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

ABSTRACT: 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.

SUBMITTER: Toure V

PROVIDER: S-EPMC7904049 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Gold-standard annotated corpora have become important resources for the training and testing of natural-language-processing (NLP) systems designed to support biocuration efforts, and ontologies are increasingly used to facilitate curational consistency and semantic integration across disparate resources. Bringing together the respective power of these, the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of full-length, open-access biomedical journal articles with extensive manually created syntactic, formatting and semantic markup, was previously created and released. This initial public release has already been used in multiple projects to drive development of systems focused on a variety of biocuration, search, visualization, and semantic and syntactic NLP tasks. Building on its demonstrated utility, we have expanded the CRAFT Corpus with a large set of manually created semantic annotations relying on Uberon, an ontology representing anatomical entities and life-cycle stages of multicellular organisms across species as well as types of multicellular organisms defined in terms of life-cycle stage and sexual characteristics. This newly created set of annotations, which has been added for v2.1 of the corpus, is by far the largest publicly available collection of gold-standard anatomical markup and is the first large-scale effort at manual markup of biomedical text relying on the entirety of an anatomical terminology, as opposed to annotation with a small number of high-level anatomical categories, as performed in previous corpora. In addition to presenting and discussing this newly available resource, we apply it to provide a performance baseline for the automatic annotation of anatomical concepts in biomedical text using a prominent concept recognition system. The full corpus, released with a CC BY 3.0 license, may be downloaded from http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml. Database URL: http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml.

Dataset Information

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

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