https://wiki.geneontology.org/index.php?title=LEGO_May_9,_2016&feed=atom&action=historyLEGO May 9, 2016 - Revision history2024-03-29T04:42:18ZRevision history for this page on the wikiMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=LEGO_May_9,_2016&diff=60734&oldid=prevDavid: /* Capturing Extent of Causally Upstream Of in a GAF/GPAD */2016-05-11T10:54:41Z<p><span dir="auto"><span class="autocomment">Capturing Extent of Causally Upstream Of in a GAF/GPAD</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>*Contrast the translation upstream vs the acylation upstream - the former is not known to be Wnt-specific, but the latter is Wnt-specific</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>*Contrast the translation upstream vs the acylation upstream - the former is not known to be Wnt-specific, but the latter is Wnt-specific</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>** DOS: But note - *this* could be captured under a broader term for cell-cell signaling by wnt - with parts for ligand processing, secretion, intercellular transport/presentation, & signal transduction. The advantage of this is that it makes it explicit what it means to be wnt-specific. If we leave this to the LEGO model, then it comes down to an undocumented curator choice about when to use place causally_upstream_of links. Are we confident of curator consistency on this?</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>** DOS: But note - *this* could be captured under a broader term for cell-cell signaling by wnt - with parts for ligand processing, secretion, intercellular transport/presentation, & signal transduction. The advantage of this is that it makes it explicit what it means to be wnt-specific. If we leave this to the LEGO model, then it comes down to an undocumented curator choice about when to use place causally_upstream_of links. Are we confident of curator consistency on this?</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>** DPH: It could but we would need to be really careful. This seems straightforward on the surface, but the underlying biology might be more complex than first thought. The reason that the signaling group decided to start and classify a signaling cascade based on the receptor, was because they found examples of different types of ligands binding different types of receptors, not always named for the ligand. This could lead to confusion in annotation. To avoid this using the suggested strategy, it would be necessary to define the signal transduction in the 'cell-cell signaling process by X' as a signal transduction that starts with the reception of a signal enabled by X. This doesn't contradict any of the work already done.</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>** DPH: It could but we would need to be really careful. This seems straightforward on the surface, but the underlying biology might be more complex than first thought. The reason that the signaling group decided to start and classify a signaling cascade based on the receptor, was because they found examples of different types of ligands binding different types of receptors, not always named for the ligand. This could lead to confusion in annotation. To avoid this using the suggested strategy, it would be necessary to define the signal transduction in the 'cell-cell signaling process by X' as a signal transduction that starts with the reception of a signal enabled by X. This doesn't contradict any of the work already done<ins style="font-weight: bold; text-decoration: none;">. This should be an ontology discussion</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>*Proposal is to add these qualifiers to the GAF so we can get the annotations curators would normally make in the GAF:</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>*Proposal is to add these qualifiers to the GAF so we can get the annotations curators would normally make in the GAF:</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>** DOS: The logically consistent way to do this would be to add the qualifiers whether the relationship was asserted or inferred. DH arguing for this only where the link is asserted by a curator (?) </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>** DOS: The logically consistent way to do this would be to add the qualifiers whether the relationship was asserted or inferred. DH arguing for this only where the link is asserted by a curator (?) </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>** DPH: No, but in the conventional gaf, it would not be straightforward to attribute evidence to the inferred annotation with the qualifier. To get things moving, for now we would simply want the asserted ones. In the future we might want to have the ability to see when an asserted relation and an inferred relation 'contradict' one another. For example if a gene product executes a function that is inferred to be part of a process, but is asserted to execute a function that regulates the process.</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>** DPH: No, but in the conventional gaf, it would not be straightforward to attribute evidence to the inferred annotation with the qualifier. To get things moving, for now we would simply want the asserted ones. In the future we might want to have the ability to see when an asserted relation and an inferred relation 'contradict' one another. For example if a gene product executes a function that is inferred to be part of a process, but is asserted to execute a function that regulates the process<ins style="font-weight: bold; text-decoration: none;">. Further in the future, I am sure that we will want to make associations between gene products and processes based on property chains in models. Here is where I think DOS's point really comes into play. If models contain very long causal chains that are true, but not necessarily useful, then this could become very messy. For example RNA polymerase being upstream of any process mediated by a gene product wouldn't be useful. A few weeks ago Stacia suggested that the practical way to handle this would be to only populate the model with things that a curator deems relevant to the biology being modeled. Maybe this is the best rout to take</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>** DOS: Making a qualifier for causally_upstream_of could be dangerous. Casual chains can potentially become very long => associations that most biologists would consider wrong. Our protection against this is to rely on curators not to add the links in question. But are there clear rules for this? If so, can we codify them? (how) do they map to all/some patterns for relationships (which, strictly, don't apply in LEGO!)? If there are no clear rules, is it sufficient to rely on curator instinct? To assess this, I think we need to look at many more examples. It is easy to be fooled into thinking we have a generally safe method on the basis of a small number of cases where the correct way to annotate is clear.</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>** DOS: Making a qualifier for causally_upstream_of could be dangerous. Casual chains can potentially become very long => associations that most biologists would consider wrong. Our protection against this is to rely on curators not to add the links in question. But are there clear rules for this? If so, can we codify them? (how) do they map to all/some patterns for relationships (which, strictly, don't apply in LEGO!)? If there are no clear rules, is it sufficient to rely on curator instinct? To assess this, I think we need to look at many more examples. It is easy to be fooled into thinking we have a generally safe method on the basis of a small number of cases where the correct way to annotate is clear.</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>** DPH: Having been an annotator for a long time and having looked at a lot of annotations, I would say that this already happens. Annotators create annotations for processes that are a result of very long chains of causally_upstream_of with no indication in the current methodology to indicate this. Adding the qualifier will only make things more explicit. Right now the existing annotations consist of a gene product and a GO term and in my experience include every possible qualifier we could think of adding. We are looking for improvement over the current method.</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>** DPH: Having been an annotator for a long time and having looked at a lot of annotations, I would say that this already happens. Annotators create annotations for processes that are a result of very long chains of causally_upstream_of with no indication in the current methodology to indicate this. Adding the qualifier will only make things more explicit. Right now the existing annotations consist of a gene product and a GO term and in my experience include every possible qualifier we could think of adding. We are looking for improvement over the current method<ins style="font-weight: bold; text-decoration: none;">. But yes, it is still very up to curator judgement</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;"><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>==Documentation Week==</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>==Documentation Week==</div></td></tr>
</table>Davidhttps://wiki.geneontology.org/index.php?title=LEGO_May_9,_2016&diff=60694&oldid=prevDavid: /* Capturing Extent of Causally Upstream Of in a GAF/GPAD */2016-05-10T12:42:20Z<p><span dir="auto"><span class="autocomment">Capturing Extent of Causally Upstream Of in a GAF/GPAD</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 08:42, 10 May 2016</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>** DPH: No, but in the conventional gaf, it would not be straightforward to attribute evidence to the inferred annotation with the qualifier. To get things moving, for now we would simply want the asserted ones. In the future we might want to have the ability to see when an asserted relation and an inferred relation 'contradict' one another. For example if a gene product executes a function that is inferred to be part of a process, but is asserted to execute a function that regulates the process.</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>** DPH: No, but in the conventional gaf, it would not be straightforward to attribute evidence to the inferred annotation with the qualifier. To get things moving, for now we would simply want the asserted ones. In the future we might want to have the ability to see when an asserted relation and an inferred relation 'contradict' one another. For example if a gene product executes a function that is inferred to be part of a process, but is asserted to execute a function that regulates the process.</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>** DOS: Making a qualifier for causally_upstream_of could be dangerous. Casual chains can potentially become very long => associations that most biologists would consider wrong. Our protection against this is to rely on curators not to add the links in question. But are there clear rules for this? If so, can we codify them? (how) do they map to all/some patterns for relationships (which, strictly, don't apply in LEGO!)? If there are no clear rules, is it sufficient to rely on curator instinct? To assess this, I think we need to look at many more examples. It is easy to be fooled into thinking we have a generally safe method on the basis of a small number of cases where the correct way to annotate is clear.</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>** DOS: Making a qualifier for causally_upstream_of could be dangerous. Casual chains can potentially become very long => associations that most biologists would consider wrong. Our protection against this is to rely on curators not to add the links in question. But are there clear rules for this? If so, can we codify them? (how) do they map to all/some patterns for relationships (which, strictly, don't apply in LEGO!)? If there are no clear rules, is it sufficient to rely on curator instinct? To assess this, I think we need to look at many more examples. It is easy to be fooled into thinking we have a generally safe method on the basis of a small number of cases where the correct way to annotate is clear.</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>** DPH: Having been an annotator for a long time and having looked at a lot of annotations, I would say that this already happens. Annotators create annotations for processes that are a result of very long chains of <del style="font-weight: bold; text-decoration: none;">causally upstream of </del>with no indication in the current methodology to indicate this.Adding the qualifier will only make things more explicit. Right now the <del style="font-weight: bold; text-decoration: none;">exisiting </del>annotations consist of a gene product and a GO term and in my experience include every possible qualifier we could think of adding. We are looking for improvement over the current method.</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>** DPH: Having been an annotator for a long time and having looked at a lot of annotations, I would say that this already happens. Annotators create annotations for processes that are a result of very long chains of <ins style="font-weight: bold; text-decoration: none;">causally_upstream_of </ins>with no indication in the current methodology to indicate this. Adding the qualifier will only make things more explicit. Right now the <ins style="font-weight: bold; text-decoration: none;">existing </ins>annotations consist of a gene product and a GO term and in my experience include every possible qualifier we could think of adding. We are looking for improvement over the current method.</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"></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>==Documentation Week==</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>==Documentation Week==</div></td></tr>
</table>Davidhttps://wiki.geneontology.org/index.php?title=LEGO_May_9,_2016&diff=60693&oldid=prevDavid: /* Capturing Extent of Causally Upstream Of in a GAF/GPAD */2016-05-10T11:42:41Z<p><span dir="auto"><span class="autocomment">Capturing Extent of Causally Upstream Of in a GAF/GPAD</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>*Contrast the translation upstream vs the acylation upstream - the former is not known to be Wnt-specific, but the latter is Wnt-specific</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>*Contrast the translation upstream vs the acylation upstream - the former is not known to be Wnt-specific, but the latter is Wnt-specific</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>** DOS: But note - *this* could be captured under a broader term for cell-cell signaling by wnt - with parts for ligand processing, secretion, intercellular transport/presentation, & signal transduction. The advantage of this is that it makes it explicit what it means to be wnt-specific. If we leave this to the LEGO model, then it comes down to an undocumented curator choice about when to use place causally_upstream_of links. Are we confident of curator consistency on this?</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>** DOS: But note - *this* could be captured under a broader term for cell-cell signaling by wnt - with parts for ligand processing, secretion, intercellular transport/presentation, & signal transduction. The advantage of this is that it makes it explicit what it means to be wnt-specific. If we leave this to the LEGO model, then it comes down to an undocumented curator choice about when to use place causally_upstream_of links. Are we confident of curator consistency on this?</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;">** DPH: It could but we would need to be really careful. This seems straightforward on the surface, but the underlying biology might be more complex than first thought. The reason that the signaling group decided to start and classify a signaling cascade based on the receptor, was because they found examples of different types of ligands binding different types of receptors, not always named for the ligand. This could lead to confusion in annotation. To avoid this using the suggested strategy, it would be necessary to define the signal transduction in the 'cell-cell signaling process by X' as a signal transduction that starts with the reception of a signal enabled by X. This doesn't contradict any of the work already done.</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>*Proposal is to add these qualifiers to the GAF so we can get the annotations curators would normally make in the GAF:</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>*Proposal is to add these qualifiers to the GAF so we can get the annotations curators would normally make in the GAF:</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>** DOS: The logically consistent way to do this would be to add the qualifiers whether the relationship was asserted or inferred. DH arguing for this only where the link is asserted by a curator (?) </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>** DOS: The logically consistent way to do this would be to add the qualifiers whether the relationship was asserted or inferred. DH arguing for this only where the link is asserted by a curator (?) </div></td></tr>
</table>Davidhttps://wiki.geneontology.org/index.php?title=LEGO_May_9,_2016&diff=60692&oldid=prevDavid: /* Capturing Extent of Causally Upstream Of in a GAF/GPAD */2016-05-10T11:28:25Z<p><span dir="auto"><span class="autocomment">Capturing Extent of Causally Upstream Of in a GAF/GPAD</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 07:28, 10 May 2016</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>*Proposal is to add these qualifiers to the GAF so we can get the annotations curators would normally make in the GAF:</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>*Proposal is to add these qualifiers to the GAF so we can get the annotations curators would normally make in the GAF:</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>** DOS: The logically consistent way to do this would be to add the qualifiers whether the relationship was asserted or inferred. DH arguing for this only where the link is asserted by a curator (?) </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>** DOS: The logically consistent way to do this would be to add the qualifiers whether the relationship was asserted or inferred. DH arguing for this only where the link is asserted by a curator (?) </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;">** DPH: No, but in the conventional gaf, it would not be straightforward to attribute evidence to the inferred annotation with the qualifier. To get things moving, for now we would simply want the asserted ones. In the future we might want to have the ability to see when an asserted relation and an inferred relation 'contradict' one another. For example if a gene product executes a function that is inferred to be part of a process, but is asserted to execute a function that regulates the process.</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>** DOS: Making a qualifier for causally_upstream_of could be dangerous. Casual chains can potentially become very long => associations that most biologists would consider wrong. Our protection against this is to rely on curators not to add the links in question. But are there clear rules for this? If so, can we codify them? (how) do they map to all/some patterns for relationships (which, strictly, don't apply in LEGO!)? If there are no clear rules, is it sufficient to rely on curator instinct? To assess this, I think we need to look at many more examples. It is easy to be fooled into thinking we have a generally safe method on the basis of a small number of cases where the correct way to annotate is clear.</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>** DOS: Making a qualifier for causally_upstream_of could be dangerous. Casual chains can potentially become very long => associations that most biologists would consider wrong. Our protection against this is to rely on curators not to add the links in question. But are there clear rules for this? If so, can we codify them? (how) do they map to all/some patterns for relationships (which, strictly, don't apply in LEGO!)? If there are no clear rules, is it sufficient to rely on curator instinct? To assess this, I think we need to look at many more examples. It is easy to be fooled into thinking we have a generally safe method on the basis of a small number of cases where the correct way to annotate is clear.</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;">** DPH: Having been an annotator for a long time and having looked at a lot of annotations, I would say that this already happens. Annotators create annotations for processes that are a result of very long chains of causally upstream of with no indication in the current methodology to indicate this.Adding the qualifier will only make things more explicit. Right now the exisiting annotations consist of a gene product and a GO term and in my experience include every possible qualifier we could think of adding. We are looking for improvement over the current method.</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;"><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>==Documentation Week==</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>==Documentation Week==</div></td></tr>
</table>Davidhttps://wiki.geneontology.org/index.php?title=LEGO_May_9,_2016&diff=60691&oldid=prevDavid os: /* Capturing Extent of Causally Upstream Of in a GAF/GPAD */2016-05-10T10:32:22Z<p><span dir="auto"><span class="autocomment">Capturing Extent of Causally Upstream Of in a GAF/GPAD</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 06:32, 10 May 2016</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>*Implications for current ontology development</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>*Implications for current ontology development</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 you characterize signaling by ligand type, do you run into problems?</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 you characterize signaling by ligand type, do you run into problems?</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>*** Need to be clear what we mean here: cell-cell signaling vs <del style="font-weight: bold; text-decoration: none;">signaling </del>transduction.</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>*** Need to be clear what we mean here: cell-cell signaling vs <ins style="font-weight: bold; text-decoration: none;">signal </ins>transduction. <ins style="font-weight: bold; text-decoration: none;"> The latter is mostly defined by receptor. The former covers secretion, transport between cells, presentation to a receptor and signal transduction. It can potentially be defined by ligand. Doesn't it make sense to do so in cases where there is a specific pathway for processing of a ligand?</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>*Current GAF generation only generates AE to immediate downstream step.</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>*Current GAF generation only generates AE to immediate downstream step.</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>*Additional AEs to downstream steps can only come from direct links between an activity and a process.</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>*Additional AEs to downstream steps can only come from direct links between an activity and a process.</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>*This leads to question of how to generate these annotations in the GAF and the issue of expanding the qualifier column to make the association between the activity and the process clearer.</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>*This leads to question of how to generate these annotations in the GAF and the issue of expanding the qualifier column to make the association between the activity and the process clearer.</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>** DOS: The 'qualifier' column = the GP : GO relationship. If we expand the range of these, then <del style="font-weight: bold; text-decoration: none;">they change </del></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>** DOS: The 'qualifier' column = the GP : GO relationship. If we expand the range of these, then <ins style="font-weight: bold; text-decoration: none;">we explicitly broaden the meaning of annotation. Need to think through the implications of this for general use of GO annotations.</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>*Contrast the translation upstream vs the acylation upstream - the former is not known to be Wnt-specific, but the latter is Wnt-specific</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>*Contrast the translation upstream vs the acylation upstream - the former is not known to be Wnt-specific, but the latter is Wnt-specific</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>** DOS: But note - *this* could be captured under a broader term for cell-cell signaling by wnt - with parts for ligand processing, secretion, intercellular transport/presentation, & signal transduction. The advantage of this is that it makes it explicit what it means to be wnt-specific. If we leave this to the LEGO model, then it comes down to an undocumented curator choice about when to use place causally_upstream_of links. Are we confident of curator consistency on this?</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>** DOS: But note - *this* could be captured under a broader term for cell-cell signaling by wnt - with parts for ligand processing, secretion, intercellular transport/presentation, & signal transduction. The advantage of this is that it makes it explicit what it means to be wnt-specific. If we leave this to the LEGO model, then it comes down to an undocumented curator choice about when to use place causally_upstream_of links. Are we confident of curator consistency on this?</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>*Proposal is to add these qualifiers to the GAF so we can get the annotations curators would normally make in the GAF:</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>*Proposal is to add these qualifiers to the GAF so we can get the annotations curators would normally make in the GAF:</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>** DOS: The logically consistent way to do this would be to add the qualifiers whether the relationship was asserted or inferred. DH arguing for this only where the link is asserted by a curator (?) </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>** DOS: The logically consistent way to do this would be to add the qualifiers whether the relationship was asserted or inferred. DH arguing for this only where the link is asserted by a curator (?) </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>** DOS: Making a qualifier for causally_upstream_of <del style="font-weight: bold; text-decoration: none;">is potentially </del>dangerous. Casual chains can potentially become very long => associations that most biologists would consider wrong. Our protection against this is to rely on curators not to add the links in question. But are there clear rules for this? If so, can we codify them? (how) do they map to all/some patterns for relationships (which, strictly, don't apply in LEGO!)? If there are no clear rules, is it sufficient to rely on curator instinct? To assess this, I think we need to look at many more examples. It is easy to be fooled into thinking we have a generally safe method on the basis of a small number of cases where the correct way to annotate is clear.</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>** DOS: Making a qualifier for causally_upstream_of <ins style="font-weight: bold; text-decoration: none;">could be </ins>dangerous. Casual chains can potentially become very long => associations that most biologists would consider wrong. Our protection against this is to rely on curators not to add the links in question. But are there clear rules for this? If so, can we codify them? (how) do they map to all/some patterns for relationships (which, strictly, don't apply in LEGO!)? If there are no clear rules, is it sufficient to rely on curator instinct? To assess this, I think we need to look at many more examples. It is easy to be fooled into thinking we have a generally safe method on the basis of a small number of cases where the correct way to annotate is clear.</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"></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>==Documentation Week==</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>==Documentation Week==</div></td></tr>
</table>David oshttps://wiki.geneontology.org/index.php?title=LEGO_May_9,_2016&diff=60690&oldid=prevDavid os: /* Capturing Extent of Causally Upstream Of in a GAF/GPAD */2016-05-10T09:55:48Z<p><span dir="auto"><span class="autocomment">Capturing Extent of Causally Upstream Of in a GAF/GPAD</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 05:55, 10 May 2016</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l94">Line 94:</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>*Implications for current ontology development</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>*Implications for current ontology development</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 you characterize signaling by ligand type, do you run into problems?</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 you characterize signaling by ligand type, do you run into problems?</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;">*** Need to be clear what we mean here: cell-cell signaling vs signaling transduction.</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>*Current GAF generation only generates AE to immediate downstream step.</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>*Current GAF generation only generates AE to immediate downstream step.</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>*Additional AEs to downstream steps can only come from direct links between an activity and a process.</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>*Additional AEs to downstream steps can only come from direct links between an activity and a process.</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>*This leads to question of how to generate these annotations in the GAF and the issue of expanding the qualifier column to make the association between the activity and the process clearer.</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>*This leads to question of how to generate these annotations in the GAF and the issue of expanding the qualifier column to make the association between the activity and the process clearer.</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;">** DOS: The 'qualifier' column = the GP : GO relationship. If we expand the range of these, then they change </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>*Contrast the translation upstream vs the acylation upstream - the former is not known to be Wnt-specific, but the latter is Wnt-specific</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>*Contrast the translation upstream vs the acylation upstream - the former is not known to be Wnt-specific, but the latter is Wnt-specific</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>*Proposal is to add these qualifiers to the GAF so we can get the annotations curators would normally make in the GAF</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;"> ** DOS: But note - *this* could be captured under a broader term for cell-cell signaling by wnt - with parts for ligand processing, secretion, intercellular transport/presentation, & signal transduction. The advantage of this is that it makes it explicit what it means to be wnt-specific. If we leave this to the LEGO model, then it comes down to an undocumented curator choice about when to use place causally_upstream_of links. Are we confident of curator consistency on this?</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>*Proposal is to add these qualifiers to the GAF so we can get the annotations curators would normally make in the GAF<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;">** DOS: The logically consistent way to do this would be to add the qualifiers whether the relationship was asserted or inferred. DH arguing for this only where the link is asserted by a curator (?) </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;">** DOS: Making a qualifier for causally_upstream_of is potentially dangerous. Casual chains can potentially become very long => associations that most biologists would consider wrong. Our protection against this is to rely on curators not to add the links in question. But are there clear rules for this? If so, can we codify them? (how) do they map to all/some patterns for relationships (which, strictly, don't apply in LEGO!)? If there are no clear rules, is it sufficient to rely on curator instinct? To assess this, I think we need to look at many more examples. It is easy to be fooled into thinking we have a generally safe method on the basis of a small number of cases where the correct way to annotate is clear.</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> </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>==Documentation Week==</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>==Documentation Week==</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>*David H and Kimberly will be working on LEGO documentation and a training manual this week</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>*David H and Kimberly will be working on LEGO documentation and a training manual this week</div></td></tr>
</table>David oshttps://wiki.geneontology.org/index.php?title=LEGO_May_9,_2016&diff=60670&oldid=prevVanaukenk at 16:34, 9 May 20162016-05-09T16:34:31Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:34, 9 May 2016</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l99">Line 99:</td>
<td colspan="2" class="diff-lineno">Line 99:</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>*Contrast the translation upstream vs the acylation upstream - the former is not known to be Wnt-specific, but the latter is Wnt-specific</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>*Contrast the translation upstream vs the acylation upstream - the former is not known to be Wnt-specific, but the latter is Wnt-specific</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>*Proposal is to add these qualifiers to the GAF so we can get the annotations curators would normally make in the GAF</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>*Proposal is to add these qualifiers to the GAF so we can get the annotations curators would normally make in the GAF</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;">==Documentation Week==</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;">*David H and Kimberly will be working on LEGO documentation and a training manual this week</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;">*Stacia and Kevin at SGD will be helping to create Noctua videos</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;"><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;"><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>
</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=LEGO_May_9,_2016&diff=60669&oldid=prevVanaukenk: /* Capturing Extent of Causally Upstream Of in a GAF/GPAD */2016-05-09T16:33:03Z<p><span dir="auto"><span class="autocomment">Capturing Extent of Causally Upstream Of in a GAF/GPAD</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:33, 9 May 2016</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l96">Line 96:</td>
<td colspan="2" class="diff-lineno">Line 96:</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>*Current GAF generation only generates AE to immediate downstream step.</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>*Current GAF generation only generates AE to immediate downstream step.</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>*Additional AEs to downstream steps can only come from direct links between an activity and a process.</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>*Additional AEs to downstream steps can only come from direct links between an activity and a process.</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;">*This leads to question of how to generate these annotations in the GAF and the issue of expanding the qualifier column to make the association between the activity and the process clearer.</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;">*Contrast the translation upstream vs the acylation upstream - the former is not known to be Wnt-specific, but the latter is Wnt-specific</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;">*Proposal is to add these qualifiers to the GAF so we can get the annotations curators would normally make in the GAF</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;"></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;"><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;"><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>
</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=LEGO_May_9,_2016&diff=60668&oldid=prevVanaukenk: /* Capturing Extent of Causally Upstream Of in a GAF/GPAD */2016-05-09T16:19:32Z<p><span dir="auto"><span class="autocomment">Capturing Extent of Causally Upstream Of in a GAF/GPAD</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:19, 9 May 2016</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l90">Line 90:</td>
<td colspan="2" class="diff-lineno">Line 90:</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>*To capture this in a LEGO model we need to make a direct connection between the acyltransferase and the Wnt signaling pathway</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>*To capture this in a LEGO model we need to make a direct connection between the acyltransferase and the Wnt signaling pathway</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>*Distinguish between a logically redundant assertion with specific evidence vs a stronger assertion with specific evidence</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>*Distinguish between a logically redundant assertion with specific evidence vs a stronger assertion with specific evidence</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;">**The mom-1 relation to Wnt signaling is currently logically redundant but with specific evidence</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;">*Also look at Wntless and its annotations, currently in GAFs as some form of regulation of Wnt secretion or Wnt protein signaling</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;">*Implications for current ontology development</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;">**If you characterize signaling by ligand type, do you run into problems?</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;">*Current GAF generation only generates AE to immediate downstream step.</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;">*Additional AEs to downstream steps can only come from direct links between an activity and a process.</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;"><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;"><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>
</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=LEGO_May_9,_2016&diff=60667&oldid=prevVanaukenk at 16:09, 9 May 20162016-05-09T16:09:44Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:09, 9 May 2016</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l84">Line 84:</td>
<td colspan="2" class="diff-lineno">Line 84:</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>****Sentences would be part_of a publication</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>****Sentences would be part_of a publication</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>****Sentences would then support an assertion</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>****Sentences would then support an assertion</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;">==Capturing Extent of Causally Upstream Of in a GAF/GPAD==</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;">*Example using Wnt pathway</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;">*Wnts need to be lipid modified to be secreted</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;">*Wnt acyltransferases are all currently annotated to some flavor of Wnt signaling or Wnt protein secretion</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;">*To capture this in a LEGO model we need to make a direct connection between the acyltransferase and the Wnt signaling pathway</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;">*Distinguish between a logically redundant assertion with specific evidence vs a stronger assertion with specific evidence</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;"><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;"><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>
</table>Vanaukenk