From: <no...@us...> - 2008-02-20 21:13:33
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Revision: 1544 http://obo.svn.sourceforge.net/obo/?rev=1544&view=rev Author: nomi Date: 2008-02-20 13:12:40 -0800 (Wed, 20 Feb 2008) Log Message: ----------- I'm sure these were committed by accident--I just happened to notice them. Removed Paths: ------------- phenote/trunk/doc/phenote-website/related.shtml~ phenote/trunk/doc/phenote-website/release-notes.shtml~ phenote/trunk/doc/phenote-website/resources.shtml~ phenote/trunk/doc/phenote-website/screenshots.shtml~ phenote/trunk/doc/phenote-website/team.shtml~ phenote/trunk/doc/phenote-website/users.shtml~ Deleted: phenote/trunk/doc/phenote-website/related.shtml~ =================================================================== --- phenote/trunk/doc/phenote-website/related.shtml~ 2008-02-20 20:24:24 UTC (rev 1543) +++ phenote/trunk/doc/phenote-website/related.shtml~ 2008-02-20 21:12:40 UTC (rev 1544) @@ -1,173 +0,0 @@ -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml"> - <head> - - <!--#include virtual="ssi/head.html" --> - <title>Phenote</title> - - </head> - <body> - - <!--#include virtual="ssi/header.html" --> - - <div id="main_container_aux"> - <div id="main_content_aux"> - <div class="catch_phrase"> - Related Projects - </div> - <h1>Ontologies</h1> - <h2> - <a href="http://www.bioontology.org/wiki/index.php/PATO:Main_Page"> - Phenotype and Trait Ontology (PATO)</a> - </h2> - <p> - An ontology of phenotypic qualities (properties). This ontology - can be used in conjunction with other ontologies such as GO or - anatomical ontologies to refer to phenotypes. Examples of - qualities are red, ectopic, high temperature, fused, small, - edematous and arrested. - </p> - <h2> - <a href="http://www.geneontology.org/"> - Gene Ontology (GO)</a> - </h2> - <p> - The Gene Ontology (GO) project is a collaborative effort to address - the need for consistent descriptions of gene products in different - databases. - The Gene Ontology project provides a controlled vocabulary to - describe gene and gene product attributes in any organism. There - are three distinct ontologies developed by GO: molecular function, - biological process, and cellular component. - <h2> - <a href="http://obi.sourceforge.net/"> - Ontologies for Biomedical Investigations - </a> - </h2> - <p> - The Ontology for Biomedical Investigations (OBI) project is - developing an integrated ontology for the description of - biological and medical experiments and investigations. This - ontology will support the consistent annotation of - biomedical investigations, regardless of the particular - field of study. - </p> - - - <h1>Resources</h1> - <h2> - <a href="http://www.bioontology.org/"> - National Center for Biomedical Ontology</a> - </h2> - <p> - The NCBO is a consortium of leading biologists, clinicians, - informaticians, and ontologists who develop innovative technology - and methods that allow scientists to create, disseminate, and - manage biomedical information and knowledge in machine-processable - form. - </p> - <h2> - <a href="http://www.obofoundry.org/"> - OBO Foundry</a> - </h2> - <p> - The OBO Foundry is an open, inclusive, and collaborative core of - interoperable ontologies developed by the research community. The - goal is to facilitate the creation of consistent, compatible, and - unambiguous ontologies thereby supporting the biomedical research - community. The contributors are those biological researchers and - ontology developers who have agreed to work together on an evolving - set of design principles that can foster interoperability of - ontologies, and ensure a gradual improvement of quality and formal - rigor in ontologies, in ways designed to meet the increasing needs - of data and information integration in the biomedical domain. - - </p> - <h2> - <a href="http://www.gmod.org/"> - Generic Model Organism Databases</a> - </h2> - <p> - The Generic Model Organism Project (GMOD) is a joint effort - by the model organism system databases WormBase, FlyBase, - MGI, SGD, Gramene, Rat Genome Database, EcoCyc, and TAIR to - develop reusable components suitable for creating new - community databases of biology. - </p> - - <h2> - <a href="http://ifomis.org"> - Institute for Formal Ontology and Medical Information - Science (IFOMIS) - </a> - </h2> - <p> - The Institute for Formal Ontology and Medical Information - Science (IFOMIS) comprehends an interdisciplinary research - group with members from Philosophy, Computer and Information - Science, Logic, Medicine, and Medical Informatics, focusing - on theoretically grounded research in both formal and - applied ontology. - </p> - - <h2> - <a href="http://mged.sf.net/"> - MGED - </a> - </h2> - <p> - The Microarray Gene Expression Data (MGED) Society is an - international organisation of biologists, computer - scientists, and data analysts that aims to facilitate the - sharing of microarray data generated by functional genomics - and proteomics experiments. - </p> - - <h2> - <a href="http://www.ebi.ac.uk/ontology-lookup/"> - Ontology Lookup Service - </a> - </h2> - <p> - The Ontology Lookup Service is a spin-off of the PRIDE - project, which required a centralized query interface for - ontology and controlled vocabulary lookup. While many of the - ontologies queriable by the OLS are available online, each - has its own query interface and output format. The OLS - provides a web service interface to query multiple - ontologies from a single location with a unified output - format. - </p> - - <h2> - <a href="http://www.plantontology.org/"> - Plant Ontology Consortium - </a> - </h2> - <p> - The Plant Ontology Consortium (POC) aims to develop, curate - and share structured controlled vocabularies (ontologies) - that describe plant structures and growth/developmental - stages. Through this effort, the project aims to facilitate - cross database querying by fostering consistent use of these - vocabularies in the annotation of tissue and/or growth stage - specific expression of genes, proteins and phenotypes. - </p> - - <h2> - <a href="http://www.psidev.info/index.php?q=node/258"> - Proteomics Standards Initiative - </a> - </h2> - <p> - Is also interested in guidelines for the development of - Controlled Vocabularies. - </p> - - </div> - </div> - - <!--#include virtual="ssi/footer.html" --> - - </body> -</html> Deleted: phenote/trunk/doc/phenote-website/release-notes.shtml~ =================================================================== --- phenote/trunk/doc/phenote-website/release-notes.shtml~ 2008-02-20 20:24:24 UTC (rev 1543) +++ phenote/trunk/doc/phenote-website/release-notes.shtml~ 2008-02-20 21:12:40 UTC (rev 1544) @@ -1,579 +0,0 @@ -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml"> - <head> - - <!--#include virtual="ssi/head.html" --> - <title>Phenote: A Phenotype Annotation Tool using Ontologies</title> - - </head> - <body> - - <!--#include virtual="ssi/header.html" --> - - <div id="main_container"> - <div id="main_content"> - <div class="catch_phrase"> - Phenote Release Notes - </div> - - <h1>1.4 </h1> - <h2>08.28.2007, version <a href="phenote/1.4-beta3/phenote.jnlp">1.4-beta3</a></h2> - <ul> - <li>feature: Native look-and-feel enabled for interface. Users should now see Mac or Windows style depending on their system.</li> - <li>feature: read-only field (needs work)</li> - <li>feature: config disabling of copy of field (for db ids)</li> - <li>feature: display property values of terms in term info</li> - <li>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.</li> - <li>feature: term fields can be nullified</li> - <li>feature: separate queries to backend for different groups, implemented in worm</li> - <li>feature: ID field type, requires ":"</li> - <li>feature: can get unique list of deleted annots</li> - <li>feature: added group adapter framework</li> - <li>feature: fly genotype group adapter makes fly genotype strings from tab/group</li> - <li>feature: worm group adapter makes reference terms from ref query</li> - <li>change: on term completion if adding a letter use previous completion list</li> - <li>change: worm adapter query tab working properly</li> - <li>change: build file takes param for webstart version deployment, and puts in jnlp</li> - <li>change: group adapters can listen for CharList changes</li> - <li>change: added/corrected birn ontologies</li> - <li>bugfix: load of file doesnt crash on post comp parsing bug</li> - <li>bugfix: doesnt load obo files specified twice twice</li> - <li>bugfix: view menu show up at initialization</li> - <li>bugfix: layout of term history with split pane proper</li> -</ul> - -<h2>07.20.2007, version <a href="phenote/1.4-beta2/phenote.jnlp">1.4-beta2</a></h2> - -<ul> - - <li>feature: RESTful data input for BIRN's smart atlas</li> - - <li>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.</li> - - <li>feature: Progress on gui for config (in progress)</li> - - <li>feature: Progress on field groups (genotype maker, pub querying...)</li> - - <li>feature: right-click editing functions for free-text fields in data input frame. right-click copy in table.</li> - - <li>feature: incorporation of help documentation into Phenote under menu item Help->PhenoteHelp </li> - - <li>feature: added plant_grammene.cfg configuration, plus appropriate obo files.</li> - - <li>feature: navigation bar added to top of term info; buttons to traverse worn paths; term name moved up to top of box [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1685540&group_id=76834&atid=887913">1685540</a>]</li> - - <li>feature: dbxrefs are listed in term info (no external links yet) [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1739399&group_id=76834&atid=887913">1739399</a>]</li> - - <li>change: ontology files can be read with dangling references</li> - - <li>change: Command line read & write of .tab</li> - - <li>change: 'use term' button moved and replaced with checkmark button in navigation bar</li> - - <li>change: ncbo.cfg changed to always update from master file at url</li> - - <li>change: birn2.cfg gene_ontology replaced with gene_ontology_edit.obo reference</li> - - <li>change: Windows splash screen text edited from 'biomedial' to 'biomedical'</li> - - <li>bugfix: obsolete terms were not being read in from annotation files as Ontology.getTerm was only looking at non obsoleted terms</li> - - <li>known bug: ontology files using import statements not properly read</li> - -</ul> - - -<h2>version 1.4-beta1 - oops - skipped!</h2> - - - -<h1>1.3</h1> - - -<h2>05.24.2007, version <a href="phenote/1.3/phenote.jnlp">1.3 release</a></h2> - -<ul> - - <li>feature: <a href="http://www.phenote.org/help/">Web-based documentation and Help features.</a></li> - - <li>feature: Metadata fields added to configuration. User can name their configuration, add a description, and author [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1676756&group_id=76834&atid=887913">1676756</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1672080&group_id=76834&atid=887913">1672080</a>]</li> - - <li>feature: Descriptions can be added for fields </li> - - <li>feature: Master-to-local overwrite stuff</li> - - <li>feature: Dialog allows user to back out of exiting from File->Exit</li> - - <li>feature: Autocompletion search default settings configurable <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1677411&group_id=76834&atid=887913">1677411</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1669579&group_id=76834&atid=887913">1669579</a>] - </li> - - <li>feature: User can save search setting defaults if changed during Phenote session</li> - - <li>change: File->New is disabled until next version</li> - - <li>change: ncbo, zfin-standalone, flybase, demo configurations -modified to include master-overwrite feature; keeping track of revision -history in file comments </li> - - <li>change: can read http, https, ftp, ftps for ontology update URLs, not just http [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1718945&group_id=76834&atid=887913">1718945</a>]</li> - - <li>bugfix: Bulk-editing functions are working again</li> - - <li>bugfix: Undo wasn't working for several functions due to a bug in the Copy function [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721044&group_id=76834&atid=887913"> 1721044</a>]</li> - - <li>bugfix: multi-select deletes free-text content replaces with * [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721032&group_id=76834&atid=887913">1721032</a>]</li> - - <li>bugfix: pre 1.2 post comp data wasnt able to load<big> </big>[<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721470&group_id=76834&atid=887913">1721470</a>]</li> - -</ul> - - - - -<h2>05.09.2007, version <a href="phenote/1.3-beta1/phenote.jnlp">1.3-beta1</a></h2> - - - -<ul> - - <li>feature: Added sample config for BIRN</li> - - <li>feature: Added SAO.obo ontology for BIRN</li> - - <li>feature: Namespace config writes back</li> - - <li>feature: Can specify more than one website for ontology update</li> - - <li>feature: Empty field shows all terms in ontology rather than none</li> - - <li>feature: Can add more differentia to post comp</li> - - <li>bugfix: Config update/merge bug where fields in wrong order fixed.</li> - - <li>known bug: can't read post-compositions from phenote versions 1.1 and prior</li> - -</ul> - - - - -<h1>1.2</h1> - -<h2>05.02.2007, version <a href="phenote/1.2/phenote.jnlp">1.2</a></h2> -<ul> - - <li>feature: Can post-compose with >2 terms </li> - - <li>feature: Term history display can be toggled on/off (Settings->Term History menu)</li> - - <li>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 <i>related</i> synonym H2O, which has the category of a chemical <i>formula</i>.</li> - - <li>feature: Obsolete replacements or consideration terms are displayed in term info with links</li> - - <li>feature: Display term comments in Term Info beneath relationships</li> - - <li>feature: Loading splash screen </li> - - <li>feature: Can configure by namespace for ontologies</li> - - <li>feature: Can automatically update ontologies during startup (configurable)</li> - - <li>feature: Timer added to configuration during ontology update check (configurable)</li> - - <li>feature: Can check which version of phenote is running by selecting Help->About.</li> - - <li>feature: Added common configuration for OMIM curation for use by NCBO (ncbo.cfg).</li> - - <li>feature: can forward and reverse sort columns by repeatedly clicking on column header [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574916&group_id=76834&atid=887913">1574916</a>]</li> - - <li>feature: display ontology namespace in term info box [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1598048&group_id=76834&atid=887913">1598048</a>]</li> - - <li>change: Search filters moved into menu </li> - - <li>change: Updates to the zfin-standalone.cfg for the zebrafish community annotation; only includes GO and ZFanatomy ontologies. </li> - - <li>bugfix: Free-text field text not sticking in "new" or blank rows </li> - -</ul> - - - - -<h1>1.1</h1> - - - -<h2>04.06.2007, version <a href="phenote/1.1/phenote.jnlp">1.1.3</a></h2> - - -<ul> - - <li>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).</li> - -</ul> - - - -<h2>03.28.2007, version 1.1.1</h2> - -<ul> - - <li>feature: Phenote is now a single webstart app; user chooses -their configuration at startup (used to be hard wired to a -configuration)</li> - - <li>feature: Phenote will merge its default configuration with users' configuration, -preserving user changes as well as adding anything new from phenote -upgrade.</li> - - <li>feature: Beginnings of term history to display recently used ontology terms. Will be clickable in future.</li> - - <li>feature: Data entry panel will spill over into multiple tabs if >12 fields included</li> - - <li>feature: Tab delimited data adapter; data in/output format compatible with excel and other spreadsheet software [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661778&group_id=76834&atid=887913">1661778</a>]</li> - - <li>feature: QueryableDataAdapter interface for developers; enables -connection between input fields and a database backend for quering. -Queryable fields get a retrieve button.</li> - - <li>feature: Autocompletion search with ALL ontologies in a field instead of just one [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1575241&group_id=76834&atid=887913">1575241</a>]</li> - - <li>feature: Retrieve ontology files from URL if more up to date or no local found; only from a single repository for all [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1648337&group_id=76834&atid=887913">1648337</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574906&group_id=76834&atid=887913">1574906</a>]</li> - - <li>feature: fixed releases available for checkout via sourceforge [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1670345&group_id=76834&atid=887913">1670345</a>]</li> - - <li>feature: display xtns in load/save menu choices [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1594508&group_id=76834&atid=887913">1594508</a>]</li> - - <li>change: Refactored code for field guis</li> - - <li>change: Layout improved</li> - - <li>change: OBSOLETE is displayed in red next to obsolete term in term info [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1581589&group_id=76834&atid=887913">1581589</a>]</li> - - <li>change: human.cfg configuration to include obo foundary ontologies GO, SO, CL, ChEBI, PATO, OBI, Relations, unit, and spatial [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1633287&group_id=76834&atid=887913">1633287</a>]</li> - - <li>bugfix: Ontology chooser reflects current term</li> - - <li>bugfix: phenosyntax reader broken [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1684591&group_id=76834&atid=887913">1684591</a>]</li> - - <li>bugfix: post-composed terms not loading [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661728&group_id=76834&atid=887913">1661728</a>]</li> - -</ul> - - - -<h1>1.0</h1> - - - -<h2>02.06.2007, version <a href="phenote/1.0/phenote-flybase.jnlp">1.0.5-fly</a>, <a href="1.0/phenote-zfin.jnlp">1.0.5-zfin</a></h2> - - - -<h2>01.12.2007, version1.0, -<a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby -Phenote(components used by Zfin)</a></h2> - -<ul> - <li>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. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574912&group_id=76834&atid=887913">1574912</a>]</li> - - <li>change: Webby phenote is now using JSP and Spring.</li> - - <li>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.</li> - - <li>bugfix: absent fields not displaying in human 1.03 [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661973&group_id=76834&atid=887913">1661973</a>]</li> - -</ul> - - - -<h1>0.9</h1> - -<h2>11.15.2006, version <a href="phenote/0.9/phenote-flybase.jnlp">0.9-fly</a>, -<a href="phenote/0.9/phenote-zfin.jnlp">0.9-zfin</a>, -<a href="http://165.124.152.194/web/html/interface.html">DictyBase -webby phenote</a></h2> - -<h2>11.09.2006, version 0.9</h2> - - - -<ul> - - - - <li>feature: Undo - can step backward through previous actions</li> - - <li>feature: Quartz scheduler used to schedule when to check for new obo files. Added by Christian Pich of Zfin. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1588669&group_id=76834&atid=887913">1588669</a>]</li> - - <li>change: upgraded PhenoteServlet to Spring framework. Added by Christian Pich [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1588670&group_id=76834&atid=887913">1588670</a>]</li> - - <li>feature: Synonyms are displayed from autocomplete with [syn]; when -selected the term name (not the synonym) goes into the field and table (webby & standalone)</li> - - <li>feature: obsoletes are displayed from autocomplete with [obs]</li> - - <li>feature: Bulk update & copy in standalone. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1579885&group_id=76834&atid=887913">1579885</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1579882&group_id=76834&atid=887913">1579882</a>] </li> - - <li>change: search types interface changed from radio buttons to checkboxes (j. balhoff)</li> - - <li>bugfix: file-save button changed to say "save" not "load"</li> - - <li>feature: file-save recognizes and chooses appropriate data -adapter based on file extension (.psx for phenosyntax and .xml for -phenoxml)</li> - - <li>change: Single quotes escaped for javascript fns.</li> - -</ul> - - - -<h1>0.8</h1> - - -<h2>10.02.2006, version <a href="phenote/0.8/phenote-flybase.jnlp">0.8-fly</a>, -<a href="phenote/0.8/phenote-zfin.jnlp">0.8-zfin</a>, -<a href="http://165.124.152.194/web/html/interface.html">DictyBase -webby phenote</a></h2> -<ul> - - <li>feature: Added post composition to standalone phenote. </li> - - <li>feature: Actions are logged for both webby/servlet & standalone.</li> - - <li>feature: Pheno-xml reader (thanks to Jim Balhoff) and improvements to pheno-xml -writer (does pub & genetic context)</li> - - <li> feature: Command line reading & writing of phenoxml & phenosyntax.</li> - - <li>feature: Application exits on window exit (unless servlet)</li> - - <li>feature: Can filter out stage terms from zfin anatomy</li> - -</ul> - - - - -<h1>0.7</h1> - - - -<h2>08.23.2007, version <a href="phenote/0.7/phenote-flybase.jnlp">0.7-fly.</a>, -<a href="0.7/phenote-zfin.jnlp">0.7-zfin</a></h2> - -<ul> - <li>feature: entity chooser (web)</li> - - <li>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).</li> - - <li>feature: entity field and term info installed into zfin (web) -phenotype site. Term info & completion are scrollable.</li> - - <li>feature: standalone version can read & write pheno-syntax with ids & term names in comments</li> - - <li>feature: standalone entity chooser</li> - - <li>feature: added pub field</li> - - <li>feature: added 'use term' button in term info</li> - - <li>feature: can sort table by any field in forward order by clicking on headers</li> - - <li>change: personal config file gets copied out of jar</li> - - <li>change: directory for file load/save remembered</li> - - <li>change: layout fixed</li> - - <li>bugfix: paste for mac fixed</li> - -</ul> - - - -<h1>0.6</h1> - - - -<h2>07.28.2006, version <a href="phenote/0.6/phenote-flybase.jnlp">0.6-fly</a>, <a href="phenote/0.6/phenote-zfin.jnlp">0.6-zfin</a>, -<a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby Phenote -(0.6)</a></h2> -<ul> - <li>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! </li> - - <li> feature: writing pheno-xml format, and uses the latest -PATO ontology (as of July 28, 2006).</li> -</ul> - -<h1>0.5</h1> - -<h2>05.12.2006, version <a href="phenote/0.5/phenote-flybase.jnlp">0.5-FlyBase</a>, <a href="phenote/0.5/phenote-zfin.jnlp">0.5-ZFIN</a></h2> -<p> -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.</p> - - -<h1>0.4</h1> -<h2>04.26.2006, version <a href="phenote/0.4/phenote-flybase.jnlp">0.4-flybase</a>, <a href="phenote/0.4/phenote-zfin.jnlp">0.4-zfin</a></h2> - -<ul> - - <li>feature: Added Genetic Context field.</li> - - <li>feature: Parent & child terms in term info are now clickable/navigable.</li> - - <li>feature: HTML Links in descriptions are clickable (should bring up default browser)</li> - - <li>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.</li> - - <li>bugfix: can't delete to 0 rows</li> - - <li>bugfix: synonym search duplicates removed</li> - - <li>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.</li> - - <li>Development: Renamed Phenotype to Character. Added Character interface CharacterI.</li> - - <li>Development: Added tests to test suite.</li> - -</ul> - - -<h1>0.3</h1> - - - -<h2>04.07.2006, version <a href="phenote/0.3/phenote-webstart.jnlp">0.3</a>, <a href="phenote/0.3.1/phenote-webstart.jnlp">0.3.1 (for CToL)</a></h2> - -<p>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.</p> -<p> 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.</p> - -<ul> - - <li>feature: Completion terms now sorted alphabeitcally.</li> - - <li>feature: Obsoletes are now in addition to regular terms, not in lieu of.</li> - - <li>feature: Filtering out attribute values (todo: change to actually filter in -values)</li> - - <li>change: Html formatting of term info (todo: make terms selectable)</li> - - <li>feature: Children relations are in term info</li> - - <li>change: Term info layout greatly improved</li> - - <li>change: Term info in scroller</li> - - <li>change: Border with label around term info</li> - - <li>change: Put definition at end of term info</li> - - <li>bugfix: Backspace in ontology combo box</li> - - <li>bugfix: Selection of item in comp list causing exception, not going in term box</li> - - <li>bugfix: No terms with just 1 char</li> - - <li>bugfix: Popup was staying up after selection</li> - - <li>development: Test suite added! (todo: add more tests)</li> - - <li>development: Migrated to jdk 1.5 (which caused some of the bugs above)</li> - - <li>development: Ant file made build.xml.</li> - - <li>development: CompletionList refactored into Ontology (prompted by sorting)</li> - -</ul> - - - - -<h1>0.2</h1> - -<h2>03.27.2006, version <a href="phenote/0.2/phenote-webstart.jnlp">0.2</a></h2> -<ul> - - <li>feature: term completion on Synonyms, Definitions and Obsoletes</li> - - <li>feature: mouse-over on term in completion list displays info in 'term info' text area</li> - - <li>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.</li> - - <li>known bugs: If you hit backspace in term completion fields it gets wacky </li> - -</ul> - -<h1>0.1</h1> - -<h2>03.01.2006, version <a href="phenote/0.1/phenote-webstart.jnlp">0.1</a></h2> -<p> 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.</p> - </div> - </div> - - <!--#include virtual="ssi/footer.html" --> - -</body> -</html> Deleted: phenote/trunk/doc/phenote-website/resources.shtml~ =================================================================== --- phenote/trunk/doc/phenote-website/resources.shtml~ 2008-02-20 20:24:24 UTC (rev 1543) +++ phenote/trunk/doc/phenote-website/resources.shtml~ 2008-02-20 21:12:40 UTC (rev 1544) @@ -1,71 +0,0 @@ -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml"> - <head> - - <!--#include virtual="ssi/head.html" --> - <title>Phenote</title> - - </head> - <body> - - <!--#include virtual="ssi/header.html" --> - - <div id="main_container_aux"> - <div id="main_content_aux"> - <div class="catch_phrase"> - Ontology Resources - </div> - <p>You can find out more about available ontologies for use during - annotation with Phenote software:<p> - <h3> - <a href="http://www.bioontology.org/ncbo/faces/pages/ontology_list.xhtml"> - NCBO Bioportal - </a> - </h3> - <p> - On this page you can find a listing of biomedical ontologies - that have been submitted to the NCBO. From there you can link - to their project websites, download the ontology files, and search - their contents. - </p> - - <h3> - <a href="http://www.obofoundry.org">OBO Foundry - </a> - </h3> - <p> - The OBO Foundry is an open, inclusive, and collaborative core of - interoperable ontologies developed by the research community. - The goal is to facilitate the creation of consistent, compatible, - and unambiguous ontologies thereby supporting the biomedical - research community. The contributors are those biological - researchers and ontology developers who have agreed to work - together on an evolving set of design principles that can - foster interoperability of ontologies, and ensure a gradual - improvement of quality and formal rigor in ontologies, in ways - designed to meet the increasing needs of data and information - integration in the biomedical domain. - </p> - - <h3> - <a href="http://www.ebi.ac.uk/ontology-lookup/"> - Ontology Lookup Service (OLS) - </a> - </h3> - <p> - The Ontology Lookup Service is a spin-off of the PRIDE project, - which required a centralized query interface for ontology and - controlled vocabulary lookup. While many of the ontologies - queriable by the OLS are available online, each has its own - query interface and output format. The OLS provides a web - service interface to query multiple ontologies from a single - location with a unified output format. - </p> - - </div> - </div> - - <!--#include virtual="ssi/footer.html" --> - - </body> -</html> Deleted: phenote/trunk/doc/phenote-website/screenshots.shtml~ =================================================================== --- phenote/trunk/doc/phenote-website/screenshots.shtml~ 2008-02-20 20:24:24 UTC (rev 1543) +++ phenote/trunk/doc/phenote-website/screenshots.shtml~ 2008-02-20 21:12:40 UTC (rev 1544) @@ -1,26 +0,0 @@ -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml"> - <head> - - <!--#include virtual="ssi/head.html" --> - <title>Phenote</title> - - </head> - <body> - - <!--#include virtual="ssi/header.html" --> - - <div id="main_container_aux"> - <div id="main_content_aux"> - <div class="catch_phrase"> - Phenote Screenshots - </div> - <div class="clearall"></div> - <p><img src="http://www.phenote.org/images/phenote_screenshot.jpg" title="Phenote in action" alt="Phenote screenshot" width="100%"/></p> - </div> - </div> - - <!--#include virtual="ssi/footer.html" --> - - </body> -</html> Deleted: phenote/trunk/doc/phenote-website/team.shtml~ =================================================================== --- phenote/trunk/doc/phenote-website/team.shtml~ 2008-02-20 20:24:24 UTC (rev 1543) +++ phenote/trunk/doc/phenote-website/team.shtml~ 2008-02-20 21:12:40 UTC (rev 1544) @@ -1,78 +0,0 @@ -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml"> - <head> - - <!--#include virtual="ssi/head.html" --> - <title>Phenote: The Team</title> - - </head> - <body> - - <!--#include virtual="ssi/header.html" --> - - <div id="main_container_aux"> - <div id="main_content_aux"> - <div class="catch_phrase"> - Project Team - </div> - <h2 class="bio"><a name="exec" id="exec"></a> - Development</h2> - <div class="third_bio"> - <p><img src="http://www.bioontology.org/images/team/gibson.jpg" title="Mark Gibson" alt="Mark Gibson" height="130"/></p> - <p><a href="http://www.berkeleybop.org/content/about/people/" title="Mark Gibson">Mark Gibson</a>, MSE</p> - </div> - <div class="third_bio"> - <p><img src="http://www.bioontology.org/images/team/washington.jpg" title="Nicole Washington" alt="Nicole Washington" height="130" /> </p> - <p><a href="http://berkeleybop.org/content/about/people/nlwashington/" title="Nicole Washington">Nicole Washington</a>, PhD </p> - </div> - <div class="third_bio"> - <p><img src="http://www.bioontology.org/images/team/mungall.jpg" title="Chris Mungall" alt="Chris Mungall" height="130" /></p> - <p><a href="http://www.fruitfly.org/%7Ecjm/" title="Chris Mungall">Chris Mungall</a>, BSc</p> - </div> - <div class="clearall"></div> - - <div class="third_bio"> - <p><img src="http://www.bioontology.org/images/team/lewis.jpg" title="Suzanna Lewis" alt="Suzanna Lewis" height="130" /> </p> - <p><a href="http://www.berkeleybop.org/content/about/people/" title="Suzanna Lewis">Suzanna Lewis</a>, MS</p> - </div> - <div class="clearall"></div> - - <h1>Affiliations</h1> - - <h3> - <a href="http://bioontology.org/"> - National Center for Biomedical Ontology (NCBO) - </a> - </h3> - <p> - The NCBO is a consortium of leading biologists, clinicians, - informaticians, and ontologists who develop innovative - technology and methods that allow scientists to create, - disseminate, and manage biomedical information and knowledge - in machine-processable form. - </p> - - <h3> - <a href="http://www.berkeleybop.org/"> - Berkeley Bioinformatics and Ontologies Project (BBOP) - </a> - </h3> - <p> - The BBOP is located at the Lawrence Berkeley National Labs, - is a diverse group of scientific researchers and software - engineers dedicated to developing tools and applying - computational technologies to solve biological - problems. Members of the group contribute to a number of - projects, including The Gene Ontology, The National Center - for Biomedical Ontology, the Model Organism Encyclopedia - of DNA Elements (modENCODE), and the Generic Model Organism - Database Project. - </p> - - </div> - </div> - - <!--#include virtual="ssi/footer.html" --> - - </body> -</html> Deleted: phenote/trunk/doc/phenote-website/users.shtml~ =================================================================== --- phenote/trunk/doc/phenote-website/users.shtml~ 2008-02-20 20:24:24 UTC (rev 1543) +++ phenote/trunk/doc/phenote-website/users.shtml~ 2008-02-20 21:12:40 UTC (rev 1544) @@ -1,79 +0,0 @@ -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml"> - <head> - - <!--#include virtual="ssi/head.html" --> - <title>Phenote</title> - - </head> - <body> - - <!--#include virtual="ssi/header.html" --> - - <div id="main_container_aux"> - <div id="main_content_aux"> - <div class="catch_phrase"> - Phenote User Community - </div> - <h1>Collaborations</h1> - - <p>Phenote development is a community effort. We welcome input and feedback from our users. The following groups are using Phenote:</p> - <table border="0"> - <tr> - <td><a href="http://flybase.bio.indiana.edu/"> <img src="/images/fly_logo.png" alt="Flybase" /></a> - </td> - <td>Flybase</td> - </tr> - <tr> - <td><a href="http://www.zfin.org/"> <img height="50" src="/images/zfin_logo.gif" alt="Zfin" /></a> - </td> - <td>Zebrafish Information Network (Zfin)</td> - </tr> - <tr> - <td><a href="http://www.nbirn.net/research/mouse/index.shtm"> - <img src="/images/BIRN_logo.gif" alt="BIRN" /></a> - </td> - <td>mouse Biomedical Informatics Research Network (mouseBIRN)</td> - </tr> - <tr> - <td><a href="http://www.dictybase.org/"><img height="50" src="/images/dicty_logo.png" alt="Dictybase" /></a> - </td> - <td>Dictyostelium Model Organism Database (Dictybase)</td> - </tr> - <tr> - <td><a href="http://www.geneontology.org/"><img height="50" src="/images/go_logo.gif" alt="GO" /></a> - </td> - <td>The Gene Ontology</td> - </tr> - <tr> - <td><a href="http://www.wormbase.org/"><img src="/images/worm_logo.jpg" height="50" alt="WB" /></a> - </td> - <td>The <i>C. elegans</i> Genome Database (Wormbase)</td> - </tr> - <tr> - <td><a href="http://www.nescent.org/"> - <img src="/images/nescent_logo.gif" height="50" alt="Nescent" /></a> - </td> - <td>National Evolutionary Synthesis Center (NESCent)</td> - </tr> - <tr> - <td><a href="http://www.pharmgkb.org/"><img src="/images/pgkb_logo.png" height="50" alt="PharmGKB" /></a> - </td> - <td>PharmacoGenomics KnowledgeBase (PharmGKB)</td> - </tr> - <tr> - <td><a href="http://www.xenbase.org/"><img src="/images/xenbase_logo.gif" height="50" alt="Xenbase" /></a> - </td> - <td>Xenopus Model Organism Database (Xenbase)</td> - </tr> -</table> - - <p>If you are an active user and would like to be listed on our webpage, please <a href="contact.shtml">contact us</a>.</p> - - </div> - </div> - - <!--#include virtual="ssi/footer.html" --> - - </body> -</html> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |