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The Da Vinci European BioBank: A Metabolomics-Driven Infrastructure.

Carotenuto D, Luchinat C, Marcon G, Rosato A, Turano P - J Pers Med (2015)

Bottom Line: We present here the organization of the recently-constituted da Vinci European BioBank (daVEB, https://www.davincieuropeanbiobank.org/it).The biobank was created as an infrastructure to support the activities of the Fiorgen Foundation (http://www.fiorgen.net/), a nonprofit organization that promotes research in the field of pharmacogenomics and personalized medicine.The way operating procedures concerning samples and data have been developed at daVEB largely stems from the strong metabolomics connotation of Fiorgen and from the involvement of the scientific collaborators of the foundation in international/European projects aimed to tackle the standardization of pre-analytical procedures and the promotion of data standards in metabolomics.

View Article: PubMed Central - PubMed

Affiliation: Da Vinci European BioBank, FiorGen Foundation, via Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy. dario.carotenuto@gmail.com.

ABSTRACT
We present here the organization of the recently-constituted da Vinci European BioBank (daVEB, https://www.davincieuropeanbiobank.org/it). The biobank was created as an infrastructure to support the activities of the Fiorgen Foundation (http://www.fiorgen.net/), a nonprofit organization that promotes research in the field of pharmacogenomics and personalized medicine. The way operating procedures concerning samples and data have been developed at daVEB largely stems from the strong metabolomics connotation of Fiorgen and from the involvement of the scientific collaborators of the foundation in international/European projects aimed to tackle the standardization of pre-analytical procedures and the promotion of data standards in metabolomics.

No MeSH data available.


Example of first-level daVEB metadata table.
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jpm-05-00107-f003: Example of first-level daVEB metadata table.

Mentions: The meaning of the fields in a table such as that of Figure 2 is defined in higher-level metadata table, as shown in Figure 3. Such table contains the definition of the metadata associated to each collection of the daVEB biobank. This is done by defining for each field of the data table of the collection the name of the field, its reference to a specific ontology, and the type of data (numeric, string, link, etc.) that can be associated to each field (see Figure 3). Each record of the metadata table corresponds to a specific field (defined by the combination of TableRef and FieldRef fields). The OntoRef field indicates the ontology used for that particular field of the data table, which can be an internally defined ontology or a public reference ontology. The reference used for the field is indicated by the DataRef field, whereas the allowed data type is defined by the daVEBDescr field. Each data type, as mentioned, can be a single instance field, e.g., “Coeliac Disease”, or a type set. If the ontology used is an external one, then the DataRef field can point directly to external RESTful ontology, as shown in the example. This allows the unequivocal definition of the term “Coeliac Disease”. However, it is possible to use multiple ontologies, if necessary, by providing multiple records for each term, with pointers to the appropriate external vocabularies.


The Da Vinci European BioBank: A Metabolomics-Driven Infrastructure.

Carotenuto D, Luchinat C, Marcon G, Rosato A, Turano P - J Pers Med (2015)

Example of first-level daVEB metadata table.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4493490&req=5

jpm-05-00107-f003: Example of first-level daVEB metadata table.
Mentions: The meaning of the fields in a table such as that of Figure 2 is defined in higher-level metadata table, as shown in Figure 3. Such table contains the definition of the metadata associated to each collection of the daVEB biobank. This is done by defining for each field of the data table of the collection the name of the field, its reference to a specific ontology, and the type of data (numeric, string, link, etc.) that can be associated to each field (see Figure 3). Each record of the metadata table corresponds to a specific field (defined by the combination of TableRef and FieldRef fields). The OntoRef field indicates the ontology used for that particular field of the data table, which can be an internally defined ontology or a public reference ontology. The reference used for the field is indicated by the DataRef field, whereas the allowed data type is defined by the daVEBDescr field. Each data type, as mentioned, can be a single instance field, e.g., “Coeliac Disease”, or a type set. If the ontology used is an external one, then the DataRef field can point directly to external RESTful ontology, as shown in the example. This allows the unequivocal definition of the term “Coeliac Disease”. However, it is possible to use multiple ontologies, if necessary, by providing multiple records for each term, with pointers to the appropriate external vocabularies.

Bottom Line: We present here the organization of the recently-constituted da Vinci European BioBank (daVEB, https://www.davincieuropeanbiobank.org/it).The biobank was created as an infrastructure to support the activities of the Fiorgen Foundation (http://www.fiorgen.net/), a nonprofit organization that promotes research in the field of pharmacogenomics and personalized medicine.The way operating procedures concerning samples and data have been developed at daVEB largely stems from the strong metabolomics connotation of Fiorgen and from the involvement of the scientific collaborators of the foundation in international/European projects aimed to tackle the standardization of pre-analytical procedures and the promotion of data standards in metabolomics.

View Article: PubMed Central - PubMed

Affiliation: Da Vinci European BioBank, FiorGen Foundation, via Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy. dario.carotenuto@gmail.com.

ABSTRACT
We present here the organization of the recently-constituted da Vinci European BioBank (daVEB, https://www.davincieuropeanbiobank.org/it). The biobank was created as an infrastructure to support the activities of the Fiorgen Foundation (http://www.fiorgen.net/), a nonprofit organization that promotes research in the field of pharmacogenomics and personalized medicine. The way operating procedures concerning samples and data have been developed at daVEB largely stems from the strong metabolomics connotation of Fiorgen and from the involvement of the scientific collaborators of the foundation in international/European projects aimed to tackle the standardization of pre-analytical procedures and the promotion of data standards in metabolomics.

No MeSH data available.