The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)

Abstract

A large variety of molecular interactions occurs between biomolecular components in cells. When one or a cascade of molecular interactions results in a regulatory effect, by one component onto a downstream component, a so-called ‘causal interaction’ takes place. Causal interactions constitute the building blocks in our understanding of larger regulatory networks in cells. These causal interactions and the biological processes they enable (e.g., gene regulation) need to be described with a careful appreciation of molecular interactions that occur between entities. A proper description of this information enables archiving, sharing, and reuse by humans and for computational science. Various representations of causal relationships between biological components are currently used in a variety of resources. Here, we propose a checklist that accommodates current representations, and call it the Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). This checklist defines both the required core information, as well as a comprehensive set of other contextual details valuable to the end user and relevant for reusing and reproducing causal molecular interaction information. The MI2CAST checklist can be used as reporting guidelines when annotating and curating causal statements, while assuring uniformity and interoperability of the data across resources.

The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling

“…The utility of these various sources of causal interaction data holds room for improvement. Molecular causal interactions as such may be improved if producers adhere to the recently proposed Minimum Information about a Molecular Interaction Causal Statement (MI2CAST, [ 3 ]) guidelines, which guides curators to add a wide range of annotation details (see Table 2 ) that will significantly increase the utility of the information for logical modelers. MI2CAST has been proposed through the collaboration of scientific communities involved in causal representation (e.g.…”

“…the regulator) affects and changes a target entity (i.e. the regulated entity), in a specific context and with defined biological states of the entities [ 3 ]. For example, a protein can affect and regulate the expression of a gene, or it can regulate the activity of another protein or even its own activity (e.g.…”

The Status of Causality in Biological Databases for Logical Modeling: Data Resources and Data Retrieval Possibilities

“…The unification of the description of molecular causal interactions goes through agreed-on guidelines for scientists to lean on when producing, accessing or using causal statements. To this end, the Minimum Information about a Molecular Interaction Causal Statement (MI2CAST, see Table 2) [3] has been recently put in place through the collaboration of scientific communities involved in causal representation (e.g., NTNU, IMEx consortium, GREEKC consortium (http://greekc.org/), Swiss Bioinformatics Institute), which organized discussions between data curators, data providers and data users with the desire to improve and homogenize the curation of causal molecular interactions. The establishment of these guidelines encourages the communities (PSI-MITAB2.8, GO-CAM, BEL) to update data formats and curation protocols to comply with MI2CAST and offer better interoperability possibilities between resources supporting these formats.…”

“…Systems biology aspires to understand cellular behavior emerging from molecular mechanisms, and causality constitutes a key concept to clarify how biological entities interact and affect each other, and how they are implicated in cellular activities. A causal interaction is defined as a biological event where a source entity (i.e., the regulator) affects and changes a target entity (i.e., the regulated entity), in a certain context and with defined biological states of the entities [3]. For example, a protein can affect and regulate the expression of a gene; or it can regulate the activity of another protein or even its own activity (e.g., when a version of a protein stimulates the modification of itself into a different form, or by autocatalysis); or a miRNA can affect its target.…”

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

“…Recently, the Minimum Information about a Molecular Interaction Causal Statement (MI2CAST) has been developed to guide the curation of causal statements ( 1 ). The MI2CAST checklist serves as a framework for standardizing the production of high-quality causal interaction information, in several ways.…”