The MIRRI Information System (MIRRI-IS)
The MIRRI Information System (MIRR-IS) is the reference database and analysis platform of the Microbial Resources Research Infrastructure (MIRRI). It includes data from catalogues of partner Culture Collections (CCs) plus reference taxonomy databases and software tools for phylogenomic analysis of microorganisms collected and characterized by CCs.
In order to integrate all catalogues into one database, CCs have agreed on shared specifications of relevant information for the different resource types. Guidelines including a description of the datasets have therefore been approved and published. CCs have finally submitted the data of their catalogues according to the shared specifications.
Format of MIRRI-IS specifications
Information included in one of the MIRRI-IS specifications is described on the basis of the following data:
- Name: the name assigned to the information
- Description: a description of the meaning and contents of the information
- Syntax: the syntax of the information, including e.g. its type and syntactic components. Not all information has an associated syntax.
- Values: the values allowed for the information, or a link to a reference list or nomenclature or ontology. Not all information has a restricted list of allowed values, e.g. free text information.
- Validation: the list of actions carried out by MIRRI in order to validate the information.
- Examples: some examples of valid data for the information.
Specifications for plasmids and for viruses also include the following data:
- Short name: a simplified version of the name, usually a single term following the camel format.
- Correspondence with Guidelines for microorganisms: specifies whether the information is also available in the specifications for microorganisms and the relative name.
Mandatory and non-mandatory information
At present, only some of the information included in the specifications are mandatory and they are highlighted in the specifications. MIRRI-IS will discard records missing mandatory data fields. All other data fields are strongly recommended and collections are invited to submit all data they have. The presence or absence of some non-mandatory information is a criterium for defining the quality of the submitted data and for ordering results of user queries.
Results of queries carried out on the MIRRI-IS integrated catalog will therefore be sorted by relevance first and then by completeness of data. A list of non-mandatory fields which are used for sorting results, have been defined for each resource type.
MIRRI-IS data specifications
Here, we report the list of approved documents as a reference for users willing to link their information systems to the MIRRI-IS through its APIs.
Microbial strains (archaea, bacteria, yeasts, filamentous fungi, microalgae)
- Specifications (version 3, 2022-04-07)
- Guide to create an Excel file for uploading data (version 2, 2020-06-01)
- Excel template (version 3, 2022-04-07)
- Data exchange format (JSON)
- Web Services (APIs)
- Dataverse platform