ComplexViewer: visualization of curated macromolecular complexes

Combe, Colin; Sivade, M.; Hermjakob, Henning; Heimbach, Joshua; Meldal, Birgit; Micklem, Gos; Orchard, Sandra; Rappsilber, Juri

doi:10.1093/bioinformatics/btx497

Cited by 13 publications

(11 citation statements)

References 9 publications

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“…Lastly, in order to represent proteins belonging to a common group, for instance, protein complexes, it is possible to envelop with gray hulls nodes belonging to user defined lists of entities, which, on mouse hover, turn red showing the group name. Protein complexes visualization goes beyond the purpose of SVP due to the intrinsic complexity of such biological entities for which a dedicated JavaScript visualizer called ComplexViewer, a visualization tool for Complex Portal ( Meldal et al , 2015 ), was recently released ( Combe et al , 2017 ).…”

Section: Methodsmentioning

confidence: 99%

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SPV: a JavaScript Signaling Pathway Visualizer

Calderone

2018

Bioinformatics

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SummaryThe visualization of molecular interactions annotated in web resources is useful to offer to users such information in a clear intuitive layout. These interactions are frequently represented as binary interactions that are laid out in free space where, different entities, cellular compartments and interaction types are hardly distinguishable. Signaling Pathway Visualizer is a free open source JavaScript library, which offers a series of pre-defined elements, compartments and interaction types meant to facilitate the representation of signaling pathways consisting of causal interactions without neglecting simple protein–protein interaction networks.Availability and implementationFreely available under Apache version 2 license; Source code: https://github.com/Sinnefa/SPV_Signaling_Pathway_Visualizer_v1.0. Language: JavaScript; Web technology: Scalable Vector Graphics; Libraries: D3.js.

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Section: Methodsmentioning

confidence: 99%

“…The IMEx Consortium promotes the Proteomics Standards Initiative-Molecular Interaction (PSI-MI) in order to facilitate data exchange ( Hermjakob et al , 2004 ). In particular, the JavaScript Object Notation format MI-JSON will soon be published ( Combe et al , 2017 ) and integrated in SPV.…”

Section: Compatibilitymentioning

confidence: 99%

SPV: a JavaScript Signaling Pathway Visualizer

Calderone

2018

Bioinformatics

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“…The HTML format is intended for quick human consumption via a web browser, and is currently hardwired in JAMI to produce a consistent layout and appearance although further CSS extensibility is planned in the future, if there is user demand. The MI-JSON output is designed for ease of use with JavaScript-based client applications, such as the ComplexViewer [ 6 ] described later in the results section. As described above, JAMI is designed to be readily extensible.…”

Section: Methodsmentioning

confidence: 99%

“…The ComplexViewer pictured in Figs. 2 and 3 is a powerful visualisation tool which can show its users exactly how the molecules in complex interactions interact with each other, with interactive controls to allow data exploration [ 6 ]. Unlike other network viewers, this interaction viewer details the binding sites and regions, when known, and enables the topology of a macromolecular complex to be fully represented.…”

Section: Complexviewermentioning

confidence: 99%

JAMI: a Java library for molecular interactions and data interoperability

et al. 2018

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BackgroundA number of different molecular interactions data download formats now exist, designed to allow access to these valuable data by diverse user groups. These formats include the PSI-XML and MITAB standard interchange formats developed by Molecular Interaction workgroup of the HUPO-PSI in addition to other, use-specific downloads produced by other resources. The onus is currently on the user to ensure that a piece of software is capable of read/writing all necessary versions of each format. This problem may increase, as data providers strive to meet ever more sophisticated user demands and data types.ResultsA collaboration between EMBL-EBI and the University of Cambridge has produced JAMI, a single library to unify standard molecular interaction data formats such as PSI-MI XML and PSI-MITAB. The JAMI free, open-source library enables the development of molecular interaction computational tools and pipelines without the need to produce different versions of software to read different versions of the data formats.ConclusionSoftware and tools developed on top of the JAMI framework are able to integrate and support both PSI-MI XML and PSI-MITAB. The use of JAMI avoids the requirement to chain conversions between formats in order to reach a desired output format and prevents code and unit test duplication as the code becomes more modular. JAMI’s model interfaces are abstracted from the underlying format, hiding the complexity and requirements of each data format from developers using JAMI as a library.

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“…The EBI Complex Portal [1] (www.ebi.ac.uk/intact/complex) provides a unifying, easy-to-search-and-retrieve resource for protein complexes and a custom-made visualisation tool, ComplexViewer [2] (Figure 1 and Figure 2). …”

Section: Bodymentioning

confidence: 99%

Complex Portal - A Unifying Protein Complex Database

Meldal

Combe

Bye-A-Jee

et al. 2017

Genomics Comput Biol

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SUMMARYThe EBI Complex Portal is a manually curated, unifying resource of macromolecular complexes from model organisms.Each entry has a unique and stable identifier and links participating molecule to their unique reference database (UniProt, ChEBI and RNAcentral). Each complex is annotated with information about their stoichiometry, topology and structural assembly, function, complex-centric Gene Ontology terms and evidence codes. Complexes are extensively cross-referenced to ChEMBL, EMDB, Experimental Factor Ontology, Intenz, MatrixDB, the PDB and Reactome. Bespoke visualisation tools for the general topology and stoichiometry, crystal structures, molecular reactions and gene expression data are provided. All data is open-source and available in PSI-MI xml2.5 and xml3.0 standard formats, MI-JSON and tab-delineated ComplexTAB format.

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ComplexViewer: visualization of curated macromolecular complexes

Cited by 13 publications

References 9 publications

SPV: a JavaScript Signaling Pathway Visualizer

SPV: a JavaScript Signaling Pathway Visualizer

JAMI: a Java library for molecular interactions and data interoperability

Complex Portal - A Unifying Protein Complex Database

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