https://wiki.phenoscape.org/wg/phenoscape/index.php?title=EQ_for_character_matrices&feed=atom&action=historyEQ for character matrices - Revision history2024-03-29T14:40:00ZRevision history for this page on the wikiMediaWiki 1.31.10https://wiki.phenoscape.org/wg/phenoscape/index.php?title=EQ_for_character_matrices&diff=4904&oldid=prevHilmar at 23:42, 10 January 20092009-01-10T23:42:39Z<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>* If an ancestor-descendant relationship between attributes and values is desired, this coding would not be robust to future rearrangements of PATO (where a value may not descend from a particular attribute in the future, and so becomes an invalid statement).</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>* If an ancestor-descendant relationship between attributes and values is desired, this coding would not be robust to future rearrangements of PATO (where a value may not descend from a particular attribute in the future, and so becomes an invalid statement).</div></td></tr>
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</table>Hilmarhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=EQ_for_character_matrices&diff=2347&oldid=prevHilmar: /* EQ statements vs. character matrices */2007-11-07T23:36:23Z<p><span dir="auto"><span class="autocomment">EQ statements vs. character matrices</span></span></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;"></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>So the problem is that the existing EQ system (and formats such as [http://www.fruitfly.org/~cjm/obd/formats.html PhenoSyntax and PhenoXML]) only stores a list of character states, and cannot group those states into characters.  Storing only character states would be perfectly adequate for most of the data integration benefits provided by the <del class="diffchange diffchange-inline">PhenoMap </del>project.  However, evolutionary data is often described in the character+character state framework, and a few reasons why we may want to preserve this are listed below.  Possible solutions to this problem for evolutionary data are: 1) Only storing character values and automatically generating characters when a matrix is desired, or 2) Finding a way to code and store EQ statements for both characters and character states.</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>So the problem is that the existing EQ system (and formats such as [http://www.fruitfly.org/~cjm/obd/formats.html PhenoSyntax and PhenoXML]) only stores a list of character states, and cannot group those states into characters.  Storing only character states would be perfectly adequate for most of the data integration benefits provided by the <ins class="diffchange diffchange-inline">PhenoScape </ins>project.  However, evolutionary data is often described in the character+character state framework, and a few reasons why we may want to preserve this are listed below.  Possible solutions to this problem for evolutionary data are: 1) Only storing character values and automatically generating characters when a matrix is desired, or 2) Finding a way to code and store EQ statements for both characters and character states.</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>==Possible solutions==</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>==Possible solutions==</div></td></tr>
</table>Hilmarhttps://wiki.phenoscape.org/wg/phenoscape/index.php?title=EQ_for_character_matrices&diff=1922&oldid=prevJpb15 at 17:57, 22 May 20072007-05-22T17:57:31Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 17:57, 22 May 2007</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</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>Encoding evolutionary character matrices using the [http://www.bioontology.org/wiki/index.php/PATO:About EQ format] (PATO formalism) currently presents some problems that may need to be resolved.  I will try to describe the issues here.</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>Encoding evolutionary character matrices using the [http://www.bioontology.org/wiki/index.php/PATO:About EQ format] (PATO formalism) currently presents some problems that may need to be resolved.  I will try to describe the issues here.</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>
<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;">==Background==</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;"></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>===EQ statements vs. character matrices===</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>===EQ statements vs. character matrices===</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l44" >Line 44:</td>
<td colspan="2" class="diff-lineno">Line 46:</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>So the problem is that the existing EQ system (and formats such as [http://www.fruitfly.org/~cjm/obd/formats.html PhenoSyntax and PhenoXML]) only stores a list of character states, and cannot group those states into characters.  Storing only character states would be perfectly adequate for most of the data integration benefits provided by the PhenoMap project.  However, evolutionary data is often described in the character+character state framework, and a few reasons why we may want to preserve this are listed below.  Possible solutions to this problem for evolutionary data are: 1) Only storing character values and automatically generating characters when a matrix is desired, or 2) Finding a way to code and store EQ statements for both characters and character states.</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>So the problem is that the existing EQ system (and formats such as [http://www.fruitfly.org/~cjm/obd/formats.html PhenoSyntax and PhenoXML]) only stores a list of character states, and cannot group those states into characters.  Storing only character states would be perfectly adequate for most of the data integration benefits provided by the PhenoMap project.  However, evolutionary data is often described in the character+character state framework, and a few reasons why we may want to preserve this are listed below.  Possible solutions to this problem for evolutionary data are: 1) Only storing character values and automatically generating characters when a matrix is desired, or 2) Finding a way to code and store EQ statements for both characters and character states.</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>===<del class="diffchange diffchange-inline">1. </del>Automatically inferring characters from character states using PATO===</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">==Possible solutions==</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>===Automatically inferring characters from character states using PATO===</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>PATO does not distinguish qualities representing values from those representing attributes, except that values descend from attributes in the hierarchy.  But given an arbitrary value, it is not possible to automatically infer the attribute it is a value for.  Many values are children of other values - for example, "bright blue" and "dark blue" are children of "blue".  You need to traverse up two levels to reach the attribute "color".  Also, some terminal terms in PATO are not values - they are attributes for which no values are defined in PATO.  Examples are "acceleration" and "buoyancy".</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>PATO does not distinguish qualities representing values from those representing attributes, except that values descend from attributes in the hierarchy.  But given an arbitrary value, it is not possible to automatically infer the attribute it is a value for.  Many values are children of other values - for example, "bright blue" and "dark blue" are children of "blue".  You need to traverse up two levels to reach the attribute "color".  Also, some terminal terms in PATO are not values - they are attributes for which no values are defined in PATO.  Examples are "acceleration" and "buoyancy".</div></td></tr>
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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>* The original publication may have valuable textual information describing the character, independent of particular character states.  We may want a place to preserve this.</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>* The original publication may have valuable textual information describing the character, independent of particular character states.  We may want a place to preserve this.</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>===<del class="diffchange diffchange-inline">2. </del>Storing EQ statements for both characters and character states===</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>===Storing EQ statements for both characters and character states===</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>It would be possible to store EQ statements for both characters (Entity+Attribute) and character states (maybe just Value), either by defining a custom data format or by extending PhenoXML and PhenoSyntax.  Probably, given a character such as "dorsal fin color", valid values would only be PATO descendants of "color", such as "red" or "bright blue".  However this approach may have some problems as well:</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>It would be possible to store EQ statements for both characters (Entity+Attribute) and character states (maybe just Value), either by defining a custom data format or by extending PhenoXML and PhenoSyntax.  Probably, given a character such as "dorsal fin color", valid values would only be PATO descendants of "color", such as "red" or "bright blue".  However this approach may have some problems as well:</div></td></tr>
</table>Jpb15https://wiki.phenoscape.org/wg/phenoscape/index.php?title=EQ_for_character_matrices&diff=1921&oldid=prevJpb15 at 01:45, 22 May 20072007-05-22T01:45:50Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 01:45, 22 May 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>Problems:</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>Problems:</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>* In order for this to work, the Attribute and Value slims must continue to be maintained by curators as terms are added to PATO.  However no one else seems to be using these slims at this time.</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>* In order for this to work, the Attribute and Value slims must continue to be maintained by curators as terms are added to PATO.  However no one else seems to be using these slims at this time.</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>* A researcher may be interested in coding a character such as "fin morphology", with various species having values "lobate", "stubby", and "elongated".  However, without a way to store the desired character attribute, the current Phenote NEXUS exporter would see these phenotypes as states for the separate characters "fin shape", "fin size", and "fin length", respectively.  Conversely, if the researcher was generating a matrix from a database of EQ statements by choosing an entity-attribute pair such as "fin morphology", what should happen if a given species has values for both "fin lobate" and "fin elongated" - i.e. would this be a different character state from another species which was only coded for "fin lobate"?</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>* A researcher may be interested in coding a character such as "fin morphology", with various species having values "lobate", "stubby", and "elongated".  However, without a way to store the desired character attribute, the current Phenote NEXUS exporter would see these phenotypes as states for the separate characters "fin shape", "fin size", and "fin length", respectively <ins class="diffchange diffchange-inline">("morphology" is a deeper ancestor of these 3 attributes)</ins>.  Conversely, if the researcher was generating a matrix from a database of EQ statements by choosing an entity-attribute pair such as "fin morphology", what should happen if a given species has values for both "fin lobate" and "fin elongated" - i.e. would this be a different character state from another species which was only coded for "fin lobate"?</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>* The original publication may have valuable textual information describing the character, independent of particular character states.  We may want a place to preserve this.</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>* The original publication may have valuable textual information describing the character, independent of particular character states.  We may want a place to preserve this.</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>Jpb15https://wiki.phenoscape.org/wg/phenoscape/index.php?title=EQ_for_character_matrices&diff=1920&oldid=prevJpb15 at 20:55, 21 May 20072007-05-21T20:55:35Z<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<col class="diff-marker" />
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<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 20:55, 21 May 2007</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l42" >Line 42:</td>
<td colspan="2" class="diff-lineno">Line 42:</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>|}</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>|}</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>So the problem is that the existing EQ system (and formats such as [http://www.fruitfly.org/~cjm/obd/formats.html PhenoSyntax and PhenoXML]) only stores a list of character states, and cannot group those states into characters.  Storing only character states would be perfectly adequate for most of the data integration benefits provided by the PhenoMap project.  However, <del class="diffchange diffchange-inline">  </del>Possible solutions to this problem for evolutionary data are: 1) Only storing character values and automatically generating characters when a matrix is desired, or 2) Finding a way to code and store EQ statements for both characters and character states.</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>So the problem is that the existing EQ system (and formats such as [http://www.fruitfly.org/~cjm/obd/formats.html PhenoSyntax and PhenoXML]) only stores a list of character states, and cannot group those states into characters.  Storing only character states would be perfectly adequate for most of the data integration benefits provided by the PhenoMap project.  However, <ins class="diffchange diffchange-inline">evolutionary data is often described in the character+character state framework, and a few reasons why we may want to preserve this are listed below.  </ins>Possible solutions to this problem for evolutionary data are: 1) Only storing character values and automatically generating characters when a matrix is desired, or 2) Finding a way to code and store EQ statements for both characters and character states.</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>===1. Automatically inferring characters from character states using PATO===</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>===1. Automatically inferring characters from character states using PATO===</div></td></tr>
</table>Jpb15https://wiki.phenoscape.org/wg/phenoscape/index.php?title=EQ_for_character_matrices&diff=1919&oldid=prevJpb15: /* EQ statements vs. character matrices */2007-05-21T20:52:57Z<p><span dir="auto"><span class="autocomment">EQ statements vs. character matrices</span></span></p>
<table class="diff diff-contentalign-left" 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: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 20:52, 21 May 2007</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l42" >Line 42:</td>
<td colspan="2" class="diff-lineno">Line 42:</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>|}</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>|}</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>So the problem is that the existing EQ system (and formats such as [http://www.fruitfly.org/~cjm/obd/formats.html PhenoSyntax and PhenoXML]) only stores a list of character states, and cannot group those states into characters.  Possible solutions to this problem for evolutionary data are: 1) Only storing character values and automatically generating characters when a matrix is desired, or 2) Finding a way to code and store EQ statements for both characters and character states.</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>So the problem is that the existing EQ system (and formats such as [http://www.fruitfly.org/~cjm/obd/formats.html PhenoSyntax and PhenoXML]) only stores a list of character states, and cannot group those states into characters.  <ins class="diffchange diffchange-inline">Storing only character states would be perfectly adequate for most of the data integration benefits provided by the PhenoMap project.  However,    </ins>Possible solutions to this problem for evolutionary data are: 1) Only storing character values and automatically generating characters when a matrix is desired, or 2) Finding a way to code and store EQ statements for both characters and character states.</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>===1. Automatically inferring characters from character states using PATO===</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>===1. Automatically inferring characters from character states using PATO===</div></td></tr>
</table>Jpb15https://wiki.phenoscape.org/wg/phenoscape/index.php?title=EQ_for_character_matrices&diff=1917&oldid=prevJpb15: /* 1. Automatically inferring attributes from values in PATO */2007-05-21T20:07:29Z<p><span dir="auto"><span class="autocomment">1. Automatically inferring attributes from values in PATO</span></span></p>
<table class="diff diff-contentalign-left" 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: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 20:07, 21 May 2007</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l44" >Line 44:</td>
<td colspan="2" class="diff-lineno">Line 44:</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>So the problem is that the existing EQ system (and formats such as [http://www.fruitfly.org/~cjm/obd/formats.html PhenoSyntax and PhenoXML]) only stores a list of character states, and cannot group those states into characters.  Possible solutions to this problem for evolutionary data are: 1) Only storing character values and automatically generating characters when a matrix is desired, or 2) Finding a way to code and store EQ statements for both characters and character states.</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>So the problem is that the existing EQ system (and formats such as [http://www.fruitfly.org/~cjm/obd/formats.html PhenoSyntax and PhenoXML]) only stores a list of character states, and cannot group those states into characters.  Possible solutions to this problem for evolutionary data are: 1) Only storing character values and automatically generating characters when a matrix is desired, or 2) Finding a way to code and store EQ statements for both characters and character states.</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>===1. Automatically inferring <del class="diffchange diffchange-inline">attributes </del>from <del class="diffchange diffchange-inline">values in </del>PATO===</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>===1. Automatically inferring <ins class="diffchange diffchange-inline">characters </ins>from <ins class="diffchange diffchange-inline">character states using </ins>PATO===</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>PATO does not distinguish qualities representing values from those representing attributes, except that values descend from attributes in the hierarchy.  But given an arbitrary value, it is not possible to automatically infer the attribute it is a value for.  Many values are children of other values - for example, "bright blue" and "dark blue" are children of "blue".  You need to traverse up two levels to reach the attribute "color".  Also, some terminal terms in PATO are not values - they are attributes for which no values are defined in PATO.  Examples are "acceleration" and "buoyancy".</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>PATO does not distinguish qualities representing values from those representing attributes, except that values descend from attributes in the hierarchy.  But given an arbitrary value, it is not possible to automatically infer the attribute it is a value for.  Many values are children of other values - for example, "bright blue" and "dark blue" are children of "blue".  You need to traverse up two levels to reach the attribute "color".  Also, some terminal terms in PATO are not values - they are attributes for which no values are defined in PATO.  Examples are "acceleration" and "buoyancy".</div></td></tr>
</table>Jpb15https://wiki.phenoscape.org/wg/phenoscape/index.php?title=EQ_for_character_matrices&diff=1916&oldid=prevJpb15: /* 1. Automatically inferring attributes from values in PATO */2007-05-21T20:06:55Z<p><span dir="auto"><span class="autocomment">1. Automatically inferring attributes from values in PATO</span></span></p>
<table class="diff diff-contentalign-left" 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: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 20:06, 21 May 2007</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l54" >Line 54:</td>
<td colspan="2" class="diff-lineno">Line 54:</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>* In order for this to work, the Attribute and Value slims must continue to be maintained by curators as terms are added to PATO.  However no one else seems to be using these slims at this time.</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>* In order for this to work, the Attribute and Value slims must continue to be maintained by curators as terms are added to PATO.  However no one else seems to be using these slims at this time.</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>* A researcher may be interested in coding a character such as "fin morphology", with various species having values "lobate", "stubby", and "elongated".  However, without a way to store the desired character attribute, the current Phenote NEXUS exporter would see these phenotypes as states for the separate characters "fin shape", "fin size", and "fin length", respectively.  Conversely, if the researcher was generating a matrix from a database of EQ statements by choosing an entity-attribute pair such as "fin morphology", what should happen if a given species has values for both "fin lobate" and "fin elongated" - i.e. would this be a different character state from another species which was only coded for "fin lobate"?</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>* A researcher may be interested in coding a character such as "fin morphology", with various species having values "lobate", "stubby", and "elongated".  However, without a way to store the desired character attribute, the current Phenote NEXUS exporter would see these phenotypes as states for the separate characters "fin shape", "fin size", and "fin length", respectively.  Conversely, if the researcher was generating a matrix from a database of EQ statements by choosing an entity-attribute pair such as "fin morphology", what should happen if a given species has values for both "fin lobate" and "fin elongated" - i.e. would this be a different character state from another species which was only coded for "fin lobate"?</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>* The original publication may have valuable textual information describing the character, independent of particular <del class="diffchange diffchange-inline">values</del>.  We may want a place to preserve this.</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>* The original publication may have valuable textual information describing the character, independent of particular <ins class="diffchange diffchange-inline">character states</ins>.  We may want a place to preserve this.</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>===2. Storing EQ statements for both characters and character states===</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>===2. Storing EQ statements for both characters and character states===</div></td></tr>
</table>Jpb15https://wiki.phenoscape.org/wg/phenoscape/index.php?title=EQ_for_character_matrices&diff=1915&oldid=prevJpb15: /* EQ statements vs. character matrices */2007-05-21T20:03:30Z<p><span dir="auto"><span class="autocomment">EQ statements vs. character matrices</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 20:03, 21 May 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>|}</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>|}</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>If these fish are different species, you can see that there are 2 values for the character "dorsal fin shape", 1 value for "dorsal fin color", and 1 value for "pectoral fin color".  But nowhere in the existing EQ data formats is the character stored.  We <del class="diffchange diffchange-inline">had </del>to infer it from the PATO hierarchy to generate a matrix like this:</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>If these fish are different species, you can see that there are 2 values for the character "dorsal fin shape", 1 value for "dorsal fin color", and 1 value for "pectoral fin color".  But nowhere in the existing EQ data formats is the character stored.  We <ins class="diffchange diffchange-inline">have </ins>to infer it from the PATO hierarchy to generate a matrix like this:</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>{| border="1" cellpadding="3"</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>{| border="1" cellpadding="3"</div></td></tr>
</table>Jpb15https://wiki.phenoscape.org/wg/phenoscape/index.php?title=EQ_for_character_matrices&diff=1914&oldid=prevJpb15: /* EQ statements vs. character matrices */2007-05-21T20:02:23Z<p><span dir="auto"><span class="autocomment">EQ statements vs. character matrices</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 20:02, 21 May 2007</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l11" >Line 11:</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>[[Image:EQmatrix.png|center|500px]]</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>[[Image:EQmatrix.png|center|500px]]</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>The character (a column header in the matrix) is composed of an Entity and a Quality representing an attribute (e.g. "shape").  Values for this character are entered into the cells (e.g. "round).  So you can see that the Q of EQ is represented in both the character and the character state.  When EQ is used to describe mutant phenotypes, typically only the value is stated, since one can traverse back through the PATO hierarchy to find ancestor terms representing attributes - "round" is a child of "shape".</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>The character (a column header in the matrix) is composed of an Entity<ins class="diffchange diffchange-inline">, </ins>and a Quality representing an attribute (e.g. "shape").  Values for this character are entered into the cells (e.g. "round<ins class="diffchange diffchange-inline">"</ins>).  So you can see that the Q of EQ is represented in both the character and the character state.  When EQ is used to describe mutant phenotypes, typically only the value is stated, since one can traverse back through the PATO hierarchy to find ancestor terms representing attributes - "round" is a child of "shape".</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>Clearly, evolutionary characters and character states can be represented using an EQ system as mutant phenotypes are.  However there is a major difference in the two data models: the data formats being developed for mutant phenotype EQ statements store only a list of phenotype value statements, with no place to reference an independent character.  So you may have a data set like this:</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>Clearly, evolutionary characters and character states can be represented using an EQ system as mutant phenotypes are.  However there is a major difference in the two data models: the data formats being developed for mutant phenotype EQ statements store only a list of phenotype value statements, with no place to reference an independent character.  So you may have a data set like this:</div></td></tr>
</table>Jpb15