added tools

jeevangelista · jeevangelista · commit 639ee44f9168 · 2025-01-23T13:47:03.000-05:00
diff --git a/script/process_markdown.ipynb b/script/process_markdown.ipynb
@@ -659,7 +659,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 21,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -676,13 +676,218 @@
     "\t\t\t\tyml[k] = v\n",
     "\t\t\telse:\n",
     "\t\t\t\tdescription = v\n",
-    "\tfilename = \"PMID: %s\"%str(int(yml['pmid'])) if \"pmid\" in yml else \"DOI: %s\"%yml['doi'].replace(\"/\", \"-\")\n",
+    "\tfilename = yml['title']\n",
     "\twith open('out/partnerships/%s.md'%filename, 'w') as o:\n",
     "\t\to.write('---\\n')\n",
     "\t\to.write(yaml.dump(yml))\n",
     "\t\to.write('---\\n')\n",
     "\t\to.write(description)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>label</th>\n",
+       "      <th>tutorial</th>\n",
+       "      <th>description</th>\n",
+       "      <th>url</th>\n",
+       "      <th>icon</th>\n",
+       "      <th>short_description</th>\n",
+       "      <th>image</th>\n",
+       "      <th>featured</th>\n",
+       "      <th>doi</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>Playbook Workflow Builder</td>\n",
+       "      <td>[  \"https://www.youtube.com/watch?v=xfnaNJL5-8...</td>\n",
+       "      <td>The Playbook Workflow Builder (PWB) is a web-b...</td>\n",
+       "      <td>https://playbook-workflow-builder.cloud/</td>\n",
+       "      <td>https://cfde-drc.s3.us-east-2.amazonaws.com/as...</td>\n",
+       "      <td>Web-based platform to construct biomedical wor...</td>\n",
+       "      <td>/img/pwb-screenshot.png</td>\n",
+       "      <td>True</td>\n",
+       "      <td></td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>GDLPA</td>\n",
+       "      <td>[  \"https://www.youtube.com/watch?v=eO9zsT6Tyz...</td>\n",
+       "      <td>Gene and Drug Landing Page Aggregator (GDLPA) ...</td>\n",
+       "      <td>https://cfde-gene-pages.cloud/</td>\n",
+       "      <td>/img/gdlpa.png</td>\n",
+       "      <td>Query 53 gene-centric, 18 variant-centric, and...</td>\n",
+       "      <td>/img/gdlpa-screenshot.png</td>\n",
+       "      <td></td>\n",
+       "      <td>https://doi.org/10.1093/bioadv/vbac013</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>ReproTox-KG</td>\n",
+       "      <td>[ \"https://www.youtube.com/watch?v=Gt3CCsvTppc...</td>\n",
+       "      <td>To further characterize associations between s...</td>\n",
+       "      <td>https://maayanlab.cloud/reprotox-kg</td>\n",
+       "      <td>/img/reprotox-kg-logo.png</td>\n",
+       "      <td>Toxicology knowledge graph for structural birt...</td>\n",
+       "      <td>/img/reprotox-kg-screenshot.png</td>\n",
+       "      <td>True</td>\n",
+       "      <td>https://doi.org/10.1038/s43856-023-00329-2</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>FAIRshake</td>\n",
+       "      <td></td>\n",
+       "      <td>The FAIRshake toolkit was developed to enable ...</td>\n",
+       "      <td>https://fairshake.cloud/</td>\n",
+       "      <td>/img/fairshake.png</td>\n",
+       "      <td>Toolkit to evaluate the FAIRness of research d...</td>\n",
+       "      <td>/img/fairshake-screenshot.png</td>\n",
+       "      <td></td>\n",
+       "      <td>https://doi.org/10.1016/j.cels.2019.09.011</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>Data Distillery Knowledge Graph</td>\n",
+       "      <td></td>\n",
+       "      <td>The Unified Biomedical Knowledge Graph (UBKG) ...</td>\n",
+       "      <td>https://dd-kg-ui.cfde.cloud/</td>\n",
+       "      <td>/img/ubkg.png</td>\n",
+       "      <td>KG database represents interrelated biomedical...</td>\n",
+       "      <td>/img/ubkg-screenshot.png</td>\n",
+       "      <td></td>\n",
+       "      <td></td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                             label  \\\n",
+       "0        Playbook Workflow Builder   \n",
+       "1                            GDLPA   \n",
+       "2                      ReproTox-KG   \n",
+       "3                        FAIRshake   \n",
+       "4  Data Distillery Knowledge Graph   \n",
+       "\n",
+       "                                            tutorial  \\\n",
+       "0  [  \"https://www.youtube.com/watch?v=xfnaNJL5-8...   \n",
+       "1  [  \"https://www.youtube.com/watch?v=eO9zsT6Tyz...   \n",
+       "2  [ \"https://www.youtube.com/watch?v=Gt3CCsvTppc...   \n",
+       "3                                                      \n",
+       "4                                                      \n",
+       "\n",
+       "                                         description  \\\n",
+       "0  The Playbook Workflow Builder (PWB) is a web-b...   \n",
+       "1  Gene and Drug Landing Page Aggregator (GDLPA) ...   \n",
+       "2  To further characterize associations between s...   \n",
+       "3  The FAIRshake toolkit was developed to enable ...   \n",
+       "4  The Unified Biomedical Knowledge Graph (UBKG) ...   \n",
+       "\n",
+       "                                        url  \\\n",
+       "0  https://playbook-workflow-builder.cloud/   \n",
+       "1            https://cfde-gene-pages.cloud/   \n",
+       "2       https://maayanlab.cloud/reprotox-kg   \n",
+       "3                  https://fairshake.cloud/   \n",
+       "4              https://dd-kg-ui.cfde.cloud/   \n",
+       "\n",
+       "                                                icon  \\\n",
+       "0  https://cfde-drc.s3.us-east-2.amazonaws.com/as...   \n",
+       "1                                     /img/gdlpa.png   \n",
+       "2                          /img/reprotox-kg-logo.png   \n",
+       "3                                 /img/fairshake.png   \n",
+       "4                                      /img/ubkg.png   \n",
+       "\n",
+       "                                   short_description  \\\n",
+       "0  Web-based platform to construct biomedical wor...   \n",
+       "1  Query 53 gene-centric, 18 variant-centric, and...   \n",
+       "2  Toxicology knowledge graph for structural birt...   \n",
+       "3  Toolkit to evaluate the FAIRness of research d...   \n",
+       "4  KG database represents interrelated biomedical...   \n",
+       "\n",
+       "                             image featured  \\\n",
+       "0          /img/pwb-screenshot.png     True   \n",
+       "1        /img/gdlpa-screenshot.png            \n",
+       "2  /img/reprotox-kg-screenshot.png     True   \n",
+       "3    /img/fairshake-screenshot.png            \n",
+       "4         /img/ubkg-screenshot.png            \n",
+       "\n",
+       "                                          doi  \n",
+       "0                                              \n",
+       "1      https://doi.org/10.1093/bioadv/vbac013  \n",
+       "2  https://doi.org/10.1038/s43856-023-00329-2  \n",
+       "3  https://doi.org/10.1016/j.cels.2019.09.011  \n",
+       "4                                              "
+      ]
+     },
+     "execution_count": 22,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "tools = pd.read_csv('data/tools.tsv', sep=\"\\t\")\n",
+    "tools = tools.fillna('')\n",
+    "tools.head()\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 24,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "for i, row in tools.iterrows():\n",
+    "\tyml = {\"layout\": \"../../layouts/Tools.astro\"}\n",
+    "\tdescription = ''\n",
+    "\tfor k,v in row.items():\n",
+    "\t\tif not v == '':\n",
+    "\t\t\tif not k == 'description':\n",
+    "\t\t\t\tif k == 'dccs':\n",
+    "\t\t\t\t\tv = v.split(\"; \")\n",
+    "\t\t\t\tif k == 'lead_dccs':\n",
+    "\t\t\t\t\tv = v.split(\"; \")\n",
+    "\t\t\t\tyml[k] = v\n",
+    "\t\t\telse:\n",
+    "\t\t\t\tdescription = v\n",
+    "\tfilename = yml['label']\n",
+    "\twith open('out/tools/%s.md'%filename, 'w') as o:\n",
+    "\t\to.write('---\\n')\n",
+    "\t\to.write(yaml.dump(yml))\n",
+    "\t\to.write('---\\n')\n",
+    "\t\to.write(description)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
diff --git a/src/pages/tools/CFDE-GSE.md b/src/pages/tools/CFDE-GSE.md
@@ -0,0 +1,11 @@
+---
+featured: false
+image: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/GSE-screenshot.png
+label: CFDE-GSE
+layout: ../../layouts/Tools.astro
+short_description: CFDE-GSE is web-based application that serves gene set libraries
+  created from CF programs datasets to provide an integrated cross program enrichment
+  analysis.
+url: https://gse.cfde.cloud/
+---
+Here we introduce the Common Fund Data Ecosystem (CFDE) Gene Set Enrichment (GSE) app, a web-based application that serves gene sets extracted from CF programs datasets to provide an integrated cross programs enrichment analysis tool. So far, 10 gene set libraries were created for CFDE-GSE by processing datasets from 8 programs: LINCS, GTEx, Metabolomics, IDG, GlyGen, KOMP2, MoTrPAC, and HuBMAP. To use CFDE-GSE, gene sets obtained from omics experiments by individual investigators can be submitted to the tool using a simple input form. The results produced by CFDE-GSE illuminates connections between the input gene set and various CF gene sets that overlap with the queried gene set. Such analysis enables users to explore CF datasets for further hypothesis generation for their research. Besides enrichment analysis, CFDE-GSE can be used to query the consolidated CF abstracted knowledge by searching for cross-CF dataset associations for a gene or a biological term, for example, a drug, a metabolite, a tissue, a cell type, or a phenotype. 
diff --git a/src/pages/tools/Data Distillery Knowledge Graph.md b/src/pages/tools/Data Distillery Knowledge Graph.md
@@ -0,0 +1,9 @@
+---
+icon: /img/ubkg.png
+image: /img/ubkg-screenshot.png
+label: Data Distillery Knowledge Graph
+layout: ../../layouts/Tools.astro
+short_description: KG database represents interrelated biomedical ontologies and vocabularies
+url: https://dd-kg-ui.cfde.cloud/
+---
+The Unified Biomedical Knowledge Graph (UBKG) is a knowledge graph database that represents a set of interrelated concepts from biomedical ontologies and vocabularies. The UBKG combines information from the National Library of Medicine's Unified Medical Language System (UMLS) with assertions from “non-UMLS” ontologies or vocabularies.
diff --git a/src/pages/tools/FAIRshake.md b/src/pages/tools/FAIRshake.md
@@ -0,0 +1,10 @@
+---
+doi: https://doi.org/10.1016/j.cels.2019.09.011
+icon: /img/fairshake.png
+image: /img/fairshake-screenshot.png
+label: FAIRshake
+layout: ../../layouts/Tools.astro
+short_description: Toolkit to evaluate the FAIRness of research digital resources
+url: https://fairshake.cloud/
+---
+The FAIRshake toolkit was developed to enable the establishment of community-driven FAIR metrics and rubrics paired with manual and automated FAIR assessments. FAIR assessments are visualized as an insignia that can be embedded within digital-resources-hosting websites. Using FAIRshake, a variety of biomedical digital resources were manually and automatically evaluated for their level of FAIRness.
diff --git a/src/pages/tools/GDLPA.md b/src/pages/tools/GDLPA.md
@@ -0,0 +1,13 @@
+---
+doi: https://doi.org/10.1093/bioadv/vbac013
+icon: /img/gdlpa.png
+image: /img/gdlpa-screenshot.png
+label: GDLPA
+layout: ../../layouts/Tools.astro
+short_description: Query 53 gene-centric, 18 variant-centric, and 19 drug-centric
+  repositories
+tutorial: '[  "https://www.youtube.com/watch?v=eO9zsT6Tyzk",  "https://www.youtube.com/watch?v=up8WY7N44ws"
+  ]'
+url: https://cfde-gene-pages.cloud/
+---
+Gene and Drug Landing Page Aggregator (GDLPA) has links to 53 gene, 18 variant and 19 drug repositories that provide direct links to gene and drug landing pages. You can search by gene or drug name and then choose the sites that contain knowledge about your gene or drug of interest. Resources supported by the NIH Common Fund are listed first and have the CFDE logo at their top right corner.
diff --git a/src/pages/tools/GeneSetCart.md b/src/pages/tools/GeneSetCart.md
@@ -0,0 +1,12 @@
+---
+featured: false
+icon: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/g2sg-logo.png
+image: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/g2sg-screenshot.png
+label: GeneSetCart
+layout: ../../layouts/Tools.astro
+short_description: GeneSetCart is interactive web-based application that enables users
+  to fetch gene sets, augment, perform set operations, visualize, and analyze gene
+  sets in a single session.
+url: https://g2sg.cfde.cloud/
+---
+GeneSetCart is an interactive web-based application that enables users to fetch gene sets from various Common Fund programs data sources, augment these sets with gene-gene co-expression correlations or protein-protein interactions, perform set operations such as union, consensus, and intersection on multiple sets, visualize and analyze these gene sets in a single session. GeneSetCart provides access to CFDE generated gene sets through a term query interface that returns gene sets related to all biomedical terms sourced from most CFDE DCCs. 
diff --git a/src/pages/tools/PIGEAN.md b/src/pages/tools/PIGEAN.md
@@ -0,0 +1,11 @@
+---
+featured: false
+icon: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/cfde_kc_logo.png
+image: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/PIGEAN-diagram.png
+label: PIGEAN
+layout: ../../layouts/Tools.astro
+short_description: PIGEAN (Priors Inferred from GEne ANnotations) is a Bayesian method
+  to compute relationships between phenotypes and gene sets.
+url: https://cfdeknowledge.org/r/kc_gene_set_browser_source?source=all
+---
+PIGEAN (Priors Inferred from GEne ANnotations) is a Bayesian method to compute relationships between phenotypes and gene sets.
diff --git a/src/pages/tools/Playbook Workflow Builder.md b/src/pages/tools/Playbook Workflow Builder.md
@@ -0,0 +1,12 @@
+---
+featured: true
+icon: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/PWB-logo-2024.png
+image: /img/pwb-screenshot.png
+label: Playbook Workflow Builder
+layout: ../../layouts/Tools.astro
+short_description: Web-based platform to construct biomedical workflows
+tutorial: '[  "https://www.youtube.com/watch?v=xfnaNJL5-8c",  "https://www.youtube.com/watch?v=k_3wLDWDj8M"
+  ]'
+url: https://playbook-workflow-builder.cloud/
+---
+The Playbook Workflow Builder (PWB) is a web-based platform that facilitates knowledge resolution by enabling users to traverse an ever-growing network of input datasets, semantically annotated API endpoints, and data visualization tools. Via a user-friendly user-interface, workflows can be constructed from these building-blocks without technical expertise. The output of these workflows is provided as reports containing textual descriptions, interactive figures, and downloadable tables.
diff --git a/src/pages/tools/ReproTox-KG.md b/src/pages/tools/ReproTox-KG.md
@@ -0,0 +1,13 @@
+---
+doi: https://doi.org/10.1038/s43856-023-00329-2
+featured: true
+icon: /img/reprotox-kg-logo.png
+image: /img/reprotox-kg-screenshot.png
+label: ReproTox-KG
+layout: ../../layouts/Tools.astro
+short_description: Toxicology knowledge graph for structural birth defects
+tutorial: '[ "https://www.youtube.com/watch?v=Gt3CCsvTppc", "https://www.youtube.com/watch?v=nqzDOsDFJ7g"
+  ]'
+url: https://maayanlab.cloud/reprotox-kg
+---
+To further characterize associations between small molecule compounds and their potential to induce specific birth abnormalities, we gathered knowledge from multiple sources to construct a reproductive toxicity Knowledge Graph (ReproTox-KG) with a focus on associations between birth defects, drugs, and genes.
diff --git a/src/pages/tools/Standard RNA-seq Processing Pipelines.md b/src/pages/tools/Standard RNA-seq Processing Pipelines.md
@@ -0,0 +1,10 @@
+---
+featured: true
+image: /img/rna-seq_pipeline.png
+label: Standard RNA-seq Processing Pipelines
+layout: ../../layouts/Tools.astro
+short_description: Revised STAR RNA-seq aligner to update RNA-seq pipelines across
+  CF programs
+url: https://github.com/hubmapconsortium/salmon-rnaseq
+---
+The CFDE RNA-seq Pipeline Harmonization partnership is a collaboration between multiple DCCs (GTEx, UDN, KF, HuBMAP, SPARC, MoTrPAC) to update their RNA-seq pipelines across the DCCs with a revised version of the STAR RNA-seq aligner. The goal is to enable uniform alignment to a reference genome by reprocessing all the existing accessible bulk-tissue RNA-seq datasets.
