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‎script/process_markdown.ipynb‎

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"\t\to.write(description)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 25,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/html": [
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"<div>\n",
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"<style scoped>\n",
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" .dataframe tbody tr th:only-of-type {\n",
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" vertical-align: middle;\n",
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" }\n",
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"\n",
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" .dataframe tbody tr th {\n",
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" vertical-align: top;\n",
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" }\n",
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"\n",
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" .dataframe thead th {\n",
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" text-align: right;\n",
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" }\n",
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"</style>\n",
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"<table border=\"1\" class=\"dataframe\">\n",
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" <thead>\n",
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" <tr style=\"text-align: right;\">\n",
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" <th></th>\n",
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" <th>tool_name</th>\n",
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" <th>title</th>\n",
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" <th>tutorial</th>\n",
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" <th>tool_icon</th>\n",
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" <th>short_description</th>\n",
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" <th>description</th>\n",
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" <th>inputs</th>\n",
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" <th>sources</th>\n",
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" <th>link</th>\n",
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" <th>image</th>\n",
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" <th>featured</th>\n",
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" <th>featured_image</th>\n",
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" <th>creator_dcc</th>\n",
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" <th>source_dcc</th>\n",
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" </tr>\n",
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" </thead>\n",
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" <tbody>\n",
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" <tr>\n",
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" <th>0</th>\n",
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" <td>Playbook Workflow Builder</td>\n",
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" <td>Explain Drug-Drug Interactions</td>\n",
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" <td>https://www.youtube.com/watch?v=7_Xir0jVisM</td>\n",
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" <td>https://cfde-drc.s3.us-east-2.amazonaws.com/as...</td>\n",
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" <td>For an adverse event known to be caused by dru...</td>\n",
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" <td>Give two drugs and an adverse event that is kn...</td>\n",
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" <td>phenotype; drug; drug</td>\n",
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" <td>KOMP; HPO; GWAS; Geneshot; LINCS</td>\n",
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" <td>https://playbook-workflow-builder.cloud/report...</td>\n",
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" <td>/img/playbook_usecase1.png</td>\n",
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" <td></td>\n",
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" <td></td>\n",
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" <td>LINCS</td>\n",
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" <td>LINCS; KOMP2</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>1</th>\n",
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" <td>Playbook Workflow Builder</td>\n",
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" <td>Explain MOAs of Side Effects for Approved Drugs</td>\n",
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" <td>https://www.youtube.com/watch?v=Y_stZ7wIx_A</td>\n",
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" <td>https://cfde-drc.s3.us-east-2.amazonaws.com/as...</td>\n",
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" <td>For a side effect and a drug, find differentia...</td>\n",
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" <td>For a side effect and a drug, find differentia...</td>\n",
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" <td>phenotype; drug</td>\n",
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" <td>GWAS; KOMP; LINCS</td>\n",
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" <td>https://playbook-workflow-builder.cloud/report...</td>\n",
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" <td>/img/playbook_usecase2.png</td>\n",
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" <td></td>\n",
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" <td></td>\n",
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" <td>LINCS</td>\n",
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" <td>LINCS; KOMP2</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>2</th>\n",
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" <td>Playbook Workflow Builder</td>\n",
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" <td>Small Molecules to Induce a Biological Process</td>\n",
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" <td>https://www.youtube.com/watch?v=EXdzdZR3C0I</td>\n",
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" <td>https://cfde-drc.s3.us-east-2.amazonaws.com/as...</td>\n",
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" <td>We identify genes associated with a biological...</td>\n",
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" <td>We identify genes associated with a biological...</td>\n",
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" <td>phenotype</td>\n",
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" <td>HPO; KOMP; KEGG; WikiPathways; GO; LINCS</td>\n",
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" <td>https://playbook-workflow-builder.cloud/report...</td>\n",
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" <td>/img/playbook_usecase5.png</td>\n",
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" <td></td>\n",
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" <td>/img/usecase5.png</td>\n",
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" <td>LINCS</td>\n",
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" <td>LINCS; KOMP2</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>3</th>\n",
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" <td>Playbook Workflow Builder</td>\n",
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" <td>Cell Surface Targets for Individual Cancer Pat...</td>\n",
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" <td>https://www.youtube.com/watch?v=LV2354qryXk&amp;li...</td>\n",
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" <td>https://cfde-drc.s3.us-east-2.amazonaws.com/as...</td>\n",
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" <td>Given RNA-seq samples from a patient tumor, we...</td>\n",
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" <td>Given RNA-seq samples from a patient tumor, we...</td>\n",
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" <td>gene count matrix</td>\n",
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" <td>Kids First; LINCS; GTEx; exRNA; GlyGen; Metabo...</td>\n",
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" <td>https://playbook-workflow-builder.cloud/report...</td>\n",
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" <td>https://cfde-drc.s3.us-east-2.amazonaws.com/as...</td>\n",
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" <td>True</td>\n",
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" <td>https://cfde-drc.s3.us-east-2.amazonaws.com/as...</td>\n",
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" <td>LINCS</td>\n",
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" <td>Kids First; LINCS; GTEx; ExRNA; GlyGen; Metabo...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>4</th>\n",
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" <td>Playbook Workflow Builder</td>\n",
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" <td>Compounds to Reverse Disease Signatures</td>\n",
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" <td></td>\n",
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" <td>https://cfde-drc.s3.us-east-2.amazonaws.com/as...</td>\n",
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" <td>Using differential expression signatures from ...</td>\n",
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" <td>Using differential expression signatures from ...</td>\n",
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" <td>gene signature; gene signature</td>\n",
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" <td>GTEx; GEO; LINCS</td>\n",
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" <td>https://playbook-workflow-builder.cloud/report...</td>\n",
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" <td>/img/playbook_usecase3.png</td>\n",
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" <td></td>\n",
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" <td>/img/usecase3.png</td>\n",
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" <td>LINCS</td>\n",
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" <td>GTEx; LINCS</td>\n",
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" </tr>\n",
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" </tbody>\n",
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"</table>\n",
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"</div>"
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],
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"text/plain": [
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" tool_name \\\n",
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"0 Playbook Workflow Builder \n",
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"1 Playbook Workflow Builder \n",
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"2 Playbook Workflow Builder \n",
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"3 Playbook Workflow Builder \n",
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"4 Playbook Workflow Builder \n",
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"\n",
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" title \\\n",
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"0 Explain Drug-Drug Interactions \n",
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"1 Explain MOAs of Side Effects for Approved Drugs \n",
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"2 Small Molecules to Induce a Biological Process \n",
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"3 Cell Surface Targets for Individual Cancer Pat... \n",
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"4 Compounds to Reverse Disease Signatures \n",
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"\n",
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" tutorial \\\n",
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"0 https://www.youtube.com/watch?v=7_Xir0jVisM \n",
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"1 https://www.youtube.com/watch?v=Y_stZ7wIx_A \n",
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"2 https://www.youtube.com/watch?v=EXdzdZR3C0I \n",
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"3 https://www.youtube.com/watch?v=LV2354qryXk&li... \n",
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"4 \n",
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"\n",
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" tool_icon \\\n",
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"0 https://cfde-drc.s3.us-east-2.amazonaws.com/as... \n",
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"1 https://cfde-drc.s3.us-east-2.amazonaws.com/as... \n",
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"2 https://cfde-drc.s3.us-east-2.amazonaws.com/as... \n",
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"3 https://cfde-drc.s3.us-east-2.amazonaws.com/as... \n",
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"4 https://cfde-drc.s3.us-east-2.amazonaws.com/as... \n",
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"\n",
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" short_description \\\n",
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"0 For an adverse event known to be caused by dru... \n",
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"1 For a side effect and a drug, find differentia... \n",
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"2 We identify genes associated with a biological... \n",
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"3 Given RNA-seq samples from a patient tumor, we... \n",
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"4 Using differential expression signatures from ... \n",
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"\n",
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" description \\\n",
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"0 Give two drugs and an adverse event that is kn... \n",
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"1 For a side effect and a drug, find differentia... \n",
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"2 We identify genes associated with a biological... \n",
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"3 Given RNA-seq samples from a patient tumor, we... \n",
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"4 Using differential expression signatures from ... \n",
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"\n",
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" inputs \\\n",
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"0 phenotype; drug; drug \n",
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"1 phenotype; drug \n",
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"2 phenotype \n",
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"3 gene count matrix \n",
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"4 gene signature; gene signature \n",
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"\n",
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" sources \\\n",
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"0 KOMP; HPO; GWAS; Geneshot; LINCS \n",
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"1 GWAS; KOMP; LINCS \n",
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"2 HPO; KOMP; KEGG; WikiPathways; GO; LINCS \n",
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"3 Kids First; LINCS; GTEx; exRNA; GlyGen; Metabo... \n",
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"4 GTEx; GEO; LINCS \n",
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"\n",
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" link \\\n",
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"0 https://playbook-workflow-builder.cloud/report... \n",
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"1 https://playbook-workflow-builder.cloud/report... \n",
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"2 https://playbook-workflow-builder.cloud/report... \n",
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"3 https://playbook-workflow-builder.cloud/report... \n",
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"4 https://playbook-workflow-builder.cloud/report... \n",
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"\n",
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" image featured \\\n",
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"0 /img/playbook_usecase1.png \n",
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"1 /img/playbook_usecase2.png \n",
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"2 /img/playbook_usecase5.png \n",
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"3 https://cfde-drc.s3.us-east-2.amazonaws.com/as... True \n",
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"4 /img/playbook_usecase3.png \n",
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"\n",
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" featured_image creator_dcc \\\n",
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"0 LINCS \n",
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"1 LINCS \n",
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"2 /img/usecase5.png LINCS \n",
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"3 https://cfde-drc.s3.us-east-2.amazonaws.com/as... LINCS \n",
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"4 /img/usecase3.png LINCS \n",
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"\n",
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" source_dcc \n",
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"0 LINCS; KOMP2 \n",
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"1 LINCS; KOMP2 \n",
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"2 LINCS; KOMP2 \n",
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"3 Kids First; LINCS; GTEx; ExRNA; GlyGen; Metabo... \n",
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"4 GTEx; LINCS "
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]
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},
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"execution_count": 25,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"usecase = pd.read_csv('data/usecase.tsv', sep=\"\\t\")\n",
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"usecase = usecase.fillna('')\n",
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"usecase.head()\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 29,
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"metadata": {},
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"outputs": [],
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"source": [
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"for i, row in usecase.iterrows():\n",
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"\tyml = {\"layout\": \"../../layouts/UseCase.astro\"}\n",
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"\tdescription = ''\n",
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"\tfor k,v in row.items():\n",
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"\t\tif not v == '':\n",
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"\t\t\tif not k == 'description':\n",
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"\t\t\t\tif k == 'source_dcc':\n",
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"\t\t\t\t\tv = v.split(\"; \")\n",
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"\t\t\t\tif k == 'creator_dcc':\n",
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"\t\t\t\t\tv = v.split(\"; \")\n",
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"\t\t\t\tyml[k] = v\n",
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"\t\t\telse:\n",
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"\t\t\t\tdescription = v\n",
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"\tfilename = \"%s: %s\"%(yml['tool_name'], yml[\"title\"])\n",
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"\tfilename = filename.replace(\"/\", \"-\")\n",
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"\twith open('out/usecase/%s.md'%filename, 'w') as o:\n",
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"\t\to.write('---\\n')\n",
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"\t\to.write(yaml.dump(yml))\n",
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"\t\to.write('---\\n')\n",
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"\t\to.write(description)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,

‎src/pages/usecase/Data Distillery Knowledge Graph: Breast Epitheliumn Use Case.md‎

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---
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creator_dcc:
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- LINCS
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image: /img/usecase_BreastEpithelium.png
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inputs: tissue
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layout: ../../layouts/UseCase.astro
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link: https://dd-kg-ui.cfde.cloud/use_cases/tissue2drugs?edge_labels=true
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short_description: Find the genes that are highly expressed in breast epithelium as
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well as drugs that target these genes.
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source_dcc:
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- GTEx
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- IDG
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- LINCS
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title: Breast Epitheliumn Use Case
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tool_icon: /img/ubkg.png
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tool_name: Data Distillery Knowledge Graph
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---
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Find the genes that are highly expressed in breast epithelium as well as drugs that target these genes.

‎src/pages/usecase/Data Distillery Knowledge Graph: CES1 Use Case.md‎

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---
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creator_dcc:
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- LINCS
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image: /img/usecase_ces1.png
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inputs: gene
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layout: ../../layouts/UseCase.astro
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link: https://dd-kg-ui.cfde.cloud/use_cases/enzyminer?edge_labels=true
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short_description: Display drugs that up or down regulate the gene CES1 from LINCS
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as well as tissues where it is highly expressed based on assertions from GTEx.
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source_dcc:
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- LINCS
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- GTEx
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sources: LINCS; GTEx
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title: CES1 Use Case
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tool_icon: /img/ubkg.png
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tool_name: Data Distillery Knowledge Graph
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---
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Display drugs that up or down regulate the gene CES1 from LINCS as well as tissues where it is highly expressed based on assertions from GTEx.

‎src/pages/usecase/Data Distillery Knowledge Graph: EnzymeMiner.md‎

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---
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creator_dcc:
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- LINCS
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image: /img/app_EnzymeMiner.png
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inputs: gene
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layout: ../../layouts/UseCase.astro
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link: https://dd-kg-ui.cfde.cloud/dd_apps/enzymeminer?edge_labels=true
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short_description: Select a drug processing enzyme to view drugs that up or down regulate
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it from LINCS as well as tissues where it is highly expressed based on data from
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GTEx.
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source_dcc:
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- LINCS
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- GTEx
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sources: LINCS; GTEx
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title: EnzymeMiner
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tool_icon: /img/ubkg.png
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tool_name: Data Distillery Knowledge Graph
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---
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Select a drug processing enzyme to view drugs that up or down regulate it from LINCS as well as tissues where it is highly expressed based on data from GTEx.

‎src/pages/usecase/Data Distillery Knowledge Graph: Frontotemporal Dementia Use Case.md‎

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---
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creator_dcc:
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- ExRNA
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image: /img/usecase_dementia.png
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inputs: disease; phenotype
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layout: ../../layouts/UseCase.astro
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link: https://dd-kg-ui.cfde.cloud/use_cases/disease2exrna?edge_labels=true
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short_description: For genes that are correlated with frontotemporal dementia, identify
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extracellular RNAs (exRNAs) that may be detected in human biofluids and thus serve
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as non-invasive disease biomarkers.
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source_dcc:
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- ExRNA
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title: Frontotemporal Dementia Use Case
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tool_icon: /img/ubkg.png
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tool_name: Data Distillery Knowledge Graph
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---
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For genes that are correlated with frontotemporal dementia, identify extracellular RNAs (exRNAs) that may be detected in human biofluids and thus serve as non-invasive disease biomarkers.

‎src/pages/usecase/Data Distillery Knowledge Graph: Liquid Biopsy of Condition.md‎

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---
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creator_dcc:
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- ExRNA
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image: /img/app_LiquidBiopsyOfCondition.png
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inputs: disease; phenotype
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layout: ../../layouts/UseCase.astro
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link: https://dd-kg-ui.cfde.cloud/dd_apps/disease2exrna?edge_labels=true
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short_description: For a given set of genes that are highly expressed in a specific
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disease, identify extracellular RNAs (exRNAs) that may be detected in human biofluids
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and thus serve as non-invasive disease biomarkers.
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source_dcc:
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- ExRNA
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title: Liquid Biopsy of Condition
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tool_icon: /img/ubkg.png
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tool_name: Data Distillery Knowledge Graph
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---
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For a given set of genes that are highly expressed in a specific disease, identify extracellular RNAs (exRNAs) that may be detected in human biofluids and thus serve as non-invasive disease biomarkers.

‎src/pages/usecase/Data Distillery Knowledge Graph: Liquid Biopsy of Dexamethasone Response.md‎

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---
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creator_dcc:
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- ExRNA
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image: /img/usecase_dex.png
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inputs: compound
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layout: ../../layouts/UseCase.astro
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link: https://dd-kg-ui.cfde.cloud/use_cases/drug2exrna?edge_labels=true
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short_description: Find genes that are up-regulated by dexamethasone, (2) loci expressed
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in exRNA that overlap RBP binding regions, (3) the RBP that overlaps the locus,
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and (4) the biofluid(s) where locus was expressed in exRNA.
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source_dcc:
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- ExRNA
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- LINCS
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title: Liquid Biopsy of Dexamethasone Response
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tool_icon: /img/ubkg.png
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tool_name: Data Distillery Knowledge Graph
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---
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Find genes that are up-regulated by dexamethasone, (2) loci expressed in exRNA that overlap RBP binding regions, (3) the RBP that overlaps the locus, and (4) the biofluid(s) where locus was expressed in exRNA.

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