Christopher J. Mungall

Lawrence Berkeley National Laboratory

Biochemistry, Genetics and Molecular BiologyComputer Science

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 1%percentile

44.1Author DataRank

Indexed papers

29in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 29 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

A promoter-level mammalian expression atlas

Nature(2014)10.1038/nature13182

Top 2%

8.9DataRank

Top 2%2192 citations

Alistair R. R. Forrest, J. Kenneth Baillie, Michiel de Hoon, Timo Lassmann, Ivan V. Kulakovskiy +262 more

Papers

Driven by 101 papers — median percentile 72. Top paper: “The Gene Ontology resource: enriching a GOld mine”.

The Gene Ontology resource: enriching a GOld mine

Nucleic Acids Research(2020)10.1093/nar/gkaa1113

N/A

13.0DataRank · unranked

3876 citations

Eric Douglass, Benjamin M . Good, Deepak R Unni, Nomi L. Harris, Christopher J. Mungall +95 more

A promoter-level mammalian expression atlas

Nature(2014)10.1038/nature13182

Top 2%

8.9DataRank

Top 2%2192 citations

Alistair R. R. Forrest, J. Kenneth Baillie, Michiel de Hoon, Timo Lassmann, Ivan V. Kulakovskiy +262 more

The Human Phenotype Ontology in 2021

Nucleic Acids Research(2020)10.1093/nar/gkaa1043

Top 3%

7.0DataRank

Top 3%1255 citations

Michael Gargano, Nicolas Matentzoglu, Leigh C Carmody, David Lewis‐Smith, Nicole A. Vasilevsky +46 more

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

PLOS Biology(2017)10.1371/journal.pbio.2001414

N/A

6.5DataRank · unranked

148 citations

Nick Juty, Niklas Blomberg, Tony Burdett, Tom Conlin, Nathalie Conte +45 more

The Gene Ontology knowledgebase in 2023

Genetics(2023)10.1093/genetics/iyad031

Top 4%

5.8DataRank

Top 4%2744 citations

James P. Balhoff, Seth Carbon, J. Michael Cherry, Harold Drabkin, Dustin Ebert +90 more

Survey-based naming conventions for use in OBO Foundry ontology development

BMC Bioinformatics(2009)10.1186/1471-2105-10-125

N/A

5.2DataRank · unranked

86 citations

Barry Smith, Patricia L. Whetzel, Waclaw Kusnierczyk, Jane Lomax, Christopher J. Mungall +7 more

KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response

Patterns(2020)10.1016/j.patter.2020.100155

Top 7%

3.3DataRank

Top 7%95 citations

Deepak R Unni, Tiffany J. Callahan, Luca Cappelletti, Vida Ravanmehr, Seth Carbon +13 more

Mondo: Unifying diseases for the world, by the world

medRxiv(2022)10.1101/2022.04.13.22273750

Top 8%

2.7DataRank

Top 8%104 citations

Nicolas A Matentzoglu, Sabrina Toro, Joseph E Flack, Harshad Hegde, Deepak R Unni +83 more

The GA4GH Phenopacket schema defines a computable representation of clinical data

Nature Biotechnology(2022)10.1038/s41587-022-01357-4

N/A

2.4DataRank · unranked

111 citations

Michael Baudis, Gareth Baynam, J. Beckmann, Sergi Beltrán, Orion J. Buske +62 more

ECO: the Evidence and Conclusion Ontology, an update for 2022

Nucleic Acids Research(2021)10.1093/nar/gkab1025

Top 10%

2.1DataRank

Top 10%51 citations

Rebecca Jackson, James B. Munro, Federica Quaglia, Bálint Mészáros, Dustin Olley +8 more

Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities

mSystems(2021)10.1128/msystems.01194-20

N/A

2.0DataRank · unranked

72 citations

Josephine Burgin, Anjanette Johnston, Kristen L. Beck, Daniel C. Berrios, Kai Blumberg +37 more

The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species

Nucleic Acids Research(2023)10.1093/nar/gkad1082

Top 14%

1.5DataRank

Top 14%106 citations

Kevin Schaper, Nicolas A Matentzoglu, Vincent Rubinetti, Faisal Alquaddoomi, Corey Cox +39 more

A roadmap for the functional annotation of protein families: a community perspective

Database(2022)10.1093/database/baac062

Top 14%

1.5DataRank

Top 14%63 citations

Rocío Amorín, Cecilia N. Arighi, Jill Babor, Alex Bateman, Ian K. Blaby +54 more

An open source knowledge graph ecosystem for the life sciences

Scientific Data(2024)10.1038/s41597-024-03171-w

Top 15%

1.4DataRank

Top 15%63 citations

Ignacio J. Tripodi, Adrianne L. Stefanski, Luca Cappelletti, Sanya B. Taneja, Jordan M Wyrwa +27 more

FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability

Database(2018)10.1093/database/bax105

Top 16%

1.3DataRank

Top 16%39 citations

James A. Overton, Christopher J. Mungall, Alessandro Sette, Bjoern Peters, Randi Vita

The health care and life sciences community profile for dataset descriptions

PeerJ(2016)10.7717/peerj.2331

N/A

1.2DataRank · unranked

20 citations

Vladimir Alexiev, Peter Ansell, Joachim Baran, Jerven T. Bolleman, Alison Callahan +26 more

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

Nature Biotechnology(2007)10.1038/nbt1346

N/A

1.2DataRank · unranked

2611 citations

Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug +14 more

AI-readiness Criteria for Biomedical Data

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.10.23.619844

N/A

1.2DataRank · unranked

24 citations

J. Harry Caufield, Jillian A. Parker, Mohammad Sadnan Al Manir, Edilberto Amorim, James A. Eddy +26 more

The Bioperl Toolkit: Perl Modules for the Life Sciences

Genome Research(2002)10.1101/gr.361602

N/A

1.1DataRank · unranked

1704 citations

David Block, Kris Boulez, Steven E. Brenner, Stephen A. Chervitz, Chris Dagdigian +21 more

Representing Kidney Development Using the Gene Ontology

PLoS ONE(2014)10.1371/journal.pone.0099864

N/A

1.0DataRank · unranked

22 citations

David P. Hill, Emily C. Dimmer, Midori A. Harris, Rebecca E. Foulger, Susan Tweedie +11 more

Reactome and the Gene Ontology: digital convergence of data resources

Bioinformatics(2021)10.1093/bioinformatics/btab325

Top 23%

0.869DataRank

Top 23%23 citations

Kimberly Van Auken, David P. Hill, Huaiyu Mi, Seth Carbon, James P. Balhoff +6 more

A compendium of human gene functions derived from evolutionary modelling

Nature(2025)10.1038/s41586-025-08592-0

Top 24%

0.848DataRank

Top 24%35 citations

Huaiyu Mi, Pascale Gaudet, Anushya Muruganujan, Suzanna Lewis, Dustin Ebert +95 more

A guide to the BRAIN Initiative Cell Census Network data ecosystem

PLoS Biology(2023)10.1371/journal.pbio.3002133

Top 24%

0.845DataRank

Top 24%56 citations

Maryann E. Martone, Giorgio A. Ascoli, Jan G. Bjaalie, Hong‐Wei Dong, Satrajit S. Ghosh +95 more

The Gene Ontology knowledgebase in 2026

Nucleic Acids Research(2025)10.1093/nar/gkaf1292

Top 27%

0.743DataRank

Top 27%95 citations

James P. Balhoff, Seth Carbon, J. Michael Cherry, Dustin Ebert, Marc Feuermann +95 more

Transforming the study of organisms: Phenomic data models and knowledge bases

PLoS Computational Biology(2020)10.1371/journal.pcbi.1008376

Top 28%

0.706DataRank

Top 28%16 citations

Ramona L. Walls, Lars Vogt, Jessica Singer, Robert Warren, Pier Luigi Buttigieg +7 more

The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond

Journal of Biomedical Semantics(2023)10.1186/s13326-023-00283-x

Top 31%

0.648DataRank

Top 31%17 citations

Anne E. Thessen, William D. Duncan, Nicolas A Matentzoglu, Charles Schmitt, Cynthia Grondin +6 more

The Ontology of Biological Attributes (OBA)—computational traits for the life sciences

Mammalian Genome(2023)10.1007/s00335-023-09992-1

Top 33%

0.596DataRank

Top 33%21 citations

James P. Balhoff, Meghan A. Balk, Robyn L. Ball, Susan M. Bello, Anita R. Caron +21 more

Phenopacket-tools: Building and validating GA4GH Phenopackets

PLoS ONE(2023)10.1371/journal.pone.0285433

Top 36%

0.534DataRank

Top 36%12 citations

Julius O.B. Jacobsen, Alex H. Wagner, Tudor Groza, Martha A. Beckwith, Lauren Rekerle +13 more

A corpus of GA4GH phenopackets: Case-level phenotyping for genomic diagnostics and discovery

Human Genetics and Genomics Advances(2024)10.1016/j.xhgg.2024.100371

Top 39%

0.489DataRank

Top 39%12 citations

Michael J Bamshad, Yasemin Bridges, Andrés Caballero-Oteyza, Pilar Cacheiro, Leigh C Carmody +30 more

BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies

Nucleic Acids Research(2025)10.1093/nar/gkaf402

Top 40%

0.483DataRank

Top 40%14 citations

Nomi L. Harris, Michael V Dorf, Alex Skrenchuk, J. Harry Caufield, Rafael S. Gonçalves +6 more

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST)

Bioinformatics(2020)10.1093/bioinformatics/btaa622

N/A

0.477DataRank · unranked

23 citations

Steven Vercruysse, Márcio Luís Acencio, Ruth C. Lovering, Sandra Orchard, Glyn Bradley +21 more

Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science

Open MIND(2022)10.48550/arxiv.2203.13906

N/A

0.464DataRank · unranked

7 citations

Sierra A. T. Moxon, Michael Bada, Matthew Brush, Richard Bruskiewich, Paul A. Clemons +19 more

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation

Journal of Biomedical Semantics(2016)10.1186/s13326-016-0067-z

N/A

0.449DataRank · unranked

19 citations

Robin Andersson, Francesco Strozzi, Joachim Baran, Michel J. Dumontier, Robert Buels +7 more

The Unified Phenotype Ontology : a framework for cross-species integrative phenomics

Genetics(2025)10.1093/genetics/iyaf027

Top 45%

0.406DataRank

Top 45%10 citations

Susan M. Bello, Ray Stefancsik, Sarah M. Alghamdi, Anna V. Anagnostopoulos, James P. Balhoff +41 more

Announcing the Biomedical Data Translator: Initial Public Release

Clinical and Translational Science(2025)10.1111/cts.70284

N/A

0.397DataRank · unranked

9 citations

Gustavo Glusman, Sergio E. Baranzini, Chris Bizon, Matthew Brush, William E. Byrd +37 more

The health care and life sciences community profile for dataset descriptions

(2017)10.7287/peerj.preprints.1982v2

N/A

0.354DataRank · unranked

8 citations

Alasdair J. G. Gray, Vladimir Alexiev, Peter Ansell, Samirkumar B. Amin, Joachim Baran +26 more

A corpus of GA4GH Phenopackets: case-level phenotyping for genomic diagnostics and discovery

medRxiv(2024)10.1101/2024.05.29.24308104

Top 51%

0.345DataRank

Top 51%9 citations

Michael J Bamshad, Yasemin Bridges, Pilar Cacheiro, Leigh C Carmody, Jessica X. Chong +27 more

The BRAIN Initiative Cell Census Network Data Ecosystem: A User’s Guide

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.26.513573

Top 54%

0.312DataRank

Top 54%7 citations

Maryann E. Martone, Patrick R. Hof, Ed S. Lein, Aviv Regev, Giorgio A. Ascoli +94 more

The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.26.525742

Top 59%

0.254DataRank

Top 59%3 citations

James P. Balhoff, Meghan A. Balk, Robyn L. Ball, Susan M. Bello, Anita R. Caron +21 more

The Medical Action Ontology: A Tool for Annotating and Analyzing Treatments and Clinical Management of Human Disease

medRxiv(2023)10.1101/2023.07.13.23292612

Top 60%

0.246DataRank

Top 60%3 citations

Michael Gargano, Sabrina Toro, Nicole A. Vasilevsky, Margaret P Adam, Hannah Blau +21 more

OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows

Journal of Biomedical Semantics(2013)10.1186/2041-1480-4-2

N/A

0.208DataRank · unranked

3 citations

Jesualdo Tomás Fernández-Breis, Christopher J. Mungall, Erick Antezana, Alejandro Rodríguez González, Mark D D. Wilkinson +2 more

FAIR Header Reference genome: a TRUSTworthy standard

Briefings in Bioinformatics(2024)10.1093/bib/bbae122

N/A

0.165DataRank · unranked

2 citations

Mark D D. Wilkinson, Christopher J. Mungall, Scott Cain, Stephen Richards, Paul W. Sternberg +8 more

A Change Language for Ontologies and Knowledge Graphs

arXiv (Cornell University)(2024)10.48550/arxiv.2409.13906

Top 71%

0.133DataRank

Top 71%1 citations

Vendetti, Jennifer, Goutte-Gattat, Damien, Caufield, J Harry, Graybeal, John B, Nomi L. Harris +7 more

FALDO: A semantic standard for describing the location of nucleotide and protein feature annotation

bioRxiv (Cold Spring Harbor Laboratory)(2014)10.1101/002121

N/A

0.104DataRank · unranked

1 citations

Christopher J. Mungall, Francesco Strozzi, Joachim Baran, Michel J. Dumontier, Robert Buels +7 more

monarchr: an R package for querying biomedical knowledge graphs

Bioinformatics(2025)10.1093/bioinformatics/btaf549

Top 78%

0.104DataRank

Top 78%1 citations

Brian M. Schilder, Kevin Schaper, Corey Cox, Daniel Korn, Sarah Gehrke +3 more

An Open-Source Knowledge Graph Ecosystem for the Life Sciences

Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano)(2023)10.48550/arxiv.2307.05727

Top 78%

0.104DataRank

Top 78%1 citations

Ignacio J. Tripodi, Adrianne L. Stefanski, Luca Cappelletti, Sanya B. Taneja, Jordan M Wyrwa +27 more

Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery

UNC Libraries(2024)10.17615/1tsk-ff12

N/A

0DataRank · unranked

0 citations

Amy Yates, Leigh C Carmody, Emily Pfaff, Christopher G. Chute, Hao Xu +25 more

Methods for Linking Data to Online Resources and Ontologies with Applications to Neurophysiology

arXiv (Cornell University)(2024)10.48550/arxiv.2406.00063

N/A

0DataRank · unranked

0 citations

Ryan Ly, Andrew Tritt, Ben Dichter, Kristofer E. Bouchard, Christopher J. Mungall +2 more

Consistent performance of large language models in rare disease diagnosis across ten languages and 4917 cases

EBioMedicine(2025)10.1016/j.ebiom.2025.105957

N/A

0DataRank · unranked

8 citations

J. Harry Caufield, Yasemin Bridges, Nicolas A Matentzoglu, Michael Gargano, Mario Cazalla +25 more

LinkML: an open data modeling framework

GigaScience(2025)10.1093/gigascience/giaf152

N/A

0DataRank · unranked

4 citations

Harold R. Solbrig, Nomi L. Harris, Patrick Kalita, Mark A. Miller, Sagar Patil +63 more

A change language for ontologies and knowledge graphs

Database(2025)10.1093/database/baae133

N/A

0DataRank · unranked

7 citations

Jennifer Vendetti, Damien Goutte-Gattat, J. Harry Caufield, Graybeal, John, Nomi L. Harris +7 more

Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework

BMC Bioinformatics(2025)10.1186/s12859-025-06105-4

N/A

0DataRank · unranked

5 citations

Vinícius de Souza, Katherina G Cortes, Melissa A Haendel, Nomi L. Harris, Daniel Korn +10 more

Microbiome data management in action workshop: Atlanta, GA, USA, June 12–13, 2024

Environmental Microbiome(2025)10.1186/s40793-025-00702-9

N/A

0DataRank · unranked

4 citations

Mashael R. Aljumaah, Sarah R. Bordenstein, J. Rodney Brister, Patrick Chain, José Pablo Dundore-Arias +32 more

The Vertebrate Breed Ontology: Toward Effective Breed Data Standardization

Journal of Veterinary Internal Medicine(2025)10.1111/jvim.70133

N/A

0DataRank · unranked

2 citations

Imke Tammen, Nicolas A Matentzoglu, Marius Mather, James P. Balhoff, Elizabeth Esdaile +11 more

Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science

UNC Libraries(2025)10.17615/rc0v-1b82

N/A

0DataRank · unranked

0 citations

Sierra A. T. Moxon, Michael Bada, Matthew Brush, Richard Bruskiewich, J. Harry Caufield +20 more

RareLink: scalable REDCap-based framework for rare disease interoperability linking international registries to FHIR and Phenopackets

npj Genomic Medicine(2025)10.1038/s41525-025-00534-z

N/A

0DataRank · unranked

0 citations

Filip Rehburg, Samer Alkarkoukly, Daniel Daniš, Ana Grönke, Miriam Hübner +23 more

Announcing the Biomedical Data Translator: Initial Public Release

UNC Libraries(2025)10.17615/9as8-h722

N/A

0DataRank · unranked

0 citations

Gustavo Glusman, Sergio E. Baranzini, Chris Bizon, Matthew Brush, William E. Byrd +37 more

Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project

Nature Reviews Nephrology(2020)10.1038/s41581-020-00335-w

N/A

0DataRank · unranked

71 citations

Lucy Lu Wang, Jennifer A. Schaub, John F. O’Toole, Becky Steck, Avi Z. Rosenberg +24 more

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)

Preprints.org(2020)10.20944/preprints202004.0480.v1

N/A

0DataRank · unranked

8 citations

Steven Vercruysse, Márcio Luís Acencio, Ruth C. Lovering, Sandra Orchard, Glyn Bradley +20 more

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

UNC Libraries(2020)10.17615/3bz2-ch65

N/A

0DataRank · unranked

0 citations

T. Alexander Dececchi, Anne Niknejad, Wasila Dahdul, David C. Blackburn, Melissa A Haendel +13 more

A Unified Anatomy Ontology of the Vertebrate Skeletal System

UNC Libraries(2020)10.17615/dps9-e365

Top 100%

0DataRank

Top 100%0 citations

Erik Segerdell, John G. Lundberg, James P. Balhoff, Matthew K. Vickaryous, Wasila Dahdul +10 more

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies

Database(2021)10.1093/database/baab069

N/A

0DataRank · unranked

208 citations

Nicolas A Matentzoglu, James A. Overton, Randi Vita, James P. Balhoff, Pier Luigi Buttigieg +20 more

Sequence Ontology terminology for gene regulation

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms(2021)10.1016/j.bbagrm.2021.194745

N/A

0DataRank · unranked

12 citations

Michael S. Sinclair, Christopher J. Mungall, Stefan Schulz, Daniel R. Zerbino, Ruth C. Lovering +3 more

Supervised learning with word embeddings derived from PubMed captures latent knowledge about protein kinases and cancer

NAR Genomics and Bioinformatics(2021)10.1093/nargab/lqab113

N/A

0DataRank · unranked

7 citations

Hannah Blau, Luca Cappelletti, Tommaso Fontana, Leigh C Carmody, Ben D Coleman +13 more

NSAID use and clinical outcomes in COVID-19 patients: A 38-center retrospective cohort study

medRxiv(2021)10.1101/2021.04.13.21255438

N/A

0DataRank · unranked

18 citations

Ben D Coleman, Lauren E Chan, Hannah Blau, Tiffany J. Callahan, Luca Cappelletti +18 more

OBO Foundry in 2021: Operationalizing Open Data Principles to Evaluate Ontologies

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.01.446587

N/A

0DataRank · unranked

14 citations

Nicolas A Matentzoglu, James A. Overton, Randi Vita, James P. Balhoff, Pier Luigi Buttigieg +20 more

The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine

medRxiv(2021)10.1101/2021.11.27.21266944

N/A

0DataRank · unranked

14 citations

Michael Baudis, Gareth Baynam, J. Beckmann, Sergi Beltrán, Tiffany J. Callahan +42 more

SvAnna: efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencing

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.14.452267

N/A

0DataRank · unranked

2 citations

Julius O.B. Jacobsen, Parithi Balachandran, Qihui Zhu, Feyza Yilmaz, Justin T Reese +9 more

Supervised learning with word embeddings derived from PubMed captures latent knowledge about protein kinases and cancer

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.11.447943

N/A

0DataRank · unranked

1 citations

Hannah Blau, Luca Cappelletti, Tommaso Fontana, Leigh C Carmody, Ben D Coleman +12 more

Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science

Clinical and Translational Science(2022)10.1111/cts.13302

N/A

0DataRank · unranked

100 citations

Sierra A. T. Moxon, Michael Bada, Matthew Brush, Richard Bruskiewich, J. Harry Caufield +19 more

Phenotype‐driven approaches to enhance variant prioritization and diagnosis of rare disease

Human Mutation(2022)10.1002/humu.24380

N/A

0DataRank · unranked

75 citations

Catherine Kelly, Valentina Cipriani, Christopher J. Mungall, Justin T Reese, Daniel Daniš +3 more

Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies

Database(2022)10.1093/database/baac087

N/A

0DataRank · unranked

68 citations

Damien Goutte-Gattat, Shawn Zheng Kai Tan, James P. Balhoff, Seth Carbon, Anita R. Caron +22 more

SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing

Genome Medicine(2022)10.1186/s13073-022-01046-6

N/A

0DataRank · unranked

42 citations

Julius O.B. Jacobsen, Parithi Balachandran, Qihui Zhu, Feyza Yilmaz, Justin T Reese +9 more

NSAID use and clinical outcomes in COVID-19 patients: a 38-center retrospective cohort study

Virology Journal(2022)10.1186/s12985-022-01813-2

N/A

0DataRank · unranked

31 citations

Ben D Coleman, Lauren E Chan, Hannah Blau, Tiffany J. Callahan, Luca Cappelletti +18 more

GA4GH Phenopackets: A Practical Introduction

Advanced Genetics(2022)10.1002/ggn2.202200016

N/A

0DataRank · unranked

20 citations

Julius O.B. Jacobsen, Alex H. Wagner, Daniel Daniš, Bahá El Kassaby, Michael Gargano +14 more

A Simple Standard for Sharing Ontological Mappings (SSSOM)

Database(2022)10.1093/database/baac035

N/A

0DataRank · unranked

1 citations

James P. Balhoff, Susan M. Bello, Chris Bizon, Matthew Brush, Tiffany J. Callahan +39 more

Unifying the identification of biomedical entities with the Bioregistry

Scientific Data(2022)10.1038/s41597-022-01807-3

N/A

0DataRank · unranked

33 citations

Meghan A. Balk, Tiffany J. Callahan, Daniel Domingo-Fernández, Melissa A Haendel, Harshad Hegde +14 more

GraPE: fast and scalable Graph Processing and Embedding

Research Square(2022)10.21203/rs.3.rs-967145/v1

N/A

0DataRank · unranked

5 citations

Tommaso Fontana, Elena Casiraghi, Vida Ravanmehr, Tiffany J. Callahan, Marcin P. Joachimiak +5 more

Ubergraph: integrating OBO ontologies into a unified semantic graph

Zenodo (CERN European Organization for Nuclear Research)(2022)10.5281/zenodo.7249759

N/A

0DataRank · unranked

5 citations

Ugur Bayindir, Anita R. Caron, Nicolas A Matentzoglu, David Osumi-Sutherland, Christopher J. Mungall +1 more

Node-degree aware edge sampling mitigates inflated classification performance in biomedical graph representation learning

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.21.517376

N/A

0DataRank · unranked

1 citations

Lauren Rekerle, Tommaso Fontana, Peter Hansen, Elena Casiraghi, Vida Ravanmehr +12 more

KG-Hub—building and exchanging biological knowledge graphs

Bioinformatics(2023)10.1093/bioinformatics/btad418

N/A

0DataRank · unranked

35 citations

Tim Putman, Kevin Schaper, Deepak R Unni, Harshad Hegde, Tiffany J. Callahan +21 more

GRAPE for fast and scalable graph processing and random-walk-based embedding

Nature Computational Science(2023)10.1038/s43588-023-00465-8

N/A

0DataRank · unranked

32 citations

Tommaso Fontana, Elena Casiraghi, Vida Ravanmehr, Tiffany J. Callahan, Carlos Cano +6 more

The Medical Action Ontology: A tool for annotating and analyzing treatments and clinical management of human disease

Med(2023)10.1016/j.medj.2023.10.003

N/A

0DataRank · unranked

10 citations

Michael Gargano, Sabrina Toro, Nicole A. Vasilevsky, Margaret P Adam, Hannah Blau +21 more

Brain Data Standards - A method for building data-driven cell-type ontologies

Scientific Data(2023)10.1038/s41597-022-01886-2

N/A

0DataRank · unranked

20 citations

Hüseyin Kır, Brian D. Aevermann, Tom Gillespie, Nomi L. Harris, Michael Hawrylycz +15 more

Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI)

arXiv (Cornell University)(2023)10.48550/arxiv.2312.10904

N/A

0DataRank · unranked

7 citations

Anna V. Anagnostopoulos, S. Bello, Kai Blumberg, Rhiannon Cameron, Leigh C Carmody +25 more

Predicting nutrition and environmental factors associated with female reproductive disorders using a knowledge graph and random forests

medRxiv(2023)10.1101/2023.07.14.23292679

N/A

0DataRank · unranked

1 citations

Elena Casiraghi, Tim Putman, Justin T Reese, Quaker E. Harmon, Kevin Schaper +9 more

An evaluation of GPT models for phenotype concept recognition

arXiv (Cornell University)(2023)10.48550/arxiv.2309.17169

N/A

0DataRank · unranked

1 citations

Harry Caufield, Dylan Gration, Gareth Baynam, Melissa A Haendel, Peter N. Robinson +3 more

KG-Hub -- Building and Exchanging Biological Knowledge Graphs

arXiv (Cornell University)(2023)10.48550/arxiv.2302.10800

N/A

0DataRank · unranked

0 citations

Tim Putman, Kevin Schaper, Deepak R Unni, Harshad Hegde, Tiffany J. Callahan +21 more

Author Correction: Brain Data Standards - A method for building data-driven cell-type ontologies

Scientific Data(2023)10.1038/s41597-023-02165-4

N/A

0DataRank · unranked

0 citations

Hüseyin Kır, Brian D. Aevermann, Tom Gillespie, Nomi L. Harris, Michael Hawrylycz +15 more

A Simple Standard for Ontological Mappings 2023: Updates on data model, collaborations and tooling

Zenodo (CERN European Organization for Nuclear Research)(2023)10.5281/zenodo.8202395

N/A

0DataRank · unranked

0 citations

Ian Braun, Anita R. Caron, Damien Goutte-Gattat, Benjamin M. Gyori, Nomi L. Harris +11 more

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning

Bioinformatics(2024)10.1093/bioinformatics/btae104

N/A

0DataRank · unranked

105 citations

Harshad Hegde, Vincent Emonet, Nomi L. Harris, Marcin P. Joachimiak, Nicolas A Matentzoglu +7 more

Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI)

Journal of Biomedical Semantics(2024)10.1186/s13326-024-00320-3

N/A

0DataRank · unranked

47 citations

Anna V. Anagnostopoulos, Susan M. Bello, Kai Blumberg, Rhiannon Cameron, Leigh C Carmody +25 more

An evaluation of GPT models for phenotype concept recognition

BMC Medical Informatics and Decision Making(2024)10.1186/s12911-024-02439-w

N/A

0DataRank · unranked

37 citations

Harry Caufield, Dylan Gration, Gareth Baynam, Melissa A Haendel, Peter N. Robinson +3 more

Efficient reinterpretation of rare disease cases using Exomiser

npj Genomic Medicine(2024)10.1038/s41525-024-00456-2

N/A

0DataRank · unranked

20 citations

Julius O.B. Jacobsen, Susan Walker, Valentina Cipriani, Nomi L. Harris, Melissa A Haendel +4 more

Leveraging generative AI to assist biocuration of medical actions for rare disease

Bioinformatics Advances(2024)10.1093/bioadv/vbaf141

N/A

0DataRank · unranked

3 citations

J. Harry Caufield, Leigh C Carmody, Michael Gargano, Sabrina Toro, Patricia L. Whetzel +10 more

Node-degree aware edge sampling mitigates inflated classification performance in biomedical random walk-based graph representation learning

Bioinformatics Advances(2024)10.1093/bioadv/vbae036

N/A

0DataRank · unranked

8 citations

Lauren Rekerle, Tommaso Fontana, Peter Hansen, Elena Casiraghi, Vida Ravanmehr +12 more

Predicting nutrition and environmental factors associated with female reproductive disorders using a knowledge graph and random forests

International Journal of Medical Informatics(2024)10.1016/j.ijmedinf.2024.105461

N/A

0DataRank · unranked

5 citations

Elena Casiraghi, Justin T Reese, Quaker E. Harmon, Kevin Schaper, Harshad Hegde +8 more

Systematic benchmarking demonstrates large language models have not reached the diagnostic accuracy of traditional rare-disease decision support tools

medRxiv(2024)10.1101/2024.07.22.24310816

N/A

0DataRank · unranked

9 citations

Leonardo Chimirri, Yasemin Bridges, Daniel Daniš, J. Harry Caufield, Michael Gargano +16 more

CurateGPT: A flexible language-model assisted biocuration tool

arXiv (Cornell University)(2024)10.48550/arxiv.2411.00046

N/A

0DataRank · unranked

8 citations

Carlo Kroll, Shawn T. O’Neil, Justin T Reese, Marcin P. Joachimiak, Harshad Hegde +8 more

Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.06.13.598672

N/A

0DataRank · unranked

5 citations

Vinícius de Souza, Katherina G Cortes, Melissa A Haendel, Nomi L. Harris, Daniel Korn +10 more

Leveraging Generative AI to Accelerate Biocuration of Medical Actions for Rare Disease

medRxiv(2024)10.1101/2024.08.22.24310814

N/A

0DataRank · unranked

3 citations

J. Harry Caufield, Leigh C Carmody, Michael Gargano, Sabrina Toro, Trish Whetzel +10 more

Christopher J. Mungall

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