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Pathguide specifications


Unique identifier OMICS_21344
Name Pathguide
Restrictions to use None
Database management system MySQL
Community driven No
Data access Browse
User data submission Allowed
Maintained Yes


  • person_outline Gary Bader
  • person_outline Chris Sander
  • person_outline Vuk Pavlovic

Publication for Pathguide

Pathguide citations


New perspectives: systems medicine in cardiovascular disease

BMC Syst Biol
PMCID: 5921396
PMID: 29699591
DOI: 10.1186/s12918-018-0579-5
call_split See protocol

[…] databases. This ranges from genetic sequence information on GenBank [] to protein information on UniProt [] to various sites of knowledge on molecular interactions, many of which are collected on the website [], which currently lists over 600 resources related to biological pathway and interaction knowledge. The most prominent pathway databases are Reactome [], the Network Data Excha […]


From protein protein interactions to protein co expression networks: a new perspective to evaluate large scale proteomic data

EURASIP J Bioinform Syst Biol
PMCID: 5359264
PMID: 28477207
DOI: 10.1186/s13637-017-0059-z

[…] lassification in categories (primary, meta, and prediction database) according to method used to detect interactions. Moreover, an exhaustive collection of more than 500 databases is available in the Pathguide website (Fig. ) []. Fig. 2 The development of computational tools to retrieve, visualize, and analyze biological networks is a key aspect of the systems biology studies, like the production […]


Modelling the Structure and Dynamics of Biological Pathways

PLoS Biol
PMCID: 4980033
PMID: 27509052
DOI: 10.1371/journal.pbio.1002530

[…] drive forward biological research objectives.The post-genomic era has led to the generation of a massive amount of data on the interactions between molecules across cell types and disease processes. [] lists and categorises many of the available resources providing access to this information; it currently lists 547 websites and databases (as of May 2016). Many are databases of colla […]


Reactome from a WikiPathways Perspective

PLoS Comput Biol
PMCID: 4874630
PMID: 27203685
DOI: 10.1371/journal.pcbi.1004941

[…] Pathway diagrams are a common way to represent a wealth of information about biological molecules, interactions and processes. Currently, the Pathguide collection lists 45 freely available pathway databases with human data, out of which only 14 provide the data in a machine readable format [, ]. Even fewer of these provide a pathway diagram […]


Predictive Modeling of Drug Treatment in the Area of Personalized Medicine

Cancer Inform
PMCID: 4671548
PMID: 26692759
DOI: 10.4137/CIN.S1933

[…] pment of large-scale mechanistic models has been the steady increase (over the past 10–15 years) in the availability of public information sources, providing access to relevant data. Examples include PathGuide, a comprehensive list of databases and resources for molecular and cellular pathways and interaction networks, and the well-known pathway databases KEGG and Reactome. Consensus PathDB is a m […]


Open source libraries and frameworks for biological data visualisation: A guide for developers

PMCID: 4409855
PMID: 25475079
DOI: 10.1002/pmic.201400377

[…] cape desktop, network data can be exported in JSON format and visualised in a web page.Unlike Cytoscape Web, which is currently used in many bioinformatics projects (e.g. GeneMANIA [], iRefWeb [] and Pathguide []), at present Cytoscape.js has not been widely adopted yet due to its recent development. However, it is rapidly gaining momentum and expected to be widely adopted, like its predecessor [, […]

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Pathguide institution(s)
Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA

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