MiMiR – an integrated platform for microarray data sharing, mining and analysis

Additional File 1:

Stages of experimental information collection using the Online Annotation Tool. Experiment and sample information are collected using a series of online forms starting with an overview of the experiment (stages 1–4), followed by detailed information pertaining to organisms, arrays and samples (stages 5–7). Specific details of protocols used (stages 8–9) and Quality Control parameters (stages 10–12) are also collected. There are two key decision stages (stages 5 and 9) which determine the fields presented to users in subsequent stages.

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Additional File 2:

Example of context dependent stages in the Online Annotation Tool. Several stages in the data collection process are context dependent with specific compulsory fields being presented according to information provided in a previous step. For example, at stage 5 researchers define the type of array used which subsequently determines which corresponding labelling protocols and services are available and displayed in the dropdown at stage 9. The choice of one specific labelling protocol, in turn, determines the relevant Quality Control information to be collected at stage 10.

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Additional File 3:

Curation and Annotation tools user guide.

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Additional File 4:

Ethical framework for the supply of clinical data to the clinical part of MiMiR (cMiMiR) and subsequent data retrieval from researchers. Suppliers of microarray and clinical data, e.g. clinicians/researchers running a clinical trial with independent ethical approval, create and assign unique anonymisation keys (Level 4 pseudo-anonymised data) for each participating patient. All identifying information from the respective clinical record (e.g. name, address, date of birth) is removed before sending these records for storage into cMiMiR. A 'cMiMiR Supplier Agreement' between Suppliers and Custodians of cMiMiR covers the requirements and obligations of both parties regarding the import of clinical records into cMiMiR (Additional File 6). Researchers, designated "Subscribers", wishing to access data in cMiMiR for a particular project need to apply for Research Ethics Committee (REC) approval before they can be granted rights to access data (and be bound by the 'cMiMiR Subscriber Agreement', Additional File 7). Suppliers can collect and store additional information in cMiMiR for existing patients (e.g. treatment follow-up data) by updating the relevant cMiMiR record using the original anonymisation key. Trained annotators implement the updates to ensure consistency in annotation and quality and integrity of the data. Patients and volunteers involved in clinical projects have the right to withdraw their data from cMiMiR at any stage and without any justification. This is done by the Supplier who conducted the clinical trial and who holds the anonymisation key to the individual record. It is important to ensure that patients and volunteers participating in clinical trials are fully aware of the use of their anonymised clinical records for analysis by authorised researchers during the consent process. Clinical and genetic data derived from biological materials stored in licensed tissue banks are covered under standard consenting process. Prospective clinical trials explicitly consent all recruited participants using a 'cMiMiR consent form' (Additional File 8). For retrospective clinical microarray trials under present MREC guidelines, re-consent of participants is required if re-use and sharing of clinical and genetic information is not covered in the original trial consent protocol.

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Additional File 5:

Example of clinical information supplied by a clinical researcher (first three columns) and how it is codified using the Data Mapping Tool prior to import into MiMiR. Each concept must be explicitly mapped to unambiguous, uniquely identified terms. The Unified Medical Language System (UMLS version2007AB) which provides a Metathesaurus of clinical terms is used to provide the identifiers that are persisted within MiMiR.

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Additional File 6:

cMiMiR Supplier Agreement.

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Additional File 7:

cMiMiR Subscriber Agreement.

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Additional File 8:

cMiMiR Consent Form.

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Additional File 9:

cMiMiR Data Mapping Tool user guide and practical example.

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