Deploying to gh-pages from @ 5b32834 🚀

docs/edges_report.tsv

@@ -1,5 +1,5 @@
 category	subject_prefix	predicate	object_prefix	count_star()
-biolink:GenotypeToDiseaseAssociation	MGI	biolink:model_of	DOID	8031
-biolink:GenotypeToDiseaseAssociation	RGD	biolink:model_of	DOID	785
-biolink:GenotypeToDiseaseAssociation	WB	biolink:model_of	DOID	438
-biolink:GenotypeToDiseaseAssociation	ZFIN	biolink:model_of	DOID	1169
+biolink:GenotypeToDiseaseAssociation	MGI	biolink:model_of	DOID	8041
+biolink:GenotypeToDiseaseAssociation	RGD	biolink:model_of	DOID	787
+biolink:GenotypeToDiseaseAssociation	WB	biolink:model_of	DOID	440
+biolink:GenotypeToDiseaseAssociation	ZFIN	biolink:model_of	DOID	1187

docs/index.html

@@ -574,28 +574,28 @@ <h2 id="edges-report">Edges Report</h2>
 <td>MGI</td>
 <td>biolink:model_of</td>
 <td>DOID</td>
-<td>8031</td>
+<td>8041</td>
 </tr>
 <tr>
 <td>biolink:GenotypeToDiseaseAssociation</td>
 <td>RGD</td>
 <td>biolink:model_of</td>
 <td>DOID</td>
-<td>785</td>
+<td>787</td>
 </tr>
 <tr>
 <td>biolink:GenotypeToDiseaseAssociation</td>
 <td>WB</td>
 <td>biolink:model_of</td>
 <td>DOID</td>
-<td>438</td>
+<td>440</td>
 </tr>
 <tr>
 <td>biolink:GenotypeToDiseaseAssociation</td>
 <td>ZFIN</td>
 <td>biolink:model_of</td>
 <td>DOID</td>
-<td>1169</td>
+<td>1187</td>
 </tr>
 </tbody>
 </table>

docs/search/search_index.json

@@ -1 +1 @@
-{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"Alliance Disease Association Ingest Pipeline","text":""},{"location":"#overview","title":"Overview","text":"<p>The Alliance Disease Association Ingest Pipeline transforms genotype-to-disease associations from the Alliance of Genome Resources and integrates them with the Monarch Knowledge Graph, following the Biolink Model. This pipeline processes data from multiple Model Organism Databases (MODs), maps predicates according to their types, and excludes associations with experimental conditions or modifiers.</p>"},{"location":"#source-mapping","title":"Source Mapping","text":"<p>The data sources are mapped to specific information resources using the following mapping:</p> Source Description FB (FlyBase) Represents Drosophila melanogaster (fruit fly). MGI (Mouse Genome Informatics) Represents Mus musculus (mouse). RGD (Rat Genome Database) Represents Rattus norvegicus (rat). HGNC (HUGO Gene Nomenclature Committee) Represents human genes. SGD (Saccharomyces Genome Database) Represents Saccharomyces cerevisiae (yeast). WB (WormBase) Represents Caenorhabditis elegans (nematode worm). Xenbase Represents Xenopus species (African clawed frog). ZFIN (Zebrafish Information Network) Represents Danio rerio (zebrafish)."},{"location":"#pipeline-details","title":"Pipeline Details","text":"<p>The ingest pipeline processes different types of genotype-disease associations, such as gene-to-disease, variant-to-disease, and genotype-to-disease associations, while handling diverse predicate types (e.g., <code>biolink:related_to</code>, <code>biolink:biomarker_for</code>, <code>biolink:model_of</code>, etc.).</p> <p>The main steps include:</p> <ol> <li> <p>Subject Category Identification: Identifies the subject category (gene, allele, or affected genomic model) to determine the correct association type (<code>GeneToDiseaseAssociation</code>, <code>VariantToDiseaseAssociation</code>, or <code>GenotypeToDiseaseAssociation</code>).</p> </li> <li> <p>Predicate Mapping: Maps the predicate for each association based on the <code>AssociationType</code> in the data.</p> </li> <li> <p>Filtering: Excludes rows with unsupported association types, experimental conditions (other than standard conditions), or modifiers.</p> </li> <li> <p>Output Generation: Outputs the processed associations in a format compatible with the Monarch Knowledge Graph.</p> </li> </ol>"},{"location":"#resulting-biolink-class","title":"Resulting Biolink Class","text":"<p>The resulting Biolink class includes the following fields:</p> <ul> <li>Category: <code>biolink:GenotypeToDiseaseAssociation</code></li> <li>Subject: <code>MGI:123456</code></li> <li>Predicate: <code>biolink:model_of</code></li> <li>Object: <code>MONDO:0001234</code></li> <li>Publications: <code>PMID:123456</code></li> <li>Primary Knowledge Source: <code>infores:mgi</code></li> <li>Aggregator Knowledge Source: <code>infores:monarchinitiative, infores:agrkb</code></li> <li>Knowledge Level: <code>knowledge_assertion</code></li> <li>Agent Type: <code>manual_agent</code></li> </ul>"},{"location":"#edges-report","title":"Edges Report","text":"category subject_prefix predicate object_prefix count_star() biolink:GenotypeToDiseaseAssociation MGI biolink:model_of DOID 8031 biolink:GenotypeToDiseaseAssociation RGD biolink:model_of DOID 785 biolink:GenotypeToDiseaseAssociation WB biolink:model_of DOID 438 biolink:GenotypeToDiseaseAssociation ZFIN biolink:model_of DOID 1169 <p>The edges report provides a summary of the number of genotype-to-disease associations from different sources, categorized by subject prefix and predicate: This table captures the total number of associations processed from each source, categorized by their specific predicates and object prefixes. The \"MOD\" (Model Organism Databases) sources such as MGI, RGD, WB, and ZFIN provide the foundational data for these associations.</p>"}]}
+{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"Alliance Disease Association Ingest Pipeline","text":""},{"location":"#overview","title":"Overview","text":"<p>The Alliance Disease Association Ingest Pipeline transforms genotype-to-disease associations from the Alliance of Genome Resources and integrates them with the Monarch Knowledge Graph, following the Biolink Model. This pipeline processes data from multiple Model Organism Databases (MODs), maps predicates according to their types, and excludes associations with experimental conditions or modifiers.</p>"},{"location":"#source-mapping","title":"Source Mapping","text":"<p>The data sources are mapped to specific information resources using the following mapping:</p> Source Description FB (FlyBase) Represents Drosophila melanogaster (fruit fly). MGI (Mouse Genome Informatics) Represents Mus musculus (mouse). RGD (Rat Genome Database) Represents Rattus norvegicus (rat). HGNC (HUGO Gene Nomenclature Committee) Represents human genes. SGD (Saccharomyces Genome Database) Represents Saccharomyces cerevisiae (yeast). WB (WormBase) Represents Caenorhabditis elegans (nematode worm). Xenbase Represents Xenopus species (African clawed frog). ZFIN (Zebrafish Information Network) Represents Danio rerio (zebrafish)."},{"location":"#pipeline-details","title":"Pipeline Details","text":"<p>The ingest pipeline processes different types of genotype-disease associations, such as gene-to-disease, variant-to-disease, and genotype-to-disease associations, while handling diverse predicate types (e.g., <code>biolink:related_to</code>, <code>biolink:biomarker_for</code>, <code>biolink:model_of</code>, etc.).</p> <p>The main steps include:</p> <ol> <li> <p>Subject Category Identification: Identifies the subject category (gene, allele, or affected genomic model) to determine the correct association type (<code>GeneToDiseaseAssociation</code>, <code>VariantToDiseaseAssociation</code>, or <code>GenotypeToDiseaseAssociation</code>).</p> </li> <li> <p>Predicate Mapping: Maps the predicate for each association based on the <code>AssociationType</code> in the data.</p> </li> <li> <p>Filtering: Excludes rows with unsupported association types, experimental conditions (other than standard conditions), or modifiers.</p> </li> <li> <p>Output Generation: Outputs the processed associations in a format compatible with the Monarch Knowledge Graph.</p> </li> </ol>"},{"location":"#resulting-biolink-class","title":"Resulting Biolink Class","text":"<p>The resulting Biolink class includes the following fields:</p> <ul> <li>Category: <code>biolink:GenotypeToDiseaseAssociation</code></li> <li>Subject: <code>MGI:123456</code></li> <li>Predicate: <code>biolink:model_of</code></li> <li>Object: <code>MONDO:0001234</code></li> <li>Publications: <code>PMID:123456</code></li> <li>Primary Knowledge Source: <code>infores:mgi</code></li> <li>Aggregator Knowledge Source: <code>infores:monarchinitiative, infores:agrkb</code></li> <li>Knowledge Level: <code>knowledge_assertion</code></li> <li>Agent Type: <code>manual_agent</code></li> </ul>"},{"location":"#edges-report","title":"Edges Report","text":"category subject_prefix predicate object_prefix count_star() biolink:GenotypeToDiseaseAssociation MGI biolink:model_of DOID 8041 biolink:GenotypeToDiseaseAssociation RGD biolink:model_of DOID 787 biolink:GenotypeToDiseaseAssociation WB biolink:model_of DOID 440 biolink:GenotypeToDiseaseAssociation ZFIN biolink:model_of DOID 1187 <p>The edges report provides a summary of the number of genotype-to-disease associations from different sources, categorized by subject prefix and predicate: This table captures the total number of associations processed from each source, categorized by their specific predicates and object prefixes. The \"MOD\" (Model Organism Databases) sources such as MGI, RGD, WB, and ZFIN provide the foundational data for these associations.</p>"}]}

docs/sitemap.xml

@@ -2,7 +2,7 @@
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
     <url>
          <loc>https://monarch-initiative.github.io/alliance-disease-association-ingest/</loc>
-         <lastmod>2024-12-03</lastmod>
+         <lastmod>2025-01-03</lastmod>
          <changefreq>daily</changefreq>
     </url>
 </urlset>