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From: <nl...@us...> - 2007-01-30 18:51:46
|
Revision: 312
http://svn.sourceforge.net/obo/?rev=312&view=rev
Author: nlw
Date: 2007-01-30 10:35:57 -0800 (Tue, 30 Jan 2007)
Log Message:
-----------
adding website dirs and files, largeley undeveloped
Added Paths:
-----------
phenote/trunk/doc/phenote-website/content/
phenote/trunk/doc/phenote-website/css/
phenote/trunk/doc/phenote-website/css/bbop.css
phenote/trunk/doc/phenote-website/css/style-alpha.css
phenote/trunk/doc/phenote-website/css/style-light.css
phenote/trunk/doc/phenote-website/css/style-square.css
phenote/trunk/doc/phenote-website/css/style-stark.css
phenote/trunk/doc/phenote-website/css/style-tile.css
phenote/trunk/doc/phenote-website/css/style.css
phenote/trunk/doc/phenote-website/images/
phenote/trunk/doc/phenote-website/images/NCBO_logo.jpg
phenote/trunk/doc/phenote-website/images/lbl_logo.gif
phenote/trunk/doc/phenote-website/images/oboedit_logo.gif
phenote/trunk/doc/phenote-website/index_text.shtml
phenote/trunk/doc/phenote-website/javascript/
phenote/trunk/doc/phenote-website/javascript/obfuscate.js
phenote/trunk/doc/phenote-website/ssi/
phenote/trunk/doc/phenote-website/ssi/footer.html
phenote/trunk/doc/phenote-website/ssi/footer.shtml
phenote/trunk/doc/phenote-website/ssi/header.html
phenote/trunk/doc/phenote-website/ssi/navi_about.html
phenote/trunk/doc/phenote-website/ssi/navi_home.html
phenote/trunk/doc/phenote-website/ssi/navi_home.html~
phenote/trunk/doc/phenote-website/ssi/navi_publications.html
Added: phenote/trunk/doc/phenote-website/css/bbop.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/bbop.css (rev 0)
+++ phenote/trunk/doc/phenote-website/css/bbop.css 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,657 @@
+body
+{ background: #fff;
+ margin: 5px 0;
+ font: 1em Verdana, Arial, Helvetica, sans-serif;
+ color: #000;
+}
+
+h1, h2, h3, h4
+{ font-family: "trebuchet ms", "lucida grande", arial, sans-serif;
+}
+
+h1 { font-size: 2em;
+ text-align: center; }
+h2 { font-size: 1.6em; }
+h3 { font-size: 1.4em; }
+h4 { font-size: 1.2em; }
+
+a
+{ color: #006;
+ text-decoration: none;
+ border-bottom : 1px dotted #006;
+ padding: 0.1em 2px;
+ background: #e9effa;
+}
+
+a:hover, a:active
+{ color: #fff;
+ background: #3875D7;
+ border: none;
+}
+
+a.img
+{ background: #fff;
+ border: none;
+}
+
+a.img img
+{ border: 1px solid #fff;
+ padding: 2px;
+}
+
+a.img:hover img, a.img:active img
+{ border: 1px solid #3875D7;
+}
+
+a.anchor
+{ visibility: hidden;
+}
+
+div.header, div.footer
+{ width: 100%;
+ background: #e9effa;
+ border-width: 3px 0 3px 0;
+ border-color: #3875D7;
+ border-style: solid;
+}
+
+.footer p
+{ margin: 0;
+ padding: 5px;
+ font-size: 0.7em;
+ text-align: right;
+ line-height: 1.4em;
+}
+
+.footer a
+{ border: none;
+}
+
+.footer img
+{ border: 0;
+ float: left;
+ margin: 5px 10px;
+}
+
+div.header
+{ background: url(../images/GO-head.gif) #e9effa 0 -10px no-repeat;
+}
+
+.header h1
+{ font: italic 2em "trebuchet ms", "lucida grande", arial, sans-serif;
+ margin: 0;
+ padding: 15px 5px 5px 125px;
+ color: #3875D7;
+ text-align: left;
+}
+
+.header form, .header p
+{ margin: 0;
+ padding: 3px;
+ font-size: 0.9em;
+}
+
+div.content
+{ background: url(../images/bg.gif) #fff left top repeat-y;
+}
+
+/* page layout */
+#navBox
+{ width: 180px;
+ padding: 0;
+ margin: 0;
+ float: left;
+}
+
+/* nav bar on left */
+#navLeft
+{ font-size: 0.8em;
+ line-height: 130%;
+ padding-top: 10px;
+}
+
+#navLeft ul
+{ list-style: none;
+ margin: 0;
+ padding: 0;
+}
+
+#navLeft a
+{ display: block;
+ color: #000;
+ margin: 0;
+ background: #cddcf3;
+ border-bottom: 1px solid #fff;
+ padding: 2px 15px 2px 5px;
+}
+
+#navLeft li.head a
+{ font-weight: bold;
+}
+
+#navLeft li.sub a
+{ background: #EBF1FC;
+ padding: 2px 5px 2px 15px;
+}
+
+#navLeft li a:hover
+{ color: #fff;
+ background: #3875D7;
+}
+
+#navLeft li.sub
+{ display: none;
+}
+
+#navLeft.all li
+{ display: block;
+}
+
+#navLeft li.dl
+{ display: block;
+}
+
+#navLeft.docs li.docs
+{ display: block;
+}
+
+#navLeft.abt li.abt
+{ display: block;
+}
+
+#navLeft.tools li.tools
+{ display: block;
+}
+
+#navLeft.cur li.cur
+{ display: block;
+}
+
+#navLeft li.top
+{ display: inline;
+}
+
+/* page contents */
+div.main
+{ margin-left: 180px;
+ padding: 10px;
+}
+
+/* pages without left hand navigation menu */
+div.photo
+{ padding: 10px;
+ margin: 0;
+}
+
+p.intro, div.main p
+{ padding: 10px;
+}
+
+div.main p, div.main div.block, .photo p
+{ line-height: 1.6em;
+}
+
+/* table of contents */
+div.navPage
+{ border: 2px solid #ccc;
+ background: #EBF1FC;
+ padding: 5px 5%;
+ font-size: 0.9em;
+ line-height: 1.5em;
+}
+
+div.navPage p
+{ margin: 3px 0;
+ padding: 0;
+}
+
+div.navPage ul
+{ list-style: none;
+ margin: 0;
+ padding: 0;
+}
+
+div.navPage li
+{ margin: 3px 0;
+ padding: 0;
+}
+
+div.navPage a
+{ padding: 0 2px;
+ border: solid 1px #ebf1fc;
+}
+
+div.navPage a:hover
+{ border: solid 1px #3875D7;
+ background: #fff;
+ color: #006;
+}
+
+div.navPage li.h2
+{ font-weight: bold;
+}
+
+div.navPage li.h3
+{ font-weight: normal;
+ padding-left: 20px;
+}
+/* end page navigation */
+
+/* extra class for the site map */
+div.navPage li.h1
+{ font-weight: bold;
+ margin-left: -20px;
+ padding-top: 5px;
+ font-size: 1.2em;
+}
+
+/* classes for the navBar on the 2006 annotation camp pages */
+div.navBarDiv
+{ padding: 3px 0;
+ margin: 10px -10px;
+ border-width: 3px 0 3px 0;
+ border-color: #3875D7;
+ border-style: solid;
+ background: #e9effa;
+ font-size: 1.2em;
+}
+
+ul.navBar
+{ margin: 0;
+ padding: 1px;
+ list-style: none;
+ background: #e9effa;
+ text-align: center;
+}
+
+ul.navBar li
+{ display: inline;
+ margin: 0;
+ padding: 0;
+}
+
+ul.navBar li a
+{ border: 1px solid #e9effa;
+ padding: 3px 5px;
+ margin: 0;
+}
+
+ul.navBar li a:hover, ul.navBar li a:active
+{ border: 1px solid #fff;
+ color: #fff;
+ background: #3875D7;
+}
+
+ul.navBar li a.here
+{ color: #000;
+ border: 1px solid #000;
+ background: #fff;
+}
+
+/* bibliography specific */
+h4#setViewOptions
+{ margin-bottom: 1px;
+}
+
+p#viewOptions
+{ color: #006;
+ border: solid 1px #3875D7;
+ background: #fff;
+ padding: 10px;
+ margin-top: 0;
+}
+
+div.biblio ul
+{ font-size: 0.7em;
+ margin: 0 0 0 20px;
+ padding: 0;
+}
+
+div.biblio p
+{ font-size: 0.8em;
+ margin: 15px 0 0 0;
+ padding: 0;
+}
+
+div.biblio p b
+{ font-size: 1.2em;
+}
+
+div.biblio p a
+{ font-size: 1.1em;
+}
+
+/* page contents proper */
+div.block
+{ border: 1px solid #3875D7;
+ margin: 10px 0;
+ font-size: 0.9em;
+ padding: 0 10px;
+}
+
+div.block p, div.block h4
+{ padding: 0;
+ margin: 0.5em 0;
+}
+
+div.block ul
+{ padding: 5px 0;
+ margin: 0 0 0 20px;
+}
+
+div.block li
+{ padding: 0.2em 0;
+ margin: 0;
+}
+
+div.block ul.small
+{ padding: 0 0 5px 0;
+}
+
+div.block ul.small li
+{ padding: 0;
+ margin: 0;
+}
+
+div.block h2
+{ border-bottom: 1px solid #3875D7;
+ background: #e9effa;
+ margin: 0 -10px;
+ padding: 5px 10px;
+}
+
+div.block h3, div.tool h4
+{ border-top: 1px solid #3875D7;
+ margin: 0 -10px;
+ padding: 10px 10px 5px 10px;
+ color: #006;
+ text-align: left;
+}
+
+div.block h2 + h3, div.block h2 + div.tool h4
+{ border-top: 0;
+}
+
+div.block dl
+{ margin: 0;
+ padding: 0;
+}
+
+div.block p.terminal
+{ font: 0.9em monaco, courier, monospace;
+ background: #009;
+ color: #fff;
+ border: 2px solid #ccc;
+ padding: 5px 10px;
+ margin: 0;
+}
+
+/* links at bottom of each block section */
+div.block p.toTop
+{ font-size: 0.8em;
+ line-height: 1.4em;
+ text-align: right;
+ background: #e9effa;
+ margin: 0 -10px;
+ padding: 0.3em;
+}
+
+div.block p.toTop a
+{ background: #cddcf3;
+ color: #000;
+ text-decoration: none;
+ padding: 0.3em;
+ margin: 0;
+ border: none;
+}
+
+div.block p.toTop a:hover, p.toTop a:active
+{ background: #3875D7;
+ color: #fff;
+}
+
+div.diag
+{ width: 80%;
+ margin: 10px 0 20px 10%;
+ background: #e9effa;
+ border: 3px solid #ccc;
+ padding: 5px 10px;
+}
+
+div.contents p
+{ padding: 10px 0 0 0;
+}
+
+table
+{ border: 2px solid #ccc;
+ margin: 10px 0;
+ padding: 0;
+ width: 100%;
+}
+
+div.photo table
+{ background: #ccc;
+ margin: 0;
+}
+
+th
+{ padding: 5px;
+ background: #cddcf3;
+ font-weight: bold;
+ text-align: center;
+ vertical-align: top;
+}
+
+td
+{ padding: 5px;
+ background: #e9effa;
+ vertical-align: top;
+}
+
+td.stdL
+{ background: #cddcf3;
+ font-weight: bold;
+ width: 25%;
+}
+
+.tt
+{ font-family: monaco, courier, monospace;
+}
+
+.wh
+{ background: #fff;
+}
+
+.red
+{ color: #f00;
+}
+
+.blue
+{ color: #00f;
+}
+
+.green
+{ color: #060;
+}
+
+.purple
+{ color: #909;
+}
+
+.C
+{ text-align: center;
+}
+
+.L
+{ text-align: left;
+}
+
+.R
+{ text-align: right;
+}
+
+.term
+{ color: #090;
+ font-weight: 700;
+}
+
+.small
+{ font-size: 0.8em;
+}
+
+ul.noDot
+{ list-style: none;
+}
+
+.w10
+{ width: 10%;
+}
+
+.w20
+{ width: 20%;
+}
+
+.w25
+{ width: 25%;
+}
+
+.w40
+{ width: 40%;
+}
+
+.w75
+{ width: 75%;
+}
+
+.b
+{ font-weight: bold;
+}
+
+.i
+{ font-style: italic;
+}
+
+table.annot td.sep
+{ padding: 0;
+}
+
+ul.inline
+{ margin: 0;
+ padding: 0;
+}
+
+ul.inline li
+{ display: inline;
+ list-style: none;
+ margin: 0 5px;
+ padding: 0;
+}
+
+.floatR
+{ float: right;
+ margin: 0;
+ padding-right: 10px;
+}
+
+div.floatR a
+{ background: #fff;
+ border: none;
+ padding: 3px;
+ margin: 0;
+}
+
+.clearboth
+{ clear: both;
+ height: 1px;
+ visibility: hidden;
+}
+
+.clearR
+{ clear: right;
+ height: 1px;
+ margin: 5px 0;
+ visibility: hidden;
+}
+
+dl.evidence
+{ padding: 0;
+}
+
+.evidence dt
+{ width: 15%;
+ float: left;
+ margin: 0;
+ padding: .5em;
+ border-top: 1px solid #999;
+ font-weight: bold;
+}
+
+/* commented backslash hack for mac-ie5 \*/
+dt { clear: both; }
+/* end hack */
+
+.evidence dd
+{ margin: 0 0 0 15%;
+ padding: .5em;
+ border-top: 1px solid #999;
+}
+
+div.tool div.floatR
+{ margin-top: 5px;
+ padding: 0;
+}
+
+div.tool div.floatR img
+{ margin: 0;
+ padding: 2px;
+}
+
+.block li.dir, .block li.doc, .block li.html, .block li.jpg, .block li.link, .block li.pdf, .block li.ppt, .block li.psd, .block li.sxi, .block li.txt, .block li.zip
+{ background-repeat: no-repeat;
+ background-position: 0% 50%;
+ padding-left: 18px;
+}
+
+.block li.jpg
+{ background-image: url(../images/icon-jpg.gif);
+}
+
+.block li.html
+{ background-image: url(../images/icon-html.gif);
+}
+
+.block li.ppt
+{ background-image: url(../images/icon-ppt.gif);
+}
+
+.block li.zip
+{ background-image: url(../images/icon-zip.gif);
+}
+
+.block li.psd
+{ background-image: url(../images/icon-psd.gif);
+}
+
+.block li.sxi
+{ background-image: url(../images/icon-unknown.gif);
+}
+
+.block li.txt
+{ background-image: url(../images/icon-txt.gif);
+}
+
+.block li.doc
+{ background-image: url(../images/icon-doc.gif);
+}
+
+.block li.dir
+{ background-image: url(../images/icon-dir.gif);
+}
+
+.block li.pdf
+{ background-image: url(../images/icon-pdf.gif);
+}
+
+.form textarea, .form input
+{ margin: 10px 0;
+}
Added: phenote/trunk/doc/phenote-website/css/style-alpha.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/style-alpha.css (rev 0)
+++ phenote/trunk/doc/phenote-website/css/style-alpha.css 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,178 @@
+/* Style sheet made to go with the UCSC Japanese Program. */
+
+/* ---------- Default properties. ---------- */
+body {
+ font-family: arial, helvetica, sans-serif;
+ font-size: 100%;
+ background: white url(bg-music5.jpg) repeat top right;
+ color: black;
+ margin: 0;
+ padding: 0;
+ /*border: 3px solid #f4ecd9;*/
+}
+
+/* ---------- "page_head" area. ---------- */
+
+/**/
+#page_head{
+ background-image: url(top_image.jpg);
+ background-repeat: repeat-x;
+ top: 0px;
+ height: 110px;
+ /*border: 5px solid yellow;*/
+}
+
+.ehead{
+ white-space: nowrap;
+ left: 1em;
+ font-size: 1.25em;
+ font-weight: bold;
+ color: yellow;
+ /*color: #121212;*/
+ position: absolute;
+ /*border: 5px solid red;*/
+ z-index: 2;
+}
+
+.jhead{
+ white-space: nowrap;
+ position: absolute;
+ left: 5em;
+ top: 1em;
+ font-size: 1.5em;
+ color: #dddddd;
+ /*border: 5px solid blue;*/
+ z-index: 1;
+}
+
+.language2j{
+ padding: .5em;
+ float: right;
+ color: #888888;
+ /*border: 5px solid #black;*/
+}
+
+/* ---------- "page_body" class. ---------- */
+
+/**/
+#page_body{
+ padding: 1.5em;
+/* border: 5px solid purple;*/
+}
+
+/* ---------- "page_foot" class. ---------- */
+
+/**/
+#page_foot{
+ padding: .5em;
+/* border: 5px solid grey;*/
+}
+
+/* ---------- "main_content" class. ---------- */
+
+/**/
+#main_content{
+height: auto;
+ background: #f4ecd9;
+ padding-left: 1em;
+ padding-right: 1em;
+ padding-bottom: 1em;
+ margin-left: 12em;
+ border: 2px solid black;
+}
+
+#main_content img{
+ /*float: left;*/
+ padding: 1em;
+}
+
+.portrait {
+ float: left;
+}
+
+/**/
+.contact{
+ /*float: left;*/
+ /*border: 5px solid yellow;*/
+}
+
+/* ---------- "copyright" class. ---------- */
+
+/**/
+.copyright{
+ /*float: right;*/
+ /*border: 5px solid orange;*/
+}
+
+/* ---------- "navi" id. ---------- */
+
+/* Tell us what/where a "navi" is... */
+#navi {
+ background: #f4ecd9;
+ float: left;
+ width:8em;
+ padding-top: .5em;
+ padding-bottom: 1em;
+ padding-left: 1em;
+ padding-right: 1em;
+ border: 2px solid blue;
+}
+
+/* How to display "h2"s in a "navi". */
+.navi_head {
+ font-size: 1.1em;
+ color: #36c;
+ font-weight: bold;
+ margin-bottom: .15em;
+ /*border: 1px solid red;*/
+}
+
+/* Give non-anchors a little breathing space. */
+#navi ul {
+ list-style: none;
+ margin: 0 0 0 0;
+ padding: 0;
+ /*border: 1px solid yellow;*/
+}
+
+#navi li {
+ margin: .25em;
+}
+
+#navi li a {
+ text-decoration: none;
+ display: block;
+ color: #0000c0;
+ background: #f4ecd9;
+ /*border: 1px solid grey;*/
+}
+
+/* Highlight "li"'s "a"s on hover. */
+#navi li a:hover {
+ background: #e0e0e0;
+ /*border-color: #0c0c0c;*/
+}
+
+/* */
+#navi ul li {
+ display: block;
+ background: #f4ecd9;
+ /*border: 1px solid green;*/
+}
+
+/* */
+#navi ul li ul{
+ text-decoration: none;
+ display: block;
+ margin-left: 1em;
+ /*border: 1px solid orange;*/
+}
+
+/* */
+#navi ul li ul li{
+ font-size: .85em;
+ text-decoration: none;
+ display: block;
+ background: #f4ecd9;
+ /*border: 1px solid purple;*/
+}
Added: phenote/trunk/doc/phenote-website/css/style-light.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/style-light.css (rev 0)
+++ phenote/trunk/doc/phenote-website/css/style-light.css 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,178 @@
+/* Style sheet made to go with the UCSC Japanese Program. */
+
+/* ---------- Default properties. ---------- */
+body {
+ font-family: arial, helvetica, sans-serif;
+ font-size: 100%;
+ background: white url(bg-music5.jpg) repeat top right;
+ color: black;
+ margin: 0;
+ padding: 0;
+ /*border: 3px solid #f4ecd9;*/
+}
+
+/* ---------- "page_head" area. ---------- */
+
+/**/
+#page_head{
+ background-image: url(top_image.jpg);
+ background-repeat: repeat-x;
+ top: 0px;
+ height: 110px;
+ /*border: 5px solid yellow;*/
+}
+
+.ehead{
+ white-space: nowrap;
+ left: 1em;
+ font-size: 1.25em;
+ font-weight: bold;
+ color: yellow;
+ /*color: #121212;*/
+ position: absolute;
+ /*border: 5px solid red;*/
+ z-index: 2;
+}
+
+.jhead{
+ white-space: nowrap;
+ position: absolute;
+ left: 5em;
+ top: 1em;
+ font-size: 1.5em;
+ color: #dddddd;
+ /*border: 5px solid blue;*/
+ z-index: 1;
+}
+
+.language2j{
+ padding: .5em;
+ float: right;
+ color: #888888;
+ /*border: 5px solid #black;*/
+}
+
+/* ---------- "page_body" class. ---------- */
+
+/**/
+#page_body{
+ padding: 1.5em;
+/* border: 5px solid purple;*/
+}
+
+/* ---------- "page_foot" class. ---------- */
+
+/**/
+#page_foot{
+ padding: .5em;
+/* border: 5px solid grey;*/
+}
+
+/* ---------- "main_content" class. ---------- */
+
+/**/
+#main_content{
+height: auto;
+ background: #f4ecd9;
+ padding-left: 1em;
+ padding-right: 1em;
+ padding-bottom: 1em;
+ margin-left: 12em;
+ border: 2px solid black;
+}
+
+#main_content img{
+ /*float: left;*/
+ padding: 1em;
+}
+
+.portrait {
+ float: left;
+}
+
+/**/
+.contact{
+ /*float: left;*/
+ /*border: 5px solid yellow;*/
+}
+
+/* ---------- "copyright" class. ---------- */
+
+/**/
+.copyright{
+ /*float: right;*/
+ /*border: 5px solid orange;*/
+}
+
+/* ---------- "navi" id. ---------- */
+
+/* Tell us what/where a "navi" is... */
+#navi {
+ background: #f4ecd9;
+ float: left;
+ width:8em;
+ padding-top: .5em;
+ padding-bottom: 1em;
+ padding-left: 1em;
+ padding-right: 1em;
+ border: 2px solid blue;
+}
+
+/* How to display "h2"s in a "navi". */
+.navi_head {
+ font-size: 1.1em;
+ color: #36c;
+ font-weight: bold;
+ margin-bottom: .15em;
+ /*border: 1px solid red;*/
+}
+
+/* Give non-anchors a little breathing space. */
+#navi ul {
+ list-style: none;
+ margin: 0 0 0 0;
+ padding: 0;
+ /*border: 1px solid yellow;*/
+}
+
+#navi li {
+ margin: .25em;
+}
+
+#navi li a {
+ text-decoration: none;
+ display: block;
+ color: #0000c0;
+ background: #f4ecd9;
+ /*border: 1px solid grey;*/
+}
+
+/* Highlight "li"'s "a"s on hover. */
+#navi li a:hover {
+ background: #e0e0e0;
+ /*border-color: #0c0c0c;*/
+}
+
+/* */
+#navi ul li {
+ display: block;
+ background: #f4ecd9;
+ /*border: 1px solid green;*/
+}
+
+/* */
+#navi ul li ul{
+ text-decoration: none;
+ display: block;
+ margin-left: 1em;
+ /*border: 1px solid orange;*/
+}
+
+/* */
+#navi ul li ul li{
+ font-size: .85em;
+ text-decoration: none;
+ display: block;
+ background: #f4ecd9;
+ /*border: 1px solid purple;*/
+}
Added: phenote/trunk/doc/phenote-website/css/style-square.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/style-square.css (rev 0)
+++ phenote/trunk/doc/phenote-website/css/style-square.css 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,178 @@
+/* Style sheet made to go with the UCSC Japanese Program. */
+
+/* ---------- Default properties. ---------- */
+body {
+ font-family: arial, helvetica, sans-serif;
+ font-size: 100%;
+ background: white url(bg-music.jpg) repeat top right;
+ color: black;
+ margin: 0;
+ padding: 0;
+ /*border: 3px solid #f4ecd9;*/
+}
+
+/* ---------- "page_head" area. ---------- */
+
+/**/
+#page_head{
+ background-image: url(top_image.jpg);
+ background-repeat: repeat-x;
+ top: 0px;
+ height: 110px;
+ /*border: 5px solid yellow;*/
+}
+
+.ehead{
+ white-space: nowrap;
+ left: 1em;
+ font-size: 1.25em;
+ font-weight: bold;
+ color: yellow;
+ /*color: #121212;*/
+ position: absolute;
+ /*border: 5px solid red;*/
+ z-index: 2;
+}
+
+.jhead{
+ white-space: nowrap;
+ position: absolute;
+ left: 5em;
+ top: 1em;
+ font-size: 1.5em;
+ color: #dddddd;
+ /*border: 5px solid blue;*/
+ z-index: 1;
+}
+
+.language2j{
+ padding: .5em;
+ float: right;
+ color: #888888;
+ /*border: 5px solid #black;*/
+}
+
+/* ---------- "page_body" class. ---------- */
+
+/**/
+#page_body{
+ padding: 1.5em;
+/* border: 5px solid purple;*/
+}
+
+/* ---------- "page_foot" class. ---------- */
+
+/**/
+#page_foot{
+ padding: .5em;
+/* border: 5px solid grey;*/
+}
+
+/* ---------- "main_content" class. ---------- */
+
+/**/
+#main_content{
+height: auto;
+ background: #f4ecd9;
+ padding-left: 1em;
+ padding-right: 1em;
+ padding-bottom: 1em;
+ margin-left: 12em;
+ border: 2px solid black;
+}
+
+#main_content img{
+ /*float: left;*/
+ padding: 1em;
+}
+
+.portrait {
+ float: left;
+}
+
+/**/
+.contact{
+ /*float: left;*/
+ /*border: 5px solid yellow;*/
+}
+
+/* ---------- "copyright" class. ---------- */
+
+/**/
+.copyright{
+ /*float: right;*/
+ /*border: 5px solid orange;*/
+}
+
+/* ---------- "navi" id. ---------- */
+
+/* Tell us what/where a "navi" is... */
+#navi {
+ background: #f4ecd9;
+ float: left;
+ width:8em;
+ padding-top: .5em;
+ padding-bottom: 1em;
+ padding-left: 1em;
+ padding-right: 1em;
+ border: 2px solid blue;
+}
+
+/* How to display "h2"s in a "navi". */
+.navi_head {
+ font-size: 1.1em;
+ color: #36c;
+ font-weight: bold;
+ margin-bottom: .15em;
+ /*border: 1px solid red;*/
+}
+
+/* Give non-anchors a little breathing space. */
+#navi ul {
+ list-style: none;
+ margin: 0 0 0 0;
+ padding: 0;
+ /*border: 1px solid yellow;*/
+}
+
+#navi li {
+ margin: .25em;
+}
+
+#navi li a {
+ text-decoration: none;
+ display: block;
+ color: #0000c0;
+ background: #f4ecd9;
+ /*border: 1px solid grey;*/
+}
+
+/* Highlight "li"'s "a"s on hover. */
+#navi li a:hover {
+ background: #e0e0e0;
+ /*border-color: #0c0c0c;*/
+}
+
+/* */
+#navi ul li {
+ display: block;
+ background: #f4ecd9;
+ /*border: 1px solid green;*/
+}
+
+/* */
+#navi ul li ul{
+ text-decoration: none;
+ display: block;
+ margin-left: 1em;
+ /*border: 1px solid orange;*/
+}
+
+/* */
+#navi ul li ul li{
+ font-size: .85em;
+ text-decoration: none;
+ display: block;
+ background: #f4ecd9;
+ /*border: 1px solid purple;*/
+}
Added: phenote/trunk/doc/phenote-website/css/style-stark.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/style-stark.css (rev 0)
+++ phenote/trunk/doc/phenote-website/css/style-stark.css 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,176 @@
+/* Style sheet made to go with the UCSC Japanese Program. */
+
+/* ---------- Default properties. ---------- */
+body {
+ font-family: arial, helvetica, sans-serif;
+ font-size: 100%;
+ background: white url(bg-music.jpg) repeat top right;
+ color: black;
+ margin: 0;
+ padding: 0;
+ /*border: 3px solid #f4ecd9;*/
+}
+
+/* ---------- "page_head" area. ---------- */
+
+/**/
+#page_head{
+ top: 0px;
+ height: 110px;
+ /*border: 5px solid yellow;*/
+}
+
+.ehead{
+ white-space: nowrap;
+ left: 1em;
+ font-size: 1.25em;
+ font-weight: bold;
+ color: red;
+ /*color: #121212;*/
+ position: absolute;
+ /*border: 5px solid red;*/
+ z-index: 2;
+}
+
+.jhead{
+ white-space: nowrap;
+ position: absolute;
+ left: 5em;
+ top: 1em;
+ font-size: 1.5em;
+ color: yellow;
+ /*border: 5px solid blue;*/
+ z-index: 1;
+}
+
+.language2j{
+ padding: .5em;
+ float: right;
+ color: #888888;
+ /*border: 5px solid #black;*/
+}
+
+/* ---------- "page_body" class. ---------- */
+
+/**/
+#page_body{
+ padding: 1.5em;
+/* border: 5px solid purple;*/
+}
+
+/* ---------- "page_foot" class. ---------- */
+
+/**/
+#page_foot{
+ padding: .5em;
+/* border: 5px solid grey;*/
+}
+
+/* ---------- "main_content" class. ---------- */
+
+/**/
+#main_content{
+height: auto;
+ background: #f4ecd9;
+ padding-left: 1em;
+ padding-right: 1em;
+ padding-bottom: 1em;
+ margin-left: 12em;
+ border: 2px solid black;
+}
+
+#main_content img{
+ /*float: left;*/
+ padding: 1em;
+}
+
+.portrait {
+ float: left;
+}
+
+/**/
+.contact{
+ /*float: left;*/
+ /*border: 5px solid yellow;*/
+}
+
+/* ---------- "copyright" class. ---------- */
+
+/**/
+.copyright{
+ /*float: right;*/
+ /*border: 5px solid orange;*/
+}
+
+/* ---------- "navi" id. ---------- */
+
+/* Tell us what/where a "navi" is... */
+#navi {
+ background: #f4ecd9;
+ float: left;
+ width:8em;
+ padding-top: .5em;
+ padding-bottom: 1em;
+ padding-left: 1em;
+ padding-right: 1em;
+ border: 2px solid blue;
+}
+
+/* How to display "h2"s in a "navi". */
+.navi_head {
+ font-size: 1.1em;
+ color: #36c;
+ font-weight: bold;
+ margin-bottom: .15em;
+ /*border: 1px solid red;*/
+}
+
+/* Give non-anchors a little breathing space. */
+#navi ul {
+ list-style: none;
+ margin: 0 0 0 0;
+ padding: 0;
+ /*border: 1px solid yellow;*/
+}
+
+#navi li {
+ margin: .25em;
+}
+
+#navi li a {
+ text-decoration: none;
+ display: block;
+ color: #0000c0;
+ background: #f4ecd9;
+ /*border: 1px solid grey;*/
+}
+
+/* Highlight "li"'s "a"s on hover. */
+#navi li a:hover {
+ background: #e0e0e0;
+ /*border-color: #0c0c0c;*/
+}
+
+/* */
+#navi ul li {
+ display: block;
+ background: #f4ecd9;
+ /*border: 1px solid green;*/
+}
+
+/* */
+#navi ul li ul{
+ text-decoration: none;
+ display: block;
+ margin-left: 1em;
+ /*border: 1px solid orange;*/
+}
+
+/* */
+#navi ul li ul li{
+ font-size: .85em;
+ text-decoration: none;
+ display: block;
+ background: #f4ecd9;
+ /*border: 1px solid purple;*/
+}
Added: phenote/trunk/doc/phenote-website/css/style-tile.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/style-tile.css (rev 0)
+++ phenote/trunk/doc/phenote-website/css/style-tile.css 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,176 @@
+/* Style sheet made to go with the UCSC Japanese Program. */
+
+/* ---------- Default properties. ---------- */
+body {
+ font-family: arial, helvetica, sans-serif;
+ font-size: 100%;
+ background: white url(top_image.jpg) repeat top right;
+ color: black;
+ margin: 0;
+ padding: 0;
+ /*border: 3px solid #f4ecd9;*/
+}
+
+/* ---------- "page_head" area. ---------- */
+
+/**/
+#page_head{
+ top: 0px;
+ height: 110px;
+ /*border: 5px solid yellow;*/
+}
+
+.ehead{
+ white-space: nowrap;
+ left: 1em;
+ font-size: 1.25em;
+ font-weight: bold;
+ color: yellow;
+ /*color: #121212;*/
+ position: absolute;
+ /*border: 5px solid red;*/
+ z-index: 2;
+}
+
+.jhead{
+ white-space: nowrap;
+ position: absolute;
+ left: 5em;
+ top: 1em;
+ font-size: 1.5em;
+ color: #dddddd;
+ /*border: 5px solid blue;*/
+ z-index: 1;
+}
+
+.language2j{
+ padding: .5em;
+ float: right;
+ color: #888888;
+ /*border: 5px solid #black;*/
+}
+
+/* ---------- "page_body" class. ---------- */
+
+/**/
+#page_body{
+ padding: 1.5em;
+/* border: 5px solid purple;*/
+}
+
+/* ---------- "page_foot" class. ---------- */
+
+/**/
+#page_foot{
+ padding: .5em;
+/* border: 5px solid grey;*/
+}
+
+/* ---------- "main_content" class. ---------- */
+
+/**/
+#main_content{
+height: auto;
+ background: #f4ecd9;
+ padding-left: 1em;
+ padding-right: 1em;
+ padding-bottom: 1em;
+ margin-left: 12em;
+ border: 2px solid black;
+}
+
+#main_content img{
+ /*float: left;*/
+ padding: 1em;
+}
+
+.portrait {
+ float: left;
+}
+
+/**/
+.contact{
+ /*float: left;*/
+ /*border: 5px solid yellow;*/
+}
+
+/* ---------- "copyright" class. ---------- */
+
+/**/
+.copyright{
+ /*float: right;*/
+ /*border: 5px solid orange;*/
+}
+
+/* ---------- "navi" id. ---------- */
+
+/* Tell us what/where a "navi" is... */
+#navi {
+ background: #f4ecd9;
+ float: left;
+ width:8em;
+ padding-top: .5em;
+ padding-bottom: 1em;
+ padding-left: 1em;
+ padding-right: 1em;
+ border: 2px solid blue;
+}
+
+/* How to display "h2"s in a "navi". */
+.navi_head {
+ font-size: 1.1em;
+ color: #36c;
+ font-weight: bold;
+ margin-bottom: .15em;
+ /*border: 1px solid red;*/
+}
+
+/* Give non-anchors a little breathing space. */
+#navi ul {
+ list-style: none;
+ margin: 0 0 0 0;
+ padding: 0;
+ /*border: 1px solid yellow;*/
+}
+
+#navi li {
+ margin: .25em;
+}
+
+#navi li a {
+ text-decoration: none;
+ display: block;
+ color: #0000c0;
+ background: #f4ecd9;
+ /*border: 1px solid grey;*/
+}
+
+/* Highlight "li"'s "a"s on hover. */
+#navi li a:hover {
+ background: #e0e0e0;
+ /*border-color: #0c0c0c;*/
+}
+
+/* */
+#navi ul li {
+ display: block;
+ background: #f4ecd9;
+ /*border: 1px solid green;*/
+}
+
+/* */
+#navi ul li ul{
+ text-decoration: none;
+ display: block;
+ margin-left: 1em;
+ /*border: 1px solid orange;*/
+}
+
+/* */
+#navi ul li ul li{
+ font-size: .85em;
+ text-decoration: none;
+ display: block;
+ background: #f4ecd9;
+ /*border: 1px solid purple;*/
+}
Added: phenote/trunk/doc/phenote-website/css/style.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/style.css (rev 0)
+++ phenote/trunk/doc/phenote-website/css/style.css 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,195 @@
+/* Style sheet made to go with snugglebunnies. */
+
+/* ---------- Default properties. ---------- */
+body {
+ font-family: arial, helvetica, sans-serif;
+ font-size: 100%;
+ background: white url(/images/bg_image25.jpg) repeat top right;
+ color: black;
+ margin: 0;
+}
+
+/* ---------- "page_head" area. ---------- */
+
+/**/
+#page_head{
+ /*background-image: url(top_image.jpg);*/
+ /*background-repeat: repeat-x;*/
+ /*background: #ebf1fc;*/
+ top: 0px;
+ height: 110px;
+}
+
+.ehead{
+ white-space: nowrap;
+ left: 1em;
+ font-size: 1.25em;
+ font-weight: bold;
+ color: 999999;
+ position: absolute;
+ z-index: 2;
+}
+
+.jhead{
+ white-space: nowrap;
+ position: absolute;
+ left: 5em;
+ top: 1em;
+ font-size: 1.5em;
+ color: #aabbdd;
+ z-index: 1;
+}
+
+.page_logo{
+ left: .1em;
+ top: .1em;
+ position: absolute;
+ /* padding: .25em; */
+}
+
+
+/* ---------- Effects classes. ---------- */
+
+/**/
+.small{
+ font-size: 80%;
+}
+
+.smaller{
+ font-size: 75%;
+}
+
+.smallest{
+ font-size: 50%;
+}
+
+/* ---------- "page_body" class. ---------- */
+
+/**/
+#page_body{
+ padding: 1.5em;
+}
+
+/* ---------- "page_foot" class. ---------- */
+
+/**/
+#page_foot{
+ /*color: #dddddd;*/
+ font-size: .25em;
+ /*float: right;*/
+}
+
+/* ---------- "main_content" class. ---------- */
+
+/**/
+#main_content{
+height: auto;
+ /*background: #f4ecd9;*/
+ background: #f9f9f9;
+ padding-left: 1em;
+ padding-right: 1em;
+ padding-bottom: 1em;
+ margin-left: 12em;
+ -khtml-border-radius: 1em;
+ -moz-border-radius: 1em;
+ -o-border-radius: 1em;
+ border-radius: 4px;
+ border: 2px solid black;
+}
+
+#main_content img{
+ padding-right: 1em;
+ padding-bottom: 1em;
+}
+
+#main_content .portrait {
+ float: left;
+ /*border: 1px solid brown;*/
+}
+
+#main_content .contact{
+ clear: right;
+ /*border: 1px solid brown;*/
+}
+
+/* ---------- "copyright" class. ---------- */
+
+/**/
+.copyright{
+ /*float: right;*/
+ /*border: 5px solid orange;*/
+}
+
+/* ---------- "navi" id. ---------- */
+
+/* Tell us what/where a "navi" is... */
+#navi {
+ /*background: #f4ecd9;*/
+ background: #f9f9f9;
+ float: left;
+ width:8em;
+ padding-top: .5em;
+ padding-bottom: 1em;
+ padding-left: 1em;
+ padding-right: 1em;
+ border: 2px solid blue;
+ padding: 1em;
+ -khtml-border-radius: 1em;
+ -moz-border-radius: 1em;
+ -o-border-radius: 1em;
+ border-radius: 4px;
+ border: 2px solid blue;
+}
+
+/* How to display "h2"s in a "navi". */
+.navi_head {
+ font-size: 1.1em;
+ color: #36c;
+ font-weight: bold;
+ margin-bottom: .15em;
+}
+
+/* Give non-anchors a little breathing space. */
+#navi ul {
+ list-style: none;
+ margin: 0 0 0 0;
+ padding: 0;
+}
+
+#navi li {
+ margin: .25em;
+}
+
+#navi li a {
+ text-decoration: none;
+ display: inline;
+ color: #0000c0;
+ background: #f9f9f9;
+}
+
+/* Highlight "li"'s "a"s on hover. */
+#navi li a:hover {
+ background: #aabbdd;
+ /*background: #e0e0e0;*/
+}
+
+/* */
+#navi ul li {
+ display: block;
+ background: #f9f9f9;
+}
+
+/* */
+#navi ul li ul{
+ text-decoration: none;
+ display: block;
+ margin-left: 1em;
+}
+
+/* */
+#navi ul li ul li{
+ font-size: .85em;
+ text-decoration: none;
+ display: block;
+ background: #f9f9f9;
+}
Added: phenote/trunk/doc/phenote-website/images/NCBO_logo.jpg
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/doc/phenote-website/images/NCBO_logo.jpg
___________________________________________________________________
Name: svn:executable
+ *
Name: svn:mime-type
+ application/octet-stream
Added: phenote/trunk/doc/phenote-website/images/lbl_logo.gif
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/doc/phenote-website/images/lbl_logo.gif
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: phenote/trunk/doc/phenote-website/images/oboedit_logo.gif
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/doc/phenote-website/images/oboedit_logo.gif
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: phenote/trunk/doc/phenote-website/index_text.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index_text.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/index_text.shtml 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,43 @@
+<!--#include virtual="/ssi/header.html" -->
+
+<div id="page_body">
+
+<!-- A short and funny little quote. -->
+<!--
+<div id="quote">
+<div class="quote_body">
+Here is a quote.
+</div>
+<div class="quote_ref">
+-Me
+</div>
+</div>
+-->
+
+<!--#include virtual="/ssi/navi_home.html" -->
+
+<div id="main_content">
+<h2>Welcome...</h2>
+<p>
+</p>
+
+<p>
+...to the Berkeley Bioinformatics and Ontologies Project.
+</p>
+
+<p>
+<a href="/content/jobs/">We're hiring!</a>
+</p>
+
+<p>
+The BBOP, 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 <a href="http://geneontology.org/">The Gene Ontology</a>, <a href="http://bioontology.org">The National Center for Biomedical Ontology</a>, and the <a href="http://gmod.org">Generic Model Organism Database Project</a>. Learn more about our projects <a href="/content/projects/">[here ...]</a>
+</p>
+<p>
+Since our group is focused on the development, use, and integration of ontolgies into biological data analysis, we've set up a <a href="content/faq/">FAQ</a> with answers to some common questions about ontologies.
+
+</p>
+</div>
+</div>
+
+<!--#include virtual="/ssi/footer.shtml" -->
+
Added: phenote/trunk/doc/phenote-website/javascript/obfuscate.js
===================================================================
--- phenote/trunk/doc/phenote-website/javascript/obfuscate.js (rev 0)
+++ phenote/trunk/doc/phenote-website/javascript/obfuscate.js 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,9 @@
+function obfuscate( domain, name, optionalText )
+{
+ document.write('<a href="mai' + 'lto:' + name + '@' + domain + '">');
+ if (optionalText == "")
+ document.write(name + '@' + domain);
+ else
+ document.write(optionalText);
+ document.write('<\/a>');
+}
Added: phenote/trunk/doc/phenote-website/ssi/footer.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/footer.html (rev 0)
+++ phenote/trunk/doc/phenote-website/ssi/footer.html 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1 @@
+
\ No newline at end of file
Added: phenote/trunk/doc/phenote-website/ssi/footer.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/footer.shtml (rev 0)
+++ phenote/trunk/doc/phenote-website/ssi/footer.shtml 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,23 @@
+<div id="page_foot">
+<div class="contact">
+<!-- TODO add obfuscate.js webmaster stuff here. -->
+</div>
+
+<div class="copyright">
+<!--
+©2006
+-->
+</div>
+
+<div class="last_modified">
+<!--
+<!--#config timefmt="%A %B %d, %Y" -->
+Last modified:
+<!--#echo var="LAST_MODIFIED" -->
+-->
+</div>
+</div>
+
+</body>
+
+</html>
Added: phenote/trunk/doc/phenote-website/ssi/header.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/header.html (rev 0)
+++ phenote/trunk/doc/phenote-website/ssi/header.html 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,45 @@
+<!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" xml:lang="en">
+
+<head>
+
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+
+<!-- TODO: need an icon -->
+<link rel="icon" href="" type="image/png" />
+<link rel="shortcut icon" href="" type="image/png" />
+<link rel="stylesheet" type="text/css" href="/css/style.css" title="standard" />
+<link rel="alternate stylesheet" type="text/css" href="/css/style-square.css" title="square" />
+<link rel="alternate stylesheet" type="text/css" href="/css/style-light.css" title="light" />
+<link rel="alternate stylesheet" type="text/css" href="/css/style-stark.css" title="stark" />
+<link rel="alternate stylesheet" type="text/css" href="/css/style-tile.css" title="tile" />
+<link rel="alternate stylesheet" type="text/css" href="/css/style-curve.css" title="curve" />
+<link rel="alternate stylesheet" type="text/css" href="/css/style-alpha.css" title="alpha" />
+
+<script type="text/javascript" src="/javascript/obfuscate.js"></script>
+
+<title>Phenote: A Phenotype Annotation Tool</title>
+
+<!-- My comments! -->
+
+</head>
+
+<body>
+
+<div id="page_head">
+
+<div class="ehead">
+<h1>Phenote</h1>
+</div>
+
+<div class="jhead">
+<h1>BBOP</h1>
+</div>
+
+<div class="page_logo">
+<img src="/images/stolen-logo.gif" alt="logo" />
+</div>
+
+</div>
+
Added: phenote/trunk/doc/phenote-website/ssi/navi_about.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_about.html (rev 0)
+++ phenote/trunk/doc/phenote-website/ssi/navi_about.html 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,47 @@
+<div id="navi">
+<div class="navi_head"></div>
+<ul>
+ <li>
+ <a href="/">Home</a>
+ </li>
+ <li>
+ <a href="/content/projects/">Projects</a>
+ </li>
+ <li>
+ <a href="/content/software/">Software</a>
+ </li>
+ <li>
+ <a href="/content/publications/">Publications</a>
+ </li>
+ <li>
+ <a href="/content/jobs/">Jobs</a>
+ </li>
+ <li>
+ <a href="/content/about/">About</a>
+ <ul>
+ <li>
+ <a href="/content/people/">BBOP people</a>
+ </li>
+ <li>
+ <a href="/content/about/contact.shtml">Contact us</a>
+ </li>
+ <li>
+ <a href="/content/about/directions.shtml">Directions</a>
+ </li>
+ <li>
+ <a href="/content/about/area.shtml">Area Info</a>
+ </li>
+ </ul>
+ </li>
+ <li>
+ <a href="/mediawiki">Wiki</a>
+ </li>
+ <li>
+ <a href="/content/links/">Links</a>
+ </li>
+ <li>
+ <a href="/content/faq/">FAQ</a>
+ </li>
+</ul>
+</div>
+
Added: phenote/trunk/doc/phenote-website/ssi/navi_home.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_home.html (rev 0)
+++ phenote/trunk/doc/phenote-website/ssi/navi_home.html 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,36 @@
+<div id="navi">
+<div class="navi_head"></div>
+<ul>
+<!-- <li>
+ Home
+--> </li>
+ <li>
+ <a href="/">Home</a>
+ </li>
+ <li>
+ <a href="/content/projects/">Background</a>
+ </li>
+ <li>
+ <a href="/content/software/">Downloads</a>
+ </li>
+ <li>
+ <a href="/content/software/">Documentation</a>
+ </li>
+ <li>
+ <a href="/content/publications/">References</a>
+ </li>
+ <li>
+ <a href="/content/faq/">FAQ</a>
+ </li>
+ <li>
+ <a href="/content/about/">About</a>
+ </li>
+ <li>
+ <a href="/content/links/">Links</a>
+ </li>
+ <li>
+ <a href="/mediawiki">Wiki</a>
+ </li>
+</ul>
+</div>
+
Added: phenote/trunk/doc/phenote-website/ssi/navi_home.html~
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_home.html~ (rev 0)
+++ phenote/trunk/doc/phenote-website/ssi/navi_home.html~ 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,36 @@
+<div id="navi">
+<div class="navi_head"></div>
+<ul>
+<!-- <li>
+ Home
+--> </li>
+ <li>
+ <a href="/">Home</a>
+ </li>
+ <li>
+ <a href="/content/projects/">Projects</a>
+ </li>
+ <li>
+ <a href="/content/software/">Software</a>
+ </li>
+ <li>
+ <a href="/content/publications/">Publications</a>
+ </li>
+ <li>
+ <a href="/content/jobs/">Jobs</a>
+ </li>
+ <li>
+ <a href="/content/about/">About</a>
+ </li>
+ <li>
+ <a href="/mediawiki">Wiki</a>
+ </li>
+ <li>
+ <a href="/content/links/">Links</a>
+ </li>
+ <li>
+ <a href="/content/faq/">FAQ</a>
+ </li>
+</ul>
+</div>
+
Added: phenote/trunk/doc/phenote-website/ssi/navi_publications.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/navi_publications.html (rev 0)
+++ phenote/trunk/doc/phenote-website/ssi/navi_publications.html 2007-01-30 18:35:57 UTC (rev 312)
@@ -0,0 +1,30 @@
+<div id="navi">
+<div class="navi_head"></div>
+<ul>
+ <li>
+ <a href="/">Home</a>
+ </li>
+ <li>
+ <a href="/content/projects/">Projects</a>
+ </li>
+ <li>
+ <a href="/content/people/">People</a>
+ </li>
+ <li>
+ <a href="/content/publications/">Publications</a>
+ </li>
+ <li>
+ <a href="/content/jobs/">Jobs</a>
+ </li>
+ <li>
+ <a href="/content/about/">Contact</a>
+ </li>
+ <li>
+ <a href="/mediawiki">Wiki</a>
+ </li>
+ <li>
+ <a href="/content/faq/">FAQ</a>
+ </li>
+</ul>
+</div>
+
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-01-30 18:08:13
|
Revision: 311
http://svn.sourceforge.net/obo/?rev=311&view=rev
Author: mgibson
Date: 2007-01-30 10:02:20 -0800 (Tue, 30 Jan 2007)
Log Message:
-----------
changed ant jar to put obo files in subdir in the jar - otherwise the obo jar
file will get loaded before the .phenote/obo-files obo file cache
Modified Paths:
--------------
phenote/trunk/build.xml
phenote/trunk/obo-files/quality.obo
phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml 2007-01-30 15:25:56 UTC (rev 310)
+++ phenote/trunk/build.xml 2007-01-30 18:02:20 UTC (rev 311)
@@ -133,7 +133,7 @@
</java>
</target>
<target name="run-jar" >
- <java classname="phenote.main.Phenote" fork="yes" jvmargs="-Xmx200M">
+ <java classname="phenote.main.Phenote" fork="yes" jvmargs="-Xmx300M">
<!-- arg value="-c configfilehereventually"/ -->
<classpath>
<fileset dir="${lib}">
@@ -190,7 +190,7 @@
<!-- JAR The jar target compiles everything, and produces a phenote.jar in
phenote/jars/phenote.jar. -->
- <target name="jar" depends="compile">
+ <target name="jar-pase" depends="compile">
<jar destfile="${jarfile}">
<fileset dir="${classfiles}"/>
<fileset file="${obo}/*.obo"/>
@@ -198,6 +198,14 @@
</jar>
</target>
+ <target name="jar" depends="compile">
+ <jar destfile="${jarfile}">
+ <fileset dir="${classfiles}"/>
+ <fileset dir="." includes="obo-files/" excludes="obo-files/old"/>
+ <fileset file="${conf}/*.cfg"/>
+ </jar>
+ </target>
+
<target name="jar-web" depends="compile">
<jar destfile="${jarfile}">
<fileset dir="${classfiles}"/>
Modified: phenote/trunk/obo-files/quality.obo
===================================================================
--- phenote/trunk/obo-files/quality.obo 2007-01-30 15:25:56 UTC (rev 310)
+++ phenote/trunk/obo-files/quality.obo 2007-01-30 18:02:20 UTC (rev 311)
@@ -1,5 +1,5 @@
format-version: 1.0
-date: 22:01:2007 16:16
+date: 26:01:2007 16:23
saved-by: George Gkoutos
auto-generated-by: OBO-Edit 1.100-beta16
subsetdef: abnormal_slim "Abnormal/normal slim"
@@ -289,9 +289,10 @@
[Term]
id: PATO:0000048
name: hardness
-def: "A physical quality inhering in a bearer as the constant of proportionality of the force on its elastic body to its body's extension." [: "http://thesaurus.maths.org/"]
+def: "A physical quality inhering in a bearer by virtue of its capability of being turned, bowed, or twisted without breaking." [merriam-webster:merriam-webster "http://www.m-w.com/"]
subset: attribute_slim
-related_synonym: "stiffness" []
+related_synonym: "impenetrability" []
+related_synonym: "toughness" []
is_a: PATO:0001018 ! physical quality
[Term]
@@ -2128,6 +2129,8 @@
name: hard
def: "A hardness quality of being rigid and resistant to pressure." [PATO :GVG]
subset: value_slim
+related_synonym: "impenetrable" []
+related_synonym: "tough" []
is_a: PATO:0000048 ! hardness
[Term]
@@ -5603,7 +5606,7 @@
[Term]
id: PATO:0001018
name: physical quality
-def: "A quality that exists through action of continuants at the physical level of organisation" [PATO:GVG]
+def: "A quality that exists through action of continuants at the physical level of organisation." [PATO:GVG]
subset: attribute_slim
is_a: PATO:0001237 ! monadic quality of continuant
@@ -5692,7 +5695,7 @@
[Term]
id: PATO:0001031
name: elasticity
-def: "A physical quality inhering in a bearer by \nvirtue of the ratio of its extension to its original length." [PATO :GVG]
+def: "A physical quality inhering in a bearer by virtue of its capability to recover its size and shape after deformation in any way." [merriam-webster:merriam-webster "http://www.m-w.com/ "]
subset: attribute_slim
is_a: PATO:0001018 ! physical quality
@@ -6427,14 +6430,14 @@
[Term]
id: PATO:0001171
name: elastic
-def: "An elasticity that is larger than zero." [PATO :GVG]
+def: "An elasticity quality inhering in a bearer by virtue of itsability to recover its size and shape after deformation in any way." [merriam-webster:merriam-webster "http://www.m-w.com/"]
subset: value_slim
is_a: PATO:0001031 ! elasticity
[Term]
id: PATO:0001172
name: inelastic
-def: "An elasticity that equals to zero." [PATO :GVG]
+def: "An elasticity quality inhering in a bearer by virtue of its inability to recover its size and shape after deformation in any way." [merriam-webster:merriam-webster "http://www.m-w.com/ "]
subset: value_slim
is_a: PATO:0001031 ! elasticity
@@ -8896,6 +8899,44 @@
subset: value_slim
is_a: PATO:0000083 ! phase
+[Term]
+id: PATO:0001543
+name: flexibility
+def: "A physical quality inhering in a bearer by virtue of its capability of being turned, bowed, or twisted without breaking." [merriam-webster:merriam-webster "http://www.m-w.com/"]
+is_a: PATO:0001018 ! physical quality
+
+[Term]
+id: PATO:0001544
+name: flexible
+def: "A physical quality inhering in a bearer by virtue of its ability of being turned, bowed, or twisted without breaking." [merriam-webster:merriam-webster "http://www.m-w.com/ "]
+exact_synonym: "bendy" []
+is_a: PATO:0001543 ! flexibility
+
+[Term]
+id: PATO:0001545
+name: inflexible
+def: "A physical quality inhering in a bearer by virtue of its inability of being turned, bowed, or twisted without breaking." [merriam-webster:merriam-webster "http://www.m-w.com/ "]
+exact_synonym: "stiff" []
+is_a: PATO:0001543 ! flexibility
+
+[Term]
+id: PATO:0001546
+name: quality of a solid
+exact_synonym: "solidity" []
+is_a: PATO:0001018 ! physical quality
+
+[Term]
+id: PATO:0001547
+name: quality of a gas
+exact_synonym: "gaseous" []
+is_a: PATO:0001018 ! physical quality
+
+[Term]
+id: PATO:0001548
+name: quality of a liquid
+exact_synonym: "liquidity" []
+is_a: PATO:0001018 ! physical quality
+
[Typedef]
id: is_magnitude_of
name: is_magnitude_of
Modified: phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java 2007-01-30 15:25:56 UTC (rev 310)
+++ phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java 2007-01-30 18:02:20 UTC (rev 311)
@@ -168,6 +168,7 @@
/** If repository is configured loads obo from repos if local out of date */
private void loadOboSessionCheckRepos(Ontology o,OntologyConfig oc)
throws OntologyException {
+ // first get normal/cached/local ontology
String filename = oc.getFile();
URL url = findFile(filename); // throws OntologyEx if file not found
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-01-30 15:25:57
|
Revision: 310
http://svn.sourceforge.net/obo/?rev=310&view=rev
Author: mgibson
Date: 2007-01-30 07:25:56 -0800 (Tue, 30 Jan 2007)
Log Message:
-----------
woops thought i already comitted this anyways
fixes for ontology chooser bug - now ontology chooser reflects what term is in
the field - for undo selection and post comp
one bug - if post comp term selected in main window main field cant find it -
needs to pick off genus term OR post comp needs to be added to obo session - i
think the latter actually as then it will be searchable in comp list which i
think would be helpful
Modified Paths:
--------------
phenote/trunk/src/java/phenote/datamodel/CharField.java
phenote/trunk/src/java/phenote/datamodel/Ontology.java
phenote/trunk/src/java/phenote/datamodel/OntologyManager.java
phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java
phenote/trunk/src/java/phenote/gui/field/PostCompGui.java
phenote/trunk/src/java/phenote/gui/field/RelationCompList.java
phenote/trunk/src/java/phenote/gui/field/TermCompList.java
phenote/trunk/src/java/phenote/main/PhenoteVersion.java
phenote/trunk/src/java/phenote/servlet/PhenoteController.java
Modified: phenote/trunk/src/java/phenote/datamodel/CharField.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/CharField.java 2007-01-30 00:53:37 UTC (rev 309)
+++ phenote/trunk/src/java/phenote/datamodel/CharField.java 2007-01-30 15:25:56 UTC (rev 310)
@@ -121,7 +121,7 @@
else {
OBOClass oboClass=null;
for (Ontology ont : ontologyList) {
- try { oboClass = ont.getOboClass(valueString); }
+ try { oboClass = ont.getTerm(valueString); }
catch (TermNotFoundException e) {} // move on to next ontology
}
if (oboClass != null)
Modified: phenote/trunk/src/java/phenote/datamodel/Ontology.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/Ontology.java 2007-01-30 00:53:37 UTC (rev 309)
+++ phenote/trunk/src/java/phenote/datamodel/Ontology.java 2007-01-30 15:25:56 UTC (rev 310)
@@ -95,7 +95,7 @@
/** returns null if dont have class for id, throws OntologyException if id is not
found */
- public OBOClass getOboClass(String id) throws TermNotFoundException {
+ public OBOClass getTerm(String id) throws TermNotFoundException {
// this aint right - if its a slim should only search slim
//OBOClass oc = oboSession.getTerm(id);
for (OBOClass term : sortedTerms) {
@@ -107,10 +107,10 @@
//return oc;
}
- /** Returns true if ontology holds obo class */
- boolean hasOboClass(OBOClass oboClass) {
+ /** Returns true if ontology holds term/oboClass */
+ boolean hasTerm(OBOClass term) {
// if this is too slow can do optimizations with prefixes
- try {getOboClass(oboClass.getID()); }
+ try {getTerm(term.getID()); }
catch (TermNotFoundException e) { return false; }
return true; // no exception - it has it
}
Modified: phenote/trunk/src/java/phenote/datamodel/OntologyManager.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/OntologyManager.java 2007-01-30 00:53:37 UTC (rev 309)
+++ phenote/trunk/src/java/phenote/datamodel/OntologyManager.java 2007-01-30 15:25:56 UTC (rev 310)
@@ -90,7 +90,7 @@
//while (iter.hasNext()) {
for (Ontology o : getAllOntologies()) {
//Ontology o = iter.next();
- try { oboClass = o.getOboClass(id); }
+ try { oboClass = o.getTerm(id); }
catch (TermNotFoundException e) { continue; }
if (oboClass != null)
return oboClass;
@@ -144,28 +144,18 @@
return OboUtil.makePostCompTerm(gTerm,p,dTerm);
}
-// /** util fn! */
-// private OBOClass makePostCompTerm(OBOClass genus, String relation, OBOClass diff) {
-// String nm = pcString(genus.getName(),diff.getName());
-// String id = pcString(genus.getID(),diff.getID());
-// OBOClass postComp = new OBOClassImpl(nm,id);
-// OBOProperty ISA = OBOProperty.IS_A;
-// OBORestrictionImpl gRel = new OBORestrictionImpl(postComp,ISA,genusTerm);
-// return postComp;
-// }
-
- /** for obo class find its char field enum via ontology & char field */
- public CharFieldEnum getCharFieldEnumForOboClass(OBOClass oboClass) {
+ /** Currently iterates through every ontology looking for term, if this proves too
+ inefficient we could do something with ID prefixes */
+ public Ontology getOntologyForTerm(OBOClass term) throws OntologyException {
for (CharField cf : charFieldList) {
- //if (!cf.hasOntologies()) continue; // is this needed? not sure
- for (Ontology ont : cf.getOntologyList()) {
- if (ont.hasOboClass(oboClass))
- return cf.getCharFieldEnum();
- }
+ for (Ontology o : cf.getOntologyList())
+ if (o.hasTerm(term))
+ return o;
}
- return null; // this shouldnt happen - err msg?
- }
+ throw new OntologyException(term+" not found in ontologies");
+ }
+
private Logger log;
private Logger log() {
if (log == null) log = Logger.getLogger(getClass());
@@ -174,6 +164,28 @@
}
+ // previously used by term info
+// /** for obo class find its char field enum via ontology & char field */
+// public CharFieldEnum getCharFieldEnumForOboClass(OBOClass oboClass) {
+// for (CharField cf : charFieldList) {
+// //if (!cf.hasOntologies()) continue; // is this needed? not sure
+// for (Ontology ont : cf.getOntologyList()) {
+// if (ont.hasOboClass(oboClass))
+// return cf.getCharFieldEnum();
+// }
+// }
+// return null; // this shouldnt happen - err msg?
+// }
+
+// /** util fn! */
+// private OBOClass makePostCompTerm(OBOClass genus, String relation, OBOClass diff) {
+// String nm = pcString(genus.getName(),diff.getName());
+// String id = pcString(genus.getID(),diff.getID());
+// OBOClass postComp = new OBOClassImpl(nm,id);
+// OBOProperty ISA = OBOProperty.IS_A;
+// OBORestrictionImpl gRel = new OBORestrictionImpl(postComp,ISA,genusTerm);
+// return postComp;
+// }
// private void addOntologyList(List<Ontology> l) {
// allOntologyList.addAll(l);
// }
@@ -182,56 +194,3 @@
// allOntologyList.add(o);
// }
-
- // i think char field now does this
- //fieldToOntologyList = new HashMap<CharFieldEnum,List<Ontology>>();
- //private Map<CharFieldEnum,List<Ontology>> fieldToOntologyList;
-// private List<Ontology> entityOntologyList;
- //private Ontology geneticContextOntology;
- //private Ontology lumpOntology;
- //private Ontology entityOntology;
- //private Ontology patoOntology;
-
-// final static String ANATOMY = "Anatomy";
-// final static String PATO = "Pato";
-// final static String TAXONOMY = "Taxonomy";
- // for now...
- // if hasOnlyOne? for (Ontology :...)?
-// if (cf.isGeneticContext())
-// setGeneticContextOntology(cf.getFirstOntology());
-
- // for now i know that only genetic context is in char field list...
-// public CharField getGeneticContextCharField() {
-// if (charFieldList == null || charFieldList.isEmpty())
-// return null;
-// return charFieldList.get(0); // revisit this!!!!
-// }
-
-
-// private void addOntologyToMap(CharFieldEnum c, Ontology o) {
-// List<Ontology> l = fieldToOntologyList.get(c);
-// if (l == null) {
-// l = new ArrayList<Ontology>(3);
-// fieldToOntologyList.put(c,l);
-// }
-// l.add(o);
-// }
-
-
- // public List<Ontology> getOntologyList(CharFieldEnum e) {}
-
-// public boolean haveLumpOntology() { return getLumpOntology() != null; }
-
-// public void setLumpOntology(Ontology lo) {
-// lumpOntology = lo;
-// addOntology(lumpOntology);
-// }
-
-// public Ontology getLumpOntology() {
-// return lumpOntology;
-// }
-
-// public void setEntityOntologyList(List<Ontology> entList) {
-// entityOntologyList = entList;
-// }
-
Modified: phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java 2007-01-30 00:53:37 UTC (rev 309)
+++ phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java 2007-01-30 15:25:56 UTC (rev 310)
@@ -59,7 +59,7 @@
/** @param editModel if false then ACB doesnt edit model directly (post comp)
can abstract classes have constructors - if not init() */
- protected AbstractAutoCompList(CompListSearcher s,boolean editModel) {
+ protected AbstractAutoCompList(CompListSearcher s,boolean editModel,CharField cf) {
// this inner class enables retrieving of JList for mouse over
// this will probably throw errors if non metal look & feel is used
setUI(new MetalListComboUI());
@@ -82,6 +82,7 @@
setFont(new Font("Monospaced",Font.PLAIN,10));
//setOntology(ontology);
//searchParams = sp; // singleton access? part of ontology?
+ setCharField(cf);
compListSearcher = s;
//enableTermInfoListening(true); // default - hardwired in rel & term subclasses
//addCompletionListListener(compList);
@@ -101,6 +102,10 @@
protected CharField getCharField() { return charField; }
+ protected boolean hasMoreThanOneOntology() {
+ return charField.hasMoreThanOneOntology();
+ }
+
protected boolean editModelEnabled() { return editModel; }
/** char in table changed - adjust - not needed for rel(at least not yet)
Modified: phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java 2007-01-30 00:53:37 UTC (rev 309)
+++ phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java 2007-01-30 15:25:56 UTC (rev 310)
@@ -47,7 +47,7 @@
private boolean isCompList = false;
private CharField charField;
private FieldPanel fieldPanel;
- private JComboBox ontologyChooserCombo;
+ //private JComboBox ontologyChooserCombo;
private String label;
private boolean enableListeners = true;
private boolean addCompButton = true;
@@ -95,6 +95,7 @@
EditManager.inst().addCharChangeListener(new FieldCharChangeListener());
}
+ // FreeTextField.updateModel uses this
boolean updateGuiOnly() { return updateGuiOnly; }
/** edits from post comp come in here i believe (term info used to but now
@@ -193,13 +194,13 @@
fieldPanel.addLabel(getLabel(),charField.hasMoreThanOneOntology());
// if has more than one ontology(entity) then add ontology choose list
- if (charField.hasMoreThanOneOntology())
- initOntologyChooser(charField);
+// if (charField.hasMoreThanOneOntology())
+// initOntologyChooser(charField);
- createCompList();
+ createCompList(); // comp list now makes ontologyChooser (if >1 ont)
fieldPanel.addFieldGui(getCompList());
- getCompList().setCharField(charField);
+ //getCompList().setCharField(charField);
// POST COMPOSITION button - only get post comp button if both configged for it
// AND addCompButton flag is true - PostCompGui sets to false - no post comp of
@@ -214,7 +215,7 @@
// AutoComboBox postCompCombo =
// new AutoComboBox(charField.getFirstOntology(),fieldPanel.getSearchParams());
// // postCompCombo.setVisible(false); // initial state hidden - layout?
-// postCompCombo.setCharField(charField);
+// postCompCombo.setCharField(harField);
// postCompCombo.setIsDifferentia(true); // differentia of genus in post comp
// fieldPanel.addFieldGui(postCompCombo);
}
@@ -229,23 +230,24 @@
compListSearcher =
new CompListSearcher(charField.getFirstOntology(),fieldPanel.getSearchParams());
if (isRelationshipList()) {
- relCompList = new RelationCompList(compListSearcher,enableListeners);
+ relCompList = new RelationCompList(compListSearcher,enableListeners,charField);
}
else {
- termCompList = new TermCompList(compListSearcher,enableListeners);
+ termCompList = new TermCompList(compListSearcher,enableListeners,this);
}
}
+ void addOntologyChooser(JComboBox oc) { fieldPanel.addOntologyChooser(oc); }
- private void initOntologyChooser(CharField charField) {
- ontologyChooserCombo = new JComboBox();
- // add listener....
- for (Ontology o : charField.getOntologyList()) {
- ontologyChooserCombo.addItem(o.getName());
- }
- ontologyChooserCombo.addActionListener(new OntologyChooserListener());
- fieldPanel.addOntologyChooser(ontologyChooserCombo);
- }
+// private void initOntologyChooser(CharField charField) {
+// ontologyChooserCombo = new JComboBox();
+// // add listener....
+// for (Ontology o : charField.getOntologyList()) {
+// ontologyChooserCombo.addItem(o.getName());
+// }
+// ontologyChooserCombo.addActionListener(new OntologyChooserListener());
+// fieldPanel.addOntologyChooser(ontologyChooserCombo);
+// }
private void initTextField(String label) {
isCompList = false;
@@ -324,35 +326,6 @@
return SelectionManager.inst().getFirstSelectedCharacter();
}
-// List<CharacterI> getSelectedChars() {
-// return SelectionManager.inst().getSelectedChars();
-// }
-
-// // separate char text field class?
-// /** This is where the model gets updated (for free text fields) */
-// private class TextFieldDocumentListener implements DocumentListener {
-// //private String previousVal = null;
-// public void changedUpdate(DocumentEvent e) { updateModel(); }
-// public void insertUpdate(DocumentEvent e) { updateModel(); }
-// public void removeUpdate(DocumentEvent e) { updateModel(); }
-// private void updateModel() {
-// // if only updating gui (multi select clear) then dont update model
-// if (updateGuiOnly) return;
-// // on delete last pheno row clearing of text will trigger this
-// //if (!characterTablePanel.hasRows()) return;
-// //String genotype = lumpField.getText();
-// //characterTablePanel.setSelectedGenotype(genotype);
-// List<CharacterI> chars = getSelectedChars();
-// // i believe this isnt using oboClass as we just have string
-// // of course it isnt this is free text
-// String v = getText();
-// //UpdateTransaction ut = new UpdateTransaction(char,getCharFieldEnum(),v);
-// CompoundTransaction ct = new CompoundTransaction(chars,getCharFieldEnum(),v);
-// EditManager.inst().updateModel(CharFieldGui.this,ct);
-// //previousVal = v; // undo
-// }
-// }
-
private class FieldCharSelectListener implements CharSelectionListener {
public void charactersSelected(CharSelectionEvent e) {
// if multi select then clear out fields - alternatively could do first char
@@ -361,26 +334,12 @@
setGuiForMultiSelect();
return;
}
- updateGuiOnly = true; // selection should not cause an edit!
+ updateGuiOnly = true; // selection should not cause an edit/transaction!
setValueFromChar(e.getChars().get(0));
updateGuiOnly = false;
}
}
- private class OntologyChooserListener implements ActionListener {
- public void actionPerformed(ActionEvent e) {
- String s = ontologyChooserCombo.getSelectedItem().toString();
- try {
- Ontology o = OntologyManager.inst().getOntologyForName(s);
- //getCompList().setOntology(o); // termComp?
- compListSearcher.setOntology(o);
- }
- catch (OntologyException ex) {
- log().error(ex.getMessage());
- return;
- }
- }
- }
/** I think post-comp should only be closeable if its empty (in expand collapse
inframe case - now window) */
@@ -390,8 +349,10 @@
}
}
+ /** should define a CharFieldGuiEx! */
OBOClass getCurrentOboClass() throws Exception {
- if (!isCompList || isRelationshipList())
+ //if (!isCompList || isRelationshipList)
+ if (!isTermCompList())
throw new Exception("Field has no OBO Class");
return getTermComp().getCurrentOboClass(); // throws Ex
}
@@ -402,78 +363,66 @@
return getRelComp().getCurrentRelation(); // throws Ex
}
+ private boolean isTermCompList() {
+ return isCompList && !isRelationshipList() && getTermComp()!=null;
+ // && getTermComp != null?
+ }
+
+ /** for post comp gui to set ontol chooser */
+ void setOntologyChooserFromTerm(OBOClass term) {
+ if (!isTermCompList()) return; // shouldnt happen - ex?
+ getTermComp().setOntologyChooserFromTerm(term);
+ }
+
+
private Logger log;
private Logger log() {
if (log == null) log = Logger.getLogger(getClass());
return log;
}
}
-
-// /** This is for ontology char fields, freetext returns null. returns obo class
-// selected in AutoComboBox if there is one
-// this is problematic - it can get term that was selected a while ago */
-// OBOClass getSelectedOboClass() throws Exception {
-// if (!isCompList) throw new Exception("Free text field has no OBO Class");
-// OBOClass term = getCompList().getSelectedCompListOboClass();
-// if (term == null) throw new Exception("No term selected");
-// return term;
+ // -> TermCompList
+// private class OntologyChooserListener implements ActionListener {
+// public void actionPerformed(ActionEvent e) {
+// String s = ontologyChooserCombo.getSelectedItem().toString();
+// try {
+// Ontology o = OntologyManager.inst().getOntologyForName(s);
+// //getCompList().setOntology(o); // termComp?
+// compListSearcher.setOntology(o);
+// }
+// catch (OntologyException ex) {
+// log().error(ex.getMessage());
+// return;
+// }
+// }
// }
-// private void addDocumentListener(DocumentListener dl) {
-// if (!isCombo)
-// textField.getDocument().addDocumentListener(dl);
-// }
-// private void initCombo(Ontology ontology, Container parent) {
-// // attach search params to ontology?
-// comboBox = new AutoComboBox(ontology,fieldPanel.getSearchParams());
-// // refactor... mvc - ACB talk directly to pheno model?
-// //comboBox.addActionListener(new ComboBoxActionListener(ontology.getName(),comboBox));
-// //parent.add(comboBox,makeFieldConstraint());
-// fieldPanel.addFieldGui(comboBox,parent);
+// List<CharacterI> getSelectedChars() {
+// return SelectionManager.inst().getSelectedChars();
// }
-// /** No ontology -> free text field */
-// private CharFieldGui(String label,Container parent) {
-// initTextField(label,parent);
-// }
-// /** Fields with ontology -> combo box */
-// private CharFieldGui(Ontology ontology, Container parent) {
-// if (ontology == null) // shouldnt happen
-// initTextField(null,parent);
-// else
-// initCombo(ontology,parent);
-// }
-
-// /** Listens for actions from combo boxes and puts terms into table
-// * actions come from mouse select of term as well as return & tab
-// change this - should only modify character - could be done in ACB except
-// gt text field which isnt done here anyways - then send out CharacterChangeEvent
-// for table to get and refresh itself
-// this is being phased out for AutoComboBox's more generic ComboBoxActionListener*/
-// private class ComboBoxActionListener implements ActionListener {
-// private String ontology;
-// private AutoComboBox comboBox;
-
-// private ComboBoxActionListener(String ontology,AutoComboBox cb) {
-// this.ontology = ontology;
-// comboBox = cb;
+// // separate char text field class? --> FreeTextField
+// /** This is where the model gets updated (for free text fields) */
+// private class TextFieldDocumentListener implements DocumentListener {
+// //private String previousVal = null;
+// public void changedUpdate(DocumentEvent e) { updateModel(); }
+// public void insertUpdate(DocumentEvent e) { updateModel(); }
+// public void removeUpdate(DocumentEvent e) { updateModel(); }
+// private void updateModel() {
+// // if only updating gui (multi select clear) then dont update model
+// if (updateGuiOnly) return;
+// // on delete last pheno row clearing of text will trigger this
+// //if (!characterTablePanel.hasRows()) return;
+// //String genotype = lumpField.getText();
+// //characterTablePanel.setSelectedGenotype(genotype);
+// List<CharacterI> chars = getSelectedChars();
+// // i believe this isnt using oboClass as we just have string
+// // of course it isnt this is free text
+// String v = getText();
+// //UpdateTransaction ut = new UpdateTransaction(char,getCharFieldEnum(),v);
+// CompoundTransaction ct = new CompoundTransaction(chars,getCharFieldEnum(),v);
+// EditManager.inst().updateModel(CharFieldGui.this,ct);
+// //previousVal = v; // undo
// }
-// public void actionPerformed(ActionEvent e) {
-// setTableFromField(ontology);
-// }
-
-// /** Sets table value from field. checks that text in text field from user
-// is actually an item in completion list, is an obo term. */
-// private void setTableFromField(String ontology) {
-// String input = comboBox.getText();//getInput(ontology);
-
-// // check if input is a real term - i think we can get away with checking
-// // if in present term completion list - not sure
-// boolean valid = comboBox.isInCompletionList(input);
-// if (!valid)
-// return;
-// // its valid - set the field
-// // no no no - edit model, send out model changed event
-// setTableColumn(ontology,input);
-// }
// }
+
Modified: phenote/trunk/src/java/phenote/gui/field/PostCompGui.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/PostCompGui.java 2007-01-30 00:53:37 UTC (rev 309)
+++ phenote/trunk/src/java/phenote/gui/field/PostCompGui.java 2007-01-30 15:25:56 UTC (rev 310)
@@ -95,9 +95,14 @@
//genusField.setText(getGenusString(currentTerm));
genusField.setOboClass(getGenusTerm(currentTerm));
+ // should this happen automatically from setOboClass or is that a burden/inefficiency
+ genusField.setOntologyChooserFromTerm(getGenusTerm(currentTerm));
//if (modelHasDiff(currentTerm))
try { relField.setRel(getRel(currentTerm)); } catch (Exception e){}
- try { diffField.setOboClass(getDiffTerm(currentTerm)); }
+ try {
+ diffField.setOboClass(getDiffTerm(currentTerm));
+ diffField.setOntologyChooserFromTerm(getDiffTerm(currentTerm));
+ }
catch (Exception e) {} // throws if no diff term
}
Modified: phenote/trunk/src/java/phenote/gui/field/RelationCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/RelationCompList.java 2007-01-30 00:53:37 UTC (rev 309)
+++ phenote/trunk/src/java/phenote/gui/field/RelationCompList.java 2007-01-30 15:25:56 UTC (rev 310)
@@ -7,14 +7,15 @@
import org.geneontology.oboedit.datamodel.OBOProperty;
import phenote.datamodel.CharacterI;
+import phenote.datamodel.CharField;
class RelationCompList extends AbstractAutoCompList {
private OBOProperty currentRel=null;
- RelationCompList(CompListSearcher searcher,boolean editModel) {
- super(searcher,editModel);
+ RelationCompList(CompListSearcher searcher,boolean editModel,CharField c) {
+ super(searcher,editModel,c);
// this inner class enables retrieving of JList for mouse over
// this will probably throw errors if non metal look & feel is used
// setUI(new MetalListComboUI());
Modified: phenote/trunk/src/java/phenote/gui/field/TermCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/TermCompList.java 2007-01-30 00:53:37 UTC (rev 309)
+++ phenote/trunk/src/java/phenote/gui/field/TermCompList.java 2007-01-30 15:25:56 UTC (rev 310)
@@ -1,7 +1,10 @@
package phenote.gui.field;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
import java.util.List;
import java.util.Vector;
+import javax.swing.JComboBox;
import javax.swing.JList;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
@@ -11,7 +14,11 @@
import org.geneontology.oboedit.datamodel.OBOClass;
import phenote.datamodel.CharacterI;
-import phenote.datamodel.CharFieldEnum;
+import phenote.datamodel.CharField;
+//import phenote.datamodel.CharFieldEnum;
+import phenote.datamodel.Ontology;
+import phenote.datamodel.OntologyException;
+import phenote.datamodel.OntologyManager;
import phenote.edit.EditManager;
import phenote.edit.CompoundTransaction;
//import phenote.edit.UpdateTransaction;
@@ -22,10 +29,17 @@
class TermCompList extends AbstractAutoCompList {
private OBOClass currentOboClass=null;
+ // only term comp lists need ontology choosers - if that changes move to AACL
+ private JComboBox ontologyChooserCombo;
+ private CharFieldGui charFieldGui;
- TermCompList(CompListSearcher s,boolean editModel) {
- super(s,editModel);
+ TermCompList(CompListSearcher s,boolean editModel,CharFieldGui cfg) {
+ super(s,editModel,cfg.getCharField());
+ this.charFieldGui = cfg; // pass to super? AACL subclass CFG?
enableTermInfoListening();
+ if (hasMoreThanOneOntology()) // super AACL
+ initOntologyChooser(getCharField());
+
}
@@ -43,9 +57,24 @@
// if null then user has made a new char or selected a char with no term
//if (selCharTerm == null) { } else { ??? covered above??
setOboClass(selCharTerm); // doesnt allow null
+ setOntologyChooserFromTerm(selCharTerm);
//}
}
+ void setOntologyChooserFromTerm(OBOClass term) {
+ if (term==null) return;
+ if (ontologyChooserCombo==null) return;
+ try {
+ Ontology o = OntologyManager.inst().getOntologyForTerm(term);
+ ontologyChooserCombo.setSelectedItem(o.getName());
+ }
+ catch (OntologyException e) {
+ // this happens at the moment for post comp terms - need to pick out
+ // genus for ontolo chooser or add to obo session?
+ //log().error("No ontology found for term "+term); // shouldnt happen
+ }
+ }
+
protected Vector getSearchItems(String input) {
return getCompListSearcher().getStringMatchTerms(input);
}
@@ -194,43 +223,36 @@
if (editModelEnabled()) editModel();
}
}
-
+ private void initOntologyChooser(CharField charField) {
+ ontologyChooserCombo = new JComboBox();
+ // need to add in ALL
+ for (Ontology o : charField.getOntologyList()) {
+ ontologyChooserCombo.addItem(o.getName());
+ }
+ ontologyChooserCombo.addActionListener(new OntologyChooserListener());
+ charFieldGui.addOntologyChooser(ontologyChooserCombo);
+ }
+
+
private Logger log;
private Logger log() {
if (log == null) log = Logger.getLogger(getClass());
return log;
}
+ private class OntologyChooserListener implements ActionListener {
+ public void actionPerformed(ActionEvent e) {
+ String s = ontologyChooserCombo.getSelectedItem().toString();
+ try {
+ Ontology o = OntologyManager.inst().getOntologyForName(s);
+ //getCompList().setOntology(o); // termComp?
+ getCompListSearcher().setOntology(o);
+ }
+ catch (OntologyException ex) {
+ log().error(ex.getMessage());
+ return;
+ }
+ }
+ }
}
- // this inner class enables retrieving of JList for mouse over
- // this will probably throw errors if non metal look & feel is used
-// setUI(new MetalListComboUI());
-// //setFont(new Font("Courier",Font.PLAIN,12));
-
-// setOntology(ontology);
-// searchParams = sp; // singleton access? part of ontology?
-// setEditable(true);
-// AutoTextFieldEditor autoTextFieldEditor = new AutoTextFieldEditor();
-// this.setEditor(autoTextFieldEditor);
-// setPreferredSize(new Dimension(350,22));
-
-// enableTermInfoListening(true); // default
-// //addCompletionListListener(compList);
-
-// //if (editModel) // ComboBoxActionListener edits the model
-// this.editModel = editModel;
-// addActionListener(new ComboBoxActionListener());
-// // strings get in somehow - need to figure out where they are coming from
-// private OBOClass oboClassDowncast(Object obj) throws OboException {
-// if (obj == null) throw new OboException();
-// if ( ! (obj instanceof OBOClass)) {
-// //log.info("Item in completion list not obo class "+obj.getClass());
-// throw new OboException("Item in completion list not obo class "+obj.getClass());
-// }
-// return (OBOClass)obj;
-// }
-// private OBOClass getCompListOboClass(int index) {
-// Object obj = defaultComboBoxModel.getElementAt(index);
-// return oboClassDowncast(obj);
-// }
Modified: phenote/trunk/src/java/phenote/main/PhenoteVersion.java
===================================================================
--- phenote/trunk/src/java/phenote/main/PhenoteVersion.java 2007-01-30 00:53:37 UTC (rev 309)
+++ phenote/trunk/src/java/phenote/main/PhenoteVersion.java 2007-01-30 15:25:56 UTC (rev 310)
@@ -6,7 +6,7 @@
//private static final float MAJOR_VERSION_NUM = 0.8f;
//private static final float SUB_VERSION_NUM = .3f;
- private static final String VERSION = "1.1 dev"; // ??
+ private static final String VERSION = "1.0.3 dev"; // ??
// type is "dev" or "release"
//private static final String type = " dev"; // "release"
Modified: phenote/trunk/src/java/phenote/servlet/PhenoteController.java
===================================================================
--- phenote/trunk/src/java/phenote/servlet/PhenoteController.java 2007-01-30 00:53:37 UTC (rev 309)
+++ phenote/trunk/src/java/phenote/servlet/PhenoteController.java 2007-01-30 15:25:56 UTC (rev 310)
@@ -56,7 +56,7 @@
Ontology ont = getOntology(ontologyName);
// ToDo: Put oboClass in the web session, then we do not need to pass in the ontology name in
// the html ajax call
- OBOClass oboClass = ont.getOboClass(termId);
+ OBOClass oboClass = ont.getTerm(termId);
form.setTerm(oboClass);
return new ModelAndView("term_info", "formBean", form);
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-01-30 00:53:36
|
Revision: 309
http://svn.sourceforge.net/obo/?rev=309&view=rev
Author: mgibson
Date: 2007-01-29 16:53:37 -0800 (Mon, 29 Jan 2007)
Log Message:
-----------
i to we - i think this is silly
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-java-requirements.html
Modified: phenote/trunk/doc/phenote-website/phenote-java-requirements.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-java-requirements.html 2007-01-30 00:44:50 UTC (rev 308)
+++ phenote/trunk/doc/phenote-website/phenote-java-requirements.html 2007-01-30 00:53:37 UTC (rev 309)
@@ -1,32 +1,51 @@
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
- <meta content="text/html; charset=ISO-8859-1"
- http-equiv="content-type">
+
+
+ <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">
+
+
<title>Java version for Phenote</title>
</head>
+
+
<body>
+
<h1>Java requirements for Phenote</h1>
+
<br>
-Phenote requires Java 1.5. I hope this is OK with everybody. If there
-are issues please let me know(mg...@fr...). 1.5 has been out
+
+Phenote requires Java 1.5. We hope this is OK with everybody. If there
+are issues please let us know(mg...@fr...). 1.5 has been out
for around 2 years, and has a lot of nice features. The big issue is
Macs. Mac Tiger supports 1.5 where earlier version (Panther &
-earlier) do not as far as I know. So upgrading to Tiger would then be a
+earlier) do not as far as we know. So upgrading to Tiger would then be a
requirement for using Phenote. Tiger has been out for over a year now
-and is now pretty stable, so I hope this isn't a cumbersome
-requirement. I have emailed with zfin and it seems the Mac users there
+and is now pretty stable, so we hope this isn't a cumbersome
+requirement. We have emailed with zfin and it seems the Mac users there
are actually already all upgraded to Tiger.<br>
+
<br>
+
As for windows, linux and solaris, if you do not already have jdk 1.5
it can be downloaded from sun:<br>
+
<br>
+
<a href="http://java.sun.com/j2se/1.5.0/download.jsp">http://java.sun.com/j2se/1.5.0/download.jsp</a><br>
+
<br>
+
<br>
+
<br>
+
<a href="phenote.html">Phenote main page</a><br>
+
<br>
+
<br>
+
</body>
</html>
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|
|
From: <mg...@us...> - 2007-01-30 00:44:51
|
Revision: 308
http://svn.sourceforge.net/obo/?rev=308&view=rev
Author: mgibson
Date: 2007-01-29 16:44:50 -0800 (Mon, 29 Jan 2007)
Log Message:
-----------
me to i
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote.html
Modified: phenote/trunk/doc/phenote-website/phenote.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.html 2007-01-24 21:15:31 UTC (rev 307)
+++ phenote/trunk/doc/phenote-website/phenote.html 2007-01-30 00:44:50 UTC (rev 308)
@@ -3,13 +3,17 @@
<head>
+
+
<meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">
+
+
<title>Phenote</title>
</head>
@@ -17,55 +21,71 @@
<body>
+
<h1 style="text-align: left;"><span style="font-weight: bold;"></span>Phenote<br>
+
</h1>
+
<br>
+
Phenote is a tool to annotate phenotypes using the Entity Quality
paradigm. It takes advantage of
ontologies. It uses term completion to allow curators quick access to
the ontology terms they want to use. <br>
+
<br>
+
<a href="1.0/phenote-flybase.jnlp">Phenote 1.0 for fly</a><br>
+
<br>
+
<a href="1.0/phenote-zfin.jnlp">Phenote 1.0 for zfin</a><br>
+
<br>
+
<a href="1.0/phenote-zfin.jnlp"></a><a href="1.0/phenote-human.jnlp">Phenote 1.0 for human</a><br>
+
<br>
+
To be clear the above webstart links for zfin & fly were made via
configuration not hard wired code. Thus one could in theory configure
phenote for ones own purposes.<br>
+
<br>
+
Recent addditions include the ability to add any field you like, post compose terms, bulk
update, undo, spring framework, and
synonyms now are shown in the completion list.<br>
+
<br>
+
Zebrafish requires
components of phenote(to plug into their non-public
website), not a full web app. Here is a proof of concept of some of
@@ -73,205 +93,267 @@
components:<br>
+
<br>
+
<a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby
Phenote(components used by Zfin)</a><br>
+
<br>
+
Webby phenote is a collaboration with Sohel Merchant at dictyBase.
Here is what they have done:<br>
+
<br>
+
<a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">DictyBase
webby phenote</a><br>
+
<br>
+
<br>
-I am doing these
+
+We are doing these
releases to get feedback. Please report any bugs (ideally through the <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">bug
-tracker</a>) and let me know what you
-think (mg...@fr...).<br>
+tracker</a>) and let us know what you
+think (email:<a href="mailto:mg...@be..."> mg...@be...</a>, email list: <a href="mailto:obo...@li...">obo...@li...</a>).<br>
+
<br>
+
<h4>Phenote links:<br>
+
</h4>
+
<a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote">Phenote
email list</a><br>
+
<a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">Phenote
bug tracker</a><br>
+
<a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote-bug-tracker">Bug
tracker email list</a><br>
+
<a href="https://sourceforge.net/svn/?group_id=76834">Phenote source
code (obo sourceforge svn)</a><br>
+
<a href="https://lists.sourceforge.net/lists/listinfo/obo-svn-commit">Phenote
svn commit email list</a><br>
+
<a href="http://wiki.dictybase.org/dictywiki/index.php/Phenotype_Curation_Tool_Documentation#Usage">Dicty
webby phenote wiki developer docs</a><br>
+
<a href="http://www.bioontology.org/wiki-internal/index.php/Phenotype_Annotation_Tool">Phenote
ncbo internal wiki (ncbo folk only)</a><br>
+
<br>
+
<a href="phenote-release-notes.html">Phenote Release Notes and old
webstart releases</a><br>
+
<br>
+
If the Phenote webstart link fails to do anything, then there are
probably problems
-with webstart and/or java(has to be jdk 1.5). Take a look at my <a href="webstart-troubleshooting.html">webstart troubleshooting</a><br>
+with webstart and/or java(has to be jdk 1.5). Take a look at the <a href="webstart-troubleshooting.html">webstart troubleshooting</a><br>
+
page.<br>
+
<br>
+
Click here for <a href="phenote-java-requirements.html">phenote java
requirements</a><br>
+
<br>
+
<br>
+
<br>
+
Old releases: <br>
+
<br>
+
<a href="0.9/phenote-flybase.jnlp">Phenote 0.9 for fly</a><br>
+
<a href="0.9/phenote-zfin.jnlp">Phenote (standalone) 0.9 for zfin</a><br>
+
<br>
+
<a href="0.8/phenote-flybase.jnlp">Phenote 0.8 for fly.</a><br>
+
<a href="0.8/phenote-zfin.jnlp">Phenote (standalone) 0.8 for zfin</a><br>
+
<br>
+
<a href="0.7/phenote-flybase.jnlp">Phenote 0.7 for fly.</a><br>
+
<a href="0.7/phenote-zfin.jnlp">Phenote (standalone) 0.7 for zfin</a><br>
+
<br>
+
<a href="0.6/phenote-flybase.jnlp">Phenote 0.6 with fly anatomy</a><br>
+
<br>
+
<a href="0.6/phenote-zfin.jnlp">Phenote 0.6 with zebrafish anatomy</a><br>
+
<br>
+
<a href="0.5/phenote-flybase.jnlp">Phenote 0.5 webstart for FlyBase</a><br>
+
<br>
+
<a href="0.5/phenote-zfin.jnlp">Phenote 0.5 webstart for ZFIN</a><br>
+
<br>
+
<a href="0.4/phenote-flybase.jnlp">Phenote 0.4 webstart for FlyBase</a><br>
+
<br>
+
<a href="0.4/phenote-zfin.jnlp">Phenote 0.4 webstart for ZFIN</a><br>
+
<br>
+
<a href="0.3.1/phenote-webstart.jnlp">Phenote for CToL group (0.3.1)</a>
(a special release for the CToL group that uses fish
taxonomy)<br>
+
<br>
+
<a href="0.3/phenote-webstart.jnlp">Phenote 0.3</a><br>
+
<br>
+
<a href="0.2/phenote-webstart.jnlp">Phenote 0.2</a><br>
+
<br>
+
<a href="0.1/phenote-webstart.jnlp">Phenote 0.1</a><br>
+
<br>
+
<br>
+
</body>
</html>
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|
|
From: <ba...@us...> - 2007-01-24 21:15:34
|
Revision: 307
http://svn.sourceforge.net/obo/?rev=307&view=rev
Author: balhoff
Date: 2007-01-24 13:15:31 -0800 (Wed, 24 Jan 2007)
Log Message:
-----------
Minor correction to NEXUSCharacter.hashCode().
Modified Paths:
--------------
phenote/trunk/src/java/phenote/dataadapter/nexus/NEXUSAdapter.java
Modified: phenote/trunk/src/java/phenote/dataadapter/nexus/NEXUSAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/nexus/NEXUSAdapter.java 2007-01-24 16:29:23 UTC (rev 306)
+++ phenote/trunk/src/java/phenote/dataadapter/nexus/NEXUSAdapter.java 2007-01-24 21:15:31 UTC (rev 307)
@@ -300,7 +300,7 @@
}
public int hashCode() {
- return this.entity.hashCode() * this.attribute.hashCode();
+ return this.entity.hashCode() ^ this.attribute.hashCode();
}
public String toString() {
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|
|
From: <mg...@us...> - 2007-01-24 16:29:32
|
Revision: 306
http://svn.sourceforge.net/obo/?rev=306&view=rev
Author: mgibson
Date: 2007-01-24 08:29:23 -0800 (Wed, 24 Jan 2007)
Log Message:
-----------
fixed quoting bug in pheno syntax - free text fields are now quoted as they
should be and quotes are stripped on reading in
Modified Paths:
--------------
phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxChar.java
phenote/trunk/src/java/phenote/datamodel/CharField.java
Modified: phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java 2007-01-23 17:59:48 UTC (rev 305)
+++ phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java 2007-01-24 16:29:23 UTC (rev 306)
@@ -173,6 +173,7 @@
// if ontCfg.hasSynchUrl() ?
// URL synchUrl = ontCfg.getSynchUrl
+ startTimer("checking with repos... loading obo session "+filename);
if (oc.hasReposUrl()) {
try {
URL reposUrl = oc.getReposUrl();//new URL("http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/evidence_code.obo");
@@ -180,7 +181,6 @@
// url may be jar/obo-files or svn/obo-files but this function may put file
// in cache ~/.phenote/obo-files
url = synchWithRepositoryUrl(url,reposUrl,o.getName());
-
// to do - if from repos need to load repos into local obo cache!
@@ -188,6 +188,7 @@
}
loadOboSessionFromUrl(o,url,filename);
+ stopTimer();
}
/** url is either local file or repos url */
@@ -214,14 +215,23 @@
if (repos > loc)
useRepos = queryUserAboutRepos(ontol);
if (useRepos) {
+
+ // i think its always better to download as http/repos is slow
+// boolean downloadToLocal = false; // from Config!
+// if (!downloadToLocal) {
+// LOG.info("Using obo file straight from repository "+reposUrl+
+// " NOT downloading to local cache");
+// return reposUrl; // just use straight from repos
+// }
+
+ // download obo to local cache (takes time!)
String file = FileUtil.getNameOfFile(localUrl);
try {
localUrl = new File(FileUtil.getUserOboCacheDir(),file).toURL();
- LOG.info("Loading new ontology from repository "+reposUrl+" to "+localUrl);
+ LOG.info("Downloading new ontology from repository "+reposUrl+" to "+localUrl);
copyReposToLocal(reposUrl,localUrl);
}
catch (MalformedURLException e) { throw new OntologyException(e); }
- //return reposUrl;
}
return localUrl;
}
@@ -342,13 +352,13 @@
private void startTimer(String m) {
startTime = Calendar.getInstance();
timerMsg = m;
- LOG.debug(timerMsg+" Start clock "+startTime.getTime());
+ //LOG.debug(timerMsg+" Start clock "+startTime.getTime()); // ??
}
private void stopTimer() {
Calendar endTime = Calendar.getInstance();
long seconds = (endTime.getTimeInMillis() - startTime.getTimeInMillis())/1000;
- LOG.debug(timerMsg+" clock stopped, seconds elapsed: "+seconds);
+ LOG.debug(timerMsg+" number of seconds: "+seconds);
}
Modified: phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxChar.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxChar.java 2007-01-23 17:59:48 UTC (rev 305)
+++ phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxChar.java 2007-01-24 16:29:23 UTC (rev 306)
@@ -59,39 +59,24 @@
for (CharField cf : OntologyManager.inst().getCharFieldList()) {
if (character.hasValue(cf)) {
sb.append(Config.inst().getSyntaxAbbrevForCharField(cf)).append("=");//ex
+ if (isFreeText(cf)) sb.append('"'); // free text gets quoted
sb.append(makeValue(character.getValue(cf))).append(" ");
+ if (isFreeText(cf)) sb.append("\" ");
}
// check for entity & quality??
}
-// if (character.hasValue("Pub")) // hasPub
-// sb.append("PUB=").append(character.getValueString("Pub")); //Pub());
-// // Genotype - not strictly part of pheno syntax but lets face it we need it
-// // i would say its an omission from syntax
-// //sb.append(" GT=").append(character.getGenotype());
-// if (character.hasValue("Genotype"))
-// sb.append(" GT=").append(character.getValueString("Genotype"));
-// if (character.hasValue("Genetic Context"))
-// sb.append(" GC=").append(makeValue(character.getTerm("Genetic Context")));
-
-// if (!character.hasValue("Entity"))
-// throw new BadCharException("Error: character has no entity, ignoring");
-// //sb.append(" E=").append(makeValue(character.getEntity()));
-// sb.append(" E=").append(makeValue(character.getTerm("Entity")));
-
-// // if (character.hasValue(CharFieldEnum.STAGE))
-
-// //if (character.getQuality() == null)
-// if (!character.hasValue("Quality"))
-// throw new BadCharException("Error: character has no quality, ignoring");
-// sb.append(" Q=").append(makeValue(character.getTerm("Quality")));
-
}
catch (ConfigException e) {
throw new BadCharException(e.getMessage());
}
return sb.toString();
}
+
+ /** If a char field has ontologies it is not free text */
+ private boolean isFreeText(CharField cf) {
+ return !cf.hasOntologies();
+ }
// this may be more general than just this class
class BadCharException extends Exception {
@@ -130,6 +115,7 @@
if (found) tagEnd = m.end(); // dont need if not found (last one)
String value = line.substring(valueStart,tagStart).trim();
value = stripComments(value).trim();
+ //value = stripQuotesFromFreeText(value); // free text gets quoted
//System.out.println("tag ."+tag+". val ."+value+".");
addTagValToChar(tag,value);
}
@@ -140,6 +126,15 @@
return value;
}
+ private static final String q = "\"";
+
+ private String stripQuotesFromFreeText(String value,CharField cf) {
+ if (!isFreeText(cf)) return value;
+ if (value.startsWith(q)) value = value.substring(1);
+ if (value.endsWith(q)) value = value.substring(0,value.length()-2);
+ return value;
+ }
+
class SyntaxParseException extends Exception {
private String syntaxLine;
SyntaxParseException(String syntaxLine) {
@@ -161,8 +156,14 @@
OntologyManager om = OntologyManager.inst();
try {
+ // so this is funny but there can be more than one char field for an abbrev - for
+ // instance Tag is for both abormal and absent. with setValue only the proper char
+ // field will get set, eg abnormal char field will throw exception for "absent"
List<CharField> fields = Config.inst().getCharFieldsForSyntaxAbbrev(tag);//Ex
for (CharField cf : fields) {
+
+ value = stripQuotesFromFreeText(value,cf);
+
if (cf.getName().equals("Stage")) {
// todo - a general relationship extracter?
value = extractStageHack(value); // for now - fix for real later
@@ -182,25 +183,6 @@
log().error("Term not found "+value); // list char field?
//}
-// try {
-// if (tag.equals("PUB"))
-// character.setPub(value);
-// else if (tag.equals("GT"))
-// character.setGenotype(value);
-// else if (tag.equals("GC"))
-// character.setGeneticContext(om.getOboClassWithExcep(value)); // throws ex
-// else if (tag.equals("E"))
-// character.setEntity(om.getTermOrPostComp(value));
-// else if (tag.equals("Q"))
-// character.setQuality(om.getOboClassWithExcep(value));
-// else // throw exception? or let rest of char go through?
-// System.out.println("pheno syntax tag "+tag+" not recognized (value "+value+")");
-// }
-// catch (OntologyManager.TermNotFoundException e) {
-// log().error("Term not found for tag "+tag+" value "+value+" in loaded "
-// +"ontologies - check syntax with ontology files.");
-// return;
-// }
}
@@ -225,3 +207,43 @@
return log;
}
}
+// try {
+// if (tag.equals("PUB"))
+// character.setPub(value);
+// else if (tag.equals("GT"))
+// character.setGenotype(value);
+// else if (tag.equals("GC"))
+// character.setGeneticContext(om.getOboClassWithExcep(value)); // throws ex
+// else if (tag.equals("E"))
+// character.setEntity(om.getTermOrPostComp(value));
+// else if (tag.equals("Q"))
+// character.setQuality(om.getOboClassWithExcep(value));
+// else // throw exception? or let rest of char go through?
+// System.out.println("pheno syntax tag "+tag+" not recognized (value "+value+")");
+// }
+// catch (OntologyManager.TermNotFoundException e) {
+// log().error("Term not found for tag "+tag+" value "+value+" in loaded "
+// +"ontologies - check syntax with ontology files.");
+// return;
+// }
+// if (character.hasValue("Pub")) // hasPub
+// sb.append("PUB=").append(character.getValueString("Pub")); //Pub());
+// // Genotype - not strictly part of pheno syntax but lets face it we need it
+// // i would say its an omission from syntax
+// //sb.append(" GT=").append(character.getGenotype());
+// if (character.hasValue("Genotype"))
+// sb.append(" GT=").append(character.getValueString("Genotype"));
+// if (character.hasValue("Genetic Context"))
+// sb.append(" GC=").append(makeValue(character.getTerm("Genetic Context")));
+
+// if (!character.hasValue("Entity"))
+// throw new BadCharException("Error: character has no entity, ignoring");
+// //sb.append(" E=").append(makeValue(character.getEntity()));
+// sb.append(" E=").append(makeValue(character.getTerm("Entity")));
+
+// // if (character.hasValue(CharFieldEnum.STAGE))
+
+// //if (character.getQuality() == null)
+// if (!character.hasValue("Quality"))
+// throw new BadCharException("Error: character has no quality, ignoring");
+// sb.append(" Q=").append(makeValue(character.getTerm("Quality")));
Modified: phenote/trunk/src/java/phenote/datamodel/CharField.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/CharField.java 2007-01-23 17:59:48 UTC (rev 305)
+++ phenote/trunk/src/java/phenote/datamodel/CharField.java 2007-01-24 16:29:23 UTC (rev 306)
@@ -60,6 +60,8 @@
public List<Ontology> getOntologyList() { return ontologyList; }
+ //booelan isFreeText() return !hasOntologies() ??
+
public boolean hasOntologies() {
return ontologyList != null && !ontologyList.isEmpty();
}
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|
|
From: <mg...@us...> - 2007-01-23 17:59:49
|
Revision: 305
http://svn.sourceforge.net/obo/?rev=305&view=rev
Author: mgibson
Date: 2007-01-23 09:59:48 -0800 (Tue, 23 Jan 2007)
Log Message:
-----------
so ontology data adapter now copies repos/sourceforge obo file to local file -
~/.phenote/obo-files when local obo is out of date - the copy takes a while -
i found that nio and old io took same amount of time - buffering didnt seem to
make a difference(??)
also user may want option of not copying to local cache just use straight from
repos - need config for that - and should that be the default - should there
be a checkbox in the popup
"Do you want to copy repository obo file to local file system?"
also might want "dont ask me this next time" checkboxes
Modified Paths:
--------------
phenote/trunk/src/java/phenote/config/Config.java
phenote/trunk/src/java/phenote/config/OntologyConfig.java
phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
phenote/trunk/src/java/phenote/util/FileUtil.java
Modified: phenote/trunk/src/java/phenote/config/Config.java
===================================================================
--- phenote/trunk/src/java/phenote/config/Config.java 2007-01-22 19:44:48 UTC (rev 304)
+++ phenote/trunk/src/java/phenote/config/Config.java 2007-01-23 17:59:48 UTC (rev 305)
@@ -88,12 +88,7 @@
private String getMyPhenoteConfig(String passedInConfig,
boolean overwritePersonalCfg)
throws ConfigException {
- String home = System.getProperty("user.home");
- File dotPhenote = new File(home+"/.phenote");
- if (!dotPhenote.exists()) {
- System.out.println("creating "+dotPhenote+" directory");
- dotPhenote.mkdir();
- }
+ File dotPhenote = FileUtil.getDotPhenoteDir();
File myPhenote = new File(dotPhenote,"my-phenote.cfg");
// if file doesnt exist yet or overwrite, copy over passedInConfig
if (!myPhenote.exists() || overwritePersonalCfg) {
Modified: phenote/trunk/src/java/phenote/config/OntologyConfig.java
===================================================================
--- phenote/trunk/src/java/phenote/config/OntologyConfig.java 2007-01-22 19:44:48 UTC (rev 304)
+++ phenote/trunk/src/java/phenote/config/OntologyConfig.java 2007-01-23 17:59:48 UTC (rev 305)
@@ -114,4 +114,6 @@
public boolean hasSlim() { return slim != null; }
public String getSlim() { return slim; }
+
+ public String toString() { return name; }
}
Modified: phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java 2007-01-22 19:44:48 UTC (rev 304)
+++ phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java 2007-01-23 17:59:48 UTC (rev 305)
@@ -1,11 +1,17 @@
package phenote.dataadapter;
+import java.io.*;
+
import java.io.BufferedReader;
import java.io.File;
+import java.io.FileOutputStream;
import java.io.FileNotFoundException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.IOException;
+import java.nio.channels.FileChannel;
+import java.nio.channels.ReadableByteChannel;
+import java.nio.channels.Channels;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
@@ -13,6 +19,7 @@
import java.util.Date;
import java.text.SimpleDateFormat;
import java.text.ParsePosition;
+import java.util.Calendar;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
@@ -95,7 +102,7 @@
cf.addOntology(o);
} catch (OntologyException e) {
//System.out.println(e.getMessage()+" ignoring ontology, fix config! ");
- LOG.error(e.getMessage()+" ignoring init ontology, fix config? ");
+ LOG.error(e.getMessage()+" ignoring init ontology, fix config? "+oc);
}
}
}
@@ -130,7 +137,7 @@
if (ontCfg.hasSlim())
ontology.setSlim(ontCfg.getSlim());
- loadOboSession(ontology,ontCfg); // throws FileNotFoundEx
+ loadOboSession(ontology,ontCfg); // throws FileNotFoundEx->OntolEx
return ontology;
}
@@ -163,28 +170,24 @@
throws OntologyException {
String filename = oc.getFile();
URL url = findFile(filename); // throws OntologyEx if file not found
-
+
// if ontCfg.hasSynchUrl() ?
// URL synchUrl = ontCfg.getSynchUrl
if (oc.hasReposUrl()) {
try {
URL reposUrl = oc.getReposUrl();//new URL("http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/evidence_code.obo");
- url = checkRepositoryUrl(url,reposUrl,o.getName());
+ // if out of synch copies repos to local
+ // url may be jar/obo-files or svn/obo-files but this function may put file
+ // in cache ~/.phenote/obo-files
+ url = synchWithRepositoryUrl(url,reposUrl,o.getName());
+
// to do - if from repos need to load repos into local obo cache!
} catch (/*MalformedURL & IO*/Exception e) { LOG.error(e); }
}
loadOboSessionFromUrl(o,url,filename);
-// o.setOboSession(getOboSession(url)); // throws OntEx if error
-// fileToOntologyCache.put(filename,o);
-// File file = new File(url.getFile());
-// long date = file.lastModified();
-// if (date > 0) { // jar files have 0 date???
-// o.setTimestamp(date);
-// o.setSource(file.toString());
-// }
}
/** url is either local file or repos url */
@@ -202,7 +205,8 @@
}
}
- private URL checkRepositoryUrl(URL localUrl, URL reposUrl, String ontol)
+ /** this copies obo file to local cache (~/.phenote/obo-files */
+ private URL synchWithRepositoryUrl(URL localUrl, URL reposUrl, String ontol)
throws OntologyException {
long repos = getOboDate(reposUrl);
long loc = getOboDate(localUrl); // throws ont ex
@@ -210,21 +214,19 @@
if (repos > loc)
useRepos = queryUserAboutRepos(ontol);
if (useRepos) {
- LOG.info("Loading new ontology from repository "+reposUrl);
- return reposUrl;
+ String file = FileUtil.getNameOfFile(localUrl);
+ try {
+ localUrl = new File(FileUtil.getUserOboCacheDir(),file).toURL();
+ LOG.info("Loading new ontology from repository "+reposUrl+" to "+localUrl);
+ copyReposToLocal(reposUrl,localUrl);
+ }
+ catch (MalformedURLException e) { throw new OntologyException(e); }
+ //return reposUrl;
}
return localUrl;
}
- // is it bad to have a popup from data adapter?
- private boolean queryUserAboutRepos(String ontol) {
- String m = "There is a more current ontology in the repository for "+ontol+".\nWould"
- +" you like to load the new version? (may take a few minutes)";
- int yn = JOptionPane.showConfirmDialog(null,m,"Synch ontology?",
- JOptionPane.YES_NO_OPTION,
- JOptionPane.QUESTION_MESSAGE);
- return yn == JOptionPane.YES_OPTION;
- }
+
/** Get the date of the file from the header of the obo file - just read header dont
read in whole file. should it also query urlConnection for date first? */
@@ -239,7 +241,7 @@
if (!line.startsWith("date:")) continue;
SimpleDateFormat dateFormat = new SimpleDateFormat("dd:MM:yyyy HH:mm");
Date d = dateFormat.parse(line, new ParsePosition(6));
- LOG.debug("date "+d+" for url "+oboUrl+" line "+line);
+ //LOG.debug("date "+d+" for url "+oboUrl+" line "+line);
br.close();
if (d == null)
throw new OntologyException("couldnt parse date "+line);
@@ -248,8 +250,55 @@
throw new OntologyException("No date found in "+oboUrl);
} catch (IOException e) { throw new OntologyException(e); }
}
+
+ // is it bad to have a popup from data adapter?
+ private boolean queryUserAboutRepos(String ontol) {
+ String m = "There is a more current ontology in the repository for "+ontol+".\nWould"
+ +" you like to load the new version? (may take a few minutes)";
+ int yn = JOptionPane.showConfirmDialog(null,m,"Synch ontology?",
+ JOptionPane.YES_NO_OPTION,
+ JOptionPane.QUESTION_MESSAGE);
+ return yn == JOptionPane.YES_OPTION;
+ }
+ /** local url may be from distrib/jar dir, but needs to be set to
+ .phenote/obo-files dir as thats where the user cache is */
+ private void copyReposToLocal(URL reposUrl, URL localUrl)
+ throws OntologyException {
+ // is there a better way then just reading & writing lines? nio?
+ try {
+ // nio & old io do the same time - oh well (~1 minute for GO)
+ //startTimer("nio file copy "+reposUrl+" to "+localUrl);
+ InputStream is = reposUrl.openStream();
+ // nio actually does the same with the buffer
+ //BufferedInputStream bis = new BufferedInputStream(is);
+ ReadableByteChannel r = Channels.newChannel(is);
+ //BufferedReader br = new BufferedReader(new InputStreamReader(is));
+ File f = new File(localUrl.getFile());
+ FileOutputStream fos = new FileOutputStream(f);
+ //BufferedOutputStream bos = new BufferedOutputStream(fos);
+ //OutputStreamWriter osw = new OutputStreamWriter(fos);
+ //FileWriter fw = new FileWriter(f);
+ //BufferedWriter bw = new BufferedWriter(fw);
+ //PrintStream ps = new PrintStream(bos);
+ FileChannel w = fos.getChannel();
+ long size = 99999999999999l; // cant get actual size - whole file
+ w.transferFrom(r,0,size);
+ //byte[] buf = new byte[1024];
+// int i = 0;
+// //while((i=br.read())!=-1) {
+// String line;
+// while ((line=br.readLine())!=null) {
+// //bos.write(i); //buf, 0, i);
+// ps.print(line+"\n");
+// }
+ //stopTimer();
+ r.close();
+ w.close();
+ } catch (IOException e) { throw new OntologyException(e); }
+ }
+
/** Look for file in current directory (.) and jar file
throws OntologyException if file not found - wraps FileNFEx */
private URL findFile(String fileName) throws OntologyException {
@@ -274,7 +323,7 @@
return os;
}
catch (DataAdapterException e) {
- LOG.error("got data adapter exception: "+e); // ??
+ LOG.error("got obo data adapter exception: "+e+" for url "+oboUrl); // ??
throw new OntologyException(e);
}
}
@@ -287,6 +336,22 @@
loadOboSessionFromUrl(ont,url,ont.getSource()); // throws ex
}
+ // eventually move to util class
+ private Calendar startTime;
+ private String timerMsg;
+ private void startTimer(String m) {
+ startTime = Calendar.getInstance();
+ timerMsg = m;
+ LOG.debug(timerMsg+" Start clock "+startTime.getTime());
+ }
+
+ private void stopTimer() {
+ Calendar endTime = Calendar.getInstance();
+ long seconds = (endTime.getTimeInMillis() - startTime.getTimeInMillis())/1000;
+ LOG.debug(timerMsg+" clock stopped, seconds elapsed: "+seconds);
+ }
+
+
// private void loadRelationshipOntology() { hmmmmmm
// // for now - todo configure! post comp relationship-ontology
// // FieldConfig rfc = config.getRelationshipFieldConfig();
Modified: phenote/trunk/src/java/phenote/util/FileUtil.java
===================================================================
--- phenote/trunk/src/java/phenote/util/FileUtil.java 2007-01-22 19:44:48 UTC (rev 304)
+++ phenote/trunk/src/java/phenote/util/FileUtil.java 2007-01-23 17:59:48 UTC (rev 305)
@@ -4,6 +4,7 @@
import org.apache.commons.lang.StringUtils;
import java.io.*;
+import java.io.File;
import java.net.MalformedURLException;
import java.net.URL;
import java.nio.channels.FileChannel;
@@ -21,6 +22,42 @@
private static final Logger LOG = Logger.getLogger(FileUtil.class);
+ /** if ~/.phenote doesnt exist yet its created */
+ public static File getDotPhenoteDir() {
+ String home = System.getProperty("user.home");
+ File dotPhenote = new File(sep(home,".phenote"));
+ if (!dotPhenote.exists()) {
+ LOG.info("creating "+dotPhenote+" directory");
+ dotPhenote.mkdir();
+ }
+ return dotPhenote;
+ }
+
+ public static File getUserOboCacheDir() {
+ File d = getDotPhenoteDir();
+ File obo = new File(d,"obo-files");
+ if (!obo.exists()) {
+ LOG.info("creating "+obo+" directory");
+ obo.mkdir();
+ }
+ return obo;
+ }
+
+
+ /** get actual name of file sans path */
+ public static String getNameOfFile(URL urlFile) {
+ String path = urlFile.getPath();
+ int lastSlashIndex = path.lastIndexOf('/');
+ if (lastSlashIndex == -1) return path;
+ return path.substring(lastSlashIndex);
+ }
+
+ private static String getDotPhenoteString() {
+ return getDotPhenoteDir().getPath();
+ }
+
+ private static String sep(String a, String b) { return a + FILE_SEPARATOR + b; }
+
public static URL findUrl(String filename) throws FileNotFoundException {
List<URL> possibleUrls = getPossibleUrls(filename);
for (URL u : possibleUrls)
@@ -30,10 +67,16 @@
throw new FileNotFoundException(filename+" not found");
}
+ // this is muddling config and obo - probably should be 2 methods? or be smart about
+ // suffix - or who cares?
private static List<URL> getPossibleUrls(String filename) {
List<URL> urls = new ArrayList(5);
addFile(filename,urls); // full path or relative to pwd
addFile("conf/"+filename,urls);
+ // ~/.phenote/obo-files cache for obo files - overrides phenote obo-files
+ // eventually may have configured obo dir as well...
+ //addFile(sep(getDotPhenoteString(),"obo-files"),urls);
+ addFile(getUserOboCacheDir().getPath()+"/"+filename,urls);
addFile("obo-files/"+filename,urls);//this is obo-files specific - separate method?
// URL jarUrl = FileUtil.class.getResource(filename);
// if (jarUrl != null) urls.add(jarUrl);
@@ -46,13 +89,14 @@
try {
URL u = new File(filename).toURL();
if (u != null) urls.add(u);
+
URL jarUrl = FileUtil.class.getResource(filename);
if (jarUrl != null) urls.add(jarUrl);
jarUrl = FileUtil.class.getResource("/"+filename);
if (jarUrl != null) urls.add(jarUrl);
} catch (MalformedURLException e) {
- System.out.println("bad file url "+e);
- //LOG.error("bad file url "+e);
+ //System.out.println("bad file url "+e);
+ LOG.error("bad file url "+e);
}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ba...@us...> - 2007-01-22 19:45:12
|
Revision: 304
http://svn.sourceforge.net/obo/?rev=304&view=rev
Author: balhoff
Date: 2007-01-22 11:44:48 -0800 (Mon, 22 Jan 2007)
Log Message:
-----------
Minor improvement in NEXUS output.
Modified Paths:
--------------
phenote/trunk/src/java/phenote/dataadapter/nexus/NEXUSAdapter.java
Modified: phenote/trunk/src/java/phenote/dataadapter/nexus/NEXUSAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/nexus/NEXUSAdapter.java 2007-01-22 19:23:37 UTC (rev 303)
+++ phenote/trunk/src/java/phenote/dataadapter/nexus/NEXUSAdapter.java 2007-01-22 19:44:48 UTC (rev 304)
@@ -243,9 +243,7 @@
}
valueCount++;
}
- writer.write("\t\t\t");
- if (entryIterator.hasNext()) writer.write(",");
- writer.write("\n");
+ if (entryIterator.hasNext()) writer.write("\t\t\t,\n");
characterNum++;
}
writer.write("\t\t;\n");
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ba...@us...> - 2007-01-22 19:23:45
|
Revision: 303
http://svn.sourceforge.net/obo/?rev=303&view=rev
Author: balhoff
Date: 2007-01-22 11:23:37 -0800 (Mon, 22 Jan 2007)
Log Message:
-----------
Added file adapter for exporting phenotypes to a NEXUS file. This requires the use
of PATO with attribute and value slims. The adapter does not import NEXUS files.
Modified Paths:
--------------
phenote/trunk/obo-files/quality.obo
phenote/trunk/src/java/phenote/config/Config.java
Added Paths:
-----------
phenote/trunk/src/java/phenote/dataadapter/nexus/
phenote/trunk/src/java/phenote/dataadapter/nexus/NEXUSAdapter.java
Modified: phenote/trunk/obo-files/quality.obo
===================================================================
--- phenote/trunk/obo-files/quality.obo 2007-01-20 03:18:08 UTC (rev 302)
+++ phenote/trunk/obo-files/quality.obo 2007-01-22 19:23:37 UTC (rev 303)
@@ -1,10 +1,13 @@
format-version: 1.0
-date: 28:11:2006 13:58
+date: 22:01:2007 16:16
saved-by: George Gkoutos
-auto-generated-by: OBO-Edit 1.002
+auto-generated-by: OBO-Edit 1.100-beta16
+subsetdef: abnormal_slim "Abnormal/normal slim"
subsetdef: absent_slim "Absent/present slim"
-subsetdef: abnormal_slim "Abnormal/normal slim"
+subsetdef: attribute_slim "Attribute slim"
+subsetdef: value_slim "Value slim"
default-namespace: quality
+namespace-id-rule: * ID:$sequence(7,0,2147483647)$
[Term]
id: PATO:0000000
@@ -14,7 +17,8 @@
[Term]
id: PATO:0000001
name: quality
-def: "A dependent entity that\ninheres in a bearer by virtue of how the bearer is related to other entities." [PATO :GVG]
+def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities." [PATO :GVG]
+subset: attribute_slim
[Term]
id: PATO:0000002
@@ -30,6 +34,7 @@
id: PATO:0000004
name: mobility
def: "A quality of moving freely." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0001237 ! monadic quality of continuant
[Term]
@@ -51,6 +56,7 @@
id: PATO:0000008
name: speed/velocity
def: "A physical quality inhering in an object by virtue of the rate of change of its position." [Wikipedia:Wikipedia "http://en.wikipedia.org/"]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
@@ -66,6 +72,7 @@
[Term]
id: PATO:0000011
name: age
+subset: attribute_slim
is_a: PATO:0000165 ! time
[Term]
@@ -82,46 +89,54 @@
id: PATO:0000014
name: color
def: "A composite chromatic quality composed of hue, saturation and intensity parts." [XX:<new dbxref>]
+subset: attribute_slim
is_a: PATO:0001301 ! chromatic property
[Term]
id: PATO:0000015
name: color hue
def: "a chromatic scalar-circular quality inhering in an object that manifests in an observer by virtue of the dominant wavelength of the visible light; may be subject to fiat divisions, typically into 7 or 8 spectra" [XX:<new dbxref>]
+subset: attribute_slim
is_a: PATO:0001301 ! chromatic property
[Term]
id: PATO:0000016
name: color brightness
def: "A scalar optical quality which obtains by the bearer producing the effects of light emittance in an observer." [XX:<new dbxref>]
+subset: attribute_slim
is_a: PATO:0001300 ! optical quality
[Term]
id: PATO:0000017
name: color saturation
def: "a scalar chromatic quality that manifests by virtue of the range of wavelengths in perceived light." [XX:<new dbxref>]
+subset: attribute_slim
is_a: PATO:0001301 ! chromatic property
[Term]
id: PATO:0000018
name: fluorescence
def: "Luminosity in which the bearer emits longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together." [XX:<new dbxref>]
+subset: value_slim
is_a: PATO:0001296 ! luminosity
[Term]
id: PATO:0000019
name: color pattern
-is_obsolete: true
+subset: attribute_slim
+is_a: PATO:0001301 ! chromatic property
[Term]
id: PATO:0000020
name: relative color
+subset: attribute_slim
is_a: PATO:0001300 ! optical quality
[Term]
id: PATO:0000021
name: compatibility
def: "A quality of having or lacking the ability harmonious coexistence." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0001237 ! monadic quality of continuant
[Term]
@@ -142,7 +157,9 @@
[Term]
id: PATO:0000025
name: composition
-def: "A monadic quality of continuant inhering in an object by virtue of the quantities or relative ratios of subparts of the inhering entity; for example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood)" [PATO :GVG]
+def: "A monadic quality of continuant inhering in an object by virtue of the quantities or relative ratios of subparts of the inhering entity." [PATO :GVG]
+comment: For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood).
+subset: attribute_slim
is_a: PATO:0001237 ! monadic quality of continuant
[Term]
@@ -184,6 +201,7 @@
id: PATO:0000033
name: concentration
def: "A physical quality inhering in a substance by \nvirtue of the amount of it there is mixed with another substance." [Wikipedia:Wikipedia "http://www.wikipedia.org/"]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
@@ -205,6 +223,7 @@
id: PATO:0000037
name: consistency
def: "A physical quality that inheres in a continuant by\nvirtue of density, firmness, or viscosity." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
@@ -216,12 +235,14 @@
id: PATO:0000039
name: direction
def: "The orientation of a line in space." [: "http://thesaurus.maths.org/"]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
id: PATO:0000040
name: distance
def: "The extent of space between two objects or places." [XX:<new dbxref>]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
@@ -238,12 +259,14 @@
id: PATO:0000043
name: flavor
def: "A relational quality inhering in an object or the molecules of an object, in which the molecules are perceived by a taste and odorant receptors." [XX:<new dbxref>]
+subset: attribute_slim
is_a: PATO:0001238 ! relational quality of continuant
[Term]
id: PATO:0000044
name: frequency
def: "A physical quality which inhers to the bearer by virtue of the number of repetitive actions in a particular time." [Wikipedia:Wikipedia "http://en.wikipedia.org/"]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
@@ -260,41 +283,48 @@
id: PATO:0000047
name: biological sex
def: "A monadic quality of continuant inhering in an organism by virtue of its ability to undergo sexual reproduction in order to differentiate the individuals or types involved." [MGED:MGED]
+subset: attribute_slim
is_a: PATO:0001237 ! monadic quality of continuant
[Term]
id: PATO:0000048
name: hardness
def: "A physical quality inhering in a bearer as the constant of proportionality of the force on its elastic body to its body's extension." [: "http://thesaurus.maths.org/"]
+subset: attribute_slim
related_synonym: "stiffness" []
is_a: PATO:0001018 ! physical quality
[Term]
id: PATO:0000049
name: intensity
+subset: attribute_slim
is_a: PATO:0001237 ! monadic quality of continuant
[Term]
id: PATO:0000050
name: life span
def: "A time quality which is the expected maximum age." [XX:<new dbxref>]
+subset: attribute_slim
is_a: PATO:0000165 ! time
[Term]
id: PATO:0000051
name: morphology
def: "A quality inhering in the bearer by virtue of its size, shape and structure" [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0001237 ! monadic quality of continuant
[Term]
id: PATO:0000052
name: shape
-def: "A morphology quality inhering in a bearer by virtue of the ratios of distances between its features (points, edges, surfaces and also holes etc). " [PATO :GVG]
+def: "A morphology quality inhering in a bearer by virtue of the ratios of distances between its features (points, edges, surfaces and also holes etc)." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0000051 ! morphology
[Term]
id: PATO:0000053
name: count
+subset: attribute_slim
is_a: PATO:0001226 ! quantitative
[Term]
@@ -310,28 +340,33 @@
[Term]
id: PATO:0000056
name: nutritional
+subset: attribute_slim
is_a: PATO:0001237 ! monadic quality of continuant
[Term]
id: PATO:0000057
name: occurrence
+subset: attribute_slim
is_a: PATO:0001226 ! quantitative
[Term]
id: PATO:0000058
name: odor
-def: "A relational quality inhering in an object by virtue of the molecules being are aerially dispersed and perceived by an odorant receptor. " [XX:<new dbxref>]
+def: "A relational quality inhering in an object by virtue of the molecules being are aerially dispersed and perceived by an odorant receptor." [XX:<new dbxref>]
+subset: attribute_slim
is_a: PATO:0001238 ! relational quality of continuant
[Term]
id: PATO:0000059
name: parental type
+subset: attribute_slim
is_a: PATO:0000047 ! biological sex
[Term]
id: PATO:0000060
name: pattern
def: "A monadic quality of continuant defined by the mathematic properties of the relative position of subparts" [XX:<new dbxref>]
+subset: attribute_slim
is_a: PATO:0001237 ! monadic quality of continuant
[Term]
@@ -342,7 +377,8 @@
[Term]
id: PATO:0000062
name: sleep pattern
-is_a: PATO:0000186 ! behavioral quality
+subset: attribute_slim
+is_a: PATO:0001530 ! behavioral quality of occurent
[Term]
id: PATO:0000063
@@ -363,6 +399,7 @@
id: PATO:0000066
name: pilosity
def: "A quality of having hair." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0001237 ! monadic quality of continuant
[Term]
@@ -373,21 +410,25 @@
[Term]
id: PATO:0000068
name: qualitative
+subset: attribute_slim
is_a: PATO:0001237 ! monadic quality of continuant
[Term]
id: PATO:0000069
name: deviation(from_normal)
+subset: attribute_slim
is_a: PATO:0000068 ! qualitative
[Term]
id: PATO:0000070
name: presence
+subset: attribute_slim
is_a: PATO:0000068 ! qualitative
[Term]
id: PATO:0000071
name: relative_quantity
+subset: attribute_slim
is_a: PATO:0001226 ! quantitative
[Term]
@@ -419,12 +460,14 @@
id: PATO:0000077
name: response
def: "A quality inhering in a bearer by virtue of \nits reaction to a stimulus or an agent." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0001237 ! monadic quality of continuant
[Term]
id: PATO:0000078
name: rhythm
-is_a: PATO:0001237 ! monadic quality of continuant
+subset: attribute_slim
+is_a: PATO:0001239 ! monadic quality of occurrent
[Term]
id: PATO:0000079
@@ -434,24 +477,26 @@
[Term]
id: PATO:0000080
name: amplitude
-def: "A physical quality inhering in a bearer by \nvirtue of the size of its maximum displacement from the 'normal' position, when periodic motion is taking place" [: "http://thesaurus.maths.org/"]
-is_a: PATO:0000078 ! rhythm
-is_a: PATO:0001018 ! physical quality
+def: "A physical monadic quality of occurrent quality inhering in a bearer by virtue of the size of its maximum displacement from the 'normal' position, when periodic motion is taking place." [thesaurus.maths:thesaurus.maths "http://thesaurus.maths.org/"]
+subset: attribute_slim
+is_a: PATO:0001239 ! monadic quality of occurrent
[Term]
id: PATO:0000081
name: period
-is_a: PATO:0000078 ! rhythm
+subset: attribute_slim
is_a: PATO:0000165 ! time
[Term]
id: PATO:0000082
name: persistence
+subset: attribute_slim
is_a: PATO:0000078 ! rhythm
[Term]
id: PATO:0000083
name: phase
+subset: attribute_slim
is_a: PATO:0000078 ! rhythm
[Term]
@@ -463,6 +508,7 @@
id: PATO:0000085
name: sensitivity
def: "A relational quality of continuant inhering in an entity by virtue of its propensity to respond to stimulation." [PATO:GVG]
+subset: attribute_slim
is_a: PATO:0001238 ! relational quality of continuant
[Term]
@@ -623,7 +669,8 @@
[Term]
id: PATO:0000117
name: size
-def: "A morphology quality inhering in a bearer by virtue of its physical magnitude. " [WordNet :WordNet "wordnet.princeton.edu/"]
+def: "A morphology quality inhering in a bearer by virtue of its physical magnitude." [WordNet :WordNet "wordnet.princeton.edu/"]
+subset: attribute_slim
is_a: PATO:0000051 ! morphology
[Term]
@@ -635,6 +682,7 @@
id: PATO:0000119
name: height
def: "A physical quality which is equal to the vertical dimension of extension." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
@@ -651,6 +699,7 @@
id: PATO:0000122
name: length
def: "A physical quality which is equal to the distance between two points." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
@@ -667,6 +716,7 @@
id: PATO:0000125
name: mass
def: "A physical quality that inheres in a bearer in proportion to the amount of matter it contains." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
@@ -683,6 +733,7 @@
id: PATO:0000128
name: weight
def: "A quality inhering in an object with mass near a gravitational body." [Wikipedia:Wikipedia "http://www.wikipedia.org/"]
+subset: attribute_slim
is_a: PATO:0001035 ! force
[Term]
@@ -703,14 +754,15 @@
[Term]
id: PATO:0000132
name: spatial
+subset: attribute_slim
is_a: PATO:0001237 ! monadic quality of continuant
[Term]
id: PATO:0000133
name: angle
def: "A physical quality inhering in a figure or space formed by the junction of two lines or planes." [Wikipedia :Wikipedia "http://www.wikipedia.org/"]
+subset: attribute_slim
is_a: PATO:0000132 ! spatial
-is_a: PATO:0001018 ! physical quality
[Term]
id: PATO:0000134
@@ -725,12 +777,14 @@
[Term]
id: PATO:0000136
name: closure
+subset: attribute_slim
is_a: PATO:0000132 ! spatial
[Term]
id: PATO:0000137
name: orientation
def: "A quality of an object in which its \nlocation is defined by the angle between two axes, or an axis and another object" [XX:<new dbxref>]
+subset: attribute_slim
is_a: PATO:0000132 ! spatial
[Term]
@@ -747,12 +801,14 @@
id: PATO:0000140
name: placement
def: "A spatial quality of the way in which something is placed" [PATO:gg]
+subset: attribute_slim
is_a: PATO:0000132 ! spatial
[Term]
id: PATO:0000141
name: structure
-def: "A morphology quality inhering in a bearer by virtue of the relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.\n" [PATO :GVG]
+def: "A morphology quality inhering in a bearer by virtue of the relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0000051 ! morphology
[Term]
@@ -779,6 +835,7 @@
id: PATO:0000146
name: temperature
def: "A physical quality of the thermal energy of a system." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
@@ -799,7 +856,8 @@
[Term]
id: PATO:0000150
name: texture
-def: "A morphology quality inhering in a bearer by virtue of the relative size and distribution of its surface elements or the representation or invention of the appearance of its surface. \n" [PATO :GVG]
+def: "A morphology quality inhering in a bearer by virtue of the relative size and distribution of its surface elements or the representation or invention of the appearance of its surface." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0000051 ! morphology
[Term]
@@ -811,6 +869,7 @@
id: PATO:0000152
name: threshold
def: "A quality inhering in a bearer by virtue of its sensitivity towards a fixed location or value where a change is observed; upper limit." [Wikipedia:Wikipedia "http://www.wikipedia.org/"]
+subset: attribute_slim
is_a: PATO:0001237 ! monadic quality of continuant
[Term]
@@ -831,7 +890,8 @@
[Term]
id: PATO:0000156
name: temporal
-is_a: PATO:0001237 ! monadic quality of continuant
+subset: attribute_slim
+is_a: PATO:0001239 ! monadic quality of occurrent
[Term]
id: PATO:0000157
@@ -841,6 +901,7 @@
[Term]
id: PATO:0000158
name: incidence
+subset: attribute_slim
is_a: PATO:0000156 ! temporal
[Term]
@@ -856,6 +917,7 @@
[Term]
id: PATO:0000161
name: rate
+subset: attribute_slim
is_a: PATO:0000156 ! temporal
[Term]
@@ -877,6 +939,7 @@
id: PATO:0000165
name: time
def: "A quality in which events occur in sequence" [XX:<new dbxref>]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
@@ -887,6 +950,7 @@
[Term]
id: PATO:0000167
name: bouts
+subset: attribute_slim
is_a: PATO:0000165 ! time
[Term]
@@ -898,6 +962,7 @@
id: PATO:0000169
name: viability
def: "A quality inhering in a bearer or a population by virtue of the bearer's ability or inability to survive and develop normally or the number of surviving individuals in a given population." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0001237 ! monadic quality of continuant
[Term]
@@ -978,28 +1043,33 @@
[Term]
id: PATO:0000185
name: balance
-is_a: PATO:0001237 ! monadic quality of continuant
+subset: attribute_slim
+is_a: PATO:0001530 ! behavioral quality of occurent
[Term]
id: PATO:0000186
name: behavioral quality
+subset: attribute_slim
is_a: PATO:0001237 ! monadic quality of continuant
[Term]
id: PATO:0000187
name: consumption
-is_a: PATO:0001237 ! monadic quality of continuant
+subset: attribute_slim
+is_a: PATO:0001240 ! relational quality of occurrent
[Term]
id: PATO:0000188
name: coordination
def: "A quality of having or lacking skilful and effective interaction of movement." [PATO :GVG]
-is_a: PATO:0001237 ! monadic quality of continuant
+subset: attribute_slim
+is_a: PATO:0001530 ! behavioral quality of occurent
[Term]
id: PATO:0000189
name: discrimination
def: "A quality of perceiving differences between two or more stimuli." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0001237 ! monadic quality of continuant
[Term]
@@ -1360,6 +1430,7 @@
[Term]
id: PATO:0000261
name: maturity
+subset: attribute_slim
is_a: PATO:0001237 ! monadic quality of continuant
[Term]
@@ -1420,12 +1491,14 @@
[Term]
id: PATO:0000273
name: fecundity
-is_obsolete: true
+subset: attribute_slim
+is_a: PATO:0001434 ! reproductive quality
[Term]
id: PATO:0000274
name: fertility
def: "A quality of initiating, sustaining, or supporting reproduction." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0001434 ! reproductive quality
[Term]
@@ -1435,13 +1508,16 @@
[Term]
id: PATO:0000276
-name: litter size
-is_obsolete: true
+name: brood size
+subset: attribute_slim
+related_synonym: "litter size" []
+is_a: PATO:0001496 ! brood quality
[Term]
id: PATO:0000277
name: female fertility
def: "A fertility quality of the female of initiating, sustaining, or supporting reproduction." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0000274 ! fertility
[Term]
@@ -1453,6 +1529,7 @@
id: PATO:0000279
name: male fertility
def: "A fertility quality of the male of initiating, sustaining, or supporting reproduction." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0000274 ! fertility
[Term]
@@ -1544,6 +1621,7 @@
id: PATO:0000297
name: arrested
def: "A duration in which the end point is shorted before natural end point (prematurely finishing)." [XX:<new dbxref>]
+subset: value_slim
related_synonym: "incomplete" []
is_a: PATO:0001309 ! duration
@@ -1556,12 +1634,15 @@
id: PATO:0000299
name: mobile
def: "A mobility quality of being incapable to move freely." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000004 ! mobility
[Term]
id: PATO:0000300
name: immobile
def: "A mobility quality of being capable to move freely." [PATO :GVG]
+subset: value_slim
+related_synonym: "fixed" []
is_a: PATO:0000004 ! mobility
[Term]
@@ -1578,12 +1659,14 @@
id: PATO:0000303
name: fast speed
def: "A speed which is relative high." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000008 ! speed/velocity
[Term]
id: PATO:0000304
name: slow speed
def: "A speed which is relative low." [XX:<new dbxref>]
+subset: value_slim
is_a: PATO:0000008 ! speed/velocity
[Term]
@@ -1604,11 +1687,13 @@
[Term]
id: PATO:0000308
name: old
+subset: value_slim
is_a: PATO:0000011 ! age
[Term]
id: PATO:0000309
name: young
+subset: value_slim
is_a: PATO:0000011 ! age
[Term]
@@ -1650,46 +1735,54 @@
id: PATO:0000317
name: black
def: "A color that lacks any hues as parts." [XX:<new dbxref>]
+subset: value_slim
is_a: PATO:0000014 ! color
[Term]
id: PATO:0000318
name: blue
-def: "A color hue with low wavelength of that portion of the visible spectrum lying between green and indigo, evoked in the human observer by radiant energy with wavelengths of approximately 420 to 490 nanometers;" [Dictionary:http\://dictionary.reference.com/]
+def: "A color hue with low wavelength of that portion of the visible spectrum lying between green and indigo, evoked in the human observer by radiant energy with wavelengths of approximately 420 to 490 nanometers." [Dictionary:http\://dictionary.reference.com/]
+subset: value_slim
is_a: PATO:0000014 ! color
[Term]
id: PATO:0000319
name: cyan
+subset: value_slim
is_a: PATO:0000014 ! color
[Term]
id: PATO:0000320
name: green
def: "A color hue with medium-low wavelength of that portion of the visible spectrum lying between yellow and blue, evoked in the human observer by radiant energy with wavelengths of approximately 490 to 570 nanometers;" [Dictionary:http\://dictionary.reference.com/]
+subset: value_slim
is_a: PATO:0000014 ! color
[Term]
id: PATO:0000321
name: magenta
+subset: value_slim
is_a: PATO:0000322 ! red
[Term]
id: PATO:0000322
name: red
def: "A color hue with high wavelength of the long-wave end of the visible spectrum, evoked in the human observer by radiant energy with wavelengths of approximately 630 to 750 nanometers;" [Dictionary:http\://dictionary.reference.com/]
+subset: value_slim
is_a: PATO:0000014 ! color
[Term]
id: PATO:0000323
name: white
def: "An achromatic color of maximum lightness; the color of objects that reflect nearly all light of all visible wavelengths;" [Dictionary:http\://dictionary.reference.com/]
+subset: value_slim
is_a: PATO:0000014 ! color
[Term]
id: PATO:0000324
name: yellow
def: "A color hue with medium wavelength of that portion of the visible spectrum lying between orange and green, evoked in the human observer by radiant energy with wavelengths of approximately 570 to 590 nanometers" [Dictionary:http\://dictionary.reference.com/]
+subset: value_slim
is_a: PATO:0000014 ! color
[Term]
@@ -1705,11 +1798,13 @@
[Term]
id: PATO:0000327
name: dark
+subset: value_slim
is_a: PATO:0000016 ! color brightness
[Term]
id: PATO:0000328
name: pale
+subset: value_slim
related_synonym: "dull" []
is_a: PATO:0000017 ! color saturation
@@ -1722,11 +1817,13 @@
id: PATO:0000330
name: irregular
def: "A physical quality inhering in a bearer by virtue of lacking pattern." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000060 ! pattern
[Term]
id: PATO:0000331
name: discolored
+subset: value_slim
is_a: PATO:0000020 ! relative color
[Term]
@@ -1753,11 +1850,13 @@
[Term]
id: PATO:0000336
name: colored
+subset: value_slim
is_a: PATO:0000020 ! relative color
[Term]
id: PATO:0000337
name: colorless
+subset: value_slim
is_a: PATO:0000020 ! relative color
[Term]
@@ -1794,12 +1893,14 @@
id: PATO:0000344
name: compatible
def: "A compatibility quality of being capable of harmonious coexistence." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000021 ! compatibility
[Term]
id: PATO:0000345
name: incompatible
def: "A compatibility quality of being incapable of harmonious coexistence." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000021 ! compatibility
[Term]
@@ -1901,18 +2002,21 @@
id: PATO:0000365
name: down
def: "A direction from a higher to a lower point." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000039 ! direction
[Term]
id: PATO:0000366
name: left
def: "A direction that is similar to the direction of an object to the north when it faces east." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000039 ! direction
[Term]
id: PATO:0000367
name: right
def: "A direction that is similar to the direction of an object to the north when it faces west." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000039 ! direction
[Term]
@@ -1929,6 +2033,7 @@
id: PATO:0000370
name: up
def: "A direction from a lower to a higher point." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000039 ! direction
[Term]
@@ -1950,12 +2055,14 @@
id: PATO:0000374
name: long distance
def: "A distance which is greater relative to the normal or average." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000040 ! distance
[Term]
id: PATO:0000375
name: short distance
def: "A distance which is lesser relative to the normal or average." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000040 ! distance
[Term]
@@ -1982,12 +2089,14 @@
id: PATO:0000380
name: frequent
def: "A frequency which is relative high." [XX:<new dbxref>]
+subset: value_slim
is_a: PATO:0000044 ! frequency
[Term]
id: PATO:0000381
name: infrequent
def: "A frequency which is relative low." [XX:<new dbxref>]
+subset: value_slim
is_a: PATO:0000044 ! frequency
[Term]
@@ -1999,12 +2108,14 @@
id: PATO:0000383
name: female
def: "A biological sex quality inhering in an individual that only produces gametes that can be fertilised by male gamates." [MGED:MGED]
+subset: value_slim
is_a: PATO:0000047 ! biological sex
[Term]
id: PATO:0000384
name: male
def: "A biological sex quality inhering in an individual whose sex organs contain only male gametes." [MGED:MGED]
+subset: value_slim
is_a: PATO:0000047 ! biological sex
[Term]
@@ -2016,12 +2127,14 @@
id: PATO:0000386
name: hard
def: "A hardness quality of being rigid and resistant to pressure." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000048 ! hardness
[Term]
id: PATO:0000387
name: soft
-def: "A hardness quality of giving little resistance to pressure " [PATO :GVG]
+def: "A hardness quality of giving little resistance to pressure" [PATO :GVG]
+subset: value_slim
is_a: PATO:0000048 ! hardness
[Term]
@@ -2057,16 +2170,19 @@
[Term]
id: PATO:0000394
name: mild
+subset: value_slim
is_a: PATO:0000049 ! intensity
[Term]
id: PATO:0000395
name: moderate
+subset: value_slim
is_a: PATO:0000049 ! intensity
[Term]
id: PATO:0000396
name: severe
+subset: value_slim
is_a: PATO:0000049 ! intensity
[Term]
@@ -2097,27 +2213,33 @@
[Term]
id: PATO:0000402
name: branched
+subset: value_slim
is_a: PATO:0000052 ! shape
[Term]
id: PATO:0000403
name: cleft
+subset: value_slim
is_a: PATO:0000052 ! shape
[Term]
id: PATO:0000404
name: coiled
+subset: value_slim
is_a: PATO:0000052 ! shape
[Term]
id: PATO:0000405
name: curled
-def: "A shape quality of having parallel chains in undulate fashion on the border." [XX:<new dbxref>]
+def: "A shape quality of having parallel chains in undulate fashion on the border." [PATO:]
+subset: value_slim
is_a: PATO:0000052 ! shape
[Term]
id: PATO:0000406
name: curved
+def: "A shape quality inhering in a bearer by virtue of having or marked by a curve or smoothly rounded bend" [WordNet :WordNet "http://wordnet.princeton.edu/"]
+subset: value_slim
related_synonym: "curled" []
is_a: PATO:0000052 ! shape
@@ -2125,46 +2247,55 @@
id: PATO:0000407
name: flat
def: "A shape lacking depth." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000052 ! shape
[Term]
id: PATO:0000408
name: globular
+subset: value_slim
is_a: PATO:0000052 ! shape
[Term]
id: PATO:0000409
name: oblate
+subset: value_slim
is_a: PATO:0000052 ! shape
[Term]
id: PATO:0000410
name: pinnate
+subset: value_slim
is_a: PATO:0000052 ! shape
[Term]
id: PATO:0000411
name: round
+subset: value_slim
is_a: PATO:0000052 ! shape
[Term]
id: PATO:0000412
name: shrunken
+subset: value_slim
is_a: PATO:0000052 ! shape
[Term]
id: PATO:0000413
name: square
+subset: value_slim
is_a: PATO:0000052 ! shape
[Term]
id: PATO:0000414
name: unbranched
+subset: value_slim
is_a: PATO:0000052 ! shape
[Term]
id: PATO:0000415
name: uncoiled
+subset: value_slim
is_a: PATO:0000052 ! shape
[Term]
@@ -2185,11 +2316,13 @@
[Term]
id: PATO:0000419
name: decreased number
+subset: value_slim
is_a: PATO:0000053 ! count
[Term]
id: PATO:0000420
name: increased number
+subset: value_slim
is_a: PATO:0000053 ! count
[Term]
@@ -2200,11 +2333,13 @@
[Term]
id: PATO:0000422
name: auxotroph
+subset: value_slim
is_a: PATO:0000056 ! nutritional
[Term]
id: PATO:0000423
name: prototroph
+subset: value_slim
is_a: PATO:0000056 ! nutritional
[Term]
@@ -2220,21 +2355,25 @@
[Term]
id: PATO:0000426
name: interrupted
+subset: value_slim
is_a: PATO:0000057 ! occurrence
[Term]
id: PATO:0000427
name: recurrent
+subset: value_slim
is_a: PATO:0000057 ! occurrence
[Term]
id: PATO:0000428
name: sporadic
+subset: value_slim
is_a: PATO:0000057 ! occurrence
[Term]
id: PATO:0000429
name: uninterrupted
+subset: value_slim
is_a: PATO:0000057 ! occurrence
[Term]
@@ -2255,11 +2394,13 @@
[Term]
id: PATO:0000433
name: paternal
+subset: value_slim
is_a: PATO:0000059 ! parental type
[Term]
id: PATO:0000434
name: maternal
+subset: value_slim
is_a: PATO:0000059 ! parental type
[Term]
@@ -2281,7 +2422,9 @@
id: PATO:0000438
name: invariant
def: "The state of not having or exhibiting variation." [Dictionary:http\://dictionary.reference.com/]
+subset: value_slim
related_synonym: "constant" []
+exact_synonym: "uniform" []
is_a: PATO:0001303 ! variability
[Term]
@@ -2293,21 +2436,25 @@
id: PATO:0000440
name: regular
def: "A physical quality inhering in a bearer by virtue of having pattern." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000060 ! pattern
[Term]
id: PATO:0000441
name: repetitive
+subset: value_slim
is_a: PATO:0000057 ! occurrence
[Term]
id: PATO:0000442
name: insomnia
+subset: value_slim
is_a: PATO:0000062 ! sleep pattern
[Term]
id: PATO:0000443
name: narcolepsy
+subset: value_slim
is_a: PATO:0000062 ! sleep pattern
[Term]
@@ -2359,17 +2506,20 @@
id: PATO:0000453
name: glabrous
def: "A pilosity quality of having no hairs, projections, or pubescence" [PATO :GVG]
+subset: value_slim
is_a: PATO:0000066 ! pilosity
[Term]
id: PATO:0000454
name: hairy
def: "A pilosity quality of being covered with hair or hairlike projections" [PATO :GVG]
+subset: value_slim
is_a: PATO:0000066 ! pilosity
[Term]
id: PATO:0000455
name: pubescent
+subset: value_slim
is_a: PATO:0000261 ! maturity
[Term]
@@ -2395,33 +2545,38 @@
[Term]
id: PATO:0000460
name: abnormal
+subset: abnormal_slim
+subset: value_slim
related_synonym: "aberrant" []
related_synonym: "atypical" []
related_synonym: "defective" []
is_a: PATO:0000069 ! deviation(from_normal)
-subset: abnormal_slim
[Term]
id: PATO:0000461
name: normal
+subset: abnormal_slim
+subset: value_slim
related_synonym: "average" []
is_a: PATO:0000069 ! deviation(from_normal)
-subset: abnormal_slim
[Term]
id: PATO:0000462
name: absent
+subset: absent_slim
+subset: value_slim
is_a: PATO:0000070 ! presence
-subset: absent_slim
[Term]
id: PATO:0000463
name: conspicuous
+subset: value_slim
is_a: PATO:0000070 ! presence
[Term]
id: PATO:0000464
name: inconspicuous
+subset: value_slim
is_a: PATO:0000070 ! presence
[Term]
@@ -2437,12 +2592,15 @@
[Term]
id: PATO:0000467
name: present
+subset: absent_slim
+subset: value_slim
is_a: PATO:0000070 ! presence
-subset: absent_slim
[Term]
id: PATO:0000468
name: decreased
+subset: value_slim
+related_synonym: "reduced" []
is_a: PATO:0000071 ! relative_quantity
[Term]
@@ -2453,6 +2611,7 @@
[Term]
id: PATO:0000470
name: increased
+subset: value_slim
is_a: PATO:0000071 ! relative_quantity
[Term]
@@ -2539,12 +2698,14 @@
id: PATO:0000487
name: responsive
def: "A quality inhering in a bearer by virtue of \nthe presence of its reaction to a stimulus or an agent." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000077 ! response
[Term]
id: PATO:0000488
name: unresponsive
def: "A quality inhering in a bearer by virtue of \nthe lack of its reaction to a stimulus or an agent." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000077 ! response
[Term]
@@ -2595,44 +2756,51 @@
[Term]
id: PATO:0000498
name: prolonged period
+subset: value_slim
is_a: PATO:0000081 ! period
[Term]
id: PATO:0000499
name: shortened period
+subset: value_slim
is_a: PATO:0000081 ! period
[Term]
id: PATO:0000500
name: advanced
+subset: value_slim
is_a: PATO:0000083 ! phase
[Term]
id: PATO:0000501
name: dark phase
+subset: value_slim
is_a: PATO:0000083 ! phase
[Term]
id: PATO:0000502
name: delayed
-def: "A duration in which process ends before natural\nstart point." [XX:<new dbxref>]
+def: "A duration in which process ends before natural start point." [PATO:GVG]
+subset: value_slim
related_synonym: "late" []
-is_a: PATO:0000083 ! phase
is_a: PATO:0001309 ! duration
[Term]
id: PATO:0000503
name: light phase
+subset: value_slim
is_a: PATO:0000083 ! phase
[Term]
id: PATO:0000504
name: arrhythmic
+subset: value_slim
is_a: PATO:0000078 ! rhythm
[Term]
id: PATO:0000505
name: rhythmic
+subset: value_slim
is_a: PATO:0000078 ! rhythm
[Term]
@@ -2674,6 +2842,7 @@
id: PATO:0000513
name: insensitive
def: "A quality of lacking sensitivity." [XX:<new dbxref>]
+subset: value_slim
related_synonym: "resistant" []
is_a: PATO:0000085 ! sensitivity
@@ -2686,12 +2855,14 @@
id: PATO:0000515
name: tolerant
def: "A resistance quality inhering in a bearer by virtue of its ability to tolarete or being insensitive to a stimulus." [PATO :GVG]
+subset: value_slim
is_a: PATO:0001046 ! resistance
[Term]
id: PATO:0000516
name: sensitive
def: "A quality of having sensitivity." [XX:<new dbxref>]
+subset: value_slim
is_a: PATO:0000085 ! sensitivity
[Term]
@@ -2961,12 +3132,14 @@
id: PATO:0000569
name: short height
def: "A height which is relative high." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000119 ! height
[Term]
id: PATO:0000570
name: tall height
def: "A height which is relative small." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000119 ! height
[Term]
@@ -2983,12 +3156,14 @@
id: PATO:0000573
name: long length
def: "A length which is relative large." [XX:<new dbxref>]
+subset: value_slim
is_a: PATO:0000122 ! length
[Term]
id: PATO:0000574
name: short length
def: "A length which is relative small." [XX:<new dbxref>]
+subset: value_slim
related_synonym: "shortened" []
related_synonym: "stubby" []
is_a: PATO:0000122 ! length
@@ -3012,12 +3187,14 @@
id: PATO:0000578
name: large mass
def: "A mass which is relative large." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000125 ! mass
[Term]
id: PATO:0000579
name: small mass
def: "A mass which is relative small." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000125 ! mass
[Term]
@@ -3034,32 +3211,35 @@
id: PATO:0000582
name: heavy
def: "A weight which is relative high." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000128 ! weight
[Term]
id: PATO:0000583
name: light weight
def: "A weight which is relative low." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000128 ! weight
[Term]
id: PATO:0000584
name: hypertrophic
def: "A size quality inhering in a bearer by virtue of its exhibiting hypertrophy (enlargement or overgrowth of an organ or part of the body due to increased size of the constituent cells)." [MedTerms:MedTerms "www.medterms.com/"]
+subset: value_slim
is_a: PATO:0000117 ! size
-is_a: PATO:0000141 ! structure
[Term]
id: PATO:0000585
name: hypotrophic
def: "A size quality inhering in a bearer by virtue of the progressive degeneration of an organ or tissue caused by loss of cells." [The free dictionary:The free dictionary "www.thefreedictionary.com/"]
+subset: value_slim
is_a: PATO:0000117 ! size
-is_a: PATO:0000141 ! structure
[Term]
id: PATO:0000586
name: large size
def: "A size which is greater relative to the normal or average." [PATO :GVG]
+subset: value_slim
related_synonym: "big" []
related_synonym: "enlarged" []
related_synonym: "great" []
@@ -3069,12 +3249,14 @@
id: PATO:0000587
name: small size
def: "A size which is lesser relative to the normal or average." [PATO :GVG]
+subset: value_slim
related_synonym: "tiny" []
is_a: PATO:0000117 ! size
[Term]
id: PATO:0000588
name: vestigial
+subset: value_slim
is_a: PATO:0000117 ! size
[Term]
@@ -3091,12 +3273,14 @@
id: PATO:0000591
name: thick
def: "A thickness which is relative low" [PATO :GVG]
+subset: value_slim
is_a: PATO:0000915 ! thickness
[Term]
id: PATO:0000592
name: thin
def: "A thickness which is relative low" [PATO :GVG]
+subset: value_slim
is_a: PATO:0000915 ! thickness
[Term]
@@ -3113,12 +3297,14 @@
id: PATO:0000595
name: large volume
def: "A volume which is relative high." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000918 ! volume
[Term]
id: PATO:0000596
name: small volume
def: "A volume which is relative low." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000918 ! volume
[Term]
@@ -3135,12 +3321,14 @@
id: PATO:0000599
name: narrow
def: "A width which is relative small." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000921 ! width
[Term]
id: PATO:0000600
name: wide
def: "A width which is relative large." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000921 ! width
[Term]
@@ -3183,17 +3371,20 @@
[Term]
id: PATO:0000608
name: closed
+subset: value_slim
related_synonym: "blocked" []
is_a: PATO:0000136 ! closure
[Term]
id: PATO:0000609
name: closure incomplete
+subset: value_slim
is_a: PATO:0000136 ! closure
[Term]
id: PATO:0000610
name: open
+subset: value_slim
is_a: PATO:0000136 ! closure
[Term]
@@ -3209,69 +3400,81 @@
[Term]
id: PATO:0000613
name: disoriented
+subset: value_slim
is_a: PATO:0000137 ! orientation
[Term]
id: PATO:0000614
name: oriented
+subset: value_slim
is_a: PATO:0000137 ! orientation
[Term]
id: PATO:0000615
name: anterioralized
+subset: value_slim
is_a: PATO:0000140 ! placement
[Term]
id: PATO:0000616
name: asymmetrical
def: "A symmetry quality inhering in a bearer by virtue of lacking symmetry." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000965 ! symmetry
[Term]
id: PATO:0000617
name: bent
+subset: value_slim
is_a: PATO:0000140 ! placement
[Term]
id: PATO:0000618
name: bilateral
+subset: value_slim
is_a: PATO:0000140 ! placement
[Term]
id: PATO:0000619
name: crowded
+subset: value_slim
is_a: PATO:0000140 ! placement
[Term]
id: PATO:0000620
name: dorsalized
+subset: value_slim
is_a: PATO:0000140 ! placement
[Term]
id: PATO:0000621
name: ectopic
+subset: value_slim
is_a: PATO:0000140 ! placement
-is_a: PATO:0000141 ! structure
[Term]
id: PATO:0000622
name: erect
+subset: value_slim
is_a: PATO:0000140 ! placement
[Term]
id: PATO:0000623
name: exserted
+subset: value_slim
is_a: PATO:0000140 ! placement
[Term]
id: PATO:0000624
name: inserted
+subset: value_slim
is_a: PATO:0000140 ! placement
[Term]
id: PATO:0000625
name: inverted
def: "to be completely turned about in position or direction" [PATO :GVG]
+subset: value_slim
exact_synonym: "backward" []
exact_synonym: "reversed" []
is_a: PATO:0000140 ! placement
@@ -3279,57 +3482,68 @@
[Term]
id: PATO:0000626
name: lateralized
+subset: value_slim
is_a: PATO:0000140 ! placement
[Term]
id: PATO:0000627
name: localised
+subset: value_slim
is_a: PATO:0000140 ! placement
[Term]
id: PATO:0000628
name: mislocalised
+subset: value_slim
is_a: PATO:0000140 ! placement
[Term]
id: PATO:0000629
name: misrouted
+subset: value_slim
is_a: PATO:0000140 ! placement
[Term]
id: PATO:0000630
name: posterioralized
+subset: value_slim
is_a: PATO:0000140 ! placement
[Term]
id: PATO:0000631
name: prostrate
+subset: value_slim
is_a: PATO:0000140 ! placement
[Term]
id: PATO:0000632
name: symmetrical
def: "A symmetry quality inhering in a bearer by virtue of having symmetry." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000965 ! symmetry
[Term]
id: PATO:0000633
name: uncrowded
+subset: value_slim
is_a: PATO:0000140 ! placement
[Term]
id: PATO:0000634
name: unilateral
+subset: value_slim
is_a: PATO:0000140 ! placement
[Term]
id: PATO:0000635
name: unlocalised
+subset: value_slim
is_a: PATO:0000140 ! placement
[Term]
id: PATO:0000636
name: ventralized
+subset: value_slim
is_a: PATO:0000140 ! placement
[Term]
@@ -3340,16 +3554,19 @@
[Term]
id: PATO:0000638
name: apoptotic
+subset: value_slim
is_a: PATO:0000141 ! structure
[Term]
id: PATO:0000639
name: degenerate
+subset: value_slim
is_a: PATO:0000141 ! structure
[Term]
id: PATO:0000640
name: dysplastic
+subset: value_slim
is_a: PATO:0000141 ! structure
[Term]
@@ -3360,52 +3577,62 @@
[Term]
id: PATO:0000642
name: fused
+subset: value_slim
is_a: PATO:0000141 ! structure
[Term]
id: PATO:0000643
name: herniated
+subset: value_slim
is_a: PATO:0000141 ! structure
[Term]
id: PATO:0000644
name: hyperplastic
+subset: value_slim
is_a: PATO:0000141 ! structure
[Term]
id: PATO:0000645
name: hypoplastic
+subset: value_slim
is_a: PATO:0000141 ! structure
[Term]
id: PATO:0000646
name: malformed
+subset: value_slim
is_a: PATO:0000141 ! structure
[Term]
id: PATO:0000647
name: necrotic
-def: "A viability quality inhering in a bearer by virtue of unprogrammed cell death. " [Wikipedia:Wikipedia "http://www.wikipedia.org/"]
+def: "A viability quality inhering in a bearer by virtue of unprogrammed cell death." [Wikipedia:Wikipedia "http://www.wikipedia.org/"]
+subset: value_slim
is_a: PATO:0000169 ! viability
[Term]
id: PATO:0000648
name: obstructed
+subset: value_slim
is_a: PATO:0000141 ! structure
[Term]
id: PATO:0000649
name: perforated
+subset: value_slim
is_a: PATO:0000141 ! structure
[Term]
id: PATO:0000650
name: supernumerary
+subset: value_slim
is_a: PATO:0000053 ! count
[Term]
id: PATO:0000651
name: unfused
+subset: value_slim
is_a: PATO:0000141 ! structure
[Term]
@@ -3476,6 +3703,7 @@
[Term]
id: PATO:0000665
name: light
+subset: value_slim
is_a: PATO:0000016 ! color brightness
[Term]
@@ -3537,12 +3765,14 @@
id: PATO:0000677
name: cold
def: "A temperature which is relative low" [gg:]
+subset: value_slim
is_a: PATO:0000146 ! temperature
[Term]
id: PATO:0000678
name: hot
def: "A temperature which is relative high." [gg:]
+subset: value_slim
is_a: PATO:0000146 ! temperature
[Term]
@@ -3593,16 +3823,19 @@
[Term]
id: PATO:0000688
name: asynchronous
+subset: value_slim
is_a: PATO:0000156 ! temporal
[Term]
id: PATO:0000689
name: continuous
+subset: value_slim
is_a: PATO:0000156 ! temporal
[Term]
id: PATO:0000690
name: discontinuous
+subset: value_slim
is_a: PATO:0000156 ! temporal
[Term]
@@ -3613,6 +3846,7 @@
[Term]
id: PATO:0000692
name: heterochronic
+subset: value_slim
is_a: PATO:0000156 ! temporal
[Term]
@@ -3623,13 +3857,15 @@
[Term]
id: PATO:0000694
name: premature
-def: "A duration in which the process starts before natural start point. " [XX:<new dbxref>]
+def: "A duration in which the process starts before natural start point." [XX:<new dbxref>]
+subset: value_slim
related_synonym: "early" []
is_a: PATO:0001309 ! duration
[Term]
id: PATO:0000695
name: synchronous
+subset: value_slim
is_a: PATO:0000156 ! temporal
[Term]
@@ -3655,13 +3891,15 @@
[Term]
id: PATO:0000700
name: rough
-def: "A texture quality inhering in a bearer by virtue of its irregular surface.\n" [PATO :GVG]
+def: "A texture quality inhering in a bearer by virtue of its irregular surface." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000150 ! texture
[Term]
id: PATO:0000701
name: smooth
def: "A texture quality inhering in a bearer by virtue of pocessing a surface free of roughness or irregularities." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000150 ! texture
[Term]
@@ -3687,21 +3925,25 @@
[Term]
id: PATO:0000706
name: increased threshold
+subset: value_slim
is_a: PATO:0000152 ! threshold
[Term]
id: PATO:0000707
name: low threshold
+subset: value_slim
is_a: PATO:0000152 ! threshold
[Term]
id: PATO:0000708
name: decreased threshold
+subset: value_slim
is_a: PATO:0000152 ! threshold
[Term]
id: PATO:0000709
name: high threshold
+subset: value_slim
is_a: PATO:0000152 ! threshold
[Term]
@@ -3732,11 +3974,13 @@
[Term]
id: PATO:0000715
name: fast
+subset: value_slim
is_a: PATO:0000165 ! time
[Term]
id: PATO:0000716
name: slow
+subset: value_slim
is_a: PATO:0000165 ! time
[Term]
@@ -3748,12 +3992,14 @@
id: PATO:0000718
name: lethal (sensu genetics)
def: "A viability quality inhering in a bearer or a population by virtue of the bearer's inability to survive and develop normally or the long term survival inability of a given population." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000169 ! viability
[Term]
id: PATO:0000719
name: viable
def: "A viability quality inhering in a bearer or a population by virtue of the bearer's ability to survive and develop normally or the long term survival ability of a given population." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000169 ! viability
[Term]
@@ -3944,41 +4190,49 @@
[Term]
id: PATO:0000757
name: balanced
+subset: value_slim
is_a: PATO:0000185 ! balance
[Term]
id: PATO:0000758
name: unbalanced
+subset: value_slim
is_a: PATO:0000185 ! balance
[Term]
id: PATO:0000759
name: bang sensitive
+subset: value_slim
is_a: PATO:0000186 ! behavioral quality
[Term]
id: PATO:0000760
name: hyperactive
-is_a: PATO:0000186 ! behavioral quality
+subset: value_slim
+is_a: PATO:0001530 ! behavioral quality of occurent
[Term]
id: PATO:0000761
name: hypoactive
-is_a: PATO:0000186 ! behavioral quality
+subset: value_slim
+is_a: PATO:0001530 ! behavioral quality of occurent
[Term]
id: PATO:0000762
name: impaired
+subset: value_slim
is_a: PATO:0000186 ! behavioral quality
[Term]
id: PATO:0000763
name: paralysed
+subset: value_slim
is_a: PATO:0000186 ! behavioral quality
[Term]
id: PATO:0000764
name: passive
+subset: value_slim
is_a: PATO:0000186 ! behavioral quality
[Term]
@@ -3995,42 +4249,49 @@
id: PATO:0000767
name: increased consumption
def: "A consumption which is relative high." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000187 ! consumption
[Term]
id: PATO:0000768
name: decreased consumption
def: "A consumption which is relative low." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000187 ! consumption
[Term]
id: PATO:0000769
name: coordinated
def: "A coordination quality of having skilful and effective interaction of movement." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000188 ! coordination
[Term]
id: PATO:0000770
name: uncoordinated
def: "A coordination quality of lacking skilful and effective interaction of movement." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000188 ! coordination
[Term]
id: PATO:0000771
name: aversion
def: "A preference quality of disliking a perceived stimulus." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000773 ! preference
[Term]
id: PATO:0000772
name: indifference
def: "A preference quality of having no preference to a perceived stimulus." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000773 ! preference
[Term]
id: PATO:0000773
name: preference
def: "A discrimination quality of liking a perceived stimulus." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0000189 ! discrimination
[Term]
@@ -4607,6 +4868,7 @@
id: PATO:0000888
name: female fertile
def: "A female fertility quality of being capable of initiating, sustaining, or supporting reproduction." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000277 ! female fertility
[Term]
@@ -4618,6 +4880,7 @@
id: PATO:0000890
name: male sterile
def: "A male fertility quality of being incapable of initiating, sustaining, or supporting reproduction." [PATO :GVG]
+subset: value_slim
related_synonym: "male infertile" []
is_a: PATO:0000279 ! male fertility
@@ -4625,12 +4888,14 @@
id: PATO:0000891
name: male fertile
def: "A male fertility quality of being capable of initiating, sustaining, or supporting reproduction." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000279 ! male fertility
[Term]
id: PATO:0000892
name: female sterile
def: "A female fertility quality of being incapable of initiating, sustaining, or supporting reproduction." [PATO :GVG]
+subset: value_slim
related_synonym: "female infertile" []
is_a: PATO:0000277 ! female fertility
@@ -4730,12 +4995,16 @@
[Term]
id: PATO:0000911
-name: slow rate
+name: decreased rate
+subset: value_slim
+exact_synonym: "slow rate" []
is_a: PATO:0000161 ! rate
[Term]
id: PATO:0000912
-name: fast rate
+name: increased rate
+subset: value_slim
+exact_synonym: "fast rate" []
is_a: PATO:0000161 ! rate
[Term]
@@ -4752,6 +5021,7 @@
id: PATO:0000915
name: thickness
def: "A physical quality which is equal to the dimension through an object as opposed to its length or width." [WordNet:WordNet "wordnet.princeton.edu/"]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
@@ -4768,6 +5038,7 @@
id: PATO:0000918
name: volume
def: "A physical quality of the amount of 3-dimensional space an object occupies." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
@@ -4783,7 +5054,8 @@
[Term]
id: PATO:0000921
name: width
-def: "A physical quality which is equal to the distance from one side of an object to another side which is opposite. \n\n" [PATO :GVG]
+def: "A physical quality which is equal to the distance from one side of an object to another side which is opposite." [PATO :GVG]
+subset: attribute_slim
related_synonym: "breadth" []
is_a: PATO:0001018 ! physical quality
@@ -4860,16 +5132,19 @@
[Term]
id: PATO:0000936
name: truncated
+subset: value_slim
is_a: PATO:0000141 ! structure
[Term]
id: PATO:0000937
name: disorganized
+subset: value_slim
is_a: PATO:0000141 ! structure
[Term]
id: PATO:0000938
name: organized
+subset: value_slim
is_a: PATO:0000141 ! structure
[Term]
@@ -4885,98 +5160,115 @@
[Term]
id: PATO:0000941
name: vacuolated
+subset: value_slim
is_a: PATO:0000141 ! structure
[Term]
id: PATO:0000942
name: underdeveloped
+subset: value_slim
is_a: PATO:0000141 ! structure
[Term]
id: PATO:0000943
name: overdeveloped
+subset: value_slim
is_a: PATO:0000141 ! structure
[Term]
id: PATO:0000944
name: pointed
def: "A sharp or tapered end" [PATO :GVG]
+subset: value_slim
is_a: PATO:0000052 ! shape
[Term]
id: PATO:0000945
name: epinastic
def: "A downward bending of leaves or other plant parts." [PATO:gg]
+subset: value_slim
is_a: PATO:0000052 ! shape
[Term]
id: PATO:0000946
name: oblong
def: "Having a somewhat elongated form with approximately parallel sides" [PATO:gg]
+subset: value_slim
is_a: PATO:0000052 ! shape
[Term]
id: PATO:0000947
name: elliptic
def: "Elliptic shape" [PATO:gg]
+subset: value_slim
is_a: PATO:0000052 ! shape
[Term]
id: PATO:0000948
name: heart shaped
+subset: value_slim
is_a: PATO:0000052 ! shape
[Term]
id: PATO:0000949
name: fasciated
def: "Abnormally flattened or coalesced." [PATO:gg]
+subset: value_slim
is_a: PATO:0000052 ! shape
[Term]
id: PATO:0000950
name: grey
def: "A color that lacks saturation." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000014 ! color
[Term]
id: PATO:0000951
name: purple
def: "A colour that falls about midway between red and blue in hue" [Dictionary:http\://dictionary.reference.com/]
+subset: value_slim
is_a: PATO:0000014 ! color
[Term]
id: PATO:0000952
name: brown
+subset: value_slim
is_a: PATO:0000014 ! color
[Term]
id: PATO:0000953
name: orange
def: "A color hue with high-medium wavelengththat of that portion of the visible spectrum lying between red and yellow, evoked in the human observer by radiant energy with wavelengths of approximately 585 to 620 nanometers" [Wikipedia:Wikipedia "http://www.wikipedia.org/"]
+subset: value_slim
is_a: PATO:0000014 ! color
[Term]
id: PATO:0000954
name: pink
def: "A composite color with parts\nhigh redness, low blueness, high brightness and low\nsaturation" [PATO :GVG]
+subset: value_slim
is_a: PATO:0000014 ! color
[Term]
id: PATO:0000955
name: fertile
def: "A fertility quality of being capable of initiating, sustaining, or supporting reproduction." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000274 ! fertility
[Term]
id: PATO:0000956
name: sterile
def: "A fertility quality of being incapable of initiating, sustaining, or supporting reproduction." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000274 ! fertility
[Term]
id: PATO:0000957
name: opacity
def: "An optical quality which obtains by virtue\nof the ability of the bearer to absorb visible light" [PATO:gg]
+subset: attribute_slim
is_a: PATO:0001300 ! optical quality
[Term]
@@ -5008,12 +5300,14 @@
id: PATO:0000963
name: opaque
def: "Not clear; not transmitting or reflecting light or radiant energy" [PATO:gg]
+subset: value_slim
exact_synonym: "non-transparent" []
is_a: PATO:0000957 ! opacity
[Term]
id: PATO:0000964
name: transparent
+subset: value_slim
exact_synonym: "clear" []
is_a: PATO:0000957 ! opacity
@@ -5021,6 +5315,7 @@
id: PATO:0000965
name: symmetry
def: "A pattern quality of correspondence in size, shape, and relative position of parts on opposite sides of a dividing line or median plane or about a center or axis." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0000060 ! pattern
[Term]
@@ -5032,6 +5327,7 @@
id: PATO:0000967
name: undulate
def: "Having a sinuate margin and rippled surface." [PATO:gg]
+subset: value_slim
is_a: PATO:0000052 ! shape
[Term]
@@ -5042,12 +5338,14 @@
[Term]
id: PATO:0000969
name: dwarf
+subset: value_slim
is_a: PATO:0000117 ! size
[Term]
id: PATO:0000970
name: permeability
def: "A structure quality of being cabapble of being permeated or pervaded by a liquid (as by osmosis or diffusion)." [Biology-online :Biology-online "http://www.biology-online.org/"]
+subset: attribute_slim
is_a: PATO:0000141 ! structure
[Term]
@@ -5063,7 +5361,8 @@
[Term]
id: PATO:0000973
name: porosity
-def: "A perneability quality of admitting the passage of gas or liquid through pores or interstices." [PATO:gg]
+def: "A perneability quality of admitting the passage of gas or liquid through pores or interstices." [PATO:]
+subset: attribute_slim
is_a: PATO:0000970 ! permeability
[Term]
@@ -5110,24 +5409,28 @@
id: PATO:0000982
name: permeable
def: "A quality of being capable to be permeated or pervaded by a liquid (as by osmosis or diffusion)." [Biology-online :Biology-online "http://www.biology-online.org/"]
+subset: value_slim
is_a: PATO:0000970 ! permeability
[Term]
id: PATO:0000983
name: impermeable
def: "A permeability quality of being incapable of being permeated or pervaded by a liquid (as by osmosis or diffusion)." [Biology-online :Biology-online "http://www.biology-online.org/"]
+subset: value_slim
is_a: PATO:0000970 ! permeability
[Term]
id: PATO:0000984
name: porous
def: "A quality of being capable of admitting the passage of gas or liquid through pores or interstices." [PATO:GVG]
+subset: value_slim
is_a: PATO:0000973 ! porosity
[Term]
id: PATO:0000985
name: nonporous
def: "A quality of being incapable of admitting the passage of gas or liquid through pores or interstices." [PATO:GVG]
+subset: value_slim
is_a: PATO:0000973 ! porosity
[Term]
@@ -5164,6 +5467,7 @@
id: PATO:0000992
name: viscosity
def: "A physical quality of fluids describing their internal resistance to flow" [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
@@ -5195,11 +5499,13 @@
id: PATO:0000998
name: viscous
def: "A viscosity which relative high." [PATO :GVG]
+subset: value_slim
is_a: PATO:0000992 ! viscosity
[Term]
id: PATO:0000999
name: alternation
+subset: value_slim
is_a: PATO:0001226 ! quantitative
[Term]
@@ -5231,6 +5537,7 @@
id: PATO:0001005
name: latency
def: "The time that elapses between a stimulus and the response to it" [PATO:gg]
+subset: attribute_slim
is_a: PATO:0000165 ! time
[Term]
@@ -5297,53 +5604,62 @@
id: PATO:0001018
name: physical quality
def: "A quality that exists through action of continuants at the physical level of organisation" [PATO:GVG]
+subset: attribute_slim
is_a: PATO:0001237 ! monadic quality of continuant
[Term]
id: PATO:0001019
name: density
def: "A physical quality which inhers to the bearer by virtue of some influence exerted by its mass." [Wikipedia:Wikipedia "http://en.wikipedia.org/"]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
id: PATO:0001020
name: damage
+subset: attribute_slim
is_a: PATO:0001237 ! monadic quality of continuant
[Term]
id: PATO:0001021
name: energy
def: "A physical quality inhering in a bearer by virtue of its capacity to do work." [Wikipedia:Wikipedia "http://en.wikipedia.org/"]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
id: PATO:0001022
name: impulse
def: "A physical quality inhering in a bearer by virtue of the change in its momentum." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
id: PATO:0001023
name: momentum
-def: "A physical quality inhering in a bearer by \nvirtue of its velocity multiplied by its mass\n" [PATO :GVG]
+def: "A physical quality inhering in a bearer by \nvirtue of its velocity multiplied by its mass" [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
id: PATO:0001024
name: power
def: "A physical quality inhering in a object by virtue of the rate of doing work." [Wikipedia:Wikipedia "http://en.wikipedia.org/"]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
id: PATO:0001025
name: pressure
def: "A physical quality that inheres in a bearer in proportion to the amount of force per unit area it exerts." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
id: PATO:0001026
name: work
def: "A physical quality which is equal to the energy transferred by a force to a moving object." [Wikipedia:Wikipedia "http://www.wikipedia.org/"]
+subset: attribute_slim
exact_synonym: "W" []
is_a: PATO:0001018 ! physical quality
@@ -5355,33 +5671,38 @@
[Term]
id: PATO:0001028
name: acceleration
-def: "A physical quality inhering in a bearer by \nvirtue of therate of change of its velocity in either speed or direction." [Wikipedia:Wikipedia "http://www.wikipedia.org/"]
+def: "A physical quality inhering in a bearer by virtue of therate of change of its velocity in either speed or direction." [Wikipedia:Wikipedia "http://www.wikipedia.org/"]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
id: PATO:0001029
name: efficiency
def: "A physical quality inhering in a bearer by \nvirtue of ratio of the output to the input." [WordNet :WordNet "wordnet.princeton.edu/"]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
id: PATO:0001030
name: flux
def: "A physical quality that exists by virtue of the amount of flow per unit time." [PATO :GVG]
-is_a: PATO:0001018 ! physical quality
+subset: attribute_slim
+is_a: PATO:0000156 ! temporal
[Term]
id: PATO:0001031
name: elasticity
-def: "A physical quality inhering in a bearer by \nvirtue of the ratio of its extension to its original length. " [PATO :GVG]
+def: "A physical quality inhering in a bearer by \nvirtue of the ratio of its extension to its original length." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
id: PATO:0001032
name: position
def: "The particular portion of space occupied by a physical object." [XX:<new dbxref>]
+subset: attribute_slim
related_synonym: "location" []
-is_a: PATO:0001018 ! physical quality
+is_a: PATO:0000132 ! spatial
[Term]
id: PATO:0001033
@@ -5392,12 +5713,14 @@
id: PATO:0001034
name: strain
def: "A physical quality inhering in a bearer by \nvirtue of the relative change in its length or its volume when being stretched or squashed." [PATO :GVG]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
id: PATO:0001035
name: force
def: "A physical quality inhering in a object affecting its acceleration." [: "http://thesaurus.maths.org/"]
+subset: attribute_slim
is_a: PATO:0001018 ! physical quality
[Term]
@@ -5438,6 +5761,7 @@
[Term]
id: PATO:0001043
name: susceptibility
+subset: attribute_slim
is_a: PATO:0000085 ! sensitivity
[Term]
@@ -5454,6 +5778,7 @@
id: PATO:0001046
na...
[truncated message content] |
|
From: <cmu...@us...> - 2007-01-20 03:18:07
|
Revision: 302
http://svn.sourceforge.net/obo/?rev=302&view=rev
Author: cmungall
Date: 2007-01-19 19:18:08 -0800 (Fri, 19 Jan 2007)
Log Message:
-----------
Modified Paths:
--------------
obolog/trunk/README
Modified: obolog/trunk/README
===================================================================
--- obolog/trunk/README 2007-01-20 03:17:34 UTC (rev 301)
+++ obolog/trunk/README 2007-01-20 03:18:08 UTC (rev 302)
@@ -30,4 +30,5 @@
example, for detecting certain classes of inconsistency, converting to
DL or EL++ may be fine. For instance-level reasoning, it may be
necessary to transform to rows in a relational database (and lose
-certain semantics in order to gain reasonable performance)
+certain semantics in order to gain reasonable performance). For a
+balance between these, a prolog toolkit like blipkit may be used
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <cmu...@us...> - 2007-01-20 03:17:33
|
Revision: 301
http://svn.sourceforge.net/obo/?rev=301&view=rev
Author: cmungall
Date: 2007-01-19 19:17:34 -0800 (Fri, 19 Jan 2007)
Log Message:
-----------
Modified Paths:
--------------
obolog/trunk/obolog.lisp
Modified: obolog/trunk/obolog.lisp
===================================================================
--- obolog/trunk/obolog.lisp 2007-01-20 03:14:36 UTC (rev 300)
+++ obolog/trunk/obolog.lisp 2007-01-20 03:17:34 UTC (rev 301)
@@ -23,9 +23,11 @@
(subrelation ?x ?z))
;; universal-level relations
-;; we specify this as (link ?rel ?C1 ?C2)
-;; this is a bit ugly, but we do want to write (?rel ?C1 ?C2) as we
-;; take this to mean an instance-level relation
+;; we specify these as (link ?rel ?C1 ?C2)
+;; this is a bit ugly, but we don't want to write (?rel ?C1 ?C2) as we
+;; take this to mean an instance-level relation. Since we use
+;; the same identifiers for instance and universal level relations
+;; we have to distinguish them at the relation instantiation level
;; (all_some_all_times ?relation)
;; EXAMPLE: (all_some_all_times part_of) (link part_of cell_nucleus cell)
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|
|
From: <cmu...@us...> - 2007-01-20 03:14:35
|
Revision: 300
http://svn.sourceforge.net/obo/?rev=300&view=rev
Author: cmungall
Date: 2007-01-19 19:14:36 -0800 (Fri, 19 Jan 2007)
Log Message:
-----------
Modified Paths:
--------------
obolog/trunk/README
obolog/trunk/obolog.lisp
Modified: obolog/trunk/README
===================================================================
--- obolog/trunk/README 2007-01-20 02:48:01 UTC (rev 299)
+++ obolog/trunk/README 2007-01-20 03:14:36 UTC (rev 300)
@@ -21,3 +21,13 @@
At the moment there are only 2 proofs - one for universal-level
relations (called "links" in obo-ese for now) and one for
instance-level relations
+
+=== WHY??? ===
+
+Yes, OWL is far more computable, but it is important to state
+reference ontologies in an unambiguous way. This task is orthogonal to
+computing over ontologies/data for a particular application. For
+example, for detecting certain classes of inconsistency, converting to
+DL or EL++ may be fine. For instance-level reasoning, it may be
+necessary to transform to rows in a relational database (and lose
+certain semantics in order to gain reasonable performance)
Modified: obolog/trunk/obolog.lisp
===================================================================
--- obolog/trunk/obolog.lisp 2007-01-20 02:48:01 UTC (rev 299)
+++ obolog/trunk/obolog.lisp 2007-01-20 03:14:36 UTC (rev 300)
@@ -2,37 +2,19 @@
;; upper case for universals, lower case for instances
;; - but remember, most KIF implementations are case insenstivite
-;; -- OBO Relation Ontology --
-
-;; additional formulae that cannot be extracted from obo format
-
-;; OBO_REL:part_of
-;; make this implicit in obo-format?
-(all_some_all_times "OBO_REL:part_of")
-
-;; part_of holds between 2 continuants OR 2 occurrents
-(=>
- (part_of ?x ?y ?t)
- (or (and (instance_of ?x "bfo:Continuant" ?t)
- (instance_of ?y "bfo:Continuant" ?t))
- (and (instance_of ?x "bfo:Occurrent" ?t)
- (instance_of ?y "bfo:Occurrent" ?t))))
-
+;; -----------
;; -- logic --
+;; -----------
-;; is_a
-;; (this is defined in OBO-RO but it is also part of the default logic)
-;; TODO: move to RO section?
-(transitive is_a)
-(reflexive is_a)
-(anti_symmetric is_a)
-(synonym is_a "subtype_of")
+;; (instance_of ?instance ?Universal ?time)
+;; right now ALL instantiations are time-indexed
+;; this is not necessary for processes?
(=>
(and (instance_of ?i ?X ?t)
- (link is_a ?X ?Y))
+ (link is_a ?X ?Y)) ;; TODO - change to OBO_REL:is_a?
(instance_of ?i ?Y ?t))
-;; sub-relations
+;; (subrelation ?relation ?parent_relation)
(=> (and (subrelation ?r1 ?r2)
(?r1 ?x ?y))
(?r2 ?x ?y))
@@ -40,7 +22,14 @@
(subrelation ?y ?z))
(subrelation ?x ?z))
-;; ALL-SOME
+;; universal-level relations
+;; we specify this as (link ?rel ?C1 ?C2)
+;; this is a bit ugly, but we do want to write (?rel ?C1 ?C2) as we
+;; take this to mean an instance-level relation
+
+;; (all_some_all_times ?relation)
+;; EXAMPLE: (all_some_all_times part_of) (link part_of cell_nucleus cell)
+;;
;; most relations follow the OBO-RO all-some pattern
;; ie ALL instances of U1 stand in relation ?rel to SOME instance U2 at ALL times
(=>
@@ -64,7 +53,9 @@
(=> (reflexive ?rel)
(?rel ?x ?x)))
-;; reciprocal relatons
+;; reciprocal relations
+;; remember, this is just at the instance-level
+;; not( X part_of Y <=> Y has_part X)
(=> (and (reciprocal ?rel ?inv)
(?rel ?x ?y))
(?rel ?y ?x))
@@ -72,13 +63,14 @@
;; transitivity at the universal level
(=>
(and (transitive ?rel)
+ (all_some_all_times ?rel)
(link ?rel ?X ?Y)
(link ?rel ?Y ?Z))
(link ?rel ?X ?Z))
;; transitivity at the instance level
;; temporally-subsumed-by/2 is defined in SNARK
-;; (default-use-temporal-reasoning) - not working in my v of snark
+;; (default-use-temporal-reasoning) - hmmm, not working in my v of snark
(=>
(and (transitive ?rel)
(?rel ?x ?y ?t1)
@@ -87,3 +79,34 @@
(temporally-subsumed-by ?ti ?t2)
(?rel ?x ?z ?ti)))
+;; TODO
+;; disjoint_union/N
+;; genus_differentia/N
+;; can we use lisp lists here and have these predicates with arbitrary arity?
+
+;; other predicates have no semantics
+;; eg comment/2, annotation/3
+
+;; -- OBO Relation Ontology --
+
+;; additional formulae that cannot be extracted from obo format
+
+;; NOTE: We are double-quoting the IDs to prevent parse errors
+;; this probably slows things down as lisp will not intern the
+;; string (as happens with a symbol). In future we may have
+;; some other way of doing this. quoting is ugly too..
+
+;; OBO_REL:part_of
+;; make this implicit in obo-format?
+;; obof1.3 will have a way of stating this - for
+;; now we add in this supplemental file
+(all_some_all_times "OBO_REL:part_of")
+
+;; part_of holds between 2 continuants OR 2 occurrents
+(=>
+ (part_of ?x ?y ?t)
+ (or (and (instance_of ?x "bfo:Continuant" ?t)
+ (instance_of ?y "bfo:Continuant" ?t))
+ (and (instance_of ?x "bfo:Occurrent" ?t)
+ (instance_of ?y "bfo:Occurrent" ?t))))
+
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|
|
From: <cmu...@us...> - 2007-01-20 01:57:11
|
Revision: 298
http://svn.sourceforge.net/obo/?rev=298&view=rev
Author: cmungall
Date: 2007-01-19 17:57:12 -0800 (Fri, 19 Jan 2007)
Log Message:
-----------
initial commit - FOL semantics for obo
Added Paths:
-----------
obolog/
obolog/trunk/
obolog/trunk/obolog-test-data.lisp
obolog/trunk/obolog-theorem-prover.lisp
obolog/trunk/obolog-theorem-prover.sh
obolog/trunk/obolog.lisp
Added: obolog/trunk/obolog-test-data.lisp
===================================================================
--- obolog/trunk/obolog-test-data.lisp (rev 0)
+++ obolog/trunk/obolog-test-data.lisp 2007-01-20 01:57:12 UTC (rev 298)
@@ -0,0 +1,5 @@
+;; data
+(link "OBO_REL:part_of" spliceosome nucleus)
+(link "OBO_REL:part_of" nucleus cell)
+(instance_of CN_0001 nucleus t1)
+
Added: obolog/trunk/obolog-theorem-prover.lisp
===================================================================
--- obolog/trunk/obolog-theorem-prover.lisp (rev 0)
+++ obolog/trunk/obolog-theorem-prover.lisp 2007-01-20 01:57:12 UTC (rev 298)
@@ -0,0 +1,29 @@
+(in-package :snark-user)
+
+(defun read-assertions-from-file (f)
+ (let ((stream (open f)))
+ (loop for next-expr = (read stream nil 'EOF)
+ until (eq next-expr 'EOF)
+ do (progn
+ (format nil "asserting: ~A " next-expr)
+ (assert next-expr)))))
+
+(defun obolog-prove (proof)
+ (initialize)
+ ;;(use-temporal-reasoning t)
+ (use-resolution t)
+ ;; read
+ (read-assertions-from-file "obolog.lisp")
+ ;(read-assertions-from-file "ro.obolog")
+ (read-assertions-from-file "obolog-test-data.lisp")
+
+ ;; prove it!
+ (print (prove
+ (cdr (assoc proof '((part_of1 . (instance_of ?x cell ?t))
+ (transitive . (link "OBO_REL:part_of" spliceosome cell))))))))
+
+(defun test ()
+ (obolog-proove 'part_of1))
+
+
+
Added: obolog/trunk/obolog-theorem-prover.sh
===================================================================
--- obolog/trunk/obolog-theorem-prover.sh (rev 0)
+++ obolog/trunk/obolog-theorem-prover.sh 2007-01-20 01:57:12 UTC (rev 298)
@@ -0,0 +1,2 @@
+#!/bin/sh
+sbcl --core $HOME/src/snark/snark-sbcl.core --load obolog-theorem-prover.lisp --eval "(in-package :snark-user)" --eval "(obolog-prove '$1)"
Property changes on: obolog/trunk/obolog-theorem-prover.sh
___________________________________________________________________
Name: svn:executable
+
Added: obolog/trunk/obolog.lisp
===================================================================
--- obolog/trunk/obolog.lisp (rev 0)
+++ obolog/trunk/obolog.lisp 2007-01-20 01:57:12 UTC (rev 298)
@@ -0,0 +1,89 @@
+;; CONVENTIONS:
+;; upper case for universals, lower case for instances
+;; - but remember, most KIF implementations are case insenstivite
+
+;; -- OBO Relation Ontology --
+
+;; additional formulae that cannot be extracted from obo format
+
+;; OBO_REL:part_of
+;; make this implicit in obo-format?
+(all_some_all_times "OBO_REL:part_of")
+
+;; part_of holds between 2 continuants OR 2 occurrents
+(=>
+ (part_of ?x ?y ?t)
+ (or (and (instance_of ?x "bfo:Continuant" ?t)
+ (instance_of ?y "bfo:Continuant" ?t))
+ (and (instance_of ?x "bfo:Occurrent" ?t)
+ (instance_of ?y "bfo:Occurrent" ?t))))
+
+;; -- logic --
+
+;; is_a
+;; (this is defined in OBO-RO but it is also part of the default logic)
+;; TODO: move to RO section?
+(transitive is_a)
+(reflexive is_a)
+(anti_symmetric is_a)
+(synonym is_a "subtype_of")
+(=>
+ (and (instance_of ?i ?X ?t)
+ (link is_a ?X ?Y))
+ (instance_of ?i ?Y ?t))
+
+;; sub-relations
+(=> (and (subrelation ?r1 ?r2)
+ (?r1 ?x ?y))
+ (?r2 ?x ?y))
+(=> (and (subrelation ?x ?y)
+ (subrelation ?y ?z))
+ (subrelation ?x ?z))
+
+;; ALL-SOME
+;; most relations follow the OBO-RO all-some pattern
+;; ie ALL instances of U1 stand in relation ?rel to SOME instance U2 at ALL times
+(=>
+ (and (all_some_all_times ?rel)
+ (link ?rel ?U1 ?U2)
+ (instance_of ?i1 ?U1 ?t))
+ (exists (?i2)
+ (and (instance_of ?i2 ?U2 ?t)
+ (?rel ?i1 ?i2 ?t))))
+
+;; domain and range constraints
+(=> (and (domain ?rel ?D)
+ (?rel ?i1 ?i2))
+ (instance_of ?i2 ?D))
+(=> (and (range ?rel ?R)
+ (?rel ?i1 ?i2))
+ (instance_of ?i1 ?D))
+
+;; reflexivity
+(forall (?x)
+ (=> (reflexive ?rel)
+ (?rel ?x ?x)))
+
+;; reciprocal relatons
+(=> (and (reciprocal ?rel ?inv)
+ (?rel ?x ?y))
+ (?rel ?y ?x))
+
+;; transitivity at the universal level
+(=>
+ (and (transitive ?rel)
+ (link ?rel ?X ?Y)
+ (link ?rel ?Y ?Z))
+ (link ?rel ?X ?Z))
+
+;; transitivity at the instance level
+;; temporally-subsumed-by/2 is defined in SNARK
+;; (default-use-temporal-reasoning) - not working in my v of snark
+(=>
+ (and (transitive ?rel)
+ (?rel ?x ?y ?t1)
+ (?rel ?y ?z ?t2)
+ (temporally-subsumed-by ?ti ?t1)
+ (temporally-subsumed-by ?ti ?t2)
+ (?rel ?x ?z ?ti)))
+
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|
|
From: <mg...@us...> - 2007-01-18 22:49:11
|
Revision: 297
http://svn.sourceforge.net/obo/?rev=297&view=rev
Author: mgibson
Date: 2007-01-18 14:49:12 -0800 (Thu, 18 Jan 2007)
Log Message:
-----------
Can now check with sourceforge repos (or any http really) to see if obo file
is up to date and if not can grab that one - doesnt yet stuff it in the cache
so it would be grabbing it every time
theres configuration now for specifying repository/url to check for obo file
and theres a config for specifying the base dir for repository for convenience
<obo-repository url-dir="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/"/>
<field name="Quality" file="quality.obo" syntax-abbrev="Q" repos-subdir="phenotype"/>
next is to download into cache - though the bummer there is it will take even
longer - maybe should be user option?
Modified Paths:
--------------
phenote/trunk/conf/flybase.cfg
phenote/trunk/conf/human.cfg
phenote/trunk/conf/phenote-config.rnc
phenote/trunk/conf/phenote-config.xsd
phenote/trunk/conf/zfin-standalone.cfg
phenote/trunk/jars/phenoteconfigbeans.jar
phenote/trunk/phenote
phenote/trunk/src/java/phenote/config/Config.java
phenote/trunk/src/java/phenote/config/OntologyConfig.java
phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
phenote/trunk/src/java/phenote/main/PhenoteVersion.java
Modified: phenote/trunk/conf/flybase.cfg
===================================================================
--- phenote/trunk/conf/flybase.cfg 2007-01-18 16:56:13 UTC (rev 296)
+++ phenote/trunk/conf/flybase.cfg 2007-01-18 22:49:12 UTC (rev 297)
@@ -8,6 +8,8 @@
<uvic-graph enable="false"/>
+ <obo-repository url-dir="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/"/>
+
<field name="Pub" syntax-abbrev="PUB"/>
<field name="Genotype" syntax-abbrev="GT" type="free_text"/>
@@ -15,13 +17,14 @@
<field name="Genetic Context" file="context.obo" syntax-abbrev="GC"/>
<field name="Entity" syntax-abbrev="E">
- <postcomp relationship-ontology="relationship.obo"/>
- <ontology name="Fly" file="fly_anatomy.obo" />
- <ontology name="GO" file="gene_ontology.obo"/>
+ <postcomp relationship-ontology="relationship.obo" repos-subdir="OBO_REL"/>
+ <ontology name="Fly" file="fly_anatomy.obo"
+ repos-subdir="anatomy/gross_anatomy/animal_gross_anatomy/fly"/>
+ <ontology name="GO" file="gene_ontology.obo" repos-subdir="genomic-proteomic"/>
<ontology name="SP" file="spatial.obo"/>
</field>
- <field name="Quality" file="quality.obo" syntax-abbrev="Q"/>
+ <field name="Quality" file="quality.obo" syntax-abbrev="Q" repos-subdir="phenotype"/>
<field name="Absent" file="quality.obo" slim="absent_slim" syntax-abbrev="Tag"/>
<field name="Abnormal" file="quality.obo" slim="abnormal_slim" syntax-abbrev="Tag"/>
Modified: phenote/trunk/conf/human.cfg
===================================================================
--- phenote/trunk/conf/human.cfg 2007-01-18 16:56:13 UTC (rev 296)
+++ phenote/trunk/conf/human.cfg 2007-01-18 22:49:12 UTC (rev 297)
@@ -8,6 +8,8 @@
<uvic-graph enable="false"/>
+ <obo-repository url-dir="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/"/>
+
<field name="Pub" syntax-abbrev="PUB"/>
<field name="Genotype" syntax-abbrev="GT" type="free_text"/>
@@ -15,17 +17,17 @@
<field name="Genetic Context" file="context.obo" syntax-abbrev="GC"/>
<field name="Entity" syntax-abbrev="E">
- <postcomp relationship-ontology="relationship.obo"/>
+ <postcomp relationship-ontology="relationship.obo" repos-subdir="OBO_REL"/>
<ontology name="Human Anatomy" file="fma_obo.obo"/>
- <ontology name="Gene Ontology" file="gene_ontology.obo"/>
- <ontology name="Chemical" file="chebi.obo"/>
- <ontology name="Cell Type" file="cell.obo"/>
+ <ontology name="Gene Ontology" file="gene_ontology.obo" repos-subdir="genomic-proteomic"/>
+ <ontology name="Chemical" file="chebi.obo" repos-subdir="chemical"/>
+ <ontology name="Cell Type" file="cell.obo" repos-subdir="anatomy/cell_type"/>
<ontology name="Spatial" file="spatial.obo"/>
</field>
<field name="Quality" syntax-abbrev="Q">
- <ontology name="Quality" file="quality.obo"/>
- <ontology name="MamPheno" file="mammalian_phenotype.obo"/>
+ <ontology name="Quality" file="quality.obo" repos-subdir="phenotype"/>
+ <ontology name="MamPheno" file="mammalian_phenotype.obo" repos-subdir="phenotype"/>
</field>
</phenote-configuration>
Modified: phenote/trunk/conf/phenote-config.rnc
===================================================================
--- phenote/trunk/conf/phenote-config.rnc 2007-01-18 16:56:13 UTC (rev 296)
+++ phenote/trunk/conf/phenote-config.rnc 2007-01-18 22:49:12 UTC (rev 297)
@@ -7,6 +7,7 @@
log,
dataadapter*,
uvic-graph,
+ obo-repository,
field*
}
@@ -31,6 +32,8 @@
uvic-graph = element uvic-graph { attribute enable { xsd:boolean } }
+obo-repository = element obo-repository { attribute url-dir {text} }
+
field =
element field {
##attribute name { "Pub" | "Genotype" | "Genetic Context" | "Entity" | "Quality" },
@@ -44,6 +47,7 @@
attribute file { text },
attribute filter-out { text },
attribute slim { text },
+ attribute repos-subdir {text},
postcomp?,
ontology*
}
@@ -54,7 +58,8 @@
## obo file for ontology
attribute file { text },
attribute filter-out { text },
- attribute slim { text }
+ attribute slim { text },
+ attribute repos-subdir {text}
}
postcomp =
Modified: phenote/trunk/conf/phenote-config.xsd
===================================================================
--- phenote/trunk/conf/phenote-config.xsd 2007-01-18 16:56:13 UTC (rev 296)
+++ phenote/trunk/conf/phenote-config.xsd 2007-01-18 22:49:12 UTC (rev 297)
@@ -6,6 +6,7 @@
<xs:element ref="x:log"/>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="x:dataadapter"/>
<xs:element ref="x:uvic-graph"/>
+ <xs:element ref="x:obo-repository"/>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="x:field"/>
</xs:sequence>
<xs:attribute name="version" use="required" type="xs:float"/>
@@ -37,6 +38,11 @@
<xs:attribute name="enable" use="required" type="xs:boolean"/>
</xs:complexType>
</xs:element>
+ <xs:element name="obo-repository">
+ <xs:complexType>
+ <xs:attribute name="url-dir" use="required"/>
+ </xs:complexType>
+ </xs:element>
<xs:element name="field">
<xs:complexType>
<xs:sequence>
@@ -68,6 +74,7 @@
</xs:attribute>
<xs:attribute name="filter-out" use="required"/>
<xs:attribute name="slim" use="required"/>
+ <xs:attribute name="repos-subdir" use="required"/>
</xs:complexType>
</xs:element>
<xs:element name="ontology">
@@ -80,6 +87,7 @@
</xs:attribute>
<xs:attribute name="filter-out" use="required"/>
<xs:attribute name="slim" use="required"/>
+ <xs:attribute name="repos-subdir" use="required"/>
</xs:complexType>
</xs:element>
<xs:element name="postcomp">
Modified: phenote/trunk/conf/zfin-standalone.cfg
===================================================================
--- phenote/trunk/conf/zfin-standalone.cfg 2007-01-18 16:56:13 UTC (rev 296)
+++ phenote/trunk/conf/zfin-standalone.cfg 2007-01-18 22:49:12 UTC (rev 297)
@@ -7,6 +7,8 @@
<uvic-graph enable="false"/>
+ <obo-repository url-dir="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/"/>
+
<field name="Pub" syntax-abbrev="PUB"/>
<field name="Genotype" syntax-abbrev="GT" type="free_text"/>
@@ -14,21 +16,22 @@
<field name="Genetic Context" file="context.obo" syntax-abbrev="GC"/>
<field name="Entity" syntax-abbrev="E">
- <postcomp relationship-ontology="relationship.obo"/>
- <ontology name="ZF" file="zebrafish_anatomy.obo" filter-out="ZFS:" />
- <ontology name="GO" file="gene_ontology.obo"/>
+ <postcomp relationship-ontology="relationship.obo" repos-subdir="OBO_REL"/>
+ <ontology name="ZF" file="zebrafish_anatomy.obo" filter-out="ZFS:"
+ repos-subdir="anatomy/gross_anatomy/animal_gross_anatomy/fish"/>
+ <ontology name="GO" file="gene_ontology.obo" repos-subdir="genomic-proteomic"/>
<ontology name="SP" file="spatial.obo"/>
</field>
<field name="Stage" file="zebrafish_anatomy.obo" filter-out="ZFA:" syntax-abbrev="T"/>
- <field name="Quality" file="quality.obo" syntax-abbrev="Q" />
+ <field name="Quality" file="quality.obo" syntax-abbrev="Q" repos-subdir="phenotype"/>
<field name="Absent" file="quality.obo" slim="absent_slim" syntax-abbrev="Tag"/>
<field name="Abnormal" file="quality.obo" slim="abnormal_slim" syntax-abbrev="Tag"/>
<field name="Evidence" file="evidence_code.obo" syntax-abbrev="EV"/>
- <field name="Description" syntax-abbrev="Desc"/>
+ <field name="Description" syntax-abbrev="Desc" repos-subdir="."/>
</phenote-configuration>
Modified: phenote/trunk/jars/phenoteconfigbeans.jar
===================================================================
(Binary files differ)
Modified: phenote/trunk/phenote
===================================================================
--- phenote/trunk/phenote 2007-01-18 16:56:13 UTC (rev 296)
+++ phenote/trunk/phenote 2007-01-18 22:49:12 UTC (rev 297)
@@ -8,6 +8,6 @@
fi;
done
-java -Xmx650M -classpath ${PHENOTE_CLASSPATH} phenote.main.Phenote $@
+java -Xmx700M -classpath ${PHENOTE_CLASSPATH} phenote.main.Phenote $@
##java -Xmx300M -classpath classfiles:jars/oboedit.jar:jars/org.geneontology.jar:jars/BrowserLauncher2-10rc4.jar:jars/junit-4.0.jar:jars/tomcat-servlet.jar:jars/xbean.jar:jars/jsr173_1.0_api.jar:jars/phenoxmlbeans.jar:jars/phenoteconfigbeans.jar:jars/log4j-1.2.13.jar:jars/te-common.jar phenote.main.Phenote $@
Modified: phenote/trunk/src/java/phenote/config/Config.java
===================================================================
--- phenote/trunk/src/java/phenote/config/Config.java 2007-01-18 16:56:13 UTC (rev 296)
+++ phenote/trunk/src/java/phenote/config/Config.java 2007-01-18 22:49:12 UTC (rev 297)
@@ -30,6 +30,7 @@
import phenote.config.xml.OntologyDocument.Ontology;
import phenote.config.xml.LogDocument.Log;
import phenote.config.xml.UvicGraphDocument.UvicGraph;
+import phenote.config.xml.OboRepositoryDocument.OboRepository;
import phenote.util.FileUtil;
import phenote.datamodel.CharField;
@@ -52,6 +53,7 @@
//private int newOntologyCheckMinutes = 10;
private String logConfigFile = "conf/log4j.xml"; // default log config file
private boolean uvicGraphEnabled = false; // default false for now
+ private String reposUrlDir;
/** singleton */
private Config() {
@@ -222,6 +224,8 @@
throw new ConfigException("Syn Abbrev for "+cf+" not found");
}
+ String getReposUrlDir() { return reposUrlDir; }
+
/** should this just be a part of fieldConfigList? and main window would filter it
out when making up fields? rel is for post comp gui - or maybe FieldConfig
should have isPostComp, getPostCompRelFile - yes! */
@@ -257,6 +261,11 @@
if (gr != null)
uvicGraphEnabled = gr.getEnable();
+ // Repos url dir
+ OboRepository or = pc.getOboRepository();
+ if (or != null && or.getUrlDir() != null)
+ reposUrlDir = or.getUrlDir().getStringValue();
+
// FIELDS
Field[] fields = pc.getFieldArray();
for (Field f : fields) {
@@ -319,28 +328,16 @@
fc.setPostCompRelOntCfg(makeOntologyConfig("Relationship",relFile));
}
+
// ONTOLOGIES if only one ontology file is an attribute... (convenience)
if (field.getFile() != null) {
- String file = field.getFile().getStringValue();
- // downside of strogly types xml beans is filterOut has to be dealt with
- // separately for field & ontology - annoying - & all other attribs
- String filterOut =
- field.getFilterOut()!=null ? field.getFilterOut().getStringValue() : null;
- String slim = field.getSlim()!=null ? field.getSlim().getStringValue() : null;
- fc.addOntologyConfig(makeOntologyConfig(name,file,filterOut,slim));
+ fc.addOntologyConfig(new OntologyConfig(field));
}
// otherwise its multiple ontologies listed in ontology elements (entity)
else {
Ontology[] ontologies = field.getOntologyArray();
for (Ontology o : ontologies) {
- String oName = o.getName().getStringValue();
- String oFile = o.getFile().getStringValue();
- String filterOut=null;
- if (o.getFilterOut() != null)
- filterOut = o.getFilterOut().getStringValue();
- String slim = o.getSlim()!=null ? o.getSlim().getStringValue() : null;
- OntologyConfig oc = makeOntologyConfig(oName,oFile,filterOut,slim);
- fc.addOntologyConfig(oc);
+ fc.addOntologyConfig(new OntologyConfig(o));
}
}
fieldList.add(fc);
@@ -352,16 +349,48 @@
OntologyConfig oc = new OntologyConfig(name,file);
return oc;
}
- private OntologyConfig makeOntologyConfig(String name, String file, String filterOut) {
- return new OntologyConfig(name,file,filterOut);
- }
- private OntologyConfig makeOntologyConfig(String name, String file, String filterOut,
- String slim) {
- return new OntologyConfig(name,file,filterOut,slim);
- }
-
}
+// String oName = o.getName().getStringValue();
+// String oFile = o.getFile().getStringValue();
+// String filterOut=null;
+// if (o.getFilterOut() != null)
+// filterOut = o.getFilterOut().getStringValue();
+// String slim = o.getSlim()!=null ? o.getSlim().getStringValue() : null;
+// OntologyConfig oc = makeOntologyConfig(oName,oFile,filterOut,slim);
+// String file = field.getFile().getStringValue();
+// // downside of strogly types xml beans is filterOut has to be dealt with
+// // separately for field & ontology - annoying - & all other attribs
+// String filterOut =
+// field.getFilterOut()!=null ? field.getFilterOut().getStringValue() : null;
+// String slim = field.getSlim()!=null ? field.getSlim().getStringValue() : null;
+// if (field.getReposSubdir() != null)
+// fc.setReposSubdir(field.getReposSubdir().getStringValue());
+
+// private OntologyConfig makeOntologyConfig(Field field) {
+// String name = field.getName().getStringValue();
+// String file = field.getFile().getStringValue();
+// // downside of strongly types xml beans is filterOut has to be dealt with
+// // separately for field & ontology - annoying - & all other attribs
+// String filterOut =
+// field.getFilterOut()!=null ? field.getFilterOut().getStringValue() : null;
+// String slim = field.getSlim()!=null ? field.getSlim().getStringValue() : null;
+// String rs = field.getReposSubdir()!=null ?
+// field.getReposSubdir().getStringValue() : null;
+// return makeOntologyConfig(name,file,filterOut,slim,rs);
+// //fc.addOntologyConfig(makeOntologyConfig(name,file,filterOut,slim));
+// }
+
+// private OntologyConfig makeOntologyConfig(String name, String file, String filterOut) {
+// return new OntologyConfig(name,file,filterOut);
+// }
+// private OntologyConfig makeOntologyConfig(String name, String file, String filterOut,
+// String slim,String reposSubdir) {
+// return new OntologyConfig(name,file,filterOut,slim,reposSubdir);
+// }
+
+
+
// // CHECK FOR ONTOLOGIES
// CheckForNewOntologies cfno = pc.getCheckForNewOntologies();
// if (cfno != null) { // ?
Modified: phenote/trunk/src/java/phenote/config/OntologyConfig.java
===================================================================
--- phenote/trunk/src/java/phenote/config/OntologyConfig.java 2007-01-18 16:56:13 UTC (rev 296)
+++ phenote/trunk/src/java/phenote/config/OntologyConfig.java 2007-01-18 22:49:12 UTC (rev 297)
@@ -1,5 +1,11 @@
package phenote.config;
+import java.net.MalformedURLException;
+import java.net.URL;
+
+import phenote.config.xml.FieldDocument.Field;
+import phenote.config.xml.OntologyDocument.Ontology;
+
/** May not even have ontology file (free text eg genotype) rename FieldConfig? */
public class OntologyConfig {
@@ -8,6 +14,7 @@
//public String nameSpace; // not used yet - or was this what filter out ended up
public String filterOut; // public?
private String slim;
+ private String reposSubdir;
//static OntologyConfig defaultPato = new OntologyConfig("Pato","attribute_and_value.obo");
@@ -29,6 +36,28 @@
this.slim = slim;
}
+ /** Ontology stuff in field itself (field only has one ontology) */
+ OntologyConfig(Field field) {
+ name = field.getName().getStringValue();
+ ontologyFile = field.getFile().getStringValue();
+ // downside of strongly types xml beans is filterOut has to be dealt with
+ // separately for field & ontology - annoying - & all other attribs
+ filterOut = field.getFilterOut()!=null ? field.getFilterOut().getStringValue() : null;
+ slim = field.getSlim()!=null ? field.getSlim().getStringValue() : null;
+ reposSubdir = field.getReposSubdir()!=null ?
+ field.getReposSubdir().getStringValue() : null;
+ }
+
+ OntologyConfig(Ontology o) {
+ name = o.getName().getStringValue();
+ ontologyFile = o.getFile().getStringValue();
+ if (o.getFilterOut() != null)
+ filterOut = o.getFilterOut().getStringValue();
+ slim = o.getSlim()!=null ? o.getSlim().getStringValue() : null;
+ if (o.getReposSubdir()!=null)
+ reposSubdir = o.getReposSubdir().getStringValue();
+ }
+
boolean hasName() {
return !isBad(name);
}
@@ -48,6 +77,30 @@
}
public String getFile() { return ontologyFile; }
+ void setReposSubdir(String rs) { reposSubdir = rs; }
+
+ public URL getReposUrl() throws MalformedURLException {
+ String urlString="";
+ String urlDir = getReposBaseDir();
+ if (urlDir != null)
+ urlString = urlDir;
+ urlString += "/" + reposSubdir + "/" + getFile();
+ return new URL(urlString);
+ }
+
+ private String getReposBaseDir() {
+ return Config.inst().getReposUrlDir();
+ }
+
+ public boolean hasReposUrl() {
+ if (getFile() == null) return false; // shouldnt happen
+ // repos base dir is just a convenience
+ if (reposSubdir == null) //&& getReposBaseDir() == null)
+ return false;
+ //try { getReposUrl(); } catch (MalformedURLException e) { return false; } ??
+ return true;
+ }
+
private boolean isBad(String s) {
return s == null || s.trim().equals("");
}
Modified: phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java 2007-01-18 16:56:13 UTC (rev 296)
+++ phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java 2007-01-18 22:49:12 UTC (rev 297)
@@ -1,16 +1,25 @@
package phenote.dataadapter;
+import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Date;
+import java.text.SimpleDateFormat;
+import java.text.ParsePosition;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+import javax.swing.JOptionPane;
import org.apache.log4j.Logger;
import org.geneontology.oboedit.datamodel.OBOSession;
@@ -121,18 +130,18 @@
if (ontCfg.hasSlim())
ontology.setSlim(ontCfg.getSlim());
- loadOboSession(ontology,ontCfg.getFile()); // throws FileNotFoundEx
+ loadOboSession(ontology,ontCfg); // throws FileNotFoundEx
return ontology;
}
/** Load obo session with obo edit adapter, unless previously loaded - reuse */
- private void loadOboSession(Ontology o,String filename) throws OntologyException {
+ private void loadOboSession(Ontology o,OntologyConfig oc) throws OntologyException {
// check cache of ontologies to see if ontology file already loaded
- if (fileIsInCache(filename)) {
- loadOboSessionFromCache(o,filename);
+ if (fileIsInCache(oc.getFile())) {
+ setOboSessionFromCache(o,oc.getFile());
}
else {
- loadOboSessionIgnoreCache(o,filename);
+ loadOboSessionCheckRepos(o,oc);
}
}
@@ -140,7 +149,7 @@
return fileToOntologyCache.containsKey(filename);
}
- private void loadOboSessionFromCache(Ontology o,String filename)
+ private void setOboSessionFromCache(Ontology o,String filename)
throws OntologyException {
Ontology previousOntol = fileToOntologyCache.get(filename);
o.setOboSession(previousOntol.getOboSession()); // throws OntEx if error
@@ -149,11 +158,42 @@
o.setSource(previousOntol.getSource());
}
- private void loadOboSessionIgnoreCache(Ontology o,String filename)
+ /** If repository is configured loads obo from repos if local out of date */
+ private void loadOboSessionCheckRepos(Ontology o,OntologyConfig oc)
throws OntologyException {
+ String filename = oc.getFile();
URL url = findFile(filename); // throws OntologyEx if file not found
+
+ // if ontCfg.hasSynchUrl() ?
+ // URL synchUrl = ontCfg.getSynchUrl
+ if (oc.hasReposUrl()) {
+ try {
+ URL reposUrl = oc.getReposUrl();//new URL("http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/evidence_code.obo");
+ url = checkRepositoryUrl(url,reposUrl,o.getName());
+
+ // to do - if from repos need to load repos into local obo cache!
+
+ } catch (/*MalformedURL & IO*/Exception e) { LOG.error(e); }
+ }
+
+ loadOboSessionFromUrl(o,url,filename);
+// o.setOboSession(getOboSession(url)); // throws OntEx if error
+// fileToOntologyCache.put(filename,o);
+// File file = new File(url.getFile());
+// long date = file.lastModified();
+// if (date > 0) { // jar files have 0 date???
+// o.setTimestamp(date);
+// o.setSource(file.toString());
+// }
+ }
+
+ /** url is either local file or repos url */
+ private void loadOboSessionFromUrl(Ontology o, URL url, String filename)
+ throws OntologyException {
+ //URL url = findFile(filename); // throws OntologyEx if file not found
o.setOboSession(getOboSession(url)); // throws OntEx if error
- fileToOntologyCache.put(filename,o);
+ if (filename!=null)
+ fileToOntologyCache.put(filename,o); // ??
File file = new File(url.getFile());
long date = file.lastModified();
if (date > 0) { // jar files have 0 date???
@@ -161,6 +201,53 @@
o.setSource(file.toString());
}
}
+
+ private URL checkRepositoryUrl(URL localUrl, URL reposUrl, String ontol)
+ throws OntologyException {
+ long repos = getOboDate(reposUrl);
+ long loc = getOboDate(localUrl); // throws ont ex
+ boolean useRepos = false;
+ if (repos > loc)
+ useRepos = queryUserAboutRepos(ontol);
+ if (useRepos) {
+ LOG.info("Loading new ontology from repository "+reposUrl);
+ return reposUrl;
+ }
+ return localUrl;
+ }
+
+ // is it bad to have a popup from data adapter?
+ private boolean queryUserAboutRepos(String ontol) {
+ String m = "There is a more current ontology in the repository for "+ontol+".\nWould"
+ +" you like to load the new version? (may take a few minutes)";
+ int yn = JOptionPane.showConfirmDialog(null,m,"Synch ontology?",
+ JOptionPane.YES_NO_OPTION,
+ JOptionPane.QUESTION_MESSAGE);
+ return yn == JOptionPane.YES_OPTION;
+ }
+
+ /** Get the date of the file from the header of the obo file - just read header dont
+ read in whole file. should it also query urlConnection for date first? */
+ private long getOboDate(URL oboUrl) throws OntologyException {
+ try {
+ InputStream is = oboUrl.openStream();
+ BufferedReader br = new BufferedReader(new InputStreamReader(is));
+ // just try first 15 lines? try til hit [Term]?
+ for (int i=1; i<=15; i++) {
+ String line = br.readLine();
+ // eg date: 22:08:2006 15:38
+ if (!line.startsWith("date:")) continue;
+ SimpleDateFormat dateFormat = new SimpleDateFormat("dd:MM:yyyy HH:mm");
+ Date d = dateFormat.parse(line, new ParsePosition(6));
+ LOG.debug("date "+d+" for url "+oboUrl+" line "+line);
+ br.close();
+ if (d == null)
+ throw new OntologyException("couldnt parse date "+line);
+ return d.getTime();
+ }
+ throw new OntologyException("No date found in "+oboUrl);
+ } catch (IOException e) { throw new OntologyException(e); }
+ }
/** Look for file in current directory (.) and jar file
@@ -175,7 +262,7 @@
// String -> url to handle web start jar obo files
private OBOSession getOboSession(URL oboUrl) throws OntologyException {
if (oboUrl == null)
- return new OBOSessionImpl(); // ??
+ throw new OntologyException("No url to retrieve");//return new OBOSessionImpl();
OBOFileAdapter fa = new OBOFileAdapter();
FileAdapterConfiguration cfg = new OBOFileAdapter.OBOAdapterConfiguration();
@@ -196,7 +283,8 @@
to reload itself from its file - in other words there is a new obo file to load
in place of old one */
public void reloadOntology(Ontology ont) throws OntologyException {
- loadOboSessionIgnoreCache(ont,ont.getSource()); // throws ex
+ URL url = findFile(ont.getSource()); // ex
+ loadOboSessionFromUrl(ont,url,ont.getSource()); // throws ex
}
// private void loadRelationshipOntology() { hmmmmmm
Modified: phenote/trunk/src/java/phenote/main/PhenoteVersion.java
===================================================================
--- phenote/trunk/src/java/phenote/main/PhenoteVersion.java 2007-01-18 16:56:13 UTC (rev 296)
+++ phenote/trunk/src/java/phenote/main/PhenoteVersion.java 2007-01-18 22:49:12 UTC (rev 297)
@@ -6,7 +6,7 @@
//private static final float MAJOR_VERSION_NUM = 0.8f;
//private static final float SUB_VERSION_NUM = .3f;
- private static final String VERSION = "1.0.2 dev"; // ??
+ private static final String VERSION = "1.1 dev"; // ??
// type is "dev" or "release"
//private static final String type = " dev"; // "release"
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-01-18 16:56:21
|
Revision: 296
http://svn.sourceforge.net/obo/?rev=296&view=rev
Author: mgibson
Date: 2007-01-18 08:56:13 -0800 (Thu, 18 Jan 2007)
Log Message:
-----------
copy jnlp webstart files into latest dir as well for webstart deployment
Modified Paths:
--------------
phenote/trunk/build.xml
Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml 2007-01-18 16:15:13 UTC (rev 295)
+++ phenote/trunk/build.xml 2007-01-18 16:56:13 UTC (rev 296)
@@ -417,6 +417,9 @@
<copy todir="phenote-webstart/${env.PHENOTE_VERSION}">
<fileset file="doc/phenote-website/*.jnlp"/>
</copy>
+ <copy todir="phenote-webstart/latest">
+ <fileset file="doc/phenote-website/*.jnlp"/>
+ </copy>
</target>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-01-18 16:15:14
|
Revision: 295
http://svn.sourceforge.net/obo/?rev=295&view=rev
Author: mgibson
Date: 2007-01-18 08:15:13 -0800 (Thu, 18 Jan 2007)
Log Message:
-----------
added the rest of the html files from the website -
should phenote-website be taken out of doc dir and given its own dir?
Added Paths:
-----------
phenote/trunk/doc/phenote-website/phenote-java-requirements.html
phenote/trunk/doc/phenote-website/webstart-troubleshooting.html
Added: phenote/trunk/doc/phenote-website/phenote-java-requirements.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-java-requirements.html (rev 0)
+++ phenote/trunk/doc/phenote-website/phenote-java-requirements.html 2007-01-18 16:15:13 UTC (rev 295)
@@ -0,0 +1,32 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+ <meta content="text/html; charset=ISO-8859-1"
+ http-equiv="content-type">
+ <title>Java version for Phenote</title>
+</head>
+<body>
+<h1>Java requirements for Phenote</h1>
+<br>
+Phenote requires Java 1.5. I hope this is OK with everybody. If there
+are issues please let me know(mg...@fr...). 1.5 has been out
+for around 2 years, and has a lot of nice features. The big issue is
+Macs. Mac Tiger supports 1.5 where earlier version (Panther &
+earlier) do not as far as I know. So upgrading to Tiger would then be a
+requirement for using Phenote. Tiger has been out for over a year now
+and is now pretty stable, so I hope this isn't a cumbersome
+requirement. I have emailed with zfin and it seems the Mac users there
+are actually already all upgraded to Tiger.<br>
+<br>
+As for windows, linux and solaris, if you do not already have jdk 1.5
+it can be downloaded from sun:<br>
+<br>
+<a href="http://java.sun.com/j2se/1.5.0/download.jsp">http://java.sun.com/j2se/1.5.0/download.jsp</a><br>
+<br>
+<br>
+<br>
+<a href="phenote.html">Phenote main page</a><br>
+<br>
+<br>
+</body>
+</html>
Added: phenote/trunk/doc/phenote-website/webstart-troubleshooting.html
===================================================================
--- phenote/trunk/doc/phenote-website/webstart-troubleshooting.html (rev 0)
+++ phenote/trunk/doc/phenote-website/webstart-troubleshooting.html 2007-01-18 16:15:13 UTC (rev 295)
@@ -0,0 +1,103 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+ <meta content="text/html; charset=ISO-8859-1"
+ http-equiv="content-type">
+ <title>Phenote webstart trouble shooting</title>
+</head>
+<body>
+<h2>Phenote Webstart Troubleshooting<br>
+</h2>
+<br>
+Webstart is a way of launching java applications from the web. Just
+click
+on a link and the application will download to your computer, and come
+up. Webstart is somewhat difficult, but I've got it working in some
+situations for Phenote.
+Future clicks on the link should recognize that you've already
+downloaded
+it, and will just bring up the downloaded application. If the
+application
+changes/upgrades on the server, this will be recognized and a click on
+the
+link will download the new upgraded application. So its more or less a
+web
+installer. On the <a href="phenote.html">main phenote page</a>
+there are links to the latest phenote webstart links to try.<br>
+<p>The indication that a link works is that you get a popup
+that says "Java Loading", or something like that and then a bunch of
+files get downloaded and eventually the application actually comes up.
+For this to work with a browser, the browser has to recognize java
+webstart links, which have a jnlp suffix. Macs tend to have
+webstart pre-installed on their browsers. Windows seems to as
+well. Linux does not and I don't know about Solaris. If its not
+working what you basically have to do is set up an association in the
+browser between whats called a mime type, which is
+"application/x-java-jnlp-file" in this case, and the webstart
+application, which you need to find on your computer(more on this
+below).<br>
+<br>
+These are the steps I had to go through to get webstart installed on my
+Mozilla browser on Linux, which does not come with webstart
+pre-installed. <br>
+<br>
+First you need to see if you have webstart already installed on your
+computer. If you have java on your computer then usually webstart comes
+with java so you should have it. So if you have java you first need to
+find out where it is installed. In linux you type "which java" at the
+command line. For me this comes back with<br>
+<br>
+/usr/lib/java/bin/java</p>
+<p>You then need to make sure you are using java 1.5, phenote requires
+1.4. Do a "java-version" at the command line. If you have anything less
+than 1.5, you need to install java 1.5, or if you have 1.5 installed
+somewhere (but its not the default) you need to find it and grab its
+javaws. If you try to webstart phenote with a java less than 1.5
+nothing will happen and it won't even indicate that its the wrong java,
+you just have to know.<br>
+<br>
+So what I found is in java 1.5 javaws is in both the bin and jre
+directory. So cd to
+/usr/lib/java and do a "ls jre" and "ls bin" (on windows "dir jre"
+& "dir bin") and look for a file called "javaws", which is the
+webstart application. The full path plus javaws is what you will need
+below. So for me its "/usr/lib/java/jre/javaws"<br>
+<br>
+If webstart is not on your computer (or network) you can download it
+from(make sure its from java 1.5):<br>
+<br>
+<a href="http://java.sun.com/products/javawebstart/download.jsp">http://java.sun.com/products/javawebstart/download.jsp</a><br>
+<br>
+<br>
+Now that we've found the webstart application we are ready to associate
+it with a mime type in the browser. Here is how it is done in Mozilla
+on linux, I hope other browsers are somewhat similar.<br>
+<br>
+Hit the "Edit" menu, and its "Preferences" sub menu to get the
+Preferences dialog. Expand the "Navigator" category, and under
+that click on "Helper Application", which is where mime types get
+associated with applications. Click the "New Type" button, which brings
+up a New Type dialog box. In the "MIME Type" field enter
+"application/x-java-jnlp-file". Under "Description" you can just
+put "Java Webstart". Under "Extension" put "jnlp". Click on "Open it
+with:" and in the associated field either entor or browse for the
+location of webstart on your computer. This is what you were digging
+for above. For my computer I enter "/usr/lib/java/jre/javaws", the
+location of my webstart app. then deselect "Always ask me before
+handling files of this type", as who wants to keep being asked, and hit
+"OK" and hit "OK" as well in the Helper Applications dialog.<br>
+<br>
+You now need to restart your browser for it to pick up the new mime
+type association for webstart and hopefully the above link should now
+work. <br>
+<br>
+One thing thats also handy if there are problems bringing up webstart
+is to bring up the browsers java console (this may not be supported by
+all browsers). This should give some feedback on things happening
+behind the scenes of the webstart application, so its good for trouble
+shooting. In mozilla this can be brought up with menu <br>
+Tools->Web Development->Java Console.<br>
+<br>
+</p>
+</body>
+</html>
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|
|
From: <ba...@us...> - 2007-01-17 19:46:48
|
Revision: 294
http://svn.sourceforge.net/obo/?rev=294&view=rev
Author: balhoff
Date: 2007-01-17 11:45:58 -0800 (Wed, 17 Jan 2007)
Log Message:
-----------
Added "nexus" to list of possible adapters in schema.
Modified Paths:
--------------
phenote/trunk/conf/phenote-config.rnc
phenote/trunk/conf/phenote-config.xsd
Modified: phenote/trunk/conf/phenote-config.rnc
===================================================================
--- phenote/trunk/conf/phenote-config.rnc 2007-01-16 21:27:09 UTC (rev 293)
+++ phenote/trunk/conf/phenote-config.rnc 2007-01-17 19:45:58 UTC (rev 294)
@@ -12,8 +12,8 @@
dataadapter =
element dataadapter {
- ## for now just 2 dataadapters, phenoxml & phenosyntax
- attribute name {"phenoxml" | "phenosyntax"}
+ ## for now just 2 dataadapters, phenoxml & phenosyntax (and now also nexus)
+ attribute name {"phenoxml" | "phenosyntax" | "nexus"}
}
## Whether to check if ontology(obo) has been updated/more current obo file
Modified: phenote/trunk/conf/phenote-config.xsd
===================================================================
--- phenote/trunk/conf/phenote-config.xsd 2007-01-16 21:27:09 UTC (rev 293)
+++ phenote/trunk/conf/phenote-config.xsd 2007-01-17 19:45:58 UTC (rev 294)
@@ -15,12 +15,13 @@
<xs:complexType>
<xs:attribute name="name" use="required">
<xs:annotation>
- <xs:documentation>for now just 2 dataadapters, phenoxml & phenosyntax</xs:documentation>
+ <xs:documentation>for now just 2 dataadapters, phenoxml & phenosyntax (and now also nexus)</xs:documentation>
</xs:annotation>
<xs:simpleType>
<xs:restriction base="xs:token">
<xs:enumeration value="phenoxml"/>
<xs:enumeration value="phenosyntax"/>
+ <xs:enumeration value="nexus"/>
</xs:restriction>
</xs:simpleType>
</xs:attribute>
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|
|
From: <mg...@us...> - 2007-01-16 21:27:20
|
Revision: 293
http://svn.sourceforge.net/obo/?rev=293&view=rev
Author: mgibson
Date: 2007-01-16 13:27:09 -0800 (Tue, 16 Jan 2007)
Log Message:
-----------
separate html webstart install
Modified Paths:
--------------
phenote/trunk/build.xml
Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml 2007-01-16 21:24:30 UTC (rev 292)
+++ phenote/trunk/build.xml 2007-01-16 21:27:09 UTC (rev 293)
@@ -396,17 +396,22 @@
<!-- need to test if PHENOTE_VERSION is defined - possible?? -->
- <target name="webstart" depends="copy-jnlps">
+ <target name="webstart" depends="webstart-html,copy-jnlps">
<echo message="Env Var PHENOTE VERSION is set to ${env.PHENOTE_VERSION}" />
- <copy todir="phenote-webstart">
- <fileset file="doc/phenote-website/*.html"/>
- </copy>
<mkdir dir="phenote-webstart/${env.PHENOTE_VERSION}"/>
<copy todir="phenote-webstart/${env.PHENOTE_VERSION}/jars">
<fileset file="${lib}/*.jar"/>
</copy>
</target>
+ <target name="webstart-html">
+ <echo message="Env Var PHENOTE VERSION is set to ${env.PHENOTE_VERSION}" />
+ <copy todir="phenote-webstart">
+ <fileset file="doc/phenote-website/*.html"/>
+ </copy>
+ </target>
+
+
<target name="copy-jnlps">
<echo message="Env Var PHENOTE VERSION is set to ${env.PHENOTE_VERSION}" />
<copy todir="phenote-webstart/${env.PHENOTE_VERSION}">
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|
|
From: <mg...@us...> - 2007-01-16 21:25:47
|
Revision: 292
http://svn.sourceforge.net/obo/?rev=292&view=rev
Author: mgibson
Date: 2007-01-16 13:24:30 -0800 (Tue, 16 Jan 2007)
Log Message:
-----------
dichty -> dicty
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote.html
phenote/trunk/src/java/phenote/main/PhenoteVersion.java
Modified: phenote/trunk/doc/phenote-website/phenote.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.html 2007-01-16 20:53:57 UTC (rev 291)
+++ phenote/trunk/doc/phenote-website/phenote.html 2007-01-16 21:24:30 UTC (rev 292)
@@ -2,194 +2,276 @@
<html>
<head>
+
+
<meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">
+
+
<title>Phenote</title>
</head>
<body>
+
<h1 style="text-align: left;"><span style="font-weight: bold;"></span>Phenote<br>
+
</h1>
+
<br>
+
Phenote is a tool to annotate phenotypes using the Entity Quality
paradigm. It takes advantage of
ontologies. It uses term completion to allow curators quick access to
the ontology terms they want to use. <br>
+
<br>
+
<a href="1.0/phenote-flybase.jnlp">Phenote 1.0 for fly</a><br>
+
<br>
+
<a href="1.0/phenote-zfin.jnlp">Phenote 1.0 for zfin</a><br>
+
<br>
+
<a href="1.0/phenote-zfin.jnlp"></a><a href="1.0/phenote-human.jnlp">Phenote 1.0 for human</a><br>
+
<br>
+
To be clear the above webstart links for zfin & fly were made via
configuration not hard wired code. Thus one could in theory configure
phenote for ones own purposes.<br>
+
<br>
+
Recent addditions include the ability to add any field you like, post compose terms, bulk
update, undo, spring framework, and
synonyms now are shown in the completion list.<br>
+
<br>
+
Zebrafish requires
components of phenote(to plug into their non-public
website), not a full web app. Here is a proof of concept of some of
those
components:<br>
+
<br>
+
<a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby
Phenote(components used by Zfin)</a><br>
+
<br>
+
Webby phenote is a collaboration with Sohel Merchant at dictyBase.
Here is what they have done:<br>
+
<br>
-<a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">DichtyBase
+
+<a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">DictyBase
webby phenote</a><br>
+
<br>
+
<br>
+
I am doing these
releases to get feedback. Please report any bugs (ideally through the <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">bug
tracker</a>) and let me know what you
think (mg...@fr...).<br>
+
<br>
+
<h4>Phenote links:<br>
+
</h4>
+
<a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote">Phenote
email list</a><br>
+
<a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">Phenote
bug tracker</a><br>
+
<a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote-bug-tracker">Bug
tracker email list</a><br>
+
<a href="https://sourceforge.net/svn/?group_id=76834">Phenote source
code (obo sourceforge svn)</a><br>
+
<a href="https://lists.sourceforge.net/lists/listinfo/obo-svn-commit">Phenote
svn commit email list</a><br>
-<a href="http://wiki.dictybase.org/dictywiki/index.php/Phenotype_Curation_Tool_Documentation#Usage">Dichty
+
+<a href="http://wiki.dictybase.org/dictywiki/index.php/Phenotype_Curation_Tool_Documentation#Usage">Dicty
webby phenote wiki developer docs</a><br>
+
<a href="http://www.bioontology.org/wiki-internal/index.php/Phenotype_Annotation_Tool">Phenote
ncbo internal wiki (ncbo folk only)</a><br>
+
<br>
+
<a href="phenote-release-notes.html">Phenote Release Notes and old
webstart releases</a><br>
+
<br>
+
If the Phenote webstart link fails to do anything, then there are
probably problems
with webstart and/or java(has to be jdk 1.5). Take a look at my <a href="webstart-troubleshooting.html">webstart troubleshooting</a><br>
+
page.<br>
+
<br>
+
Click here for <a href="phenote-java-requirements.html">phenote java
requirements</a><br>
+
<br>
+
<br>
+
<br>
+
Old releases: <br>
+
<br>
+
<a href="0.9/phenote-flybase.jnlp">Phenote 0.9 for fly</a><br>
+
<a href="0.9/phenote-zfin.jnlp">Phenote (standalone) 0.9 for zfin</a><br>
+
<br>
+
<a href="0.8/phenote-flybase.jnlp">Phenote 0.8 for fly.</a><br>
+
<a href="0.8/phenote-zfin.jnlp">Phenote (standalone) 0.8 for zfin</a><br>
+
<br>
+
<a href="0.7/phenote-flybase.jnlp">Phenote 0.7 for fly.</a><br>
+
<a href="0.7/phenote-zfin.jnlp">Phenote (standalone) 0.7 for zfin</a><br>
+
<br>
+
<a href="0.6/phenote-flybase.jnlp">Phenote 0.6 with fly anatomy</a><br>
+
<br>
+
<a href="0.6/phenote-zfin.jnlp">Phenote 0.6 with zebrafish anatomy</a><br>
+
<br>
+
<a href="0.5/phenote-flybase.jnlp">Phenote 0.5 webstart for FlyBase</a><br>
+
<br>
+
<a href="0.5/phenote-zfin.jnlp">Phenote 0.5 webstart for ZFIN</a><br>
+
<br>
+
<a href="0.4/phenote-flybase.jnlp">Phenote 0.4 webstart for FlyBase</a><br>
+
<br>
+
<a href="0.4/phenote-zfin.jnlp">Phenote 0.4 webstart for ZFIN</a><br>
+
<br>
+
<a href="0.3.1/phenote-webstart.jnlp">Phenote for CToL group (0.3.1)</a>
(a special release for the CToL group that uses fish
taxonomy)<br>
+
<br>
+
<a href="0.3/phenote-webstart.jnlp">Phenote 0.3</a><br>
+
<br>
+
<a href="0.2/phenote-webstart.jnlp">Phenote 0.2</a><br>
+
<br>
+
<a href="0.1/phenote-webstart.jnlp">Phenote 0.1</a><br>
+
<br>
+
<br>
+
</body>
</html>
Modified: phenote/trunk/src/java/phenote/main/PhenoteVersion.java
===================================================================
--- phenote/trunk/src/java/phenote/main/PhenoteVersion.java 2007-01-16 20:53:57 UTC (rev 291)
+++ phenote/trunk/src/java/phenote/main/PhenoteVersion.java 2007-01-16 21:24:30 UTC (rev 292)
@@ -6,7 +6,7 @@
//private static final float MAJOR_VERSION_NUM = 0.8f;
//private static final float SUB_VERSION_NUM = .3f;
- private static final String VERSION = "1.0.1 dev"; // ??
+ private static final String VERSION = "1.0.2 dev"; // ??
// type is "dev" or "release"
//private static final String type = " dev"; // "release"
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From: <mg...@us...> - 2007-01-16 20:47:40
|
Revision: 290
http://svn.sourceforge.net/obo/?rev=290&view=rev
Author: mgibson
Date: 2007-01-16 12:47:37 -0800 (Tue, 16 Jan 2007)
Log Message:
-----------
Tagging the 1.0 release of phenote - generic datamodel
Added Paths:
-----------
phenote/tags/release-1.0/
Copied: phenote/tags/release-1.0 (from rev 289, phenote/trunk)
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From: <mg...@us...> - 2007-01-16 19:40:51
|
Revision: 289
http://svn.sourceforge.net/obo/?rev=289&view=rev
Author: mgibson
Date: 2007-01-16 11:40:51 -0800 (Tue, 16 Jan 2007)
Log Message:
-----------
appreviated labels for search params for real estate - maybe they should go in
a row on top or bottom?
Modified Paths:
--------------
phenote/trunk/phenote
phenote/trunk/src/java/phenote/gui/field/FieldPanel.java
phenote/trunk/src/java/phenote/gui/field/SearchParamPanel.java
Modified: phenote/trunk/phenote
===================================================================
--- phenote/trunk/phenote 2007-01-16 18:30:53 UTC (rev 288)
+++ phenote/trunk/phenote 2007-01-16 19:40:51 UTC (rev 289)
@@ -8,6 +8,6 @@
fi;
done
-java -Xmx600M -classpath ${PHENOTE_CLASSPATH} phenote.main.Phenote $@
+java -Xmx650M -classpath ${PHENOTE_CLASSPATH} phenote.main.Phenote $@
##java -Xmx300M -classpath classfiles:jars/oboedit.jar:jars/org.geneontology.jar:jars/BrowserLauncher2-10rc4.jar:jars/junit-4.0.jar:jars/tomcat-servlet.jar:jars/xbean.jar:jars/jsr173_1.0_api.jar:jars/phenoxmlbeans.jar:jars/phenoteconfigbeans.jar:jars/log4j-1.2.13.jar:jars/te-common.jar phenote.main.Phenote $@
Modified: phenote/trunk/src/java/phenote/gui/field/FieldPanel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/FieldPanel.java 2007-01-16 18:30:53 UTC (rev 288)
+++ phenote/trunk/src/java/phenote/gui/field/FieldPanel.java 2007-01-16 19:40:51 UTC (rev 289)
@@ -55,7 +55,7 @@
this.setLayout(bl);
fieldPanel = new JPanel(new GridBagLayout());
// panel inside of panel - i think is a leftover no reason now
- add(fieldPanel); // default flow layout?
+ add(fieldPanel);
// search param panel - maybe search panel should be added to main frame?
add(getSearchParamPanel().getPanel());
Modified: phenote/trunk/src/java/phenote/gui/field/SearchParamPanel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/SearchParamPanel.java 2007-01-16 18:30:53 UTC (rev 288)
+++ phenote/trunk/src/java/phenote/gui/field/SearchParamPanel.java 2007-01-16 19:40:51 UTC (rev 289)
@@ -28,14 +28,14 @@
BoxLayout boxLayout = new BoxLayout(panel,BoxLayout.Y_AXIS);
panel.setLayout(boxLayout);
panel.add(new JLabel("Search:"));
- termButton = makeButton("Terms");
+ termButton = makeButton("Term");
termButton.setSelected(true);
panel.add(termButton);
- synonymButton = makeButton("Synonyms");
+ synonymButton = makeButton("Syn");
panel.add(synonymButton);
- definitionButton = makeButton("Definitions");
+ definitionButton = makeButton("Def");
panel.add(definitionButton);
- obsoleteButton = makeButton("Obsolete");
+ obsoleteButton = makeButton("Obs");
panel.add(obsoleteButton);
return panel;
}
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From: <mg...@us...> - 2007-01-16 18:30:55
|
Revision: 288
http://svn.sourceforge.net/obo/?rev=288&view=rev
Author: mgibson
Date: 2007-01-16 10:30:53 -0800 (Tue, 16 Jan 2007)
Log Message:
-----------
fiddled with layout - with human.cfg the "Human Anatomy" ontology lable was
bigger than any previous label and caused the layout to go to hell - Field
Panel holds both its own field panel and the search param panel and was using
flow layout - which is a pretty awful default layout - now using box layout
and set some minimum sizes higher - and widened the whole app - for this to fit
Modified Paths:
--------------
phenote/trunk/phenote
phenote/trunk/src/java/phenote/gui/field/FieldPanel.java
phenote/trunk/src/java/phenote/main/Phenote.java
Modified: phenote/trunk/phenote
===================================================================
--- phenote/trunk/phenote 2007-01-12 20:06:28 UTC (rev 287)
+++ phenote/trunk/phenote 2007-01-16 18:30:53 UTC (rev 288)
@@ -8,6 +8,6 @@
fi;
done
-java -Xmx300M -classpath ${PHENOTE_CLASSPATH} phenote.main.Phenote $@
+java -Xmx600M -classpath ${PHENOTE_CLASSPATH} phenote.main.Phenote $@
##java -Xmx300M -classpath classfiles:jars/oboedit.jar:jars/org.geneontology.jar:jars/BrowserLauncher2-10rc4.jar:jars/junit-4.0.jar:jars/tomcat-servlet.jar:jars/xbean.jar:jars/jsr173_1.0_api.jar:jars/phenoxmlbeans.jar:jars/phenoteconfigbeans.jar:jars/log4j-1.2.13.jar:jars/te-common.jar phenote.main.Phenote $@
Modified: phenote/trunk/src/java/phenote/gui/field/FieldPanel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/FieldPanel.java 2007-01-12 20:06:28 UTC (rev 287)
+++ phenote/trunk/src/java/phenote/gui/field/FieldPanel.java 2007-01-16 18:30:53 UTC (rev 288)
@@ -6,6 +6,7 @@
import java.util.ArrayList;
import java.util.List;
+import javax.swing.BoxLayout;
import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swing.JComponent;
@@ -39,16 +40,28 @@
}
// false for post comp panel
public FieldPanel(boolean doAllOntologies) {
- //this.setPreferredSize(new Dimension(800,750));
- // should figure depth from # of fields really
- this.setMinimumSize(new Dimension(690,490));
+ initGui();
+ if (doAllOntologies)
+ initAllOntologies();
+ }
+
+ private void initGui() {
+ // should figure y from # of fields really
+ // width of ontology labels effects x
+ this.setMinimumSize(new Dimension(730,490));//690,490));
+ //this.setPreferredSize(new Dimension(2000,750)); // irrelevant in box layout
+ //this.setMaximumSize(new Dimension(2000,750));
+ BoxLayout bl = new BoxLayout(this,BoxLayout.X_AXIS); // grid bag?
+ this.setLayout(bl);
fieldPanel = new JPanel(new GridBagLayout());
// panel inside of panel - i think is a leftover no reason now
add(fieldPanel); // default flow layout?
- if (doAllOntologies)
- initAllOntologies();
+ // search param panel - maybe search panel should be added to main frame?
+ add(getSearchParamPanel().getPanel());
+
}
+
/** from selection in plump table - hmmm mvc - get from model change event -
should ACB listen for event and change themselves? - oh wait this is for selection
not editing - no editing in table silly - should do selection event/listener */
@@ -66,7 +79,7 @@
}
// search param panel - maybe search panel should be added to main frame?
- add(getSearchParamPanel().getPanel());
+ //add(getSearchParamPanel().getPanel()); --> initGui
}
SearchParamsI getSearchParams() {
Modified: phenote/trunk/src/java/phenote/main/Phenote.java
===================================================================
--- phenote/trunk/src/java/phenote/main/Phenote.java 2007-01-12 20:06:28 UTC (rev 287)
+++ phenote/trunk/src/java/phenote/main/Phenote.java 2007-01-16 18:30:53 UTC (rev 288)
@@ -167,7 +167,7 @@
frame = new JFrame("Phenote "+PhenoteVersion.versionString());
frame.getContentPane().add(makeMainPanel());
MenuManager.createMenuManager(frame);
- frame.setPreferredSize(new Dimension(1100,700));
+ frame.setPreferredSize(new Dimension(1130,700)); //1100,700));
if (standalone) // if stand alone exit java on window close
frame.addWindowListener(new WindowExit());
frame.pack();
@@ -194,11 +194,9 @@
BoxLayout bl = new BoxLayout(upperPanel,BoxLayout.X_AXIS);
upperPanel.setLayout(bl);
- fieldPanel = new FieldPanel();
+ fieldPanel = new FieldPanel(); // field panel contains search params
upperPanel.add(fieldPanel);
-
-
termInfo = new TermInfo(); //fieldPanel);
upperPanel.add(termInfo.getComponent());
//++gbc.gridx; // ??
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|
|
From: <mg...@us...> - 2007-01-12 20:06:28
|
Revision: 287
http://svn.sourceforge.net/obo/?rev=287&view=rev
Author: mgibson
Date: 2007-01-12 12:06:28 -0800 (Fri, 12 Jan 2007)
Log Message:
-----------
hmmm
Modified Paths:
--------------
phenote/trunk/build.xml
phenote/trunk/doc/phenote-website/phenote-human.jnlp
Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml 2007-01-12 19:55:16 UTC (rev 286)
+++ phenote/trunk/build.xml 2007-01-12 20:06:28 UTC (rev 287)
@@ -396,20 +396,25 @@
<!-- need to test if PHENOTE_VERSION is defined - possible?? -->
- <target name="webstart">
+ <target name="webstart" depends="copy-jnlps">
<echo message="Env Var PHENOTE VERSION is set to ${env.PHENOTE_VERSION}" />
<copy todir="phenote-webstart">
<fileset file="doc/phenote-website/*.html"/>
</copy>
<mkdir dir="phenote-webstart/${env.PHENOTE_VERSION}"/>
- <copy todir="phenote-webstart/${env.PHENOTE_VERSION}">
- <fileset file="doc/phenote-website/*.jnlp"/>
- </copy>
<copy todir="phenote-webstart/${env.PHENOTE_VERSION}/jars">
<fileset file="${lib}/*.jar"/>
</copy>
</target>
+ <target name="copy-jnlps">
+ <echo message="Env Var PHENOTE VERSION is set to ${env.PHENOTE_VERSION}" />
+ <copy todir="phenote-webstart/${env.PHENOTE_VERSION}">
+ <fileset file="doc/phenote-website/*.jnlp"/>
+ </copy>
+ </target>
+
+
<target name="sign-webstart-jars">
<signjar keystore="plumpkey" alias="signFiles"
storepass="plumper" keypass="plumper">
@@ -420,10 +425,10 @@
</target>
<target name="webstart-just-phenote-jar" depends="build-all,jar">
- <signjar jar="${lib}/phenote.jar" keystore="plumpkey" alias="signFiles"
- storepass="plumper" keypass="plumper"/>
<copy file="${lib}/phenote.jar"
todir="phenote-webstart/${env.PHENOTE_VERSION}/jars"/>
+ <signjar jar="phenote-webstart/${env.PHENOTE_VERSION}/jars/phenote.jar" keystore="plumpkey" alias="signFiles"
+ storepass="plumper" keypass="plumper"/>
</target>
Modified: phenote/trunk/doc/phenote-website/phenote-human.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-human.jnlp 2007-01-12 19:55:16 UTC (rev 286)
+++ phenote/trunk/doc/phenote-website/phenote-human.jnlp 2007-01-12 20:06:28 UTC (rev 287)
@@ -34,8 +34,8 @@
<jar href="jars/phenoteconfigbeans.jar" />
<jar href="jars/tomcat-servlet.jar" />
<jar href="jars/xbean.jar" />
- <jar href="jars/te-common.jar" />
- <jar href="jars/log4j-1.2.13.jar" />
+ <jar href="jars/te-common.jar" />
+ <jar href="jars/log4j-1.2.13.jar" />
</resources>
<application-desc main-class="phenote.main.Phenote">
<argument>-c</argument>
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|
|
From: <mg...@us...> - 2007-01-12 19:55:18
|
Revision: 286
http://svn.sourceforge.net/obo/?rev=286&view=rev
Author: mgibson
Date: 2007-01-12 11:55:16 -0800 (Fri, 12 Jan 2007)
Log Message:
-----------
gui -> main for run
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-human.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-human.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-human.jnlp 2007-01-12 19:42:40 UTC (rev 285)
+++ phenote/trunk/doc/phenote-website/phenote-human.jnlp 2007-01-12 19:55:16 UTC (rev 286)
@@ -36,8 +36,8 @@
<jar href="jars/xbean.jar" />
<jar href="jars/te-common.jar" />
<jar href="jars/log4j-1.2.13.jar" />
-<</resources>
-<application-desc main-class="phenote.gui.Phenote">
+</resources>
+<application-desc main-class="phenote.main.Phenote">
<argument>-c</argument>
<argument>/human.cfg</argument>
</application-desc>
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