ArticleBMC bioinformatics2007
BioPP: a tool for web-publication of biological networks.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
9 citing papers in PubMed.
- Sustainable software development in science - insights from 20 years of Vanted.Journal of integrative bioinformatics · 2025Article
- Gene Expression Switching of Receptor Subunits in Human Brain Development.PLoS computational biology · 2015Article
- Gene set analysis of SNP data: benefits, challenges, and future directions.European journal of human genetics : EJHG · 2011Review
- FNV: light-weight flash-based network and pathway viewer.Bioinformatics (Oxford, England) · 2011Article
- Signaling network of dendritic cells in response to pathogens: a community-input supported knowledgebase.BMC systems biology · 2010Article
- Research resource: Gonadotropin-releasing hormone receptor-mediated signaling network in LbetaT2 cells: a pathway-based web-accessible knowledgebase.Molecular endocrinology (Baltimore, Md.) · 2010Article
- Coregulation mapping based on individual phenotypic variation in response to virus infection.Immunome research · 2010Article
- Automated seeding of specialised wiki knowledgebases with BioKb.BMC bioinformatics · 2009Article
- AVIS: AJAX viewer of interactive signaling networks.Bioinformatics (Oxford, England) · 2007Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
backgroundCellular processes depend on the function of intracellular molecular networks. The curation of the literature relevant to specific biological pathways is important for many theoretical and experimental research teams and communities. No current tool supports web publication or hosting of user-developed large scale annotated pathway diagrams. Sharing via web publication is needed to allow real-time access to the current literature pathway knowledge-base, both privately within a research team or publicly among the outside research community. Web publication also facilitates team and/or community input into the curation process while allowing centralized control of the curation and validation process. We have developed new tool to address these needs. Biological Pathway Publisher (BioPP) is a software suite for converting CellDesigner Systems Biology Markup Language (CD-SBML) formatted pathways into a web viewable format. The BioPP suite is available for private use and for depositing knowledge-bases into a newly created public repository.
resultsBioPP suite is a web-based application that allows pathway knowledge-bases stored in CD-SBML to be web published with an easily navigated user interface. The BioPP suite consists of four interrelated elements: a pathway publisher, an upload web-interface, a pathway repository for user-deposited knowledge-bases and a pathway navigator. Users have the option to convert their CD-SBML files to HTML for restricted use or to allow their knowledge-base to be web-accessible to the scientific community. All entities in all knowledge-bases in the repository are linked to public database entries as well as to a newly created public wiki which provides a discussion forum.
conclusionBioPP tools and the public repository facilitate sharing of pathway knowledge-bases and interactive curation for research teams and scientific communities. BioPP suite is accessible at http://tsb.mssm.edu/pathwayPublisher/broadcast/
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.