modified pub

Author: jeevangelista

script/process_markdown.ipynb

@@ -2,17 +2,17 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
     "import pandas as pd\n",
-    "from uuid import uuid5, NAMESPACE_URL\n"
+    "import yaml"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
@@ -182,7 +182,7 @@
        "089d8d63-3364-526f-9706-80d62d0ec88c    True  "
       ]
      },
-     "execution_count": 5,
+     "execution_count": 2,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -195,12 +195,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
     "for i, row in dccs.iterrows():\n",
-    "\tmeta = [\"layout: ../../layouts/DCC.astro\"]\n",
+    "\tyml = {\"layout\": \"../../layouts/DCC.astro\"}\n",
     "\tif row['active']:\n",
     "\t\tdescription = ''\n",
     "\t\tfor k,v in row.items():\n",
@@ -209,19 +209,19 @@
     "\t\t\t\t\tif k == 'icon' and v.startswith('/img'):\n",
     "\t\t\t\t\t\tv = \"https://cfde-drc.s3.amazonaws.com/assets\" + v\n",
     "\n",
-    "\t\t\t\t\tmeta.append(\"%s: %s\"%(k, v))\n",
+    "\t\t\t\t\tyml[k] = v\n",
     "\t\t\telse:\n",
     "\t\t\t\tdescription = v\n",
     "\t\twith open('out/dccs/%s.md'%row['short_label'], 'w') as o:\n",
     "\t\t\to.write('---\\n')\n",
-    "\t\t\to.write(\"\\n\".join(meta))\n",
-    "\t\t\to.write('\\n---\\n')\n",
+    "\t\t\to.write(yaml.dump(yml))\n",
+    "\t\t\to.write('---\\n')\n",
     "\t\t\to.write(description)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -447,7 +447,7 @@
        "[5 rows x 22 columns]"
       ]
      },
-     "execution_count": 17,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -461,63 +461,86 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "for i, row in publications.iterrows():\n",
+    "\tyml = {\"layout\": \"../../layouts/Publication.astro\"}\n",
+    "\tfor k,v in row.items():\n",
+    "\t\tif not v == '':\n",
+    "\t\t\tif k == 'dccs':\n",
+    "\t\t\t\tv = v.split(\"; \")\n",
+    "\t\t\tif k == \"pmid\":\n",
+    "\t\t\t\tv = int(v)\n",
+    "\t\t\tyml[k] = v\n",
+    "\tfilename = \"PMID: %s\"%str(int(yml['pmid'])) if \"pmid\" in yml else \"DOI: %s\"%yml['doi'].replace(\"/\", \"-\")\n",
+    "\twith open('out/publications/%s.md'%filename, 'w') as o:\n",
+    "\t\to.write('---\\n')\n",
+    "\t\to.write(yaml.dump(yml))\n",
+    "\t\to.write('\\n---')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "((85, 22), 85)"
+       "100"
       ]
      },
-     "execution_count": 22,
+     "execution_count": 7,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "publications.shape, publications.doi.nunique()"
+    "int(100.0)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "np.int64(1)"
+       "title                   Predictive analyses of regulatory sequences wi...\n",
+       "journal                                      Nature Computational Science\n",
+       "authors                 Klie A; Laub D; Talwar JV; Stites H; Jores T; ...\n",
+       "year                                                                 2023\n",
+       "page                                                              946-956\n",
+       "volume                                                                  3\n",
+       "issue                                                                  11\n",
+       "pmid                                                           38177592.0\n",
+       "pmcid                                                         PMC10768637\n",
+       "doi                                            10.1038/s43588-023-00544-w\n",
+       "landmark                                                            False\n",
+       "tool_id                                                                  \n",
+       "dccs                                                                     \n",
+       "partnerships                                                             \n",
+       "carousel                                                            False\n",
+       "carousel_title                                                           \n",
+       "carousel_link                                                            \n",
+       "carousel_description                                                     \n",
+       "image                                                                    \n",
+       "featured                                                            False\n",
+       "r03                                                                      \n",
+       "keywords                   [\"Workflow\", \"Genome\", \"Genomics\", \"Software\"]\n",
+       "Name: 84, dtype: object"
       ]
      },
-     "execution_count": 24,
+     "execution_count": 11,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "(publications.pmid == '').sum()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 28,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "for i, row in publications.iterrows():\n",
-    "\tmeta = [\"layout: ../../layouts/Publication.astro\"]\n",
-    "\tfor k,v in row.items():\n",
-    "\t\tif not v == '':\n",
-    "\t\t\tif k == 'dccs':\n",
-    "\t\t\t\tv = v.split(\"; \")\n",
-    "\n",
-    "\t\t\tmeta.append(\"%s: %s\"%(k, v))\n",
-    "\tuid = str(uuid5(NAMESPACE_URL, row['title']))\n",
-    "\twith open('out/publications/%s.md'%uid, 'w') as o:\n",
-    "\t\to.write('---\\n')\n",
-    "\t\to.write(\"\\n\".join(meta))\n",
-    "\t\to.write('\\n---')"
+    "row"
    ]
   },
   {

src/pages/publications/DOI: 10.1158-1538-7445.AM2023-6576.md

@@ -0,0 +1,20 @@
+---
+authors: Higgins D, Thibert JP, Mattioni M, DiGiovanna J, Grossman RL, Farrow BK,
+  Wenger E,  Volchenboum S, Carroll RJ,  Haendel MA, Taylor DM, Zhu Y, Ferretti V,
+  Resnick AC, Heath AP
+carousel: false
+dccs:
+- Kids First
+doi: 10.1158/1538-7445.AM2023-6576
+featured: false
+issue: '83'
+journal: Cancer Research
+landmark: true
+layout: ../../layouts/Publication.astro
+page: '6576'
+title: 'Gabriella Miller Kids First Data Resource Center (KFDRC): Empowering discovery
+  across germline and somatic variation in pediatric cancer.'
+volume: 7_Supplement
+year: 2023
+
+---

src/pages/publications/PMID: 22699609.md

@@ -0,0 +1,22 @@
+---
+authors: Human Microbiome Project Consortium
+carousel: false
+dccs:
+- HMP
+doi: 10.1038/nature11234
+featured: false
+issue: '7402'
+journal: Nature
+keywords: '["Male", "Metagenomics", "RNA, Ribosomal, 16S", "Phenotype", "Young Adult",
+  "Biodiversity", "Adult", "Bacteria", "Metabolic Networks and Pathways", "Metagenome",
+  "Female", "Ecosystem", "Health", "Adolescent", "Humans"]'
+landmark: true
+layout: ../../layouts/Publication.astro
+page: 207-14
+pmcid: PMC3564958
+pmid: 22699609
+title: Structure, function and diversity of the healthy human microbiome.
+volume: '486'
+year: 2012
+
+---

src/pages/publications/PMID: 22699610.md

@@ -0,0 +1,22 @@
+---
+authors: Human Microbiome Project Consortium
+carousel: false
+dccs:
+- HMP
+doi: 10.1038/nature11209
+featured: false
+issue: '7402'
+journal: Nature
+keywords: '["Statistics as Topic", "Male", "Metagenomics", "RNA, Ribosomal, 16S",
+  "Young Adult", "Adult", "Metagenome", "Bacteria", "Reference Standards", "Female",
+  "Adolescent", "Humans"]'
+landmark: true
+layout: ../../layouts/Publication.astro
+page: 215-21
+pmcid: PMC3377744
+pmid: 22699610
+title: A framework for human microbiome research.
+volume: '486'
+year: 2012
+
+---

src/pages/publications/PMID: 23715323.md

@@ -0,0 +1,23 @@
+---
+authors: GTEx Consortium
+carousel: false
+dccs:
+- GTEx
+doi: 10.1038/ng.2653
+featured: false
+issue: '6'
+journal: Nature genetics
+keywords: '["Gene Expression Profiling", "Gene Expression", "Government Programs",
+  "Organ Specificity", "Tissue Banks", "Molecular Sequence Annotation", "Consensus
+  Development Conferences, NIH as Topic", "Quantitative Trait Loci", "United States",
+  "Genome-Wide Association Study", "Humans"]'
+landmark: true
+layout: ../../layouts/Publication.astro
+page: 580-5
+pmcid: PMC4010069
+pmid: 23715323
+title: The Genotype-Tissue Expression (GTEx) project.
+volume: '45'
+year: 2013
+
+---

src/pages/publications/PMID: 25954001.md

@@ -0,0 +1,26 @@
+---
+authors: GTEx Consortium
+carousel: false
+dccs:
+- GTEx
+doi: 10.1126/science.1262110
+featured: false
+issue: '6235'
+journal: Science (New York, N.Y.)
+keywords: '["RNA, Untranslated", "Sequence Analysis, RNA", "ARHGAP42 protein, human",
+  "Transcriptome", "Tibial Arteries", "Blood Pressure", "GTPase-Activating Proteins",
+  "Disease", "Genotype", "Humans", "Pilot Projects", "RNA Splicing", "Genetic Variation",
+  "Organ Specificity", "Gene Regulatory Networks", "Quantitative Trait Loci", "Genome,
+  Human", "Multigene Family", "Gene Expression Regulation", "Alleles", "Genome-Wide
+  Association Study"]'
+landmark: true
+layout: ../../layouts/Publication.astro
+page: 648-60
+pmcid: PMC4547484
+pmid: 25954001
+title: 'Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue
+  gene regulation in humans.'
+volume: '348'
+year: 2015
+
+---

src/pages/publications/PMID: 26320938.md

@@ -0,0 +1,21 @@
+---
+authors: Ainsztein AM, Brooks PJ, Dugan VG, Ganguly A, Guo M, Howcroft TK, Kelley
+  CA, Kuo LS, Labosky PA, Lenzi R, McKie GA, Mohla S, Procaccini D, Reilly M, Satterlee
+  JS, Srinivas PR, Church ES, Sutherland M, Tagle DA, Tucker JM, Venkatachalam S
+carousel: false
+dccs:
+- ExRNA
+doi: 10.3402/jev.v4.27493
+featured: false
+journal: Journal of extracellular vesicles
+keywords: '["exRNA", "extracellular RNA", "ERCC"]'
+landmark: true
+layout: ../../layouts/Publication.astro
+page: '27493'
+pmcid: PMC4553264
+pmid: 26320938
+title: The NIH Extracellular RNA Communication Consortium.
+volume: '4'
+year: 2015
+
+---

src/pages/publications/PMID: 26467476.md

@@ -0,0 +1,25 @@
+---
+authors: Sud M, Fahy E, Cotter D, Azam K, Vadivelu I, Burant C, Edison A, Fiehn O,
+  Higashi R, Nair KS, Sumner S, Subramaniam S
+carousel: false
+dccs:
+- Metabolomics
+doi: 10.1093/nar/gkv1042
+featured: false
+issue: D1
+journal: Nucleic acids research
+keywords: '["Databases, Chemical", "User-Computer Interface", "Mass Spectrometry",
+  "Metabolomics", "Molecular Structure", "Magnetic Resonance Spectroscopy", "Reference
+  Standards", "Software", "Animals", "Humans"]'
+landmark: true
+layout: ../../layouts/Publication.astro
+page: D463-70
+pmcid: PMC4702780
+pmid: 26467476
+title: 'Metabolomics Workbench: An international repository for metabolomics data
+  and metadata, metabolite standards, protocols, tutorials and training, and analysis
+  tools.'
+volume: '44'
+year: 2016
+
+---