Despite the maturity of commercial graph databases, little consensus has been reached so far on the standardization of data definition languages (DDLs) for property graphs (PG). The discussion on the characteristics of PG schemas is ongoing in many standardization and community groups. Although some basic aspects of a schema are already present in Neo4j 3.5, like in most commercial graph databases, full support is missing allowing to constraint property graphs with more or less flexibility.In this paper, we focus on two different perspectives from which a PG schema should be considered, as being descriptive or prescriptive, and we show how it would be possible to switch from one to another as the application under development gains more stability. Apart from proposing concise schema DDL inspired by Cypher syntax, we show how schema validation can be enforced through homomorphisms between PG schemas and PG instances; and how schema evolution can be described through the use of graph rewriting operations. Our prototypical implementation demonstrates feasibility and shows the need of offering high-level query primitives to accommodate flexible graph schema requirements as showcased in our work. * Currently on leave at the University of Waterloo, Canada.

The fast accumulation of biological data calls for their integration, analysis and exploitation through more systematic approaches. The generation of novel, relevant hypotheses from this enormous quantity of data remains challenging. Logical models have long been used to answer a variety of questions regarding the dynamical behaviours of regulatory networks. As the number of published logical models increases, there is a pressing need for systematic model annotation, referencing and curation in community-supported and standardised formats. This article summarises the key topics and future directions of a meeting entitled ‘Annotation and curation of computational models in biology’, organised as part of the 2019 [BC]2 conference. The purpose of the meeting was to develop and drive forward a plan towards the standardised annotation of logical models, review and connect various ongoing projects of experts from different communities involved in the modelling and annotation of molecular biological entities, interactions, pathways and models. This article defines a roadmap towards the annotation and curation of logical models, including milestones for best practices and minimum standard requirements.

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The general question of what constitutes bio-curation for rule-based modelling of cellular signalling is posed. A general approach to the problem is presented, based on rewriting in hierarchies of graphs, together with a specific instantiation of the methodology that addresses our particular bio-curation problem. The current state of the ongoing development of the KAMI bio-curation tool, based on this approach, is outlined along with our plans for future development.