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Re-use "contrast weight matrix" from stato #305

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Re-use "contrast weight matrix" from stato #305

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c27da93
Import "contrast weight matrix" from stato
Apr 16, 2015
9d550e3
Re-use stato:'contrast weight matrix'
Apr 16, 2015
df5c363
Update examples and specs
Apr 16, 2015
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70 changes: 33 additions & 37 deletions doc/content/specs/nidm-results_dev.html
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Expand Up @@ -1105,7 +1105,7 @@ <h1 label="NIDM_0000144">nidm:'Resels Per Voxel Map'</h1>
<td><a title="NIDM_0000002">nidm:'Contrast Map'</a>
</td>

<td rowspan="4" style="text-align: center;">NIDM-Results Types<br/> (PROV Entity)</td>
<td rowspan="3" style="text-align: center;">NIDM-Results Types<br/> (PROV Entity)</td>

<td><a title="NIDM_0000002">nidm:'Contrast Map'</a></td>
</tr>
Expand All @@ -1117,13 +1117,6 @@ <h1 label="NIDM_0000144">nidm:'Resels Per Voxel Map'</h1>
<td><a title="NIDM_0000013">nidm:'Contrast Standard Error Map'</a></td>
</tr>

<tr>
<td><a title="NIDM_0000014">nidm:'Contrast Weights'</a>
</td>

<td><a title="NIDM_0000014">nidm:'Contrast Weights'</a></td>
</tr>

<tr>
<td><a title="NIDM_0000076">nidm:'Statistic Map'</a>
</td>
Expand All @@ -1138,7 +1131,7 @@ <h1 label="NIDM_0000144">nidm:'Resels Per Voxel Map'</h1>
<section id="section-nidm:'Contrast Estimation'">
<h1 label="NIDM_0000001">nidm:'Contrast Estimation'</h1>
<div class="glossary-ref">
A <a title="NIDM_0000001"><dfn title="NIDM_0000001">nidm:'Contrast Estimation'</dfn></a> is the process of performing a <a href="http://purl.obolibrary.org/obo/STATO_0000383) at each element (e.g., pixel, voxel, vertex, or face">obo:contrast estimation</a> of a map. <a title="NIDM_0000001">nidm:'Contrast Estimation'</a> is a prov:Activity that uses <a title="NIDM_0000014">nidm:'Contrast Weights'</a>, <a title="NIDM_0000019">nidm:'Design Matrix'</a>, <a title="NIDM_0000054">nidm:'Mask Map'</a>, <a title="NIDM_0000061">nidm:'Parameter Estimate Map'</a>, <a title="NIDM_0000066">nidm:'Residual Mean Squares Map'</a> entities. This activity generates <a title="NIDM_0000002">nidm:'Contrast Map'</a>, <a title="NIDM_0000013">nidm:'Contrast Standard Error Map'</a>, <a title="NIDM_0000076">nidm:'Statistic Map'</a> entities.
A <a title="NIDM_0000001"><dfn title="NIDM_0000001">nidm:'Contrast Estimation'</dfn></a> is the process of performing a <a href="http://purl.obolibrary.org/obo/STATO_0000383) at each element (e.g., pixel, voxel, vertex, or face">obo:contrast estimation</a> of a map. <a title="NIDM_0000001">nidm:'Contrast Estimation'</a> is a prov:Activity that uses <a title="NIDM_0000019">nidm:'Design Matrix'</a>, <a title="NIDM_0000054">nidm:'Mask Map'</a>, <a title="NIDM_0000061">nidm:'Parameter Estimate Map'</a>, <a title="NIDM_0000066">nidm:'Residual Mean Squares Map'</a>, <a title="STATO_0000323" href ="http://purl.obolibrary.org/obo/STATO_0000323">obo:'contrast weight matrix'</a> entities. This activity generates <a title="NIDM_0000002">nidm:'Contrast Map'</a>, <a title="NIDM_0000013">nidm:'Contrast Standard Error Map'</a>, <a title="NIDM_0000076">nidm:'Statistic Map'</a> entities.
</div>
<p></p>
<div class="attributes" id="attributes-nidm:'Contrast Estimation'"> A <a title="NIDM_0000001">nidm:'Contrast Estimation'</a> has attributes:
Expand Down Expand Up @@ -1214,33 +1207,6 @@ <h1 label="NIDM_0000013">nidm:'Contrast Standard Error Map'</h1>
nidm_inCoordinateSpace: niiri:coordinate_space_id_1 ;
crypto:sha512 "e43b6e01b0463fe7d40782137867a..."^^xsd:string ;
prov:wasGeneratedBy niiri:contrast_estimation_id .</pre>
</section>
<!-- nidm:'Contrast Weights' (NIDM_0000014) -->
<section id="section-nidm:'Contrast Weights'">
<h1 label="NIDM_0000014">nidm:'Contrast Weights'</h1>
<div class="glossary-ref">
A <a title="NIDM_0000014"><dfn title="NIDM_0000014">nidm:'Contrast Weights'</dfn></a> is vector defining the linear combination associated with a particular contrast. . <a title="NIDM_0000014">nidm:'Contrast Weights'</a> is a prov:Entity used by <a title="NIDM_0000001">nidm:'Contrast Estimation'</a>.
</div>
<p></p>
<div class="attributes" id="attributes-nidm:'Contrast Weights'"> A <a title="NIDM_0000014">nidm:'Contrast Weights'</a> has attributes:
<ul>
<li><span class="attribute" id="nidm:'Contrast Weights'.label">rdfs:label</span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> human readable description of the nidm:'Contrast Weights'.</li>

<li><a title="NIDM_0000085">nidm:'contrast Name'</a></span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> name of the contrast.(range <a title="string" href ="http://www.w3.org/2001/XMLSchema#string">xsd:string</a>)</li>
<li><a title="NIDM_0000123"><dfn title="NIDM_0000123">nidm:'statistic Type'</dfn></a></span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> property that associates a <a href="http://purl.obolibrary.org/obo/STATO_0000039">stato:"statistic"</a> with a StatisticMap or a ContrastWeights entity.(range <a title="STATO_0000039" href ="http://purl.obolibrary.org/obo/STATO_0000039">obo:'statistic'</a> such as <a title="STATO_0000030" href ="http://purl.obolibrary.org/obo/STATO_0000030">obo:'Chi-Squared statistic'</a>, <a title="STATO_0000282" href ="http://purl.obolibrary.org/obo/STATO_0000282">obo:'F-statistic'</a>, <a title="STATO_0000376" href ="http://purl.obolibrary.org/obo/STATO_0000376">obo:'Z-statistic'</a>, <a title="STATO_0000176" href ="http://purl.obolibrary.org/obo/STATO_0000176">obo:'t-statistic'</a>)</li>
</ul>
</div>
<pre class='example highlight'>@prefix nidm_ContrastWeights: &lt;http://purl.org/nidash/nidm#NIDM_0000014&gt; .
@prefix nidm_statisticType: &lt;http://purl.org/nidash/nidm#NIDM_0000123&gt; .
@prefix nidm_contrastName: &lt;http://purl.org/nidash/nidm#NIDM_0000085&gt; .
@prefix obo_tstatistic: &lt;http://purl.obolibrary.org/obo/STATO_0000176&gt; .


niiri:contrast_id a prov:Entity , nidm_ContrastWeights: ;
rdfs:label "Contrast: Listening &gt; Rest" ;
prov:value "[1, 0, 0]"^^xsd:string ;
nidm_statisticType: obo_tstatistic: ; # obo:'t-statistic'
nidm_contrastName: "listening &gt; rest"^^xsd:string .</pre>
</section>
<!-- nidm:'Statistic Map' (NIDM_0000076) -->
<section id="section-nidm:'Statistic Map'">
Expand All @@ -1258,7 +1224,7 @@ <h1 label="NIDM_0000076">nidm:'Statistic Map'</h1>
<li><a title="NIDM_0000093"><dfn title="NIDM_0000093">nidm:'error Degrees Of Freedom'</dfn></a></span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> degrees of freedom of the error.(range <a title="float" href ="http://www.w3.org/2001/XMLSchema#float">xsd:float</a>)</li>
<li><a title="NIDM_0000103">nidm:'has Map Header'</a></span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> a Property that associates an additional file containing the map header with a map.(range <a title="NIDM_0000053">nidm:'Map Header'</a>)</li>
<li><a title="NIDM_0000104">nidm:'in Coordinate Space'</a></span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> property of a DataArray to associate a CoordinateSpace with a physical file.(range <a title="NIDM_0000016">nidm:'Coordinate Space'</a>)</li>
<li><a title="NIDM_0000123">nidm:'statistic Type'</a></span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> property that associates a <a href="http://purl.obolibrary.org/obo/STATO_0000039">stato:"statistic"</a> with a StatisticMap or a ContrastWeights entity.(range <a title="STATO_0000039" href ="http://purl.obolibrary.org/obo/STATO_0000039">obo:'statistic'</a> such as <a title="STATO_0000030" href ="http://purl.obolibrary.org/obo/STATO_0000030">obo:'Chi-Squared statistic'</a>, <a title="STATO_0000282" href ="http://purl.obolibrary.org/obo/STATO_0000282">obo:'F-statistic'</a>, <a title="STATO_0000376" href ="http://purl.obolibrary.org/obo/STATO_0000376">obo:'Z-statistic'</a>, <a title="STATO_0000176" href ="http://purl.obolibrary.org/obo/STATO_0000176">obo:'t-statistic'</a>)</li>
<li><a title="NIDM_0000123"><dfn title="NIDM_0000123">nidm:'statistic Type'</dfn></a></span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> property that associates a <a href="http://purl.obolibrary.org/obo/STATO_0000039">stato:"statistic"</a> with a StatisticMap or a ContrastWeights entity.(range <a title="STATO_0000039" href ="http://purl.obolibrary.org/obo/STATO_0000039">obo:'statistic'</a> such as <a title="STATO_0000030" href ="http://purl.obolibrary.org/obo/STATO_0000030">obo:'Chi-Squared statistic'</a>, <a title="STATO_0000282" href ="http://purl.obolibrary.org/obo/STATO_0000282">obo:'F-statistic'</a>, <a title="STATO_0000376" href ="http://purl.obolibrary.org/obo/STATO_0000376">obo:'Z-statistic'</a>, <a title="STATO_0000176" href ="http://purl.obolibrary.org/obo/STATO_0000176">obo:'t-statistic'</a>)</li>
</ul>
</div>
<pre class='example highlight'>@prefix nidm_StatisticMap: &lt;http://purl.org/nidash/nidm#NIDM_0000076&gt; .
Expand All @@ -1282,6 +1248,36 @@ <h1 label="NIDM_0000076">nidm:'Statistic Map'</h1>
crypto:sha512 "e43b6e01b0463fe7d40782137867a..."^^xsd:string ;
prov:wasGeneratedBy niiri:contrast_estimation_id;
nidm_errorDegreesOfFreedom: "72.9999999990787"^^xsd:float .</pre>
</section>
<!-- obo:'contrast weight matrix' (STATO_0000323) -->
<section id="section-obo:'contrast weight matrix'">
<h1 label="STATO_0000323">obo:'contrast weight matrix'</h1>
<div class="glossary-ref">
A <a title="STATO_0000323" href ="http://purl.obolibrary.org/obo/STATO_0000323"><dfn title="STATO_0000323" href ="http://purl.obolibrary.org/obo/STATO_0000323">obo:'contrast weight matrix'</dfn></a> is a contrast weight matrix is a information content entity which holds a set of contrast weight, coefficient used in a weighting sum of means defining a contrast. <a title="STATO_0000323" href ="http://purl.obolibrary.org/obo/STATO_0000323">obo:'contrast weight matrix'</a> is used by <a title="NIDM_0000001">nidm:'Contrast Estimation'</a>.
</div>
<p></p>
<div class="attributes" id="attributes-obo:'contrast weight matrix'"> A <a title="STATO_0000323" href ="http://purl.obolibrary.org/obo/STATO_0000323">obo:'contrast weight matrix'</a> has attributes:
<ul>
<li><span class="attribute" id="obo:'contrast weight matrix'.label">rdfs:label</span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> human readable description of the obo:'contrast weight matrix'.</li>

<li><a title="NIDM_0000085">nidm:'contrast Name'</a></span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> name of the contrast.(range <a title="string" href ="http://www.w3.org/2001/XMLSchema#string">xsd:string</a>)</li>
<li><a title="NIDM_0000123">nidm:'statistic Type'</a></span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> property that associates a <a href="http://purl.obolibrary.org/obo/STATO_0000039">stato:"statistic"</a> with a StatisticMap or a ContrastWeights entity.(range <a title="STATO_0000039" href ="http://purl.obolibrary.org/obo/STATO_0000039">obo:'statistic'</a> such as <a title="STATO_0000030" href ="http://purl.obolibrary.org/obo/STATO_0000030">obo:'Chi-Squared statistic'</a>, <a title="STATO_0000282" href ="http://purl.obolibrary.org/obo/STATO_0000282">obo:'F-statistic'</a>, <a title="STATO_0000376" href ="http://purl.obolibrary.org/obo/STATO_0000376">obo:'Z-statistic'</a>, <a title="STATO_0000176" href ="http://purl.obolibrary.org/obo/STATO_0000176">obo:'t-statistic'</a>)</li>
</ul>
</div>
<pre class='example highlight'>[1,0,0]</pre>
</ul>
</div>
<pre class='example highlight'>@prefix nidm_statisticType: &lt;http://purl.org/nidash/nidm#NIDM_0000123&gt; .
@prefix nidm_contrastName: &lt;http://purl.org/nidash/nidm#NIDM_0000085&gt; .
@prefix obo_contrastweightmatrix: &lt;http://purl.obolibrary.org/obo/STATO_0000323&gt; .
@prefix obo_tstatistic: &lt;http://purl.obolibrary.org/obo/STATO_0000176&gt; .


niiri:contrast_id a prov:Entity , obo_contrastweightmatrix: ;
rdfs:label "Contrast: Listening &gt; Rest" ;
prov:value "[1, 0, 0]"^^xsd:string ;
nidm_statisticType: obo_tstatistic: ; # obo:'t-statistic'
nidm_contrastName: "listening &gt; rest"^^xsd:string .</pre>
</section>
</section>
<section><h1>Inference</h1>
Expand Down