Guidelines for managing data and processes in bone and cartilage tissue engineering

Abstract

Background: In the last decades, a wide number of researchers/clinicians involved in tissue engineering field published several works about the possibility to induce a tissue regeneration guided by the use of biomaterials. To this aim, different scaffolds have been proposed, and their effectiveness tested through in vitro and/or in vivo experiments. In this context, integration and meta-analysis approaches are gaining importance for analyses and reuse of data as, for example, those concerning the bone and cartilage biomarkers, the biomolecular factors intervening in cell differentiation and growth, the morphology and the biomechanical performance of a neo-formed tissue, and, in general, the scaffolds' ability to promote tissue regeneration. Therefore standards and ontologies are becoming crucial, to provide a unifying knowledge framework for annotating data and supporting the semantic integration and the unambiguous interpretation of novel experimental results.

Results: In this paper a conceptual framework has been designed for bone/cartilage tissue engineering domain, by now completely lacking standardized methods. A set of guidelines has been provided, defining the minimum information set necessary for describing an experimental study involved in bone and cartilage regenerative medicine field. In addition, a Bone/Cartilage Tissue Engineering Ontology (BCTEO) has been developed to provide a representation of the domain's concepts, specifically oriented to cells, and chemical composition, morphology, physical characterization of biomaterials involved in bone/cartilage tissue engineering research.

Conclusions: Considering that tissue engineering is a discipline that traverses different semantic fields and employs many data types, the proposed instruments represent a first attempt to standardize the domain knowledge and can provide a suitable means to integrate data across the field.

Figure 1

Simplified schema of the bone/cartilage tissue engineering approach. Cells extracted from a donor tissue are expanded and seeded in a biomaterial. Tissue growth (and cell differentiation, if starting from stem cells) can be evaluated either in vitro or in vivo. In the latter case, implant can be in ectopic or orthotopic mode, depending on the size of the model organism and the necessity to evaluate the biomechanical stress on the tissue.

Figure 2

Partial hierarchical overview of BCTEO ontology. It was created with OBO-Edit software. A relation, represented as an arrow, links each term to its parent. Exploited relations are: is_a (I), characterizes, intervenes_in, part_of (P), derives_from.

Figure 3

Relation between BCTEO and other biomedical ontologies. Domain main concepts (Biomaterial, Experiment, Organism, Tissue, Cellular Response) are shown associated to the external ontologies through the evidenced relations.

Figure 4

Distribution of the mean scores obtained by survey's questions. The whole set of questions obtained a mean score widely upper than the sufficiency (represented by score 3.0). On the basis of the mean score different guidelines' aspects are flagged as optional (to distinguish to the other, that are mandatory by default). None of the proposed aspects has been recognized as useless.