added publications

Author: jeevangelista

script/process_markdown.ipynb

@@ -2794,7 +2794,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -2805,7 +2805,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 18,
    "metadata": {},
    "outputs": [
     {
@@ -2814,28 +2814,28 @@
        "True"
       ]
      },
-     "execution_count": 4,
+     "execution_count": 18,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "pmid = '34248680'\n",
+    "pmid = '38692657'\n",
     "res = requests.get(f'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id={pmid}&format=json')\n",
     "res.ok"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 19,
    "metadata": {},
    "outputs": [],
    "source": [
     "data = res.json()['result'][pmid]\n",
     "yml = {}\n",
     "yml['authors'] = \", \".join([i['name'] for i in data['authors']])\n",
     "yml['carousel'] = False\n",
-    "yml['dccs'] = ['SPARC']\n",
+    "yml['dccs'] = ['SMaHT']\n",
     "yml['featured'] = False\n",
     "yml['journal'] = data[\"fulljournalname\"]\n",
     "yml['keywords'] = json.dumps([\"FAIR\", \"SPARC\", \"autonomic nervous system\", \"computational life sciences\", \"data annotation\", \"data curation\", \"knowledge management\", \"neural mapping\"])\n",
@@ -2844,7 +2844,7 @@
     "yml['page'] = data['pages']\n",
     "yml['title'] = data['title']\n",
     "yml['volume'] = data['volume']\n",
-    "yml['year'] = int(data['pubdate'])\n",
+    "yml['year'] = int(data['pubdate'].split(\" \")[0])\n",
     "for i in data['articleids']:\n",
     "\tidtype = i['idtype']\n",
     "\tif idtype == 'pubmed':\n",
@@ -2857,7 +2857,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 20,
    "metadata": {},
    "outputs": [],
    "source": [

src/pages/publications/DOI:10.1101-2025.08.11.666099.md

@@ -0,0 +1,22 @@
+---
+authors: Taha Mohseni Ahooyi, Benjamin Stear, J. Alan Simmons, Vincent T. Metzger, Praveen Kumar, John Erol Evangelista, Daniel J. B. Clarke, Zhuorui Xie, Heesu Kim, Sherry L. Jenkins, Mano R. Maurya, Srinivasan Ramachandran, Eoin Fahy, Fahim T. Imam, Natallia Kokash, E. Roth Matthew, Robert Fullem, Dubravka Jevtic, Aleks Mihajlovic, Michael Tiemeyer, Thomas Gillepsie, Clara Bakker, Andrew J. Schroeder, Julia Markowski, Jared Nedzel, Dave D. Hill, James Terry, Christopher Nemarich, Peter Park, Kristin Ardlie, Jeet Vora, Raja Mazumder, Rene Ranzinger, Bernard de Bono, Shankar Subramaniam, Jeffrey S. Grethe, Jeremy J. Yang, Christophe G. Lambert, Adam Resnick, Aleks Milosavljevic, Avi Ma’ayan, Jonathan C. Silverstein, Deanne Taylor
+carousel: false
+dccs:
+- 4DN
+- ExRNA
+- GlyGen
+- GTEx
+- HuBMAP
+- IDG
+- Kids First
+- LINCS
+- MoTrPAC
+- SPARC
+doi: 10.1101/2025.08.11.666099 
+featured: false
+journal: bioRxiv
+landmark: true
+layout: '@/layouts/Publication.astro'
+title: 'The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data'
+year: 2025
+---

src/pages/publications/PMID:38692657.md

@@ -0,0 +1,18 @@
+---
+authors: Hubler ZML, Cao Y
+carousel: false
+dccs:
+- SMaHT
+doi: 10.1093/clinchem/hvae003
+featured: false
+journal: Clinical chemistry
+keywords: '["FAIR", "SPARC", "autonomic nervous system", "computational life sciences",
+  "data annotation", "data curation", "knowledge management", "neural mapping"]'
+landmark: true
+layout: '@/layouts/Publication.astro'
+page: 780-781
+pii: '7660958'
+pmid: 38692657
+title: The Somatic Mosaicism across Human Tissues (SMaHT) Network, a SMART Investment?
+volume: '70'
+year: 2024

src/pages/publications/PMID:38844599.md

@@ -0,0 +1,20 @@
+---
+authors: Kwak GH, Kamdar HA, Douglas MJ, Hu H, Ack SE, Lissak IA, Williams AE, Yechoor
+  N, Rosenthal ES
+carousel: false
+dccs:
+- Bridge2AI
+doi: 10.1007/s12028-024-02007-0
+featured: false
+journal: Neurocritical care
+keywords: '["FAIR", "SPARC", "autonomic nervous system", "computational life sciences",
+  "data annotation", "data curation", "knowledge management", "neural mapping"]'
+landmark: true
+layout: '@/layouts/Publication.astro'
+page: 866-879
+pii: 10.1007/s12028-024-02007-0
+pmid: 38844599
+title: 'Social Determinants of Health and Limitation of Life-Sustaining Therapy in
+  Neurocritical Care: A CHoRUS Pilot Project.'
+volume: '41'
+year: 2024

src/pages/publications/PMID:39306498.md

@@ -0,0 +1,23 @@
+---
+authors: Awan SN, Bahr R, Watts S, Boyer M, Budinsky R, Bridge2AI-Voice Consortium,
+  Bensoussan Y
+carousel: false
+dccs:
+- Bridge2AI
+doi: 10.1016/j.jvoice.2024.08.029
+featured: false
+journal: 'Journal of voice : official journal of the Voice Foundation'
+keywords: '["FAIR", "SPARC", "autonomic nervous system", "computational life sciences",
+  "data annotation", "data curation", "knowledge management", "neural mapping"]'
+landmark: true
+layout: '@/layouts/Publication.astro'
+mid: NIHMS2032409
+page: ''
+pii: S0892-1997(24)00283-2
+pmc: PMC11922786
+pmcid: 'PMC11922786;manuscript-id: NIHMS2032409;embargo-date: 2026/03/20;'
+pmid: 39306498
+title: Evidence-Based Recommendations for Tablet Recordings From the Bridge2AI-Voice
+  Acoustic Experiments.
+volume: ''
+year: 2024

src/pages/publications/PMID:39516364.md

@@ -3,14 +3,20 @@ authors: AI-READI Consortium
 carousel: false
 dccs:
 - Bridge2AI
-doi: /10.1038/s42255-024-01165-x
+doi: 10.1038/s42255-024-01165-x
 featured: false
-journal: Nature Metabolism
-keywords: '[]'
+journal: Nature metabolism
+keywords: '["FAIR", "SPARC", "autonomic nervous system", "computational life sciences",
+  "data annotation", "data curation", "knowledge management", "neural mapping"]'
 landmark: true
 layout: '@/layouts/Publication.astro'
+mid: NIHMS2079065
+page: 2210-2212
+pii: 10.1038/s42255-024-01165-x
+pmc: PMC12126850
+pmcid: 'PMC12126850;manuscript-id: NIHMS2079065;'
 pmid: 39516364
 title: 'AI-READI: rethinking AI data collection, preparation and sharing in diabetes
-  research and beyond'
+  research and beyond.'
+volume: '6'
 year: 2024
----

src/pages/publications/PMID:40205054.md

@@ -0,0 +1,25 @@
+---
+authors: Schaffer LV, Hu M, Qian G, Moon KM, Pal A, Soni N, Latham AP, Pontano Vaites
+  L, Tsai D, Mattson NM, Licon K, Bachelder R, Cesnik A, Gaur I, Le T, Leineweber
+  W, Palar A, Pulido E, Qin Y, Zhao X, Churas C, Lenkiewicz J, Chen J, Ono K, Pratt
+  D, Zage P, Echeverria I, Sali A, Harper JW, Gygi SP, Foster LJ, Huttlin EL, Lundberg
+  E, Ideker T
+carousel: false
+dccs:
+- Bridge2AI
+doi: 10.1038/s41586-025-08878-3
+featured: false
+journal: Nature
+keywords: '["FAIR", "SPARC", "autonomic nervous system", "computational life sciences",
+  "data annotation", "data curation", "knowledge management", "neural mapping"]'
+landmark: true
+layout: '@/layouts/Publication.astro'
+mid: NIHMS2086025
+page: 222-231
+pii: 10.1038/s41586-025-08878-3
+pmc: PMC12137143
+pmcid: 'PMC12137143;manuscript-id: NIHMS2086025;'
+pmid: 40205054
+title: Multimodal cell maps as a foundation for structural and functional genomics.
+volume: '642'
+year: 2025

src/pages/tools/Data Distillery Knowledge Graph.md

@@ -5,5 +5,6 @@ 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/
+doi: https://doi.org/10.1101/2025.08.11.666099
 ---
 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.