1.6

04.15.2008, version 1.6 - beta4

• feature: in-table editing added, complete with auto-completion
• feature: large text fields can now be viewed/edited in separate panel when configured [1873002 | 1610324]
• feature: ontology tree browser is a new component, and all ontologies can be browsed. terms can be dragged/dropped from the tree to the editor []
• change: configurations birn, worm, ncbo, etc., were all updated with the "big text box" for the "description" field
• bugfix: layouts/perspectives are no longer automatically overwritten at application close [1909013]
• bugfix: post-composition window is no longer automatically displaying terms in their intersection style when selected [1927441]
• bugfix: a strange bug where a change to the configuration with the "select config" option in phenote was not preserving the change with the new windows-installer. this was a specific problem to the ncbo.cfg configuration. this originated with a bug in the configuration file, and has now been remedied. [1911327]
• bugfix: column content was being sorted with case-sensitivity. [1890712]
• bugfix: selection of a row in the annotation table is preserved when sorting on different columns. [1922443]
• bugfix: field widths in editor panel are maxed to the size of the panel so that scrolling horizontally won't have to happen. [1922353]
• bugfix: terms from the autocompletion pick-list were not highlighted in the genotype maker [1909007]

1.5

03.03.2008, version 1.5 - release

With the release of version 1.5, we are transitioning over to a new interface. We will continue to support the webstart version of phenote for a couple of releases, but will ultimately switch to the standalone version that is debuting in this release. The new 'Phenote+' will have at least the same capabilities as the original Phenote, but new components will be only added to the new interface. Be sure to choose the proper phenote (or phenote plus) when entering bug reports

• feature: if user changes their annotations since previous save, user is prompted for resave [1810448]
• feature: addition of the ProtocolEditor as a plug-in to phenote. For more information, please see the Protocol Editor demo. This plugin is being developed by the folks at the Open Microscopy Environment
• feature: Read-only fields can be configured [1737572
• feature: "Save" added as menu item to overwrite currently open file [1803824]. A dot in the titlebar will disappear upon save. [1893249
• feature: "Open" and "Save" added as toolbar icons [1811165]
• feature: User can lookup abstracts from PubMed or OMIM for "Pub" fields configured with the PubMedDataAdapter. These can be seen in the "ncbo-test" and "demo" configurations
• change: table manipulation actions such as "New", "Delete", and "Duplicate" have been moved to a iconic-toolbar at the top of the table window [1824391]
• feature: new data types added for configuration: boolean, ints, FILL ME IN
• change: all configurations have been changed to include "terminology definitions" which need to be defined for the new ontology update feature
• feature: A new ontology update interface has been added, similar to the mac-style software update. The user is presented with a single window that allows them to choose some/all ontologies to update as they start the application [1694447]
• feature: Enter the current value and advance to the next annotation while continuing to edit the same field, by pressing Cmd-Return on Mac, Ctrl-Enter on Windows
• feature: Improved sorting in tables - now uses natural sorting which takes embedded numbers in strings into account.
• feature: Added support for fields whose values are lists of other characters - this is for Phenoscape specimen lists.
• feature: Added pick list type of field. This field can choose any number of values that have been entered into another list field for a character - this is for Phenoscape specimen lists.
• bugfix: Mac-specific problem with "View" menu item names fixed [1882256]
• bugfix: Term Info box used to display empty collapsible panes - these have been removed when there are no items in them [1833088]
• bufgix: Phenote can now accomodate empty E/Q fields when mapping to the annotation model [1894065]
• bugfix: Undo with free-text type fields was broken

01.30.2008, version 1.5 - beta4

• feature: Added a scrollbar to the config chooser [1799784]
• change: post-compositions are now displayed in multi-line style [1579357]
• bugfix: Use term button now working again
• bugfix: Return/Enter key now selects first item in an auto-completion list before moving to next field [1574780]

01.22.2008, version 1.5 - beta3

12.20.2007, version 1.5 - beta2

• feature: Solaris OS now supported
• feature: New look and feel with Phenote+
  • Ability to move different panels around to customize the user experience. [1729114] These panels can be "locked" by going to the Settings->Lock Docking Components menu item. [1882110]
  • Panels can be "undocked" so that they can float independently around the screen
  • feature: Phenote can interoperate with some obo-edit components, such as the tree-like dag viewer and the graph editor. [1822371]
• feature: Term info panel updated with collapsible panes.
• bugfix: Sporatic bug fixed where phenote hangs after loading [1841122]
• bugfix: Field name is now always shown, even if there is only one ontology configured for that field. It used to default to the ontology name in this instance. [1852112]

11.09.2007, version 1.5 - beta1

1.4

10.10.2007, version 1.4 - release

• feature: Loading splash more informative about what's going on behind-the-scenes such as which ontologies are loading, if they are being updated, etc.
• feature: obo edit annotation model can now be optionally configured for backend, which will allow for more sophisticated data to be captured (like comparisons)
• feature: Error for obo parse failures to info panel
• feature: Delimited tab adapter uses column headings to map to table, rather than ordering
• feature: Autocompletion optimized with threading, cancels stale requests (min-comp-chars now pase)
• feature: Date created automatically added into data (under the hood)
• feature: If arrow hit with empty input then gets & displays all terms (used to inefficiently pre-load)
• feature: Can sort completion list by ID, needed for zfin stages
• feature: Table preserves user ordering of columns, in addition to column widths.
• feature: Filter search field allows user to narrow down displayed data rows via matching text.
• feature: See actual value in input field when multiple rows are selected and have the same value.
• feature: Copy all taxon names in specimen list as an unresolved Newick tree (for PhenoMap/NESCent)
• feature: Automatically open specimen list and phylogenetic tree files when opening data file (for PhenoMap/NESCent)
• change: Moved test suites in with source to work with eclipse
• change: Took a lot of obos out of webstart jar - less bulky - as they get automatically downloaded
• change: Phenote now follows standard log4j configuration conventions. Pass a custom log configuration to Phenote via the classpath or the system propery "log4j.configuration".
• bugfix: Terms not found are no longer dropped, a dangler is created, and error msg to info, show up in red
• bugfix: if log conf fails use backup default
• bugfix: Input fields now commit changes with either Return or Tab
• bugfix: Native lib is loaded properly for Mac interface on webstart, allowing traversal of aliases in file dialog, as well as user sidebar items in file dialog
• bugfix: Noncontiguous row selection works now on Mac

08.28.2007, version 1.4-beta3

• feature: Native look-and-feel enabled for interface. Users should now see Mac or Windows style depending on their system.
• feature: read-only field (needs work)
• feature: config disabling of copy of field (for db ids)
• feature: display property values of terms in term info
• feature: Phylogeny Chooser for NESCent/PhenoMap project. A user can import a phylogenetic tree in Newick format. The user can use the tree viewer to select rows within the character template - typically taxonomic groups.
• feature: term fields can be nullified
• feature: separate queries to backend for different groups, implemented in worm
• feature: ID field type, requires ":"
• feature: can get unique list of deleted annots
• feature: added group adapter framework
• feature: fly genotype group adapter makes fly genotype strings from tab/group
• feature: worm group adapter makes reference terms from ref query
• change: on term completion if adding a letter use previous completion list
• change: worm adapter query tab working properly
• change: build file takes param for webstart version deployment, and puts in jnlp
• change: group adapters can listen for CharList changes
• change: added/corrected birn ontologies
• bugfix: load of file doesnt crash on post comp parsing bug
• bugfix: doesnt load obo files specified twice twice
• bugfix: view menu show up at initialization
• bugfix: layout of term history with split pane proper

07.20.2007, version 1.4-beta2

• feature: RESTful data input for BIRN's smart atlas
• feature: Character Template for NESCent/CToL (Jim Balhoff). This is an additional window which edits a separate list of characters using a subset of the fields in the main window. The fields to include are denoted by a group in the config file. This functionality will be used by the PhenoMap project to create a specimen list. The same EQ statement can be applied to many specimens at once by selecting the relevant specimens and generating characters in the main window with the template fields pre-filled. All the new characters are selected and can then be bulk edited.
• feature: Progress on gui for config (in progress)
• feature: Progress on field groups (genotype maker, pub querying...)
• feature: right-click editing functions for free-text fields in data input frame. right-click copy in table.
• feature: incorporation of help documentation into Phenote under menu item Help->PhenoteHelp
• feature: added plant_grammene.cfg configuration, plus appropriate obo files.
• feature: navigation bar added to top of term info; buttons to traverse worn paths; term name moved up to top of box [1685540]
• feature: dbxrefs are listed in term info (no external links yet) [1739399]
• change: ontology files can be read with dangling references
• change: Command line read & write of .tab
• change: 'use term' button moved and replaced with checkmark button in navigation bar
• change: ncbo.cfg changed to always update from master file at url
• change: birn2.cfg gene_ontology replaced with gene_ontology_edit.obo reference
• change: Windows splash screen text edited from 'biomedial' to 'biomedical'
• bugfix: obsolete terms were not being read in from annotation files as Ontology.getTerm was only looking at non obsoleted terms
• known bug: ontology files using import statements not properly read

version 1.4-beta1 - oops - skipped!

1.3

05.24.2007, version 1.3 release

• feature: Web-based documentation and Help features.
• feature: Metadata fields added to configuration. User can name their configuration, add a description, and author [1676756, 1672080]
• feature: Descriptions can be added for fields
• feature: Master-to-local overwrite stuff
• feature: Dialog allows user to back out of exiting from File->Exit
• feature: Autocompletion search default settings configurable 1677411, 1669579]
• feature: User can save search setting defaults if changed during Phenote session
• change: File->New is disabled until next version
• change: ncbo, zfin-standalone, flybase, demo configurations modified to include master-overwrite feature; keeping track of revision history in file comments
• change: can read http, https, ftp, ftps for ontology update URLs, not just http [1718945]
• bugfix: Bulk-editing functions are working again
• bugfix: Undo wasn't working for several functions due to a bug in the Copy function [ 1721044]
• bugfix: multi-select deletes free-text content replaces with * [1721032]
• bugfix: pre 1.2 post comp data wasnt able to load [1721470]

05.09.2007, version 1.3-beta1

• feature: Added sample config for BIRN
• feature: Added SAO.obo ontology for BIRN
• feature: Namespace config writes back
• feature: Can specify more than one website for ontology update
• feature: Empty field shows all terms in ontology rather than none
• feature: Can add more differentia to post comp
• bugfix: Config update/merge bug where fields in wrong order fixed.
• known bug: can't read post-compositions from phenote versions 1.1 and prior

1.2

05.02.2007, version 1.2

• feature: Can post-compose with >2 terms
• feature: Term history display can be toggled on/off (Settings->Term History menu)
• feature: Synonyms delineated by scope in Term Info: Exact, Narrow, Broad, General, Related. If the synonym category is given, it is displayed. For example, the term 'water' has the related synonym H2O, which has the category of a chemical formula.
• feature: Obsolete replacements or consideration terms are displayed in term info with links
• feature: Display term comments in Term Info beneath relationships
• feature: Loading splash screen
• feature: Can configure by namespace for ontologies
• feature: Can automatically update ontologies during startup (configurable)
• feature: Timer added to configuration during ontology update check (configurable)
• feature: Can check which version of phenote is running by selecting Help->About.
• feature: Added common configuration for OMIM curation for use by NCBO (ncbo.cfg).
• feature: can forward and reverse sort columns by repeatedly clicking on column header [1574916]
• feature: display ontology namespace in term info box [1598048]
• change: Search filters moved into menu
• change: Updates to the zfin-standalone.cfg for the zebrafish community annotation; only includes GO and ZFanatomy ontologies.
• bugfix: Free-text field text not sticking in "new" or blank rows

1.1

04.06.2007, version 1.1.3

• feature: User can change the configuration they want to use at initialization from file menu; change takes effect after restart. (previously user had to edit the .phenote/conf/my-phenote file).

03.28.2007, version 1.1.1

• feature: Phenote is now a single webstart app; user chooses their configuration at startup (used to be hard wired to a configuration)
• feature: Phenote will merge its default configuration with users' configuration, preserving user changes as well as adding anything new from phenote upgrade.
• feature: Beginnings of term history to display recently used ontology terms. Will be clickable in future.
• feature: Data entry panel will spill over into multiple tabs if >12 fields included
• feature: Tab delimited data adapter; data in/output format compatible with excel and other spreadsheet software [1661778]
• feature: QueryableDataAdapter interface for developers; enables connection between input fields and a database backend for quering. Queryable fields get a retrieve button.
• feature: Autocompletion search with ALL ontologies in a field instead of just one [1575241]
• feature: Retrieve ontology files from URL if more up to date or no local found; only from a single repository for all [1648337, 1574906]
• feature: fixed releases available for checkout via sourceforge [1670345]
• feature: display xtns in load/save menu choices [1594508]
• change: Refactored code for field guis
• change: Layout improved
• change: OBSOLETE is displayed in red next to obsolete term in term info [1581589]
• change: human.cfg configuration to include obo foundary ontologies GO, SO, CL, ChEBI, PATO, OBI, Relations, unit, and spatial [1633287]
• bugfix: Ontology chooser reflects current term
• bugfix: phenosyntax reader broken [1684591]
• bugfix: post-composed terms not loading [1661728]

1.0

02.06.2007, version 1.0.5-fly, 1.0.5-zfin

01.12.2007, version1.0, Webby Phenote(components used by Zfin)

• change: refactoring of the data model to allow addition of any field desired, not just E,Q,GC,GT,Pub. Stage, Evidence, Description, Abnormal, and Absent have been added through this new mechanism in the newest configurations. [1574912]
• change: Webby phenote is now using JSP and Spring.
• change: There has been some recent work with UVictoria for ontology graph visualization. This is coming along well and hopefully will be seen in the next release.
• bugfix: absent fields not displaying in human 1.03 [1661973]

0.9

11.15.2006, version 0.9-fly, 0.9-zfin, DictyBase webby phenote

11.09.2006, version 0.9

• feature: Undo - can step backward through previous actions
• feature: Quartz scheduler used to schedule when to check for new obo files. Added by Christian Pich of Zfin. [1588669]
• change: upgraded PhenoteServlet to Spring framework. Added by Christian Pich [1588670]
• feature: Synonyms are displayed from autocomplete with [syn]; when selected the term name (not the synonym) goes into the field and table (webby & standalone)
• feature: obsoletes are displayed from autocomplete with [obs]
• feature: Bulk update & copy in standalone. [1579885, 1579882]
• change: search types interface changed from radio buttons to checkboxes (j. balhoff)
• bugfix: file-save button changed to say "save" not "load"
• feature: file-save recognizes and chooses appropriate data adapter based on file extension (.psx for phenosyntax and .xml for phenoxml)
• change: Single quotes escaped for javascript fns.

0.8

10.02.2006, version 0.8-fly, 0.8-zfin, DictyBase webby phenote

• feature: Added post composition to standalone phenote.
• feature: Actions are logged for both webby/servlet & standalone.
• feature: Pheno-xml reader (thanks to Jim Balhoff) and improvements to pheno-xml writer (does pub & genetic context)
• feature: Command line reading & writing of phenoxml & phenosyntax.
• feature: Application exits on window exit (unless servlet)
• feature: Can filter out stage terms from zfin anatomy

0.7

08.23.2007, version 0.7-fly., 0.7-zfin

• feature: entity chooser (web)
• feature: can configure to check for new obo files and load them. (These are installed at zfin, if anyone would like to see them publicly let me know).
• feature: entity field and term info installed into zfin (web) phenotype site. Term info & completion are scrollable.
• feature: standalone version can read & write pheno-syntax with ids & term names in comments
• feature: standalone entity chooser
• feature: added pub field
• feature: added 'use term' button in term info
• feature: can sort table by any field in forward order by clicking on headers
• change: personal config file gets copied out of jar
• change: directory for file load/save remembered
• change: layout fixed
• bugfix: paste for mac fixed

0.6

07.28.2006, version 0.6-fly, 0.6-zfin, Webby Phenote (0.6)

• new: webbified phenote. This is in its extremely early stages (very little functionality and buggy). At this point it only does Entity and Quality fields and term info and thats it, and even thats buggy, but more coming soon!
• feature: writing pheno-xml format, and uses the latest PATO ontology (as of July 28, 2006).

0.5

05.12.2006, version 0.5-FlyBase, 0.5-ZFIN

No new additions to the gui here. In preparation for my visit to Cambridge/FlyBase, I worked on a FlyBase dataadapter. This is phenote first data adapter so I also laid down the foundations for data adapters. The FlyBase data adapter simply cuts and pastes phenotype character objects to the system clipboard. The idea is that FlyBase's Proforma java application will also cut and paste to the clipboard. This is a simple way to pass objects between applications, to get us off the ground. Proforma is not there yet so this has not been tested yet with Proforma, but it works in the test suite. Added special FlyBase character wrappers that do the parsing and creating of Proforma character strings.

0.4

04.26.2006, version 0.4-flybase, 0.4-zfin

• feature: Added Genetic Context field.
• feature: Parent & child terms in term info are now clickable/navigable.
• feature: HTML Links in descriptions are clickable (should bring up default browser)
• feature: configuration files to configure ontologies & fields. This is currently at a devloper level (xml file) not a user level(gui - todo). There is a command line argument for which configuration file to use. This allows for having separate zf & fb releases without having to change the code to do it (like was done for the ctol release). The configuration for now is for developers (internal xml file), on the todo is to have a gui configuration for users.
• bugfix: can't delete to 0 rows
• bugfix: synonym search duplicates removed
• Development: Refactored for configuration & adding field. Made the internal code much more generic for adding new fields from configuration, got rid of a lot of hard wiring.  Part of this was instituring model-view-controller in some places where views were improperly talking to other views. In theory this should also make it easier to plop a web gui on top of the current phenote model & controller.
• Development: Renamed Phenotype to Character. Added Character interface CharacterI.
• Development: Added tests to test suite.

0.3

04.07.2006, version 0.3, 0.3.1 (for CToL)

Note: 0.3.1 is identical to 0.3 except that it has ontologies for CToL (fish evolution group). In particular it uses a fish taxonomy ontology for the id (in this taxonomy) choosing. On the todo is the ability to configure ontologies, but not there yet, so for now need to hardwire with seaparate jar file. This clearly makes the todo item a bit more pressing.

Release for NESCent fish eveolution meeting. No major new functionality here. Cleaned up and fixed a lot of the bugs in 0.2, which was rather buggy.

• feature: Completion terms now sorted alphabeitcally.
• feature: Obsoletes are now in addition to regular terms, not in lieu of.
• feature: Filtering out attribute values (todo: change to actually filter in values)
• change: Html formatting of term info (todo: make terms selectable)
• feature: Children relations are in term info
• change: Term info layout greatly improved
• change: Term info in scroller
• change: Border with label around term info
• change: Put definition at end of term info
• bugfix: Backspace in ontology combo box
• bugfix: Selection of item in comp list causing exception, not going in term box
• bugfix: No terms with just 1 char
• bugfix: Popup was staying up after selection
• development: Test suite added! (todo: add more tests)
• development: Migrated to jdk 1.5 (which caused some of the bugs above)
• development: Ant file made build.xml.
• development: CompletionList refactored into Ontology (prompted by sorting)

0.2

03.27.2006, version 0.2

• feature: term completion on Synonyms, Definitions and Obsoletes
• feature: mouse-over on term in completion list displays info in 'term info' text area
• Todo: layout, scrollbar, border w title, ordering & lumping parents & children, formatting. Also perhaps have children & parents be clickable in some fashion either html-like clickable text or as buttons.
• known bugs: If you hit backspace in term completion fields it gets wacky

0.1

03.01.2006, version 0.1

0.1 was the initial phenote release (known briefly as the plumper at the time). It just had a genotype, anatomy and pato fields, where anatomy and pato did term completion (just on term names) with there ontologies in a drop down list. There was also the phenotype table that tracked phenotype instances being edited in the above fields. This very limited functionality was demo'd at the cbio meeting 3/3/06 at Stanford.