ArticleBMC bioinformatics2011
A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 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
15 citing papers in PubMed.
- Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions.PloS one · 2022Article
- A Community-Driven, Openly Accessible Molecular Pathway Integrating Knowledge on Malignant Pleural Mesothelioma.Frontiers in oncology · 2022Article
- Ten simple rules for creating reusable pathway models for computational analysis and visualization.PLoS computational biology · 2021Article
- Pathway information extracted from 25 years of pathway figures.Genome biology · 2020Article
- Multifactorial Modes of Action of Arsenic Trioxide in Cancer Cells as Analyzed by Classical and Network Pharmacology.Frontiers in pharmacology · 2018Article
- Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform.F1000Research · 2018Article
- Predicted Role of NAD Utilization in the Control of Circadian Rhythms during DNA Damage Response.PLoS computational biology · 2015Article
- NetworkViewer: visualizing biochemical reaction networks with embedded rendering of molecular interaction rules.BMC systems biology · 2014Article
- SIRT1/PARP1 crosstalk: connecting DNA damage and metabolism.Genome integrity · 2013Article
- PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways.Bioinformatics (Oxford, England) · 2013Article
- Software support for SBGN maps: SBGN-ML and LibSBGN.Bioinformatics (Oxford, England) · 2012Article
- PathVisio-Validator: a rule-based validation plugin for graphical pathway notations.Bioinformatics (Oxford, England) · 2012Article
- Modeling formalisms in Systems Biology.AMB Express · 2011Article
- Guidelines for visualizing and annotating rule-based models.Molecular bioSystems · 2011Article
- PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs).Bioinformatics (Oxford, England) · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
backgroundThe Molecular Interaction Map (MIM) notation offers a standard set of symbols and rules on their usage for the depiction of cellular signaling network diagrams. Such diagrams are essential for disseminating biological information in a concise manner. A lack of software tools for the notation restricts wider usage of the notation. Development of software is facilitated by a more detailed specification regarding software requirements than has previously existed for the MIM notation.
resultsA formal implementation of the MIM notation was developed based on a core set of previously defined glyphs. This implementation provides a detailed specification of the properties of the elements of the MIM notation. Building upon this specification, a machine-readable format is provided as a standardized mechanism for the storage and exchange of MIM diagrams. This new format is accompanied by a Java-based application programming interface to help software developers to integrate MIM support into software projects. A validation mechanism is also provided to determine whether MIM datasets are in accordance with syntax rules provided by the new specification.
conclusionsThe work presented here provides key foundational components to promote software development for the MIM notation. These components will speed up the development of interoperable tools supporting the MIM notation and will aid in the translation of data stored in MIM diagrams to other standardized formats. Several projects utilizing this implementation of the notation are outlined herein. The MIM specification is available as an additional file to this publication. Source code, libraries, documentation, and examples are available at http://discover.nci.nih.gov/mim.
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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.