https://wiki.geneontology.org/index.php?title=Annotation_29Apr10&feed=atom&action=historyAnnotation 29Apr10 - Revision history2024-03-28T14:22:13ZRevision history for this page on the wikiMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=Annotation_29Apr10&diff=49599&oldid=prevGail at 20:24, 9 April 20142014-04-09T20:24:31Z<p></p>
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</table>Gailhttps://wiki.geneontology.org/index.php?title=Annotation_29Apr10&diff=27087&oldid=prevRama: /* ATP catabolism for Kinase activity */2010-04-29T16:51:58Z<p><span dir="auto"><span class="autocomment">ATP catabolism for Kinase activity</span></span></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>===ATP catabolism for Kinase activity===</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>===ATP catabolism for Kinase activity===</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>If a geneproduct has kinase activity, would you make ATP binding and ATP catabolic process annotations?</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>If a geneproduct has kinase activity, would you make ATP binding and ATP catabolic process annotations?</div></td></tr>
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</table>Ramahttps://wiki.geneontology.org/index.php?title=Annotation_29Apr10&diff=27086&oldid=prevRama at 16:51, 29 April 20102010-04-29T16:51:28Z<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>* Could the WG email lists be administered by a person in addition to Mike? As it would be handy to keep an eye on who has signed up/ who has not when sending emails round (Emily)</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>* Could the WG email lists be administered by a person in addition to Mike? As it would be handy to keep an eye on who has signed up/ who has not when sending emails round (Emily)</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">===ATP catabolism for Kinase activity===</ins></div></td></tr>
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</table>Ramahttps://wiki.geneontology.org/index.php?title=Annotation_29Apr10&diff=27061&oldid=prevPascale at 13:07, 29 April 20102010-04-29T13:07:49Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 09:07, 29 April 2010</td>
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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>Pascale: tor is widely accepted as the Target of Rapamycin. tor has a very central role in regulation of protein synthesis, so one would expect pleiotropic effects from its inactivation. In other words, I can see how this is very downstream, but it's not inconsistent with annotating RNA polymerase to embryonic development. I'll add this in the 'downstream effect discussion. </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>Pascale: tor is widely accepted as the Target of Rapamycin. tor has a very central role in regulation of protein synthesis, so one would expect pleiotropic effects from its inactivation. In other words, I can see how this is very downstream, but it's not inconsistent with annotating RNA polymerase to embryonic development. I'll add this in the 'downstream effect discussion. </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>
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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>===Management of WG email lists===</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>===Management of WG email lists===</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>* Could the WG email lists be administered by a person in addition to Mike? As it would be handy to keep an eye on who has signed up/ who has not when sending emails round (Emily)</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>* Could the WG email lists be administered by a person in addition to Mike? As it would be handy to keep an eye on who has signed up/ who has not when sending emails round (Emily)</div></td></tr>
</table>Pascalehttps://wiki.geneontology.org/index.php?title=Annotation_29Apr10&diff=27060&oldid=prevPascale at 13:06, 29 April 20102010-04-29T13:06:31Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 09:06, 29 April 2010</td>
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<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> </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;">===</ins>IMP evidence code needs clarfication.<ins style="font-weight: bold; text-decoration: none;">===</ins></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;">* </del>IMP evidence code needs clarfication.</div></td><td colspan="2" class="diff-side-added"></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>The issue is whether IMP GO annotations should be made from chemical inhibition studies in which a drug is used on whole cells to inhibit a specific protein. (Note, this is distinct from chemical genomics studies where a chemical is used in combination with a mutant collection; we do already curate these as mutant phenotypes.) An example is in this paper</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>The issue is whether IMP GO annotations should be made from chemical inhibition studies in which a drug is used on whole cells to inhibit a specific protein. (Note, this is distinct from chemical genomics studies where a chemical is used in combination with a mutant collection; we do already curate these as mutant phenotypes.) An example is in this paper</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>
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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>So, annotating based on chemical inhibition is not a good idea unless you know the chemical is very specific. This bit should be highlighted in the evidence code documentation.</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>So, annotating based on chemical inhibition is not a good idea unless you know the chemical is very specific. This bit should be highlighted in the evidence code documentation.</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 colspan="2" class="diff-side-deleted"></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;">----</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">Pascale: tor is widely accepted as the Target of Rapamycin. tor has a very central role in regulation of protein synthesis, so one would expect pleiotropic effects from its inactivation. In other words, I can see how this is very downstream, but it's not inconsistent with annotating RNA polymerase to embryonic development. I'll add this in the 'downstream effect discussion. </ins></div></td></tr>
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<tr><td colspan="2" class="diff-side-deleted"></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;">===Management of WG email lists===</ins></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>* Could the WG email lists be administered by a person in addition to Mike? As it would be handy to keep an eye on who has signed up/ who has not when sending emails round (Emily)</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>* Could the WG email lists be administered by a person in addition to Mike? As it would be handy to keep an eye on who has signed up/ who has not when sending emails round (Emily)</div></td></tr>
</table>Pascalehttps://wiki.geneontology.org/index.php?title=Annotation_29Apr10&diff=27053&oldid=prevEdimmer: /* Items */2010-04-29T10:12:48Z<p><span dir="auto"><span class="autocomment">Items</span></span></p>
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</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l16">Line 16:</td>
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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;"><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"></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>So, annotating based on chemical inhibition is not a good idea unless you know the chemical is very specific. This bit should be highlighted in the evidence code documentation.</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>So, annotating based on chemical inhibition is not a good idea unless you know the chemical is very specific. This bit should be highlighted in the evidence code documentation.</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">* Could the WG email lists be administered by a person in addition to Mike? As it would be handy to keep an eye on who has signed up/ who has not when sending emails round (Emily)</ins></div></td></tr>
</table>Edimmerhttps://wiki.geneontology.org/index.php?title=Annotation_29Apr10&diff=27050&oldid=prevRama: Created page with '==Items== * IMP evidence code needs clarfication. The issue is whether IMP GO annotations should be made from chemical inhibition studies in which a drug is used on whole cells …'2010-04-29T00:22:16Z<p>Created page with '==Items== * IMP evidence code needs clarfication. The issue is whether IMP GO annotations should be made from chemical inhibition studies in which a drug is used on whole cells …'</p>
<p><b>New page</b></p><div>==Items==<br />
<br />
* IMP evidence code needs clarfication.<br />
The issue is whether IMP GO annotations should be made from chemical inhibition studies in which a drug is used on whole cells to inhibit a specific protein. (Note, this is distinct from chemical genomics studies where a chemical is used in combination with a mutant collection; we do already curate these as mutant phenotypes.) An example is in this paper<br />
<br />
http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1000294<br />
<br />
C. albicans Tor1p is essential and there are no available reduction-of-function alleles, so they use the inhibitor rapamycin to reduce Tor1p function. Rapamycin-treated cells have increased expression of adhesin genes, so the authors conclude that Tor1p negatively regulates adhesion. Is an annotation to "negative regulation of adhesion" with IMP evidence justified? GOC documentation says that IMP can be used based on<br />
<br />
"any procedure that disturbs the expression or function of the gene, including RNAi, anti-sense RNAs,<br />
antibody depletion, or the use of any molecule or experimental condition that may disturb or affect <br />
the normal functioning of the gene, including: inhibitors, blockers, modifiers, any type of antagonists,<br />
temperature jumps, changes in pH or ionic strength." <br />
<br />
Rapamycin has a lot of effects, such as inhibiting expression of genes involved in ribosome biogenesis and other processes, which may or may not be due to its inhibition of Tor1p.<br />
<br />
So, annotating based on chemical inhibition is not a good idea unless you know the chemical is very specific. This bit should be highlighted in the evidence code documentation.</div>Rama