https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Hypodigm&feed=atom&action=historyHypodigm - Revision history2024-03-28T21:53:06ZRevision history for this page on the wikiMediaWiki 1.31.10https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Hypodigm&diff=4623&oldid=prevHilmar at 21:55, 22 November 20082008-11-22T21:55:42Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>We need to standardize the list of evidence codes and their meaning for our data.  Here is a [http://www.geneontology.org/GO.evidence.shtml GO page about them], and here is [http://obofoundry.org/cgi-bin/detail.cgi?id=evidence_code an evidence_code ontology], with many more codes:</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>We need to standardize the list of evidence codes and their meaning for our data.  Here is a [http://www.geneontology.org/GO.evidence.shtml GO page about them], and here is [http://obofoundry.org/cgi-bin/detail.cgi?id=evidence_code an evidence_code ontology], with many more codes:</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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>
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</table>Hilmarhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Hypodigm&diff=2477&oldid=prevHilmar at 05:07, 1 February 20082008-02-01T05:07:47Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 05:07, 1 February 2008</td>
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<tr><td class='diff-marker'>−</td><td style="color: #222; 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>==Problem==</div></td><td class='diff-marker'>+</td><td style="color: #222; 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 class="diffchange diffchange-inline">==Ambiguous specimen information: annotating phenotypes for specimens or species==</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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 class="diffchange diffchange-inline">=</ins>==Problem<ins class="diffchange diffchange-inline">=</ins>==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>How to handle the uncertainty of tying phenotype annotations to specimens within publications has been at issue.  Our existing data model held all phenotype annotations at the level of particular specimens.  Handling ambiguity at this level was causing difficulty in determining the proper OBO semantics, since authors often do not explicitly reference specimens, but instead discuss taxonomic groups.  Since a list of specimens is included in the paper, we know that at least one of them, and maybe more, were examined for the described character.  This "someOf" semantics is not currently available within OBO and may not be logically desirable.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>How to handle the uncertainty of tying phenotype annotations to specimens within publications has been at issue.  Our existing data model held all phenotype annotations at the level of particular specimens.  Handling ambiguity at this level was causing difficulty in determining the proper OBO semantics, since authors often do not explicitly reference specimens, but instead discuss taxonomic groups.  Since a list of specimens is included in the paper, we know that at least one of them, and maybe more, were examined for the described character.  This "someOf" semantics is not currently available within OBO and may not be logically desirable.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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 level of detail raises questions of what our goals should be: trying to model the logic within the published descriptions exactly, or rather creating a knowledge base of phenotypic diversity which uses the publications for support.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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 level of detail raises questions of what our goals should be: trying to model the logic within the published descriptions exactly, or rather creating a knowledge base of phenotypic diversity which uses the publications for support.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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>==Resolution==</div></td><td class='diff-marker'>+</td><td style="color: #222; 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 class="diffchange diffchange-inline">=</ins>==Resolution<ins class="diffchange diffchange-inline">=</ins>==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>Our discussion at the Biocuration meeting led to a new data model in which all phenotype annotations are expressed as properties of species.  Any annotation is assigned an evidence code such as those used by the GO project.  An phenotypic description explicitly tied to a specimen will be given a "strong" evidence code, such as "direct observation by author", requiring a supplemental museum catalog number or numbers.  A phenotypic description in which the author just says, "species X has phenotype Y", without pointing to a specimen, will be curated as well, but the evidence code will be something like "traceable author statement", and no catalog numbers attached (even though some for that species may be listed in the materials and methods).</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>Our discussion at the Biocuration meeting led to a new data model in which all phenotype annotations are expressed as properties of species.  Any annotation is assigned an evidence code such as those used by the GO project.  An phenotypic description explicitly tied to a specimen will be given a "strong" evidence code, such as "direct observation by author", requiring a supplemental museum catalog number or numbers.  A phenotypic description in which the author just says, "species X has phenotype Y", without pointing to a specimen, will be curated as well, but the evidence code will be something like "traceable author statement", and no catalog numbers attached (even though some for that species may be listed in the materials and methods).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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;"></td></tr>
</table>Hilmarhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Hypodigm&diff=2475&oldid=prevHilmar: Ambiguous specimen information: annotating phenotypes for specimens or species moved to Hypodigm: Shorter name2008-02-01T05:06:40Z<p><a href="/wiki/Ambiguous_specimen_information:_annotating_phenotypes_for_specimens_or_species" class="mw-redirect" title="Ambiguous specimen information: annotating phenotypes for specimens or species">Ambiguous specimen information: annotating phenotypes for specimens or species</a> moved to <a href="/wiki/Hypodigm" title="Hypodigm">Hypodigm</a>: Shorter name</p>
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<td colspan="1" style="background-color: #fff; color: #222; text-align: center;">Revision as of 05:06, 1 February 2008</td>
</tr><tr><td colspan="2" class="diff-notice" lang="en"><div class="mw-diff-empty">(No difference)</div>
</td></tr></table>Hilmarhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=Hypodigm&diff=2365&oldid=prevJpb15: /* Problem */2007-11-15T21:35:53Z<p><span dir="auto"><span class="autocomment">Problem</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 21:35, 15 November 2007</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>==Problem==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>==Problem==</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; 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>How to handle the uncertainty of tying phenotype annotations to specimens within publications has been at issue.  Our existing data model held all phenotype annotations at the level of particular specimens.  Handling ambiguity at this level was causing difficulty in determining the proper OBO semantics, since authors often do not explicitly reference specimens, but instead discuss taxonomic groups.  This level of detail raises questions of what our goals should be: trying to model the logic within the published descriptions exactly, or rather creating a knowledge base of phenotypic diversity which uses the publications for support.</div></td><td class='diff-marker'>+</td><td style="color: #222; 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>How to handle the uncertainty of tying phenotype annotations to specimens within publications has been at issue.  Our existing data model held all phenotype annotations at the level of particular specimens.  Handling ambiguity at this level was causing difficulty in determining the proper OBO semantics, since authors often do not explicitly reference specimens, but instead discuss taxonomic groups.  <ins class="diffchange diffchange-inline">Since a list of specimens is included in the paper, we know that at least one of them, and maybe more, were examined for the described character.  This "someOf" semantics is not currently available within OBO and may not be logically desirable.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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 colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; 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>This level of detail raises questions of what our goals should be: trying to model the logic within the published descriptions exactly, or rather creating a knowledge base of phenotypic diversity which uses the publications for support.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>==Resolution==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; 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>==Resolution==</div></td></tr>
</table>Jpb15https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Hypodigm&diff=2362&oldid=prevJpb15 at 21:29, 15 November 20072007-11-15T21:29:32Z<p></p>
<p><b>New page</b></p><div>==Problem==<br />
How to handle the uncertainty of tying phenotype annotations to specimens within publications has been at issue. Our existing data model held all phenotype annotations at the level of particular specimens. Handling ambiguity at this level was causing difficulty in determining the proper OBO semantics, since authors often do not explicitly reference specimens, but instead discuss taxonomic groups. This level of detail raises questions of what our goals should be: trying to model the logic within the published descriptions exactly, or rather creating a knowledge base of phenotypic diversity which uses the publications for support.<br />
<br />
==Resolution==<br />
Our discussion at the Biocuration meeting led to a new data model in which all phenotype annotations are expressed as properties of species. Any annotation is assigned an evidence code such as those used by the GO project. An phenotypic description explicitly tied to a specimen will be given a "strong" evidence code, such as "direct observation by author", requiring a supplemental museum catalog number or numbers. A phenotypic description in which the author just says, "species X has phenotype Y", without pointing to a specimen, will be curated as well, but the evidence code will be something like "traceable author statement", and no catalog numbers attached (even though some for that species may be listed in the materials and methods).<br />
<br />
The same methodology can be extended to statements about higher taxa. In this case, individual species-level phenotype annotations should be generated for every species of that taxon listed in the materials list. These will generally all get the weaker evidence code. If the author happened to point out one or more particular specimens illustrating the phenotype, these particular species can be given the stronger evidence code with catalog numbers attached.<br />
<br />
We need to standardize the list of evidence codes and their meaning for our data. Here is a [http://www.geneontology.org/GO.evidence.shtml GO page about them], and here is [http://obofoundry.org/cgi-bin/detail.cgi?id=evidence_code an evidence_code ontology], with many more codes:</div>Jpb15