Basic concepts

To properly manage all the data and experimental procedures, the LAS identifies several types of entities and defines a predefined set of possible relationships among them.

The entity types are the following:

  • Patient. This entity is the person that signed an Informed Consent to allow the collection of specimens for research purposes.

  • IC. It represents the signed Informed Consent for a Study. Without a signed IC it is not possible to collect specimens and information about the patient.

  • Study. The study can be for instance a clinical trial or a research study approved by one or more institutions. Each study has a set of associated rules that define the constraints to collect biological samples and perform research experiments.

  • Collection. It represents the collector of several specimens sharing homogeneous source/event characteristics. For instance, a collection can pertain to all the tissues collected from one patient following a surgical intervention. Different surgical interventions of the same patient are usually mapped in separated collections.

  • Aliquot. The collected specimens are splitted in aliquots according to their intrinsic characteristics. Several kind of aliquots are managed by the system (e.g, viable, RNALater, SNAP Frozen). According to the characteristics of the aliquots and the purpose of the research study, different operations can be performed: (i) storage in dedicated containers, (ii) extraction of derived aliquots (e.g., DNA, RNA), and (iii) implantation in immunocompromised animals (i.e., xenografts) or (iv) derivation of cell lines.

  • Biomouse. It represents the join of one implanted aliquot and one mouse animal. If different aliquots are implanted in the same physical mouse in different sites, different biomice are generated.

  • CellLine. This entity represents in vitro experiments. Cell lines can be generated from viable aliquots by means of generation and thawing process, or from other cells by means of expansion procedures.

Each collection and biological entity (i.e., Aliquot, Biomouse, CellLine) is identified by an unique and mnemonic key, named GenealogyID, that encodes relevant information regarding the history of the entity. This is automatically generated through formal rules by the LAS platform. The first part of the GeneaologyID (untile the instance ID field) is focused on summarizing information about the ancestors of the bioentity, while the last part is used to specify some specific features of the current bioentity (e.g., aliquot type for Aliquots, implant site for Biomice).

The relationships among the LAS entities can be represented by a graph. It possible to notice that one patient can generates more than one collection by means of the same Informed Consent and different IC of different studies. Each collection can be composed by different aliquot types and several instances of the same aliquot type. If a viable specimen is implanted in animals it generates one or several biomice. The biomice of the first passage are labeled also by a different lineage identifier. Each biomouse can generate aliquots that can be implanted in other animals to generate biomice of second passage. The implantation/explantation process can be repeated several times according to the purpose of the research study. The Viable aliquots can be also used to generates Cell Lines that can be expanded and/or archived to generate other generations.

All these relationships are stored in a graph database, while the detailed information of each entity and the description of the procedure applied are collected in relational database. A non relational database is instead exploited to store complex data and instrumental documents.