's guide is totally out of date

Changes: * Fixed some problems in graph-based editing * Added the javadocking system * Added some spellcheck features * Added dynamic error checking displays * The settings directory can now be specified with the "-Dprefsdir=" option

Release Name: 2.000-beta1

Notes: This is the first beta release of OBO-Edit 2.0. It's going to be buggier than you're used to in an OBO-Edit release, but we need user feedback on the new graph editor. Changes:

Release Name: a>

Notes:

Changes: * Fixed bug where "on reasoner" checks always ran at load, even if the reasoner was not enabled. * Fixed bug where the reasoner drew many incorrect disjoint_from inferences * Fixed bug where disjointness verification check would double-report errors * Made default size of OBO advanced configuration screen much larger, and rearranged components to make better use of available space * Fixed bug in relative path resolution of OBO "import" tags

Release Name: 1.100-beta24

Notes:

Changes: * Fixed bug where various user-defined check attributes would not load * Fixed bug where only the first non-fatal warning would display when saving * Fixed bug where user-defined checks could not be deleted

Release Name: 1.100-beta23

Notes:

Changes: * User-defined verification checks now load properly when OBO-Edit is restarted

Release Name: 1.100-beta22

Notes:

Changes: * Added diagnostic messages to help track down a rarely seen Category Manager load/save bug * Changed compilation settings to add greater usefulness to stderr output * Fixed reasoner bug caused by incomplete transitivity rules * Verification plugin no longer shows hyperlinks in situations where clicking the link would have no effect * Fixed bug where beta21 required Java 1.5 instead of Java 1.4 * Fixed reasoner bug that caused obo2obo to fail when using reasoner

Release Name: 1.100-beta21

Notes:

Changes: * A warning will appear if the screen is locked around a non-visible path * A progress bar now pops up while the reasoner is working. * Fixed broken load history browse button. * Fixed DAG Viewer slow update (at least in some circumstances) * Fixed problem where filtering seemed to always be strict (which was actually caused by an underlying bug that was probably effecting the display in other ways) * Fixed bugs in history system * Removed the sub-selection control and added buttons so the sub-selection can be controlled via the ontology editor panel

Release Name: 1.100-beta20

Notes:

Changes: * Fixed dangling propertyValue bug * Fixed bug where non-transitive paths were displayed in the DAG Viewer even when the "Show non-transitive paths" setting was disabled * Fixed bug where only obsolete search results could be selected * Layout editor now provides useful error messages when too many subtags are added to a tag that normally only allows one subtag

Release Name: 1.100-beta19

Notes:

Changes: * Fixed a number of reasoner bugs * Fixed problems with DAG Viewer performance * Fixed DAG Viewer problems in cyclic ontologies * Fixed link filter editor bugs * Fixed bug in synonym category manager * Fixed bug in 'write id rules' control in OBO file save gui

Release Name: 1.100-beta18

Notes:

Changes: * Eliminated save bottlenecks and other performance problems introduced by new datamodels * Fixed errors in filtered reasoner behavior introduced by datamodel improvements * Fixed null pointer exceptions when running "obodiff -t xml" * Fixed bad error location reporting from OBO adapter when loading files that use the import statement

Release Name: 1.100-beta17

Notes:

Changes: * Fixed bug where OBO-Edit put in line feed characters in Windows * Fixed DAG Viewer bugs * Added more detail to search summary line in filter editor * Fixed bugs when using the Root search aspect to filter * Crippled reasoner code so that the OBO-Edit gui freezes while the ontology is being re-reasoned. This sucks, but it's better than the current behavior where users see the ontology being taken apart and reassembled by the reasoner in real time (which leads to all kinds of strange graphical artifacts) * Fixed spurious "uncommitted text edits" messages from terms that have cross-product definitions AND explicit assertions of the cross product links * 100-fold speedup when the "flower button" (actually called the reasoned prefilter button) is used * Reduced lag between when a term is selected and when it appears in the text editor by around 75% * Fixed bug where ontologies with dbxref descriptions that contain commas cannot be saved

Release Name: 1.100-beta16

Notes:

Changes:

• Fixed constant exception popup caused by a verification configuration file that refers to non-existant checks

Release Name: a>

Notes:

Changes: * Fixed bug where obomerge would unobsolete some terms * Fixed bug where obomerge would create duplicate synonyms * Fixed constant NullPointException messages from the Verification Plugin * Updated documentation

Release Name: 1.100-beta14

Notes:

Changes: * Fixed giant Configuration Panel bug * Fixed bugs that occured when loading plugins with external libraries * Unsealed org.geneontology.oboedit.plugin package (which was creating problems when loading external plugins) * OBO-Edit can finally load extended characters again * Removed harmless startup NullPointerException messages * Added obomerge to platform independent version * Finished documentation (I think)

Release Name: 1.100-beta13

Notes: Additional Files:

• questionplugin.jar

Say hello to the first external OBO-Edit Plugin! This is the Question Plugin. When a term is selected, the Question Plugin displays a list of (possibly) interesting questions about the term, and the answers to those questions.

Currently all answers consist of a structured list of term names. If a term name is clicked, it will become selected in the main gui.

To get more info about how a question is being answered, mouseover the question text.

To install this plugin, place questionplugin.jar in the extensions subdirectory of your OBO-Edit installation directory.

• oboedit.jar

The recently added oboedit.jar file is a patch to fix an obomerge bug where instead of writing the merge results to disk it would just write out one of the original files in 1.2 format.

To install:

• Shut down OBO-Edit
• Copying the oboedit.jar file into the runtime/ subdirectory of your OBO-Edit installation

It's installed! Changes: * Changed the implementation of sets in the OBO-Edit datamodels. This will lead to negligibly slower performance (I would be stunned if it were a > 5% performance hit) but dramatically reduced memory usage (OBO-Edit will use 50-80% less memory with most ontologies). Many thanks to Mark Gibson and his profiling tools for pointing out the bad memory use. * Fixed problems with right-click menu when there is no selection * Fixed unhandled exception when changing the relationship type of a link and an ancestor link at the same time * Fixed bug where no warning would pop up when OBO-Edit ran out of ids * Fixed autocommit bugs that appeared after the autocommit settings had been changed * Fixed bug where asterisk did not appear on cross-product tab for terms that had cross products defined * Fixed bug where dbxrefs containing a # would be marked as containing non-URI characters * Fixed bug where some verification checks would be run on text edit even if the user had disabled them * The plugin system can now load external libraries * Completed documentation for the verification plugin

Release Name: 1.100-beta12

Notes:

Changes: * Fixed bug where last item in an OBO file would not have its namespace loaded correctly if it used the default ontology namespace * Fixed StackOverflowError when filtering ancestors in an ontology with cycles * Fixed obo2obo bugs * Fixed problem reading OBO files with curly braces in term names * Graph viewer plugin now wraps long term names on spaces, tabs, underscores, dashes and commas * Fixed bad automatic sizing of definition dbxref control * Added Quick Fix for verification warning about multiple spaces in a row * Improved messages for verification warnings about multiple spaces in a row and missing spaces around periods. * Fixed bugs where quick fixes that modified the ontology would not work in autocommit mode * Improved documentation

Release Name: 1.000-beta11

Notes:

Changes: * Fixed lost genus info * Fixed major new bugs in filter editor * Fixed bugs when starting OBO-Edit with no exiting configuration data * If id generation rules were loaded from a file, OBO-Edit now saves those rules by default

Release Name: 1.100-beta10

Notes:

Changes: * Bug fixes * Added quick-fix items to verification system * Added lots of quick fixes * Fixed bug where synonym categories with bad ids could be saved * Fixed bug where primary selector would be deselected when the configuration changed * Fixed user's guide search problems * Created local filtering checkbox in Graph Viewer * Mac installer can now create aliases

Release Name: 1.100-beta9

Notes:

Changes: * Fixed bug in text verifications that would cause verification step to crash in some circumstances. * Improved information given in unhandled exception message * Fixed bad reasoner link trimming behavior * Fixed bugs in memory setting updates from installer * Fixed Mac OS launcher bugs * Added script launching to obo2obo

Release Name: 1.100-beta8

Notes:

Changes: * Rebuilt platform independent launchers to use the same vm options passing as the installer-built launchers * Fixed bug when loading an obo file with an exclamation point inside of quotes * Fixed bugs in writing memory settings to .vmoptions and Info.plist files * Added popup message for out of memory errors * Fixed bugs in import code * Documentation improvements

Release Name: 1.100-beta7

Notes:

Changes: * Added hidden -fixdbxrefs parameter to obo2obo * Added "Always save properties" mode to OBO advanced save * Changed default layout * Added "Use default layout" button to layout editor * Documentation updates

Release Name: 1.100-beta6

Notes:

Changes: * Bug fixes * Added support for saving reasoned links to disk in obo2obo * Added support for realizing implied links as real links in OBO adapter * Added clash detection/repair in obomerge * Documentation improvements

Release Name: a>

Notes:

Changes: * Fixed problem where FindPanel forgets settings on exit * Sorted properties in CopyAction, MoveAction and TypeChangeAction menus * Rebuilt installers

Release Name: 1.100-beta4

Notes:

Changes: * Fixed OBOMerge problems * Fixed problems when deleting newly created, unmodified dbxrefs * Fixed launcher problems * Fixed bug where dbxrefs from the DbxrefPlugin would disappear from the definition refs editor when the edit button was pressed * Improved descriptions in OBODiff for several types of history items

Release Name: 1.100-beta3-rebuild

Notes: Rebuilt installers for beta3 to try to fix widespread installation problems. Changes:

Release Name: 1.100-beta3

Notes:

Changes: * Added "Root" aspect to search aspects * Added verification system * Added pre-trim type filters to save * Added root detection algorithm to save * OBO-Edit chooses much better default selection paths when a search result is selected * Non-transitive links are now hidden by default * Added isa complete filter * Added transitivity, cyclicity, symmetry controls for properties

Release Name: 1.100-beta2

Notes:

Changes: * Added "Root" aspect to search aspects * Added verification system * Added pre-trim type filters to save * Added root detection algorithm to save * OBO-Edit chooses much better default selection paths when a search result is selected * Non-transitive links are now hidden by default * Added isa complete filter

Release Name: 1.100-beta1

Notes:

Changes: * Moved to XML format for configuration files * Added buttons to add and remove data adapter profiles * Added "Are you sure you want to exit?" feature * Added graph plugin save capability for PNG, DOT and XDOT format * Lowered memory use * Added text edit autocommit mode * Added warnings for lost text edits when not in autocommit mode * Added XML sub-layouts * Added lots of new XML layout tags * Added -parsecomments and -writecomments tags to obo2obo * Added text field checks for incomplete sentences, missing title case, extra whitespace characters

Release Name: 1.002-beta3

Notes:

Changes: * Fixed bug in saving consider tags in OBO format * Fixed bug where destroy confirmation message might appear behind the main window * Fixed bug where OBO serializer was writing newlines in comments incorrectly * Added obo2obo script * Parent-child merges (or merges between any terms) are now allowed. See the user's manual for potential dangers of this new behavior. * Merged terms are now assigned a definition and comment consisting of the definition/comment of the source and target terms concatenated together. * Any number of replacement or consider terms are allowed for obsolete terms.

Release Name: OBO-Edit 1.002-beta2

Notes:

Changes:

• Fixed bug where OBO serializer was writing newlines in comments incorrectly
• Added obo2obo script
• Parent-child merges (or merges between any terms) are now allowed. (See the user's manual for potential dangers of this new behavior)
• Merged terms are now assigned a definition and comment consisting of the definition/comment of the source and target terms concatenated together.
• Any number of replacement or consider terms are allowed for obsolete terms.

Release Name: OBO-Edit 1.002-beta1

Notes:

Changes: * Fixed bug where OBO serializer was writing newlines in comments incorrectly * Added obo2obo script

Release Name: 1.000-beta27

Notes:

Changes: * Self-loops no longer allowed from Cross Product editor