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MIABIS SAMPLE TAB Format

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José Villaveces edited this page Jul 28, 2015 · 5 revisions

Introduction

The MIABIS SAMPLE TAB format describes samples, one sample per row. Columns are separated by tabulations.

Column definitions

The column contents should be as follows:

  1. Sample ID, Unique ID of the sample within a sample collection, often represented by the sample barcode; text identifier, recommendation maximum 30 characters. It corresponds to the field [MIABIS-39] (https://github.com/MIABIS/miabis/wiki/Data-describing-Sample).
  2. Parent sample ID, Unique ID within a sample collection of a parent sample. Only if the sample has a parent sample i.e. if the sample itself is an aliquot or a derivative from another sample. It corresponds to the field [MIABIS-40] (https://github.com/MIABIS/miabis/wiki/Data-describing-Sample).
  3. Material type, The biospecimen type saved from a biological entity for testing, diagnostic, propagation, treatment or research purposes. It corresponds to the field [MIABIS-41] (https://github.com/MIABIS/miabis/wiki/Data-describing-Sample) and can only take one of the values defined here.
  4. Storage Temperature, The long term storage temperature at which the samples are stored after preparation. It corresponds to the field [MIABIS-42] (https://github.com/MIABIS/miabis/wiki/Data-describing-Sample) and can only take one of the values defined here.
  5. Sampled Time, The time when the sample is taken according to ISO 8601 i.e. YYYYMMDDThhmm. It corresponds to the field [MIABIS-43] (https://github.com/MIABIS/miabis/wiki/Data-describing-Sample).
  6. Anatomical site, The anatomical position of the body where the solid sample was taken from. [MIABIS-44] (https://github.com/MIABIS/miabis/wiki/Data-describing-Sample). It is composed by several fields separated by "," in the following way: id,ontology_name,version,code,description. e.g. EFO:0000815,Experimental Factor Ontology (EFO),2.62,EFO,A myogenic muscular organ found in the cardiovascular system.
  7. Biobank ID, Textual string of letters starting with the country code (according to standard ISO1366 alpha2) followed by the underscore “_” and post-fixed by a biobank ID or name specified by its juristic person (nationally specific). It corresponds to the field [MIABIS-01] (https://github.com/MIABIS/miabis/wiki/Data-describing-Biobank).
  8. Biobank Acronym, Textual string of short name in use for the biobank. If applicable. It corresponds to the field [MIABIS-02] (https://github.com/MIABIS/miabis/wiki/Data-describing-Biobank).
  9. Biobank Name, Textual string of letters denoting the name of the biobank in English. It corresponds to the field [MIABIS-03] (https://github.com/MIABIS/miabis/wiki/Data-describing-Biobank).
  10. Biobank URL, It corresponds to the field [MIABIS-04] (https://github.com/MIABIS/miabis/wiki/Data-describing-Biobank).
  11. Biobank Juristic Person, Textual string of letters denoting the juristic person e.g. a university, concern, county council etc. for the biobank. It corresponds to the field [MIABIS-05] (https://github.com/MIABIS/miabis/wiki/Data-describing-Biobank).
  12. Biobank Contact Information, Contact information for the contact person of the biobank. It corresponds to the field [MIABIS-07] (https://github.com/MIABIS/miabis/wiki/Data-describing-Biobank). It is composed by several fields separated by "," in the following way: id,first_name,last_name,phone,email,address,zip_code,city,country. e.g. 1,Sherlock,Holmes,,sherlock@london.com,221B Baker Street,82152,London,UK.
  13. Biobank Description, Textual string of letters with a description about the biobank in English. It corresponds to the field [MIABIS-06] (https://github.com/MIABIS/miabis/wiki/Data-describing-Biobank).
  14. Biobank Country, ISO-standard (3166 alpha2), two letter code for the country of the biobank. It corresponds to the field [MIABIS-08] (https://github.com/MIABIS/miabis/wiki/Data-describing-Biobank).
  15. Sample Collection ID, Sample Collection ID that also links the sample collection to the hosting biobank or study. It corresponds to the field [MIABIS-01] (https://github.com/MIABIS/miabis/wiki/Data-describing-Sample-Collection).
  16. Sample Collection Acronym, Short name in use for the sample collection. It corresponds to the field [MIABIS-02] (https://github.com/MIABIS/miabis/wiki/Data-describing-Sample-Collection).
  17. Sample Collection Name, The name of the sample collection in english. It corresponds to the field [MIABIS-03] (https://github.com/MIABIS/miabis/wiki/Data-describing-Sample-Collection).
  18. Sample Collection Description, A description of the sample collection. Recommendation max. 2000 char. It corresponds to the field [MIABIS-08] (https://github.com/MIABIS/miabis/wiki/Data-describing-Sample-Collection).
  19. Sample Collection Sex, The sex of the individuals in the sample collection. Can be one or more of the following values: Male, Female, Unknown, Undiferrentiated. It corresponds to the field [MIABIS-09] (https://github.com/MIABIS/miabis/wiki/Data-describing-Sample-Collection). Multiple values are separated by "|".
  20. Sample Collection Age Low, Age of youngest sample donor at time of sample donation. It corresponds to the field [MIABIS-10] (https://github.com/MIABIS/miabis/wiki/Data-describing-Sample-Collection).
  21. Sample Collection Age High, Age of oldest sample donor at time of sample donation. It corresponds to the field [MIABIS-11] (https://github.com/MIABIS/miabis/wiki/Data-describing-Sample-Collection).
  22. Sample Collection Age Unit, Unit defining Age Low and Age High. Can be one of the following values: years, months, weeks, days. It corresponds to the field [MIABIS-12] (https://github.com/MIABIS/miabis/wiki/Data-describing-Sample-Collection).
  23. Sample Collection Data Category, The data categories from which data is available. It must be one of the following values: Survey data, Imaging data, Medical records, National registries, Genealogical records, Physiological/Biochemical, Other. It corresponds to the field MIABIS-13. Multiple values are separated by "|".
  24. Sample Collection Collection type, The type of the sample collection. Can be one of the following values: Case-control, Cohort, Cross-sectional, Longitudinal, Twin-study, Quality control, Population-based, Disease specific, Birth cohort, Other. It corresponds to the field [MIABIS-16] (https://github.com/MIABIS/miabis/wiki/Data-describing-Sample-Collection). Multiple values are separated by "|".
  25. Sample Collection Disease, The disease of main interest in the sample collection, if any. It corresponds to the field [MIABIS-17] (https://github.com/MIABIS/miabis/wiki/Data-describing-Sample-Collection) and is composed by several fields separated by "," in the following way: id,ontology_name,version,code,description,free_text. Multiple values are separated by "|".
  26. Sample Collection Contact information, Contact information for the contact person of the sample collection. It corresponds to the field [MIABIS-07] (https://github.com/MIABIS/miabis/wiki/Data-describing-Sample-Collection). It is composed by several fields separated by "," in the following way: id,first_name,last_name,phone,email,address,zip_code,city,country. Multiple values are separated by "|".
  27. Study ID, Contact information for the contact person of the sample collection. It corresponds to the field [MIABIS-01] (https://github.com/MIABIS/miabis/wiki/Data-describing-Study).
  28. Study Name, The name of the study in english. It corresponds to the field [MIABIS-03] (https://github.com/MIABIS/miabis/wiki/Data-describing-Study).
  29. Study Description, A description of the study. Recommendation max. 2000 char. It corresponds to the field [MIABIS-08] (https://github.com/MIABIS/miabis/wiki/Data-describing-Study).
  30. Study Principal Investigator, The name of the person responsible for the study. It corresponds to the field [MIABIS-18] (https://github.com/MIABIS/miabis/wiki/Data-describing-Study).
  31. Study Contact Information, Contact information for the contact person of the biobank. It corresponds to the field [MIABIS-07] (https://github.com/MIABIS/miabis/wiki/Data-describing-Study). It is composed by several fields separated by "," in the following way: id,first_name,last_name,phone,email,address,zip_code,city,country. e.g. 1,Sherlock,Holmes,,sherlock@london.com,221B Baker Street,82152,London,UK.
  32. Study Design, The design of the study. Can be one or more of the following values: Case-control, Cohort, Cross-sectional, Longitudinal, Twin-study, Quality control, Population-based, Disease specific, Birth cohort, Other It corresponds to the field MIABIS-19. Multiple values are separated by "|".
  33. Study Collection Sex, The sex of the individuals in the sample study. Can be one or more of the following values: Male, Female, Unknown, Undiferrentiated. It corresponds to the field [MIABIS-09] (https://github.com/MIABIS/miabis/wiki/Data-describing-Study). Multiple values are separated by "|".
  34. Study Age Low, Age of youngest sample donor at time of sample donation. It corresponds to the field [MIABIS-10] (https://github.com/MIABIS/miabis/wiki/Data-describing-Study).
  35. Study Age High, Age of oldest sample donor at time of sample donation. It corresponds to the field [MIABIS-11] (https://github.com/MIABIS/miabis/wiki/Data-describing-Study).
  36. Study Age Unit, Unit defining Age Low and Age High. Can be one of the following values: years, months, weeks, days. It corresponds to the field [MIABIS-12] (https://github.com/MIABIS/miabis/wiki/Data-describing-Study).
  37. Study Data Category, The data categories from which data is available. It must be one of the following values: Survey data, Imaging data, Medical records, National registries, Genealogical records, Physiological/Biochemical, Other. It corresponds to the field [MIABIS-13]. (https://github.com/MIABIS/miabis/wiki/Data-describing-Sample-Collection). Multiple values are separated by "|".
  38. Study Total Number of Participants, Total number of individuals recruited for the study. It corresponds to the field [MIABIS-20] (https://github.com/MIABIS/miabis/wiki/Data-describing-Study).(https://github.com/MIABIS/miabis/wiki/Data-describing-Sample-Collection). Multiple values are separated by "|".
  39. Study Total Number of Donors, Total number of individuals with biological samples in the study. It corresponds to the field [MIABIS-21] (https://github.com/MIABIS/miabis/wiki/Data-describing-Study).
  40. Study Inclusion Criteria, Information on type of parameters that determine which individuals will become study participants. 2000 char. It corresponds to the field [MIABIS-22] (https://github.com/MIABIS/miabis/wiki/Data-describing-Study).
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