PathMe: merging and exploring mechanistic pathway knowledge (Q64054035)

1

0 references

Charles Tapley Hoyt

object named as

Charles Tapley Hoyt

4

0 references

Sarah Mubeen

2

0 references

Josep Marín-Llaó

3

0 references

Martin Hofmann-Apitius

describes a project that uses

5

0 references

language of work or name

English

0 references

publication date

15 May 2019

0 references

published in

BMC Bioinformatics

0 references

volume

20

0 references

issue

1

0 references

page(s)

243

0 references

uses

PyBEL

0 references

Jupyter notebook file

1 reference

Cytoscape

2 references

Europe PubMed Central

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Hierarchical phosphorylation of the translation inhibitor 4E-BP1

1 reference

12 December 2020

The Ensembl genome database project

1 reference

12 December 2020

The HUGO Gene Nomenclature Committee (HGNC).

1 reference

12 December 2020

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

1 reference

12 December 2020

UniProt: the Universal Protein knowledgebase

1 reference

12 December 2020

Entrez Gene: gene-centered information at NCBI

1 reference

12 December 2020

ConsensusPathDB--a database for integrating human functional interaction networks

1 reference

12 December 2020

Rapamycin differentially inhibits S6Ks and 4E-BP1 to mediate cell-type-specific repression of mRNA translation

1 reference

12 December 2020

A novel signaling pathway impact analysis.

1 reference

12 December 2020

Akt-dependent and -independent mechanisms of mTOR regulation in cancer

1 reference

12 December 2020

The Systems Biology Graphical Notation

1 reference

12 December 2020

The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

1 reference

12 December 2020

The BioPAX community standard for pathway data sharing

1 reference

12 December 2020

Pathway Commons, a web resource for biological pathway data

1 reference

12 December 2020

KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats

1 reference

12 December 2020

ChEMBL: a large-scale bioactivity database for drug discovery

1 reference

12 December 2020

Critical assessment of human metabolic pathway databases: a stepping stone for future integration

1 reference

12 December 2020

Homeostasis and the importance for a balance between AKT/mTOR activity and intracellular signaling

1 reference

12 December 2020

mTORC1 and mTORC2 regulate insulin secretion through Akt in INS-1 cells

1 reference

12 December 2020

BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats

1 reference

12 December 2020

Using biological pathway data with paxtools

1 reference

12 December 2020

Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges.

1 reference

12 December 2020

PathVisio 3: an extendable pathway analysis toolbox

1 reference

12 December 2020

PathCards: multi-source consolidation of human biological pathways

1 reference

12 December 2020

Cytoscape.js: a graph theory library for visualisation and analysis

1 reference

12 December 2020

ChEBI in 2016: Improved services and an expanding collection of metabolites

1 reference

12 December 2020

NDEx, the Network Data Exchange

1 reference

12 December 2020

The Pfam protein families database: towards a more sustainable future

1 reference

12 December 2020

Reactome from a WikiPathways Perspective

1 reference

12 December 2020

Impact of outdated gene annotations on pathway enrichment analysis

1 reference

12 December 2020

OmniPath: guidelines and gateway for literature-curated signaling pathway resources.

1 reference

12 December 2020

Expansion of the Gene Ontology knowledgebase and resources

1 reference

12 December 2020

KEGG: new perspectives on genomes, pathways, diseases and drugs

1 reference

12 December 2020

PyBEL: a Computational Framework for Biological Expression Language

1 reference

12 December 2020

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research

1 reference

12 December 2020

The Reactome Pathway Knowledgebase.

1 reference

12 December 2020

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

1 reference

12 December 2020

RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites.

1 reference

12 December 2020

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

1 reference

12 December 2020

Experimenting with reproducibility: a case study of robustness in bioinformatics

1 reference

12 December 2020

metaGraphite-a new layer of pathway annotation to get metabolite networks

1 reference

12 December 2020

ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases

1 reference

12 December 2020

BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language

1 reference

12 December 2020

Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling

1 reference

12 December 2020

10.1186/S12859-019-2863-9

Identifiers

DOI

0 references

BioRxiv ID

451625

0 references

DBLP publication ID

journals/bmcbi/Domingo-Fernandez19

1 reference