VSM-box: General-purpose Interface for Biocuration and Knowledge Representation

Vercruysse, Steven; Zobolas, John; Touré, Vasundra; Andersen, Maria; Kuiper, Martin

doi:10.20944/preprints202007.0557.v1

Cited by 4 publications

(6 citation statements)

References 6 publications

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“…This is easily achieved by linking any dictionary to our reusable autocomplete web-component . UBDs can also be linked to a vsm-box ( Vercruysse et al, 2020 ) to build curation applications, like causalBuilder.…”

Section: Resultsmentioning

confidence: 99%

UniBioDicts: Unified access to Biological Dictionaries

et al. 2021

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Summary We present a set of software packages that provide uniform access to diverse biological vocabulary resources that are instrumental for current biocuration efforts and tools. The Unified Biological Dictionaries (UniBioDicts or UBDs) provide a single query-interface for accessing the online API services of leading biological data providers. Given a search string, UBDs return a list of matching term, identifier and metadata units from databases (e.g. UniProt), controlled vocabularies (e.g. PSI-MI) and ontologies (e.g. GO, via BioPortal). This functionality can be connected to input fields (user-interface components) that offer autocomplete lookup for these dictionaries. UBDs create a unified gateway for accessing life science concepts, helping curators find annotation terms across resources (based on descriptive metadata and unambiguous identifiers), and helping data users search and retrieve the right query terms. Availability and implementation The UBDs are available through npm and the code is available in the GitHub organisation UniBioDicts (https://github.com/UniBioDicts) under the Affero GPL license. Supplementary information Supplementary data are available at Bioinformatics online.

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Section: Resultsmentioning

confidence: 99%

UniBioDicts: Unified access to Biological Dictionaries

et al. 2021

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“…It is our hope that the causalBuilder example may inspire managers of curation projects to deploy the vsm-box in their curation platform, to allow their curators to benefit from the ease and flexibility of the VSM technology. The availability of the vsm-box resource ( https://github.com/vsm/vsm-box ( 8 )) facilitates the development of dedicated VSM-template annotation entry interfaces customized to the needs of various curation projects.…”

Section: Discussionmentioning

confidence: 99%

“…VSM represents information in a form that is both intuitive for curators and semantically precise for computer processing. It uses an elementary conceptual model, combined with a general-purpose user interface, called ‘vsm-box’ ( https://github.com/vsm/vsm-box ( 8 ), with lowercase ‘vsm’ as per JavaScript module naming convention). A vsm-box is a sophisticated input-component that can be embedded in a web page.…”

Section: Introductionmentioning

confidence: 99%

CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator

et al. 2021

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Molecular causal interactions are defined as regulatory connections between biological components. They are commonly retrieved from biological experiments and can be used for connecting biological molecules together to enable the building of regulatory computational models that represent biological systems. However, including a molecular causal interaction in a model requires assessing its relevance to that model, based on the detailed knowledge about the biomolecules, interaction type and biological context. In order to standardize the representation of this knowledge in ‘causal statements’, we recently developed the Minimum Information about a Molecular Interaction Causal Statement (MI2CAST) guidelines. Here, we introduce causalBuilder: an intuitive web-based curation interface for the annotation of molecular causal interactions that comply with the MI2CAST standard. The causalBuilder prototype essentially embeds the MI2CAST curation guidelines in its interface and makes its rules easy to follow by a curator. In addition, causalBuilder serves as an original application of the Visual Syntax Method general-purpose curation technology and provides both curators and tool developers with an interface that can be fully configured to allow focusing on selected MI2CAST concepts to annotate. After the information is entered, the causalBuilder prototype produces genuine causal statements that can be exported in different formats.

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“…Here we describe the design of both this method and its supporting UI. Applications, software, and links to existing technology are detailed in separate papers [31][32][33][34] . The examples assume the availability of dictionaries (=controlled vocabularies, CVs) that provide a term+ID for each shown VSM-term.…”

Section: Solutionmentioning

confidence: 99%

“…This VSM-box input-component holds one VSMsentence ( Fig. 1) and should be embedded in other software, like a web page 32 .…”

Section: Vsm As a User Interfacementioning

confidence: 99%

Intuitive Representation of Knowledge in Computable Form

Vercruysse¹,

Kuiper²

2020

Preprint

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Scientific progress is increasingly dependent on knowledge in computation-ready forms. In the life sciences, among others, many scientists carefully extract and structure knowledge from the scientific literature. In a process called manual curation, they enter knowledge into spreadsheets, or into databases where it serves their and many others' research. Valuable as these curation efforts are, the range and detail of what can practically be captured and shared remains limited, because of the constraints of current curation tools. Many important contextual aspects of observations described in literature simply do not fit in the form defined by these tools, and thus cannot be captured. Here we present the design of an easy-to-use, general-purpose method and interface, that enables the precise semantic capture of virtually unlimited types of information and details, using only a minimal set of building blocks. Scientists from any discipline can use this to convert any complex knowledge into a form that is easily readable and meaningful for both humans and computers. The method VSM forms a universal and high-level language for encoding ideas, and for interacting with digital knowledge.

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VSM-box: General-purpose Interface for Biocuration and Knowledge Representation

Cited by 4 publications

References 6 publications

UniBioDicts: Unified access to Biological Dictionaries

UniBioDicts: Unified access to Biological Dictionaries

CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator

Intuitive Representation of Knowledge in Computable Form

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