ArticleBMC genomics2025
SyBValS: a validation and error resolution service for biological pathway maps.
Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
What it found
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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.
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Who cites it
0 citing papers in PubMed.
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEffective visualization of relational data is essential for thorough analysis, including in biological research. Annotating and depicting biological models in universally recognized formats is essential. Additionally, uncovering graph-theoretical characteristics within pathways and pinpointing specific paths or subgraphs within them are vital aspects of pathway data analysis. Standard formats such as SBGN impose stringent rules regarding the interaction among biological entities. However, many users tend to overlook or disregard these rules, resulting in the need to rectify them to ensure the validity of the map model.
resultsIn response to this issue, we developed a web service called SyBValS. SyBValS begins by validating a pathway in SBGN process description format. Any encountered errors are documented along with relevant explanations and color-coded on an automatically laid out and generated map. If preferred, SyBValS can endeavor to rectify these errors whenever feasible, updating both the error list and the corresponding map image accordingly. AVAILABILITY: SyBValS is open-source, available on GitHub , and distributed freely under the MIT license. Additionally, a sample deployment is accessible here for public use.
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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.