Software support for SBGN maps: SBGN-ML and LibSBGN

Iersel, Martijn P. van; Villéger, Alice; Czauderna, Tobias; Boyd, Sarah; Bergmann, Frank; Luna, Augustin; Demir, Emek; Sorokin, Anatoly; Doğrusöz, Uğur; Matsuoka, Yoshikazu; Funahashi, Akira; Aladjem, Mirit I.; Mi, Huaiyu; Moodie, Stuart; Kitano, Hiroaki; Novère, Nicolas Le; Schreiber, Falk

doi:10.1093/bioinformatics/bts270

Cited by 78 publications

(69 citation statements)

References 16 publications

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“…Each pathway is represented as a diagram, and the PANTHER overrepresentation and enrichment analysis tools enable users to view their data overlaid on these diagrams. To support other pathway analysis and modeling tools, PANTHER Pathways can now be downloaded in three major pathway exchange formats: Systems Biology Market Language (SBML) (22), Systems Biology Graphical Notation (SBGN-ML) (23,24) and BioPAX (25). SBML is mainly used by the systems biology community for pathway network simulation and modeling tools.…”

Section: Panther Pathwaysmentioning

confidence: 99%

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

Muruganujan

Thomas

2012

Nucleic Acids Research

1,584

1,388

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The data and tools in PANTHER—a comprehensive, curated database of protein families, trees, subfamilies and functions available at http://pantherdb.org—have undergone continual, extensive improvement for over a decade. Here, we describe the current PANTHER process as a whole, as well as the website tools for analysis of user-uploaded data. The main goals of PANTHER remain essentially unchanged: the accurate inference (and practical application) of gene and protein function over large sequence databases, using phylogenetic trees to extrapolate from the relatively sparse experimental information from a few model organisms. Yet the focus of PANTHER has continually shifted toward more accurate and detailed representations of evolutionary events in gene family histories. The trees are now designed to represent gene family evolution, including inference of evolutionary events, such as speciation and gene duplication. Subfamilies are still curated and used to define HMMs, but gene ontology functional annotations can now be made at any node in the tree, and are designed to represent gain and loss of function by ancestral genes during evolution. Finally, PANTHER now includes stable database identifiers for inferred ancestral genes, which are used to associate inferred gene attributes with particular genes in the common ancestral genomes of extant species.

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Section: Panther Pathwaysmentioning

confidence: 99%

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

Muruganujan

Thomas

2012

Nucleic Acids Research

1,584

1,388

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“…STON is a standalone, Java-based framework that uses two sets of external libraries: LibSBGN [5] and a collection of Neo4j libraries. The latest version of STON 1.2 works with the LibSBGN milestone 2 and the Neo4j Community Edition version 2.3.1.…”

Section: Methodsmentioning

confidence: 99%

“…SBGN diagrams are drawn using three sets of standardized glyphs for the three SBGN languages. SBGN maps are represented in an XML-based format: the SBGN-ML [5], which is both human-readable and machine-readable. They can be exported from software tools such as SBGN-ED [6] (a VANTED add-on [7] with SBGN support) or CellDesigner [8].…”

Section: Introductionmentioning

confidence: 99%

STON: exploring biological pathways using the SBGN standard and graph databases

et al. 2016

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BackgroundWhen modeling in Systems Biology and Systems Medicine, the data is often extensive, complex and heterogeneous. Graphs are a natural way of representing biological networks. Graph databases enable efficient storage and processing of the encoded biological relationships. They furthermore support queries on the structure of biological networks.ResultsWe present the Java-based framework STON (SBGN TO Neo4j). STON imports and translates metabolic, signalling and gene regulatory pathways represented in the Systems Biology Graphical Notation into a graph-oriented format compatible with the Neo4j graph database.ConclusionSTON exploits the power of graph databases to store and query complex biological pathways. This advances the possibility of: i) identifying subnetworks in a given pathway; ii) linking networks across different levels of granularity to address difficulties related to incomplete knowledge representation at single level; and iii) identifying common patterns between pathways in the database.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1394-x) contains supplementary material, which is available to authorized users.

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“…SBGN-ED generated an automatic layout of the uploaded SBML model, which was then improved manually. The resulting Figure 1 was exported in different formats (GraphML 22 , GML ( www.fim.uni-passau.de/index.php?id=17297&L=1), PNG image, PDF, and SBGN-ML 23 ). Using WebCAT the files were uploaded to the directory and metadata was provided.…”

Section: Methodsmentioning

confidence: 99%

A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos

Scharm

Waltemath

2016

F1000Res

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COMBINE archives are standardised containers for data files related to a simulation study in computational biology. This manuscript describes a fully featured archive of a previously published simulation study, including (i) the original publication, (ii) the model, (iii) the analyses, and (iv) metadata describing the files and their origin. With the archived data at hand, it is possible to reproduce the results of the original work. The archive can be used for both, educational and research purposes. Anyone may reuse, extend and update the archive to make it a valuable resource for the scientific community.

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Software support for SBGN maps: SBGN-ML and LibSBGN

Cited by 78 publications

References 16 publications

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

STON: exploring biological pathways using the SBGN standard and graph databases

A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos

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