Update gh-pages to output generated at 2dcc6a5

api/pypath.utils.orthology.EnsemblOrthology.html

@@ -508,8 +508,7 @@ <h1>pypath.utils.orthology.EnsemblOrthology<a class="headerlink" href="#pypath-u
 <dt>Args</dt><dd><dl class="simple">
 <dt>target:</dt><dd><p>Name or NCBI Taxonomy ID of the target organism.</p>
 </dd>
-<dt>source:</dt><dd><p>Name or NCBI Taxonomy ID of the default source organism.
-Multiple source organisms can be used on the same instance.</p>
+<dt>source:</dt><dd><p>Name or NCBI Taxonomy ID of the source organism.</p>
 </dd>
 <dt>id_type:</dt><dd><p>The identifier type to use.</p>
 </dd>

api/pypath.utils.orthology.HomologeneOrthology.html

@@ -514,8 +514,7 @@ <h1>pypath.utils.orthology.HomologeneOrthology<a class="headerlink" href="#pypat
 <dt>Args</dt><dd><dl class="simple">
 <dt>target:</dt><dd><p>Name or NCBI Taxonomy ID of the target organism.</p>
 </dd>
-<dt>source:</dt><dd><p>Name or NCBI Taxonomy ID of the default source organism.
-Multiple source organisms can be used on the same instance.</p>
+<dt>source:</dt><dd><p>Name or NCBI Taxonomy ID of the source organism.</p>
 </dd>
 <dt>id_type:</dt><dd><p>The identifier type to use.</p>
 </dd>

api/pypath.utils.orthology.OmaOrthology.html

@@ -508,8 +508,7 @@ <h1>pypath.utils.orthology.OmaOrthology<a class="headerlink" href="#pypath-utils
 <dt>Args</dt><dd><dl class="simple">
 <dt>target:</dt><dd><p>Name or NCBI Taxonomy ID of the target organism.</p>
 </dd>
-<dt>source:</dt><dd><p>Name or NCBI Taxonomy ID of the default source organism.
-Multiple source organisms can be used on the same instance.</p>
+<dt>source:</dt><dd><p>Name or NCBI Taxonomy ID of the source organism.</p>
 </dd>
 <dt>id_type:</dt><dd><p>The identifier type to use.</p>
 </dd>

api/pypath.utils.orthology.OrthologyManager.html

@@ -553,14 +553,13 @@ <h1>pypath.utils.orthology.OrthologyManager<a class="headerlink" href="#pypath-u
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>target</strong> – Name or NCBI Taxonomy ID of the target organism.</p></li>
-<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the default source organism.
-Multiple source organisms can be used on the same instance.</p></li>
+<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the source organism.</p></li>
 <li><p><strong>id_type</strong> – The identifier type to use.</p></li>
 <li><p><strong>only_swissprot</strong> – Use only SwissProt IDs.</p></li>
-<li><p><strong>oma</strong> – Use homology information from the Orthologous Matrix (OMA).
-Currently this is the recommended source for homology data.</p></li>
-<li><p><strong>homologene</strong> – Use homology information from NCBI HomoloGene.</p></li>
-<li><p><strong>ensembl</strong> – Use homology information from Ensembl.</p></li>
+<li><p><strong>oma</strong> – Use orthology information from the Orthologous Matrix (OMA).
+Currently this is the recommended source for orthology data.</p></li>
+<li><p><strong>homologene</strong> – Use orthology information from NCBI HomoloGene.</p></li>
+<li><p><strong>ensembl</strong> – Use orthology information from Ensembl.</p></li>
 <li><p><strong>oma_rel_type</strong> – Restrict relations to certain types.</p></li>
 <li><p><strong>oma_score</strong> – Lower threshold for similarity metric.</p></li>
 <li><p><strong>ensembl_hc</strong> – Use only the high confidence orthology relations from Ensembl.</p></li>
@@ -587,14 +586,13 @@ <h1>pypath.utils.orthology.OrthologyManager<a class="headerlink" href="#pypath-u
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>target</strong> – Name or NCBI Taxonomy ID of the target organism.</p></li>
-<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the default source organism.
-Multiple source organisms can be used on the same instance.</p></li>
+<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the source organism.</p></li>
 <li><p><strong>id_type</strong> – The identifier type to use.</p></li>
 <li><p><strong>only_swissprot</strong> – Use only SwissProt IDs.</p></li>
-<li><p><strong>oma</strong> – Use homology information from the Orthologous Matrix (OMA).
-Currently this is the recommended source for homology data.</p></li>
-<li><p><strong>homologene</strong> – Use homology information from NCBI HomoloGene.</p></li>
-<li><p><strong>ensembl</strong> – Use homology information from Ensembl.</p></li>
+<li><p><strong>oma</strong> – Use orthology information from the Orthologous Matrix (OMA).
+Currently this is the recommended source for orthology data.</p></li>
+<li><p><strong>homologene</strong> – Use orthology information from NCBI HomoloGene.</p></li>
+<li><p><strong>ensembl</strong> – Use orthology information from Ensembl.</p></li>
 <li><p><strong>oma_rel_type</strong> – Restrict relations to certain types.</p></li>
 <li><p><strong>oma_score</strong> – Lower threshold for similarity metric.</p></li>
 <li><p><strong>ensembl_hc</strong> – Use only the high confidence orthology relations from Ensembl.</p></li>
@@ -622,14 +620,13 @@ <h1>pypath.utils.orthology.OrthologyManager<a class="headerlink" href="#pypath-u
 <li><p><strong>identifiers</strong> – One or more identifers of the source organism, of ID type
 <cite>id_type</cite>.</p></li>
 <li><p><strong>target</strong> – Name or NCBI Taxonomy ID of the target organism.</p></li>
-<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the default source organism.
-Multiple source organisms can be used on the same instance.</p></li>
+<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the source organism.</p></li>
 <li><p><strong>id_type</strong> – The identifier type to use.</p></li>
 <li><p><strong>only_swissprot</strong> – Use only SwissProt IDs.</p></li>
-<li><p><strong>oma</strong> – Use homology information from the Orthologous Matrix (OMA).
-Currently this is the recommended source for homology data.</p></li>
-<li><p><strong>homologene</strong> – Use homology information from NCBI HomoloGene.</p></li>
-<li><p><strong>ensembl</strong> – Use homology information from Ensembl.</p></li>
+<li><p><strong>oma</strong> – Use orthology information from the Orthologous Matrix (OMA).
+Currently this is the recommended source for orthology data.</p></li>
+<li><p><strong>homologene</strong> – Use orthology information from NCBI HomoloGene.</p></li>
+<li><p><strong>ensembl</strong> – Use orthology information from Ensembl.</p></li>
 <li><p><strong>oma_rel_type</strong> – Restrict relations to certain types.</p></li>
 <li><p><strong>oma_score</strong> – Lower threshold for similarity metric.</p></li>
 <li><p><strong>ensembl_hc</strong> – Use only the high confidence orthology relations from Ensembl.</p></li>
@@ -660,15 +657,14 @@ <h1>pypath.utils.orthology.OrthologyManager<a class="headerlink" href="#pypath-u
 keys are column names and values are ID types. Except this
 last case, identifiers are assumed to be <cite>id_type</cite>.</p></li>
 <li><p><strong>target</strong> – Name or NCBI Taxonomy ID of the target organism.</p></li>
-<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the default source organism.
-Multiple source organisms can be used on the same instance.</p></li>
+<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the source organism.</p></li>
 <li><p><strong>id_type</strong> – The default identifier type to use, will be used for all
 columns where ID type is not specified.</p></li>
 <li><p><strong>only_swissprot</strong> – Use only SwissProt IDs.</p></li>
-<li><p><strong>oma</strong> – Use homology information from the Orthologous Matrix (OMA).
-Currently this is the recommended source for homology data.</p></li>
-<li><p><strong>homologene</strong> – Use homology information from NCBI HomoloGene.</p></li>
-<li><p><strong>ensembl</strong> – Use homology information from Ensembl.</p></li>
+<li><p><strong>oma</strong> – Use orthology information from the Orthologous Matrix (OMA).
+Currently this is the recommended source for orthology data.</p></li>
+<li><p><strong>homologene</strong> – Use orthology information from NCBI HomoloGene.</p></li>
+<li><p><strong>ensembl</strong> – Use orthology information from Ensembl.</p></li>
 <li><p><strong>oma_rel_type</strong> – Restrict relations to certain types.</p></li>
 <li><p><strong>oma_score</strong> – Lower threshold for similarity metric.</p></li>
 <li><p><strong>ensembl_hc</strong> – Use only the high confidence orthology relations from Ensembl.</p></li>

api/pypath.utils.orthology.ProteinOrthology.html

@@ -514,8 +514,7 @@ <h1>pypath.utils.orthology.ProteinOrthology<a class="headerlink" href="#pypath-u
 <dt>Args</dt><dd><dl class="simple">
 <dt>target:</dt><dd><p>Name or NCBI Taxonomy ID of the target organism.</p>
 </dd>
-<dt>source:</dt><dd><p>Name or NCBI Taxonomy ID of the default source organism.
-Multiple source organisms can be used on the same instance.</p>
+<dt>source:</dt><dd><p>Name or NCBI Taxonomy ID of the source organism.</p>
 </dd>
 <dt>id_type:</dt><dd><p>The identifier type to use.</p>
 </dd>

api/pypath.utils.orthology.get_df.html

@@ -504,14 +504,13 @@ <h1>pypath.utils.orthology.get_df<a class="headerlink" href="#pypath-utils-ortho
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>target</strong> – Name or NCBI Taxonomy ID of the target organism.</p></li>
-<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the default source organism.
-Multiple source organisms can be used on the same instance.</p></li>
+<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the source organism.</p></li>
 <li><p><strong>id_type</strong> – The identifier type to use.</p></li>
 <li><p><strong>only_swissprot</strong> – Use only SwissProt IDs.</p></li>
-<li><p><strong>oma</strong> – Use homology information from the Orthologous Matrix (OMA).
-Currently this is the recommended source for homology data.</p></li>
-<li><p><strong>homologene</strong> – Use homology information from NCBI HomoloGene.</p></li>
-<li><p><strong>ensembl</strong> – Use homology information from Ensembl.</p></li>
+<li><p><strong>oma</strong> – Use orthology information from the Orthologous Matrix (OMA).
+Currently this is the recommended source for orthology data.</p></li>
+<li><p><strong>homologene</strong> – Use orthology information from NCBI HomoloGene.</p></li>
+<li><p><strong>ensembl</strong> – Use orthology information from Ensembl.</p></li>
 <li><p><strong>oma_rel_type</strong> – Restrict relations to certain types.</p></li>
 <li><p><strong>oma_score</strong> – Lower threshold for similarity metric.</p></li>
 <li><p><strong>ensembl_hc</strong> – Use only the high confidence orthology relations from Ensembl.</p></li>

api/pypath.utils.orthology.get_dict.html

@@ -504,14 +504,13 @@ <h1>pypath.utils.orthology.get_dict<a class="headerlink" href="#pypath-utils-ort
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>target</strong> – Name or NCBI Taxonomy ID of the target organism.</p></li>
-<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the default source organism.
-Multiple source organisms can be used on the same instance.</p></li>
+<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the source organism.</p></li>
 <li><p><strong>id_type</strong> – The identifier type to use.</p></li>
 <li><p><strong>only_swissprot</strong> – Use only SwissProt IDs.</p></li>
-<li><p><strong>oma</strong> – Use homology information from the Orthologous Matrix (OMA).
-Currently this is the recommended source for homology data.</p></li>
-<li><p><strong>homologene</strong> – Use homology information from NCBI HomoloGene.</p></li>
-<li><p><strong>ensembl</strong> – Use homology information from Ensembl.</p></li>
+<li><p><strong>oma</strong> – Use orthology information from the Orthologous Matrix (OMA).
+Currently this is the recommended source for orthology data.</p></li>
+<li><p><strong>homologene</strong> – Use orthology information from NCBI HomoloGene.</p></li>
+<li><p><strong>ensembl</strong> – Use orthology information from Ensembl.</p></li>
 <li><p><strong>oma_rel_type</strong> – Restrict relations to certain types.</p></li>
 <li><p><strong>oma_score</strong> – Lower threshold for similarity metric.</p></li>
 <li><p><strong>ensembl_hc</strong> – Use only the high confidence orthology relations from Ensembl.</p></li>

api/pypath.utils.orthology.get_manager.html

@@ -501,8 +501,8 @@ <h1>pypath.utils.orthology.get_manager<a class="headerlink" href="#pypath-utils-
 <span class="sig-prename descclassname"><span class="pre">pypath.utils.orthology.</span></span><span class="sig-name descname"><span class="pre">get_manager</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#get_manager"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.get_manager" title="Permalink to this definition">§</a></dt>
 <dd><p>Access the orthology manager.</p>
 <p>Returns the orthology manager, an object which loads and unloads the
-homology lookup tables as necessary, and provides the interface for
-querying the homology data. Normally an instance of the manager
+orthology lookup tables as necessary, and provides the interface for
+querying the orthology data. Normally an instance of the manager
 belongs to the module, and if it does not exist yet, will be created
 automatically.</p>
 </dd></dl>

api/pypath.utils.orthology.translate.html

@@ -506,14 +506,13 @@ <h1>pypath.utils.orthology.translate<a class="headerlink" href="#pypath-utils-or
 <li><p><strong>identifiers</strong> – One or more identifers of the source organism, of ID type
 <cite>id_type</cite>.</p></li>
 <li><p><strong>target</strong> – Name or NCBI Taxonomy ID of the target organism.</p></li>
-<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the default source organism.
-Multiple source organisms can be used on the same instance.</p></li>
+<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the source organism.</p></li>
 <li><p><strong>id_type</strong> – The identifier type to use.</p></li>
 <li><p><strong>only_swissprot</strong> – Use only SwissProt IDs.</p></li>
-<li><p><strong>oma</strong> – Use homology information from the Orthologous Matrix (OMA).
-Currently this is the recommended source for homology data.</p></li>
-<li><p><strong>homologene</strong> – Use homology information from NCBI HomoloGene.</p></li>
-<li><p><strong>ensembl</strong> – Use homology information from Ensembl.</p></li>
+<li><p><strong>oma</strong> – Use orthology information from the Orthologous Matrix (OMA).
+Currently this is the recommended source for orthology data.</p></li>
+<li><p><strong>homologene</strong> – Use orthology information from NCBI HomoloGene.</p></li>
+<li><p><strong>ensembl</strong> – Use orthology information from Ensembl.</p></li>
 <li><p><strong>oma_rel_type</strong> – Restrict relations to certain types.</p></li>
 <li><p><strong>oma_score</strong> – Lower threshold for similarity metric.</p></li>
 <li><p><strong>ensembl_hc</strong> – Use only the high confidence orthology relations from Ensembl.</p></li>

api/pypath.utils.orthology.translate_df.html

@@ -505,19 +505,18 @@ <h1>pypath.utils.orthology.translate_df<a class="headerlink" href="#pypath-utils
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>df</strong> – A data frame.</p></li>
 <li><p><strong>target</strong> – Name or NCBI Taxonomy ID of the target organism.</p></li>
-<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the default source organism.
-Multiple source organisms can be used on the same instance.</p></li>
+<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the source organism.</p></li>
 <li><p><strong>cols</strong> – One or more columns to be translated. It can be a single
 column name, an iterable of column names or a dict where
 keys are column names and values are ID types. Except this
 last case, identifiers are assumed to be <cite>id_type</cite>.</p></li>
 <li><p><strong>id_type</strong> – The default identifier type to use, will be used for all
 columns where ID type is not specified.</p></li>
 <li><p><strong>only_swissprot</strong> – Use only SwissProt IDs.</p></li>
-<li><p><strong>oma</strong> – Use homology information from the Orthologous Matrix (OMA).
-Currently this is the recommended source for homology data.</p></li>
-<li><p><strong>homologene</strong> – Use homology information from NCBI HomoloGene.</p></li>
-<li><p><strong>ensembl</strong> – Use homology information from Ensembl.</p></li>
+<li><p><strong>oma</strong> – Use orthology information from the Orthologous Matrix (OMA).
+Currently this is the recommended source for orthology data.</p></li>
+<li><p><strong>homologene</strong> – Use orthology information from NCBI HomoloGene.</p></li>
+<li><p><strong>ensembl</strong> – Use orthology information from Ensembl.</p></li>
 <li><p><strong>oma_rel_type</strong> – Restrict relations to certain types.</p></li>
 <li><p><strong>oma_score</strong> – Lower threshold for similarity metric.</p></li>
 <li><p><strong>ensembl_hc</strong> – Use only the high confidence orthology relations from Ensembl.</p></li>

contents.html

@@ -565,9 +565,9 @@ <h1>Contents<a class="headerlink" href="#contents" title="Permalink to this head
 <li class="toctree-l3"><a class="reference internal" href="notebooks/manual.html#Direct-access-to-ID-translation-tables">Direct access to ID translation tables</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="notebooks/manual.html#Homology-translation">Homology translation</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="notebooks/manual.html#Homology-translation-tables-as-dictionaries">Homology translation tables as dictionaries</a></li>
-<li class="toctree-l3"><a class="reference internal" href="notebooks/manual.html#Homology-translation-data-frames">Homology translation data frames</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/manual.html#Orthology-translation">Orthology translation</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="notebooks/manual.html#Orthology-translation-tables-as-dictionaries">Orthology translation tables as dictionaries</a></li>
+<li class="toctree-l3"><a class="reference internal" href="notebooks/manual.html#Orthology-translation-data-frames">Orthology translation data frames</a></li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="notebooks/manual.html#Taxonomy">Taxonomy</a><ul>