https://wiki.geneontology.org/index.php?title=OBO-Edit:_FAQ&feed=atom&action=historyOBO-Edit: FAQ - Revision history2024-03-28T09:24:55ZRevision history for this page on the wikiMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=OBO-Edit:_FAQ&diff=52518&oldid=prevGail at 19:26, 30 June 20142014-06-30T19:26:07Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Useful items from this FAQ will eventually be integrated into the main user's guide, but this page can be a useful place to check in if your question isn't in the guide at the moment...</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Useful items from this FAQ will eventually be integrated into the main user's guide, but this page can be a useful place to check in if your question isn't in the guide at the moment...</div></td></tr>
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</table>Gailhttps://wiki.geneontology.org/index.php?title=OBO-Edit:_FAQ&diff=1872&oldid=prevJrichter at 17:57, 10 April 20072007-04-10T17:57:01Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Useful items from this FAQ will eventually be integrated into the main user's guide, but this page can be a useful place to check in if your question isn't in the guide at the moment...</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Useful items from this FAQ will eventually be integrated into the main user's guide, but this page can be a useful place to check in if your question isn't in the guide at the moment...</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* '''My ontology has way too many roots! Why?''' - There <del style="font-weight: bold; text-decoration: none;">2 </del>major causes for this problem:</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* '''My ontology has way too many roots! Why?''' - There <ins style="font-weight: bold; text-decoration: none;">3 </ins>major causes for this problem:</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*# ''Cross products'' - Are there many cross products in this ontology? In a perfectly non-redundant ontology, all cross-product terms will appear to be roots unless the reasoner is turned on. When the reasoner is enabled, the cross-product terms will be placed in the graph correctly. The internal editors version of the Sequence Ontology works this way, for example. If this is the problem, turn on the reasoner.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*# ''Cross products'' - Are there many cross products in this ontology? In a perfectly non-redundant ontology, all cross-product terms will appear to be roots unless the reasoner is turned on. When the reasoner is enabled, the cross-product terms will be placed in the graph correctly. The internal editors version of the Sequence Ontology works this way, for example. If this is the problem, turn on the reasoner.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*# ''Transitivity'' - By default, OBO-Edit doesn't show non-transitive relationships in the Ontology Editor. If a term is connected to its parents only by non-transitive links, it will appear to be an orphan. To solve this problem, first check to make sure that all transitive relationships are really ''marked'' as transitive relationships. If there are still orphans after you've done that, the '''ideal''' course would be to edit your ontology and guarantee that all terms have a complete is_a path to the root (otherwise your ontology is technically incorrect). If you're happy with a broken ontology and just want to change the display, open the Global Filters plugin. Select the Link Filter that contains the condition "Link Self NOT Is Transitive" and delete that condition.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*# ''Transitivity'' - By default, OBO-Edit doesn't show non-transitive relationships in the Ontology Editor. If a term is connected to its parents only by non-transitive links, it will appear to be an orphan. To solve this problem, first check to make sure that all transitive relationships are really ''marked'' as transitive relationships. If there are still orphans after you've done that, the '''ideal''' course would be to edit your ontology and guarantee that all terms have a complete is_a path to the root (otherwise your ontology is technically incorrect). If you're happy with a broken ontology and just want to change the display, open the Global Filters plugin. Select the Link Filter that contains the condition "Link Self NOT Is Transitive" and delete that condition.</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*#<del style="font-weight: bold; text-decoration: none;">OR </del>- <del style="font-weight: bold; text-decoration: none;">the other possibility is that you</del>'ve left a filter on from the previous session - I've done this many times!</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*# <ins style="font-weight: bold; text-decoration: none;">''Old Filters'' </ins>- <ins style="font-weight: bold; text-decoration: none;">You</ins>'ve <ins style="font-weight: bold; text-decoration: none;">accidentally </ins>left a filter on from the previous session - I've done this many times!</div></td></tr>
</table>Jrichterhttps://wiki.geneontology.org/index.php?title=OBO-Edit:_FAQ&diff=1871&oldid=prevJrichter: New page: Useful items from this FAQ will eventually be integrated into the main user's guide, but this page can be a useful place to check in if your question isn't in the guide at the moment... *...2007-04-10T17:51:07Z<p>New page: Useful items from this FAQ will eventually be integrated into the main user's guide, but this page can be a useful place to check in if your question isn't in the guide at the moment... *...</p>
<p><b>New page</b></p><div>Useful items from this FAQ will eventually be integrated into the main user's guide, but this page can be a useful place to check in if your question isn't in the guide at the moment...<br />
<br />
* '''My ontology has way too many roots! Why?''' - There 2 major causes for this problem:<br />
*# ''Cross products'' - Are there many cross products in this ontology? In a perfectly non-redundant ontology, all cross-product terms will appear to be roots unless the reasoner is turned on. When the reasoner is enabled, the cross-product terms will be placed in the graph correctly. The internal editors version of the Sequence Ontology works this way, for example. If this is the problem, turn on the reasoner.<br />
*# ''Transitivity'' - By default, OBO-Edit doesn't show non-transitive relationships in the Ontology Editor. If a term is connected to its parents only by non-transitive links, it will appear to be an orphan. To solve this problem, first check to make sure that all transitive relationships are really ''marked'' as transitive relationships. If there are still orphans after you've done that, the '''ideal''' course would be to edit your ontology and guarantee that all terms have a complete is_a path to the root (otherwise your ontology is technically incorrect). If you're happy with a broken ontology and just want to change the display, open the Global Filters plugin. Select the Link Filter that contains the condition "Link Self NOT Is Transitive" and delete that condition.<br />
*#OR - the other possibility is that you've left a filter on from the previous session - I've done this many times!</div>Jrichter