produce R2RML mappings for the BacDive database transformation to RDF

[javadch]

• [x] Choose the tables to be mapped
• [ ] Choose the ontology from #14
  1. • [ ] cell_morphology | 10 | morphology data like size/shape/gram stain and motility | ID_strains/ID_reference
  2. • [ ] colony_morphology | 10 | Colony shape and colour, incubation time, hemolysis | ID_strains/ID_reference
  3. • [ ] culture_pH | 10 | data on pH values | ID_strains/ID_reference
  4. • [ ] culture_temp | 10 | data on temperature values | ID_strains/ID_reference
  5. • [ ] halophily | 10 | halophilic data | ID_strains/ID_reference
  6. • [ ] strains | 10 | central table on strain data including species name, culture collection numbers, and type strain status
  7. • [ ] enzymes | 8 | data on enzyme activity | ID_strains/ID_reference
  8. • [ ] met_antibiotica | 8 | Antibiotica data | ID_strains/ID_reference
  9. • [ ] met_production | 8 | Metabolite production data | ID_strains/ID_reference
  10. • [ ] met_util | 8 | Metabolite utilization data | ID_strains/ID_reference
  11. • [ ] origin | 8 | data on the origin and enrichment of culture, sample type is the basis for the Isolation Source TAGS | ID_strains/ID_reference
  12. • [ ] oxygen_tolerance | 8 | data on oxygen relation | ID_strains/ID_reference
  13. • [ ] reference | 8 | Metadata for the references
  14. • [ ] risk_assessment | 8 | data on pathogenicity and risk assessment | ID_strains/ID_reference
  15. • [ ] spore_formation | 8 | data on spore formation ability of the bacteria | ID_strains/ID_reference
  16. • [ ] culture_medium | 7 | Medium data for cultivation, not standardized data | ID_strains/ID_reference
  17. • [ ] met_test | 7 | Metabolite test data: methyl red, Voges-Proskauer, Indole and Citrate | ID_strains/ID_reference
  18. • [ ] nutrition_type | 7 | Nutrition type, rather general data on the nutrition of a bacterium | ID_strains/ID_reference
  19. • [ ] GC_content | 6 | GC content of the DNA | ID_strains/ID_reference
  20. • [ ] multicellular_morphology | 6 | data on multicellular complex building ability, not standardized | ID_strains/ID_reference
  21. • [ ] pigmentation | 6 | data on pigmentation of the bacteria | ID_strains/ID_reference
  22. • [ ] sequence | 6 | metadata on sequences > might be split into Genome and 16S sequence in the near future | ID_strains/ID_reference
  23. • [ ] FA_meta | 5 | metadata for fatty acid profiles
  24. • [ ] FA_profile | 5 | fatty acid profiles, connect metadata with FK_FA_META >PK FA_meta | FK_FA_META/ID_strains/ID_reference
  25. • [ ] IS_cat1 | 5 | Vocabulary of the Isolation Source TAGS Cat1 (highest)
  26. • [ ] IS_cat2 | 5 | Vocabulary of the Isolation Source TAGS Cat2 (middle) | FK_Cat1 |  
  27. • [ ] IS_cat3 | 5 | Vocabulary of the Isolation Source TAGS Cat3 (lowest) | FK_Cat2 |  
  28. • [ ] IS_link | 5 | Isolation Source Tag data | Cat1_link/Cat2_link/Cat3_link/ID_strains/ID_origin
  29. • [ ] met_antibiogram | 4 | Antibiogram test data | ID_strains/ID_reference
  30. • [ ] met_antibiogram_meta | 4 | Metadata for antibiogram tests
  31. • [ ] murein | 4 | Murein (cell wall) data | ID_strains/ID_reference
  32. • [ ] tolerance | 4 | Data on tolerances against compounds, non standardized data | ID_strains/ID_reference
  33. • [ ] strain_history | 4 | data on the history of a strain | ID_strains/ID_reference
  34. • [ ] compound_production | 3 | not so well structured data on compound production, can be later moved to metabolite and enzyme tables | ID_strains/ID_reference
  35. • [ ] kit_api_20A | 3 | Test data from API 20A | ID_strains/ID_reference
  36. • [ ] kit_api_20A_meta | 3 | Metadata for API 20A
  37. • [ ] kit_api_20E | 3 | Test data from API 20E | ID_strains/ID_reference
  38. • [ ] kit_api_20E_meta | 3 | Metadata for API 20E
  39. • [ ] kit_api_20NE | 3 | Test data from API 20NE | ID_strains/ID_reference
  40. • [ ] kit_api_20NE_meta | 3 | Metadata for API 20NE
  41. • [ ] kit_api_20STR | 3 | Test data from API 20STR | ID_strains/ID_reference
  42. • [ ] kit_api_20STR_meta | 3 | Metadata for API 20STR
  43. • [ ] kit_api_50CHac | 3 | Test data from API 50CHac | ID_strains/ID_reference
  44. • [ ] kit_api_50CHac_meta | 3 | Metadata for API 50CHac
  45. • [ ] kit_api_50CHas | 3 | Test data from API 50CHas | ID_strains/ID_reference
  46. • [ ] kit_api_50CHas_meta | 3 | Metadata for API 50CHas
  47. • [ ] kit_api_CAM | 3 | Test data from API CAM | ID_strains/ID_reference
  48. • [ ] kit_api_CAM_meta | 3 | Metadata for API CAM
  49. • [ ] kit_api_coryne | 3 | Test data from API Coryne | ID_strains/ID_reference
  50. • [ ] kit_api_coryne_meta | 3 | Metadata for API Coryne
  51. • [ ] kit_api_ID32E | 3 | Test data from API ID32E | ID_strains/ID_reference
  52. • [ ] kit_api_ID32E_meta | 3 | Metadata for API ID32E
  53. • [ ] kit_api_ID32STA | 3 | Test data from API ID32STA | ID_strains/ID_reference
  54. • [ ] kit_api_ID32STA_meta | 3 | Metadata for API ID32STA
  55. • [ ] kit_api_LIST | 3 | Test data from API LIST | ID_strains/ID_reference
  56. • [ ] kit_api_LIST_meta | 3 | Metadata for API LIST
  57. • [ ] kit_api_NH | 3 | Test data from API NH | ID_strains/ID_reference
  58. • [ ] kit_api_NH_meta | 3 | Metadata for API NH
  59. • [ ] kit_api_rID32A | 3 | Test data from API rID32A | ID_strains/ID_reference
  60. • [ ] kit_api_rID32A_meta | 3 | Metadata for API rID32A
  61. • [ ] kit_api_rID32STR | 3 | Test data from API rID32STR | ID_strains/ID_reference
  62. • [ ] kit_api_rID32STR_meta | 3 | Metadata for API rID32STR
  63. • [ ] kit_api_STA | 3 | Test data from API STA | ID_strains/ID_reference
  64. • [ ] kit_api_STA_meta | 3 | Metadata for API STA
  65. • [ ] kit_api_zym | 3 | Test data from API ZYM | ID_strains/ID_reference
  66. • [ ] kit_api_zym_ec | 3 | Metadata for API ZYM
  67. • [ ] ncbi_all | 3 | Help table for matching to NCBI | ID_strains
  68. • [ ] observation | 3 | Unstructured, not standardized data that does not fit into other data fields | ID_strains/ID_reference
  69. • [ ] biosample | 2 | NCBI Biosample data | ID_strains
  70. • [ ] countries | 1 | help table for translating ISO/Country
  71. • [ ] culture_collection | 1 | help table for structuring and analysing culture collection numbers

[javadch]

dev continues on #24