Evidence map›Paper›PMID 37900350›Full record

ArticleJournal of clinical and translational science2023

An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges.

Karamarie Fecho, Chris Bizon, Tursynay Issabekova, Sierra Moxon, Anne E Thessen, Shervin Abdollahi, Sergio E Baranzini, Basazin Belhu, William E Byrd, Lawrence Chung and 33 more

Abstract read
In one paragraph

Article in Journal of clinical and translational science, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

43 authors.

Karamarie FechoRenaissance Computing Institute (RENCI), University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.ORCID https://orcid.org/0000-0002-6704-9306
Chris BizonRenaissance Computing Institute (RENCI), University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.ORCID https://orcid.org/0000-0002-9491-7674
Tursynay IssabekovaDepartment of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.ORCID https://orcid.org/0000-0003-0842-7335
Sierra MoxonBiosystems Data Science Department, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID https://orcid.org/0000-0002-8719-7760
Anne E ThessenDepartment of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.ORCID https://orcid.org/0000-0002-2908-3327
Shervin AbdollahiDivision of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.ORCID https://orcid.org/0000-0002-2444-0014
Sergio E BaranziniDepartment of Neurology, Weill Institute for Neuroscience, University of California - San Francisco, San Francisco, CA, USA.ORCID https://orcid.org/0000-0003-0067-194X
Basazin BelhuInstitute for Systems Biology, Seattle, WA, USA.
William E ByrdThe Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, AL, USA.ORCID https://orcid.org/0000-0003-4730-5293
Lawrence ChungThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID https://orcid.org/0000-0002-6823-9275
Andrew CrouseThe Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, AL, USA.ORCID https://orcid.org/0000-0003-3499-6902
Marc P DubyThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID https://orcid.org/0000-0002-3884-6680
Stephen FergusonNational Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.ORCID https://orcid.org/0000-0003-3172-8347
Aleksandra FoksinskaThe Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, AL, USA.ORCID https://orcid.org/0000-0002-1035-3294
Laura ForeroRady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
Jennifer FriedmanRady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
Vicki GardnerRenaissance Computing Institute (RENCI), University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Gwênlyn GlusmanInstitute for Systems Biology, Seattle, WA, USA.ORCID https://orcid.org/0000-0001-8060-5955
Jennifer HadlockInstitute for Systems Biology, Seattle, WA, USA.ORCID https://orcid.org/0000-0001-6103-7606
Kristina HanspersGladstone Institutes, University of California - San Francisco, San Francisco, CA, USA.ORCID https://orcid.org/0000-0001-5410-599X
Eugene HindererTufts Clinical and Translational Science Institute, Tufts Medical Center, Boston, MA, USA.ORCID https://orcid.org/0000-0001-8045-7083
Charlotte HobbsRady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.ORCID https://orcid.org/0000-0002-3964-5952
Gregory HydeThayer School of Engineering at Dartmouth College, Hanover, NH, USA.ORCID https://orcid.org/0000-0001-5608-5224
Sui HuangInstitute for Systems Biology, Seattle, WA, USA.ORCID https://orcid.org/0000-0002-3545-4665
David KoslickiDepartments of Computer Science and Engineering, Biology, and the Huck Institutes of the Life Sciences, Penn State University, University Park, PA, USA.ORCID https://orcid.org/0000-0002-0640-954X
Philip MeaseSwedish Medical Center, St. Joseph Health, Seattle, WA, USA.ORCID https://orcid.org/0000-0002-6620-0457
Sandrine MullerThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID https://orcid.org/0000-0001-5998-3003
Christopher J MungallBiosystems Data Science Department, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID https://orcid.org/0000-0002-6601-2165
Stephen A RamseyOregon State University, Corvallis, OR, USA.ORCID https://orcid.org/0000-0002-2168-5403
Jared RoachInstitute for Systems Biology, Seattle, WA, USA.ORCID https://orcid.org/0000-0003-4524-0107
Irit RubinInstitute for Systems Biology, Seattle, WA, USA.ORCID https://orcid.org/0000-0003-2377-3498
Shepherd H SchurmanNational Institute on Aging, National Institutes of Health, Baltimore, MD, USA.ORCID https://orcid.org/0000-0002-9133-7906
Anath ShalevThe Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, AL, USA.ORCID https://orcid.org/0000-0003-2869-7228
Brett SmithInstitute for Systems Biology, Seattle, WA, USA.ORCID https://orcid.org/0000-0002-2586-5014
Karthik SomanDepartment of Neurology, Weill Institute for Neuroscience, University of California - San Francisco, San Francisco, CA, USA.ORCID https://orcid.org/0000-0002-3490-9306
Sarah StemannDivision of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.
Andrew I SuThe Scripps Research Institute, La Jolla, CA, USA.ORCID https://orcid.org/0000-0002-9859-4104
Casey TaColumbia University Irving Medical Center, New York, NY, USA.ORCID https://orcid.org/0000-0002-4679-805X
Paul B WatkinsDivision of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.ORCID https://orcid.org/0000-0001-9541-8917
Mark D WilliamsDivision of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.ORCID https://orcid.org/0000-0001-8020-916X
Chunlei WuThe Scripps Research Institute, La Jolla, CA, USA.ORCID https://orcid.org/0000-0002-2629-6124
Colleen H XuThe Scripps Research Institute, La Jolla, CA, USA.ORCID https://orcid.org/0000-0003-2975-882X
Biomedical Data Translator Consortium

Funding

Pathway Hypotheses Knowledge-base: A Knowledge Source for the Biomedical Data TranslatorOT2TR003436 · NCATS · DARTMOUTH COLLEGE · PI SANTOS, EUGENE · 2020 to 2024
$3.2M
DOCKET: accelerating knowledge extraction from biomedical data setsOT2TR003443 · NCATS · INSTITUTE FOR SYSTEMS BIOLOGY · PI GLUSMAN, GWÊNLYN, HADLOCK, JENNIFER · 2020 to 2024
$3.1M
Expanding the landscape of Translator Knowledge Providers using BioThings SDK and SmartAPIOT2TR003445 · NCATS · SCRIPPS RESEARCH INSTITUTE, THE · PI WU, CHUNLEI · 2020 to 2024
$2.8M
Translator Red Knowledge (TReK)OT2TR003434 · NCATS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI DUMONTIER, MICHEL, TA, CASEY NGHIA · 2020 to 2024
$2.3M
NCATS NIH HHS OT2 TR003434NCATS NIH HHS OT2 TR003436NCATS NIH HHS OT2 TR003443NCATS NIH HHS OT2 TR003445
6 · The paper itself

Abstract

Knowledge graphs have become a common approach for knowledge representation. Yet, the application of graph methodology is elusive due to the sheer number and complexity of knowledge sources. In addition, semantic incompatibilities hinder efforts to harmonize and integrate across these diverse sources. As part of The Biomedical Translator Consortium, we have developed a knowledge graph-based question-answering system designed to augment human reasoning and accelerate translational scientific discovery: the Translator system. We have applied the Translator system to answer biomedical questions in the context of a broad array of diseases and syndromes, including Fanconi anemia, primary ciliary dyskinesia, multiple sclerosis, and others. A variety of collaborative approaches have been used to research and develop the Translator system. One recent approach involved the establishment of a monthly "Question-of-the-Month (QotM) Challenge" series. Herein, we describe the structure of the QotM Challenge; the six challenges that have been conducted to date on drug-induced liver injury, cannabidiol toxicity, coronavirus infection, diabetes, psoriatic arthritis, and

Indexed as

bioinformaticsknowledge graphssemantic technologyteam scienceTranslational research

Identifiers

PMID37900350
PMCPMC10603356

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.