BioKC: a collaborative platform for systems biology model curation and annotation

Curation of biomedical knowledge into standardised and inter-operable systems biology models is essential for studying complex biological processes. However, systems-level curation is a laborious manual process, especially when facing ever increasing growth of domain literature. Currently, these systems-level curation efforts concentrate around dedicated pathway databases, with a limited input from the research community. The demand for systems biology knowledge increases with new findings demonstrating elaborate relationships between multiple molecules, pathways and cells. This new challenge calls for novel collaborative tools and platforms allowing to improve the quality and the output of the curation process. In particular, in the current systems biology environment, curation tools lack reviewing features and are not well suited for an open, community-based curation workflows. An important concern is the complexity of the curation process and the limitations of the tools supporting it. Currently, systems-level curation combines model-building with diagram layout design. However, diagram editing tools offer limited annotation features. On the other hand, text-oriented tools have insufficient capabilities representing and annotating relationships between biological entities. Separating model curation and annotation from diagram editing enables iterative and distributed building of annotated models. Here, we present BioKC (Biological Knowledge Curation), a web-based collaborative platform for the curation and annotation of biomedical knowledge following the standard data model from Systems Biology Markup Language (SBML).

[1]  Inna Kuperstein,et al.  NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps , 2013, BMC Systems Biology.

[2]  Fengkai Zhang,et al.  SBML Level 3 package: Multistate, Multicomponent and Multicompartment Species, Version 1, Release 1 , 2018, J. Integr. Bioinform..

[3]  Henning Hermjakob,et al.  The Reactome pathway knowledgebase , 2013, Nucleic Acids Res..

[4]  Mudita Singhal,et al.  COPASI - a COmplex PAthway SImulator , 2006, Bioinform..

[5]  Sb Ras,et al.  BioUML: VISUAL MODELING, AUTOMATED CODE GENERATION AND SIMULATION OF BIOLOGICAL SYSTEMS , 2006 .

[6]  Valentin Grouès,et al.  BioKB - Text mining and semantic technologies for the biomedical content discovery , 2017, SWAT4LS.

[7]  Nicolas Le Novère,et al.  Identifiers.org and MIRIAM Registry: community resources to provide persistent identification , 2011, Nucleic Acids Res..

[8]  Armando Blanco,et al.  Collaborative semi-automatic annotation of the biomedical literature , 2011, 2011 11th International Conference on Intelligent Systems Design and Applications.

[9]  Ugur Dogrusoz,et al.  SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps , 2015, PloS one.

[10]  D Garfinkel,et al.  Computer applications to biochemical kinetics. , 1970, Annual review of biochemistry.

[11]  Jurica Ševa,et al.  An extensive review of tools for manual annotation of documents , 2019, Briefings Bioinform..

[12]  Henning Hermjakob,et al.  The Reactome pathway Knowledgebase , 2015, Nucleic acids research.

[13]  B. Chance,et al.  The kinetics of the enzyme-substrate compound of peroxidase. 1943. , 1943, Advances in enzymology and related areas of molecular biology.

[14]  Marek Ostaszewski,et al.  Closing the gap between formats for storing layout information in systems biology , 2019, Briefings Bioinform..

[15]  Piotr Gawron,et al.  MINERVA—a platform for visualization and curation of molecular interaction networks , 2016, npj Systems Biology and Applications.

[16]  Henning Hermjakob,et al.  The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST). , 2020, Bioinformatics.

[17]  W. John Wilbur,et al.  Assisting manual literature curation for protein–protein interactions using BioQRator , 2014, Database J. Biol. Databases Curation.

[18]  Sampo Pyysalo,et al.  A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text , 2013, Bioinform..

[19]  Burkhard Rost,et al.  tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles , 2014, Database J. Biol. Databases Curation.

[20]  M Hucka,et al.  Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project. , 2004, Systems biology.

[21]  Chris J. Myers,et al.  Harmonizing semantic annotations for computational models in biology , 2018, bioRxiv.

[22]  Jacky L. Snoep,et al.  BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems , 2005, Nucleic Acids Res..

[23]  Paul T. Groth,et al.  The anatomy of a nanopublication , 2010, Inf. Serv. Use.

[24]  Mariana L. Neves,et al.  A survey on annotation tools for the biomedical literature , 2014, Briefings Bioinform..

[25]  Sampo Pyysalo,et al.  brat: a Web-based Tool for NLP-Assisted Text Annotation , 2012, EACL.

[26]  Zhiyong Lu,et al.  ezTag: tagging biomedical concepts via interactive learning , 2018, Nucleic Acids Res..

[27]  Yukiko Matsuoka,et al.  Using process diagrams for the graphical representation of biological networks , 2005, Nature Biotechnology.

[28]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[29]  A. Ruepp,et al.  CIDeR: multifactorial interaction networks in human diseases , 2012, Genome Biology.

[30]  Ryan Miller,et al.  WikiPathways: capturing the full diversity of pathway knowledge , 2015, Nucleic Acids Res..

[31]  Iryna Gurevych,et al.  WebAnno: A Flexible, Web-based and Visually Supported System for Distributed Annotations , 2013, ACL.

[32]  Minoru Kanehisa,et al.  KEGG: new perspectives on genomes, pathways, diseases and drugs , 2016, Nucleic Acids Res..

[33]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[34]  L. Levin,et al.  Biodiversity on the Rocks: Macrofauna Inhabiting Authigenic Carbonate at Costa Rica Methane Seeps , 2015, PloS one.

[35]  Hiroaki Kitano,et al.  CellDesigner: a process diagram editor for gene-regulatory and biochemical networks , 2003 .

[36]  Alfonso Valencia,et al.  MyMiner: a web application for computer-assisted biocuration and text annotation , 2012, Bioinform..