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A Simple Standard for Sharing Ontological Mappings (SSSOM)

artículo científico publicado en 2022

A Unified Framework for Rank-based Evaluation Metrics for Link Prediction in Knowledge Graphs

artículo científico

Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature

artículo científico publicado en 2020

Author-sourced capture of pathway knowledge in computable form using Biofactoid

artículo científico

Automated Network Assembly of Mechanistic Literature for Informed Evidence Identification to Support Cancer Risk Assessment

artículo científico publicado en 2022

Automated assembly of molecular mechanisms at scale from text mining and curated databases

preprint published on 31 August 2022

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

artículo científico

Capturing scientific knowledge in computable form

artículo científico publicado en 2021

ChemicalX: A Deep Learning Library for Drug Pair Scoring

preprint published on 11 February 2022

Computational Tools and Data Integration to Accelerate Vaccine Development: Challenges, Opportunities, and Future Directions

Preprint

Democratising Knowledge Representation with BioCypher

artículo científico publicado en 2022

Democratizing knowledge representation with BioCypher

Encoding Growth Factor Identity in the Temporal Dynamics of FOXO3 under the Combinatorial Control of ERK and AKT Kinases.

artículo científico publicado en 2018

FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining.

artículo científico publicado en 2018

From word models to executable models of signaling networks using automated assembly.

artículo científico publicado en 2017

GeneWalk identifies relevant gene functions for a biological context using network representation learning

artículo científico

Gilda: biomedical entity text normalization with machine-learned disambiguation as a service

preprint published on 11 September 2021

Gilda: biomedical entity text normalization with machine-learned disambiguation as a service

artículo científico publicado en 2022

INDRA-IPM: interactive pathway modeling using natural language with automated assembly

scientific article published on 01 November 2019

Integrated Network and Dynamical Reasoning Assembler

Text mining and systems biology modeling software

Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes

preprint published on 09 August 2021

Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes

artículo científico publicado en 2022

Maintenance and Enrichment of Disease Maps in Biological Expression Language

conference poster

Nociceptor neuroimmune interactomes reveal cell type- and injury-specific inflammatory pain pathways

OpenComet: an automated tool for comet assay image analysis.

artículo científico publicado en 2014

Prediction and Curation of Missing Biomedical Identifier Mappings with Biomappings

preprint published on 02 December 2022

Prediction and curation of missing biomedical identifier mappings with Biomappings

scientific article published in 2023

ProtSTonKGs: A Sophisticated Transformer Trained on Protein Sequences, Text, and Knowledge Graphs

PyBioPAX: biological pathway exchange in Python

artículo científico publicado en 2022

Re-curation and Rational Enrichment of Knowledge Graphs in Biological Expression Language

BioRxiv article

Re-curation and rational enrichment of knowledge graphs in Biological Expression Language.

artículo científico publicado en 2019

Robustness and parameter geography in post-translational modification systems

scientific article published on 04 May 2020

STonKGs: A Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs

preprint published on 18 August 2021

STonKGs: A Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs

artículo científico publicado en 2022

The Human Phenotype Ontology in 2024: phenotypes around the world

artículo científico publicado en 2023

The O3 guidelines: open data, open code, and open infrastructure for sustainable curated scientific resources

preprint published November 16th, 2023

The O3 guidelines: open data, open code, and open infrastructure for sustainable curated scientific resources

artículo científico publicado en 2024

Unifying the Identification of Biomedical Entities with the Bioregistry

preprint published on 10 July 2022

Unifying the identification of biomedical entities with the Bioregistry

artículo científico publicado en 2022