http://mx.phenomix.org/index.php?title=Guide/Ontology&feed=atom&action=history Guide/Ontology - Revision history 2024-03-29T07:40:47Z Revision history for this page on the wiki MediaWiki 1.20.0 http://mx.phenomix.org/index.php?title=Guide/Ontology&diff=1617&oldid=prev Matt at 07:04, 29 December 2006 2006-12-29T07:04:43Z <p></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 07:04, 29 December 2006</td> </tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[Guide | Guide home]]</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>One of the strengths of databasing is the possibility to cross-reference. In our project we have the potential to take advantage of this by accessing the Hymenoptera Ontology Project. Whenever you are viewing a character description ('''Fig. 11''') you can click &lt;span class=&quot;hll&quot;&gt;markup description&lt;/span&gt; in the menu to the left and MX will highlight all words in the description with a corresponding entry in the ontology. The highlights are links, each of which will take you to a definition on a public webpage also powered by MX ('''Fig. 13'''). Furthermore, there is a private part which is available to all users of the chalcid project ('''Fig. 14'''). Just click &lt;span class=&quot;hll&quot;&gt;Change projects&lt;/span&gt; at the top right of a page and choose &lt;span class=&quot;hll&quot;&gt;Hymenoptera Ontology&lt;/span&gt;. There is no need to log out first, and you can even access both projects and have multiple windows open simultaneously. &lt;br/&gt;&lt;br/&gt;</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>One of the strengths of databasing is the possibility to cross-reference. In our project we have the potential to take advantage of this by accessing the Hymenoptera Ontology Project. Whenever you are viewing a character description ('''Fig. 11''') you can click &lt;span class=&quot;hll&quot;&gt;markup description&lt;/span&gt; in the menu to the left and MX will highlight all words in the description with a corresponding entry in the ontology. The highlights are links, each of which will take you to a definition on a public webpage also powered by MX ('''Fig. 13'''). Furthermore, there is a private part which is available to all users of the chalcid project ('''Fig. 14'''). Just click &lt;span class=&quot;hll&quot;&gt;Change projects&lt;/span&gt; at the top right of a page and choose &lt;span class=&quot;hll&quot;&gt;Hymenoptera Ontology&lt;/span&gt;. There is no need to log out first, and you can even access both projects and have multiple windows open simultaneously. &lt;br/&gt;&lt;br/&gt;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> </table> Matt http://mx.phenomix.org/index.php?title=Guide/Ontology&diff=1616&oldid=prev Matt at 07:04, 29 December 2006 2006-12-29T07:04:17Z <p></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 07:04, 29 December 2006</td> </tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>One of the strengths of databasing is the possibility to cross-reference. In our project we have the potential to take advantage of this by accessing the Hymenoptera Ontology Project. Whenever you are viewing a character description ('''Fig. 11''') you can click &lt;span class=&quot;hll&quot;&gt;markup description&lt;/span&gt; in the menu to the left and MX will highlight all words in the description with a corresponding entry in the ontology. The highlights are links, each of which will take you to a definition on a public webpage also powered by MX ('''Fig. 13'''). Furthermore, there is a private part which is &#160;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>One of the strengths of databasing is the possibility to cross-reference. In our project we have the potential to take advantage of this by accessing the Hymenoptera Ontology Project. Whenever you are viewing a character description ('''Fig. 11''') you can click &lt;span class=&quot;hll&quot;&gt;markup description&lt;/span&gt; in the menu to the left and MX will highlight all words in the description with a corresponding entry in the ontology. The highlights are links, each of which will take you to a definition on a public webpage also powered by MX ('''Fig. 13'''). Furthermore, there is a private part which is available to all users of the chalcid project ('''Fig. 14'''). Just click &lt;span class=&quot;hll&quot;&gt;Change projects&lt;/span&gt; at the top right of a page and choose &lt;span class=&quot;hll&quot;&gt;Hymenoptera Ontology&lt;/span&gt;. There is no need to log out first, and you can even access both projects and have multiple windows open simultaneously. &lt;br/&gt;&lt;br/&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>available to all users of the chalcid project ('''Fig. 14'''). Just click &lt;span class=&quot;hll&quot;&gt;Change projects&lt;/span&gt; at the top right of a page and choose &lt;span class=&quot;hll&quot;&gt;Hymenoptera Ontology&lt;/span&gt;. There is no need to log out first, and you can even access both projects and have multiple windows open simultaneously. &lt;br/&gt;&lt;br/&gt;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The first view presents you with a choice of what to do. Typically you will want to either &lt;span class=&quot;hll&quot;&gt;list all the terms&lt;/span&gt; ('''Fig. 14'''), &lt;span class=&quot;hll&quot;&gt;search for term&lt;/span&gt; through the blue box, &lt;span class=&quot;hll&quot;&gt;add a new term&lt;/span&gt; ('''Fig. 15 &amp; 16''') or &lt;span class=&quot;hll&quot;&gt;edit&lt;/span&gt; an existing definition. All these procedures are pretty straightforward and all you really need to know is that when creating a new term you are not required to enter &lt;span class=&quot;hll&quot;&gt;highest taxon name to which this term applies&lt;/span&gt; ('''Fig. 16''') although we would recommend it. A term can also have a number of relationships such as the terminal button being part_of the antenna. If we would later decide on another name for terminal button this can be indicated by it being a synonym_of, ''e.g.'', reduced apical flagellomere.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The first view presents you with a choice of what to do. Typically you will want to either &lt;span class=&quot;hll&quot;&gt;list all the terms&lt;/span&gt; ('''Fig. 14'''), &lt;span class=&quot;hll&quot;&gt;search for term&lt;/span&gt; through the blue box, &lt;span class=&quot;hll&quot;&gt;add a new term&lt;/span&gt; ('''Fig. 15 &amp; 16''') or &lt;span class=&quot;hll&quot;&gt;edit&lt;/span&gt; an existing definition. All these procedures are pretty straightforward and all you really need to know is that when creating a new term you are not required to enter &lt;span class=&quot;hll&quot;&gt;highest taxon name to which this term applies&lt;/span&gt; ('''Fig. 16''') although we would recommend it. A term can also have a number of relationships such as the terminal button being part_of the antenna. If we would later decide on another name for terminal button this can be indicated by it being a synonym_of, ''e.g.'', reduced apical flagellomere. <ins class="diffchange diffchange-inline"> Or the entry could simply be destroyed.&lt;br/&gt;</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160;</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">There is actually an ontology part of the chalcid project too, but everything is set up so that the chalcid</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">project is accessing the collaborative general ontology rather than the local version which is accessible for our</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">project only. This way we can make use of the many already entered terms.&lt;br/&gt;</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160;</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">[[Image:Guide_fig_11.jpg|frame|none| '''Fig. 11.''' Single character show.]]</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160;</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">[[Image:Guide_fig_13.png|frame|none| '''Fig. 13.''' Public ontology.]]</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160;</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">[[Image:Guide_fig_14.png|frame|none| '''Fig. 14.''' Listing terms.]]</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160;</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">[[Image:Guide_fig_15.jpg|frame|none| '''Fig. 15.''' New term.]]</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160;</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">[[Image:Guide_fig_16.png|frame|none| '''Fig. 16.''' Show term.]]</ins></div></td></tr> </table> Matt http://mx.phenomix.org/index.php?title=Guide/Ontology&diff=1600&oldid=prev Matt at 20:49, 28 December 2006 2006-12-28T20:49:37Z <p></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 20:49, 28 December 2006</td> </tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>One of the strengths of databasing is the possibility to cross-reference. In our project we have the potential to take advantage of this by accessing the Hymenoptera Ontology Project. Whenever you are viewing a character description (Fig. 11) you can click markup description in the menu to the left and MX will highlight all words in the description with a corresponding entry in the ontology. The highlights are links, each of which will take you to a definition on a public webpage also powered by MX (Fig. 13). Furthermore, there is a private part which is &#160;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>One of the strengths of databasing is the possibility to cross-reference. In our project we have the potential to take advantage of this by accessing the Hymenoptera Ontology Project. Whenever you are viewing a character description (<ins class="diffchange diffchange-inline">'''</ins>Fig. 11<ins class="diffchange diffchange-inline">'''</ins>) you can click <ins class="diffchange diffchange-inline">&lt;span class=&quot;hll&quot;&gt;</ins>markup description<ins class="diffchange diffchange-inline">&lt;/span&gt; </ins>in the menu to the left and MX will highlight all words in the description with a corresponding entry in the ontology. The highlights are links, each of which will take you to a definition on a public webpage also powered by MX (<ins class="diffchange diffchange-inline">'''</ins>Fig. 13<ins class="diffchange diffchange-inline">'''</ins>). Furthermore, there is a private part which is &#160;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>available to all users of the chalcid project (Fig. 14). Just click Change projects at the top right of a page and choose Hymenoptera Ontology <del class="diffchange diffchange-inline">located immediately below the chalcid project in figure 3</del>. There is no need to log out first, and you can even access both projects and have multiple windows open simultaneously. &lt;br/&gt;&lt;br/&gt;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>available to all users of the chalcid project (<ins class="diffchange diffchange-inline">'''</ins>Fig. 14<ins class="diffchange diffchange-inline">'''</ins>). Just click <ins class="diffchange diffchange-inline">&lt;span class=&quot;hll&quot;&gt;</ins>Change projects<ins class="diffchange diffchange-inline">&lt;/span&gt; </ins>at the top right of a page and choose <ins class="diffchange diffchange-inline">&lt;span class=&quot;hll&quot;&gt;</ins>Hymenoptera Ontology<ins class="diffchange diffchange-inline">&lt;/span&gt;</ins>. There is no need to log out first, and you can even access both projects and have multiple windows open simultaneously. &lt;br/&gt;&lt;br/&gt;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The first view presents you with a choice of what to do. Typically you will want to either list all the terms (Fig. 14), search for term through the blue box, add a new term (Fig. 15 &amp; 16) or edit an existing definition. All these procedures are pretty straightforward and all you really need to know is that when creating a new term you are not required to enter highest taxon name to which this term applies (Fig. 16) although we would recommend it. A term can also have a number of relationships such as the terminal button being part_of the antenna. If we would later decide on another name for terminal button this can be indicated by it being a synonym_of, e.g., reduced apical flagellomere.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The first view presents you with a choice of what to do. Typically you will want to either <ins class="diffchange diffchange-inline">&lt;span class=&quot;hll&quot;&gt;</ins>list all the terms<ins class="diffchange diffchange-inline">&lt;/span&gt; </ins>(<ins class="diffchange diffchange-inline">'''</ins>Fig. 14<ins class="diffchange diffchange-inline">'''</ins>), <ins class="diffchange diffchange-inline">&lt;span class=&quot;hll&quot;&gt;</ins>search for term<ins class="diffchange diffchange-inline">&lt;/span&gt; </ins>through the blue box, <ins class="diffchange diffchange-inline">&lt;span class=&quot;hll&quot;&gt;</ins>add a new term<ins class="diffchange diffchange-inline">&lt;/span&gt; </ins>(<ins class="diffchange diffchange-inline">'''</ins>Fig. 15 &amp; 16<ins class="diffchange diffchange-inline">'''</ins>) or <ins class="diffchange diffchange-inline">&lt;span class=&quot;hll&quot;&gt;</ins>edit<ins class="diffchange diffchange-inline">&lt;/span&gt; </ins>an existing definition. All these procedures are pretty straightforward and all you really need to know is that when creating a new term you are not required to enter <ins class="diffchange diffchange-inline">&lt;span class=&quot;hll&quot;&gt;</ins>highest taxon name to which this term applies<ins class="diffchange diffchange-inline">&lt;/span&gt; </ins>(<ins class="diffchange diffchange-inline">'''</ins>Fig. 16<ins class="diffchange diffchange-inline">'''</ins>) although we would recommend it. A term can also have a number of relationships such as the terminal button being part_of the antenna. If we would later decide on another name for terminal button this can be indicated by it being a synonym_of, <ins class="diffchange diffchange-inline">''</ins>e.g.<ins class="diffchange diffchange-inline">''</ins>, reduced apical flagellomere.</div></td></tr> </table> Matt http://mx.phenomix.org/index.php?title=Guide/Ontology&diff=1521&oldid=prev Matt at 22:55, 22 December 2006 2006-12-22T22:55:44Z <p></p> <p><b>New page</b></p><div>One of the strengths of databasing is the possibility to cross-reference. In our project we have the potential to take advantage of this by accessing the Hymenoptera Ontology Project. Whenever you are viewing a character description (Fig. 11) you can click markup description in the menu to the left and MX will highlight all words in the description with a corresponding entry in the ontology. The highlights are links, each of which will take you to a definition on a public webpage also powered by MX (Fig. 13). Furthermore, there is a private part which is <br /> available to all users of the chalcid project (Fig. 14). Just click Change projects at the top right of a page and choose Hymenoptera Ontology located immediately below the chalcid project in figure 3. There is no need to log out first, and you can even access both projects and have multiple windows open simultaneously. &lt;br/&gt;&lt;br/&gt;<br /> <br /> The first view presents you with a choice of what to do. Typically you will want to either list all the terms (Fig. 14), search for term through the blue box, add a new term (Fig. 15 &amp; 16) or edit an existing definition. All these procedures are pretty straightforward and all you really need to know is that when creating a new term you are not required to enter highest taxon name to which this term applies (Fig. 16) although we would recommend it. A term can also have a number of relationships such as the terminal button being part_of the antenna. If we would later decide on another name for terminal button this can be indicated by it being a synonym_of, e.g., reduced apical flagellomere.</div> Matt