toxbank-investigation 0.0.1pre-x86-linux

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  1. data/.gitignore +11 -0
  2. data/Gemfile +7 -0
  3. data/Gemfile.lock +101 -0
  4. data/LICENSE +674 -0
  5. data/README +14 -0
  6. data/Rakefile +31 -0
  7. data/application.rb +246 -0
  8. data/bin/toxbank-investigation-install +76 -0
  9. data/config/production.rb +9 -0
  10. data/config.ru +5 -0
  11. data/java/config/isa_configurator/cellcount_flowcytometry.xml +1 -0
  12. data/java/config/isa_configurator/cellsorting_flowcyt.xml +5 -0
  13. data/java/config/isa_configurator/clinical_chemistry.xml +1 -0
  14. data/java/config/isa_configurator/copynumvariation_micro.xml +1 -0
  15. data/java/config/isa_configurator/dnamethylation_micro.xml +1 -0
  16. data/java/config/isa_configurator/dnamethylation_seq.xml +1 -0
  17. data/java/config/isa_configurator/envgen_survey_seq.xml +1 -0
  18. data/java/config/isa_configurator/genome_seq.xml +1 -0
  19. data/java/config/isa_configurator/hematology.xml +1 -0
  20. data/java/config/isa_configurator/heterozygosity_micro.xml +1 -0
  21. data/java/config/isa_configurator/histology.xml +1 -0
  22. data/java/config/isa_configurator/histonemodification_seq.xml +1 -0
  23. data/java/config/isa_configurator/metaboliteprofiling_ms.xml +114 -0
  24. data/java/config/isa_configurator/metaboliteprofiling_nmr.xml +114 -0
  25. data/java/config/isa_configurator/metagenome_seq.xml +1 -0
  26. data/java/config/isa_configurator/nru_assay.xml +8 -0
  27. data/java/config/isa_configurator/ppi_detection_micro.xml +1 -0
  28. data/java/config/isa_configurator/protein_dna_binding_ident_micro.xml +1 -0
  29. data/java/config/isa_configurator/protein_dna_binding_ident_seq.xml +1 -0
  30. data/java/config/isa_configurator/protein_expression_ge.xml +101 -0
  31. data/java/config/isa_configurator/protein_expression_micro.xml +1 -0
  32. data/java/config/isa_configurator/protein_expression_ms.xml +1 -0
  33. data/java/config/isa_configurator/proteinident_ms.xml +1 -0
  34. data/java/config/isa_configurator/snpanalysis_micro.xml +1 -0
  35. data/java/config/isa_configurator/studySample.xml +1 -0
  36. data/java/config/isa_configurator/tfbsident_micro.xml +1 -0
  37. data/java/config/isa_configurator/tfbsident_seq.xml +1 -0
  38. data/java/config/isa_configurator/transcription_micro.xml +1 -0
  39. data/java/config/isa_configurator/transcription_rtpcr.xml +1 -0
  40. data/java/config/isa_configurator/transcription_seq.xml +6 -0
  41. data/test/Rakefile +48 -0
  42. data/test/all.rb +3 -0
  43. data/test/authorization.rb +112 -0
  44. data/test/basic_rest.rb +98 -0
  45. data/test/data/invalid/BII-invalid.n3 +19641 -0
  46. data/test/data/invalid/a_TB-ACCUTOX-plate1.txt +97 -0
  47. data/test/data/invalid/a_TB-ACCUTOX-plate2.txt +97 -0
  48. data/test/data/invalid/a_TB-ACCUTOX-plate3.txt +97 -0
  49. data/test/data/invalid/acetaminophen-plate1-data.txt +97 -0
  50. data/test/data/invalid/acetaminophen-plate2-data.txt +97 -0
  51. data/test/data/invalid/acetaminophen-plate3-data.txt +97 -0
  52. data/test/data/invalid/i_Investigation.txt +156 -0
  53. data/test/data/invalid/ic50.txt +20 -0
  54. data/test/data/invalid/isa_TB_ACCUTOX.xls +0 -0
  55. data/test/data/invalid/isa_TB_ACCUTOX.zip +0 -0
  56. data/test/data/invalid/s_TB-ACCUTOX-acetaminophen.txt +58 -0
  57. data/test/data/valid/BII-I-1.n3 +19648 -0
  58. data/test/data/valid/BII-I-1.rdf +19648 -0
  59. data/test/data/valid/BII-I-1.zip +0 -0
  60. data/test/data/valid/isa-tab-renamed.zip +0 -0
  61. data/test/data/valid/isa_TB_BII.xls +0 -0
  62. data/test/httpd.rb +69 -0
  63. data/test/querytest.rb +42 -0
  64. data/test/upload.rb +152 -0
  65. data/test/xls_upload.rb +60 -0
  66. data/toxbank-investigation.gemspec +29 -0
  67. metadata +133 -0
data/test/data/invalid/i_Investigation.txt ADDED
@@ -0,0 +1,156 @@
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+ ONTOLOGY SOURCE REFERENCE
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+ Term Source Name OBI CHEBI UO
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+ Term Source File http://bioportal.bioontology.org/ontologies/46336 http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=UO
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+ Term Source Version
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+ Term Source Description Ontology for Biomedical Investigations Chemical entities of biological interest Unit Ontology
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+ INVESTIGATION
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+ Investigation Identifier TB-Accutox
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+ Investigation Title Investigation
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+ Investigation Description
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+ Investigation Submission Date
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+ Investigation Public Release Date
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+ Comment [Last Opened With Configuration] isaconfig-default
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+ Comment [Created With Configuration] isaconfig-default
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+ Comment [Last opened with configuration] isaconfig-default
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+ INVESTIGATION PUBLICATIONS
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+ Investigation PubMed ID
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+ Investigation Publication DOI
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+ Investigation Publication Author List
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+ Investigation Publication Title
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+ Investigation Publication Status
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+ Investigation Publication Status Term Accession Number
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+ Investigation Publication Status Term Source REF
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+ INVESTIGATION CONTACTS
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+ Investigation Person Last Name
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+ Investigation Person First Name
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+ Investigation Person Mid Initials
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+ Investigation Person Email
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+ Investigation Person Phone
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+ Investigation Person Fax
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+ Investigation Person Address
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+ Investigation Person Affiliation
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+ Investigation Person Roles
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+ Investigation Person Roles Term Accession Number
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+ Investigation Person Roles Term Source REF
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+
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+ STUDY
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+ Study Identifier TB-ACCUTOX-acetaminophen
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+ Study Title Acetaminophen dose response study
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+ Study Submission Date 40855.0
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+ Study Public Release Date 40857.0
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+ Study Description Acetaminophen dose response study
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+ Study File Name s_TB-ACCUTOX-acetaminophen.txt
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+ STUDY DESIGN DESCRIPTORS
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+ Study Design Type dose response design
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+ Study Design Type Term Accession Number obo:OBI_0001418
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+ Study Design Type Term Source REF OBI
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+ STUDY PUBLICATIONS
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+ Study PubMed ID 123456.0
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+ Study Publication DOI
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+ Study Publication Author List Grados OB
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+ Study Publication Title The laboratory in programs for enteric infection control
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+ Study Publication Status Published
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+ Study Publication Status Term Accession Number
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+ Study Publication Status Term Source REF
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+ STUDY FACTORS
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+ Study Factor Name compound dose cell_line repeat replicate
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+ Study Factor Type compound dose cell_line repeat replicate
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+ Study Factor Type Term Accession Number
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+ Study Factor Type Term Source REF
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+ STUDY ASSAYS
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+ Study Assay Measurement Type Cell viability Cell viability Cell viability
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+ Study Assay Measurement Type Term Accession Number 90.0 90.0 90.0
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+ Study Assay Measurement Type Term Source REF BAO BAO BAO
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+ Study Assay Technology Type Neutral Red Uptake Cytotoxicity Test Neutral Red Uptake Cytotoxicity Test Neutral Red Uptake Cytotoxicity Test
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+ Study Assay Technology Type Term Accession Number
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+ Study Assay Technology Type Term Source REF
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+ Study Assay Technology Platform
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+ Study Assay File Name a_TB-ACCUTOX-Plate1.txt a_TB-ACCUTOX-Plate2.txt a_TB-ACCUTOX-Plate3.txt
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+ STUDY PROTOCOLS
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+ Study Protocol Name Prepare concentrations Neutral Red Uptake (NRU) Cytotoxicity Test Hill function analysis NRU
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+ Study Protocol Type Prepare concentrations Neutral Red Uptake (NRU) Cytotoxicity Test dose response curve NRU
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+ Study Protocol Type Term Accession Number
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+ Study Protocol Type Term Source REF
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+ Study Protocol Description
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+ Study Protocol URI
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+ Study Protocol Version
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+ Study Protocol Parameters Name
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+ Study Protocol Parameters Name Term Accession Number
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+ Study Protocol Parameters Name Term Source REF
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+ Study Protocol Components Name
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+ Study Protocol Components Type
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+ Study Protocol Components Type Term Accession Number
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+ Study Protocol Components Type Term Source REF
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+ STUDY CONTACTS
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+ Study Person Last Name
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+ Study Person First Name
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+ Study Person Mid Initials
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+ Study Person Email
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+ Study Person Phone
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+ Study Person Fax
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+ Study Person Address
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+ Study Person Affiliation
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+ Study Person Roles
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+ Study Person Roles Term Accession Number
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+ Study Person Roles Term Source REF
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+
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+ STUDY
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+ Study Identifier TB-ACCUTOX-rotenone
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+ Study Title Rotenone dose response study
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+ Study Submission Date 40856.0
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+ Study Public Release Date 40858.0
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+ Study Description NRU
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+ Study File Name s_TB-ACCUTOX-Rotenone.txt
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+ STUDY DESIGN DESCRIPTORS
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+ Study Design Type dose response design
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+ Study Design Type Term Accession Number obo:OBI_0001418
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+ Study Design Type Term Source REF OBI
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+ STUDY PUBLICATIONS
109
+ Study PubMed ID
110
+ Study Publication DOI
111
+ Study Publication Author List
112
+ Study Publication Title
113
+ Study Publication Status
114
+ Study Publication Status Term Accession Number
115
+ Study Publication Status Term Source REF
116
+ STUDY FACTORS
117
+ Study Factor Name compound dose cell_line repeat
118
+ Study Factor Type compound dose cell_line repeat
119
+ Study Factor Type Term Accession Number
120
+ Study Factor Type Term Source REF
121
+ STUDY ASSAYS
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+ Study Assay Measurement Type Cell viability Cell viability Cell viability
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+ Study Assay Measurement Type Term Accession Number 90.0 90.0 90.0
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+ Study Assay Measurement Type Term Source REF BAO BAO BAO
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+ Study Assay Technology Type Neutral Red Uptake Cytotoxicity Test Neutral Red Uptake Cytotoxicity Test Neutral Red Uptake Cytotoxicity Test
126
+ Study Assay Technology Type Term Accession Number
127
+ Study Assay Technology Type Term Source REF
128
+ Study Assay Technology Platform
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+ Study Assay File Name a_TB-ACCUTOX-rotenone-Plate1.txt a_TB-ACCUTOX-rotenone-Plate3.txt a_TB-ACCUTOX-rotenone-Plate2.txt
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+ STUDY PROTOCOLS
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+ Study Protocol Name Prepare concentrations Neutral Red Uptake (NRU) Cytotoxicity Test Hill function analysis
132
+ Study Protocol Type Prepare concentrations Neutral Red Uptake (NRU) Cytotoxicity Test dose response curve
133
+ Study Protocol Type Term Accession Number
134
+ Study Protocol Type Term Source REF
135
+ Study Protocol Description
136
+ Study Protocol URI
137
+ Study Protocol Version
138
+ Study Protocol Parameters Name
139
+ Study Protocol Parameters Name Term Accession Number
140
+ Study Protocol Parameters Name Term Source REF
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+ Study Protocol Components Name
142
+ Study Protocol Components Type
143
+ Study Protocol Components Type Term Accession Number
144
+ Study Protocol Components Type Term Source REF
145
+ STUDY CONTACTS
146
+ Study Person Last Name
147
+ Study Person First Name
148
+ Study Person Mid Initials
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+ Study Person Email
150
+ Study Person Phone
151
+ Study Person Fax
152
+ Study Person Address
153
+ Study Person Affiliation
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+ Study Person Roles
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+ Study Person Roles Term Accession Number
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+ Study Person Roles Term Source REF
data/test/data/invalid/ic50.txt ADDED
@@ -0,0 +1,20 @@
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+ Dose Response Name IC50
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+ acetaminophen-plate1-ic50 3.14159
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+ acetaminophen-plate2-ic50 3.1416
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+ acetaminophen-plate3-ic50 3.14
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+ rotenone-plate1-ic50 5.14159
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+ rotenone-plate2-ic50 6.1416
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+ rotenone-plate3-ic50 7.14
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
data/test/data/invalid/s_TB-ACCUTOX-acetaminophen.txt ADDED
@@ -0,0 +1,58 @@
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+ Source Name Factor[batch number] Factor Value[compound] Term Source REF Term Accession Number Factor Value[dose] Unit Term Source REF Term Accession Number Factor Value[cell_line] Term Source REF Term Accession Number Factor Value[repeat] Protocol REF Sample Name
2
+ cell culture KKKK123 Vehicle 0.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 1.0 Prepare test concentrations VC1-plate1
3
+ cell culture Solvent 0.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 1.0 Prepare test concentrations VC2-plate1
4
+ cell culture paracetamol CHEBI CHEBI:46195 2.5 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 1.0 Prepare test concentrations C1-plate1
5
+ cell culture paracetamol CHEBI CHEBI:46195 5.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 1.0 Prepare test concentrations C2-plate1
6
+ cell culture paracetamol CHEBI CHEBI:46195 12.5 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 1.0 Prepare test concentrations C3-plate1
7
+ cell culture paracetamol CHEBI CHEBI:46195 25.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 1.0 Prepare test concentrations C4-plate1
8
+ cell culture paracetamol CHEBI CHEBI:46195 50.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 1.0 Prepare test concentrations C5-plate1
9
+ cell culture paracetamol CHEBI CHEBI:46195 100.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 1.0 Prepare test concentrations C6-plate1
10
+ cell culture paracetamol CHEBI CHEBI:46195 200.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 1.0 Prepare test concentrations C7-plate1
11
+ cell culture paracetamol CHEBI CHEBI:46195 250.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 1.0 Prepare test concentrations C8-plate1
12
+ cell culture Vehicle 0.0 mg/L UO 273.0 blank 1.0 Prepare test concentrations VCb-plate1
13
+ cell culture paracetamol CHEBI CHEBI:46195 2.5 mg/L UO 273.0 blank 1.0 Prepare test concentrations C1b-plate1
14
+ cell culture paracetamol CHEBI CHEBI:46195 5.0 mg/L UO 273.0 blank 1.0 Prepare test concentrations C2b-plate1
15
+ cell culture paracetamol CHEBI CHEBI:46195 12.5 mg/L UO 273.0 blank 1.0 Prepare test concentrations C3b-plate1
16
+ cell culture paracetamol CHEBI CHEBI:46195 25.0 mg/L UO 273.0 blank 1.0 Prepare test concentrations C4b-plate1
17
+ cell culture paracetamol CHEBI CHEBI:46195 50.0 mg/L UO 273.0 blank 1.0 Prepare test concentrations C5b-plate1
18
+ cell culture paracetamol CHEBI CHEBI:46195 100.0 mg/L UO 273.0 blank 1.0 Prepare test concentrations C6b-plate1
19
+ cell culture paracetamol CHEBI CHEBI:46195 200.0 mg/L UO 273.0 blank 1.0 Prepare test concentrations C7b-plate1
20
+ cell culture paracetamol CHEBI CHEBI:46195 250.0 mg/L UO 273.0 blank 1.0 Prepare test concentrations C8b-plate1
21
+ cell culture Vehicle 0.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 2.0 Prepare test concentrations VC1-plate2
22
+ cell culture Solvent 0.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 2.0 Prepare test concentrations VC2-plate2
23
+ cell culture paracetamol CHEBI CHEBI:46195 2.5 mg/l UO 273.0 BTO BTO 218.0 2.0 Prepare test concentrations C1-plate2
24
+ cell culture paracetamol CHEBI CHEBI:46195 5.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 2.0 Prepare test concentrations C2-plate2
25
+ cell culture paracetamol CHEBI CHEBI:46195 12.5 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 2.0 Prepare test concentrations C3-plate2
26
+ cell culture paracetamol CHEBI CHEBI:46195 25.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 2.0 Prepare test concentrations C4-plate2
27
+ cell culture paracetamol CHEBI CHEBI:46195 50.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 2.0 Prepare test concentrations C5-plate2
28
+ cell culture paracetamol CHEBI CHEBI:46195 100.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 2.0 Prepare test concentrations C6-plate2
29
+ cell culture paracetamol CHEBI CHEBI:46195 200.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 2.0 Prepare test concentrations C7-plate2
30
+ cell culture paracetamol CHEBI CHEBI:46195 250.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 2.0 Prepare test concentrations C8-plate2
31
+ cell culture Vehicle 0.0 mg/L UO 273.0 blank 2.0 Prepare test concentrations VCb-plate2
32
+ cell culture paracetamol CHEBI CHEBI:46195 2.5 mg/L UO 273.0 blank 2.0 Prepare test concentrations C1b-plate2
33
+ cell culture paracetamol CHEBI CHEBI:46195 5.0 mg/L UO 273.0 blank 2.0 Prepare test concentrations C2b-plate2
34
+ cell culture paracetamol CHEBI CHEBI:46195 12.5 mg/L UO 273.0 blank 2.0 Prepare test concentrations C3b-plate2
35
+ cell culture paracetamol CHEBI CHEBI:46195 25.0 mg/L UO 273.0 blank 2.0 Prepare test concentrations C4b-plate2
36
+ cell culture paracetamol CHEBI CHEBI:46195 50.0 mg/L UO 273.0 blank 2.0 Prepare test concentrations C5b-plate2
37
+ cell culture paracetamol CHEBI CHEBI:46195 100.0 mg/L UO 273.0 blank 2.0 Prepare test concentrations C6b-plate2
38
+ cell culture paracetamol CHEBI CHEBI:46195 200.0 mg/L UO 273.0 blank 2.0 Prepare test concentrations C7b-plate2
39
+ cell culture paracetamol CHEBI CHEBI:46195 250.0 mg/L UO 273.0 blank 2.0 Prepare test concentrations C8b-plate2
40
+ cell culture Vehicle 0.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 3.0 Prepare test concentrations VC1-plate3
41
+ cell culture Solvent 0.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 3.0 Prepare test concentrations VC2-plate3
42
+ cell culture paracetamol CHEBI CHEBI:46195 2.5 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 3.0 Prepare test concentrations C1-plate3
43
+ cell culture paracetamol CHEBI CHEBI:46195 5.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 3.0 Prepare test concentrations C2-plate3
44
+ cell culture paracetamol CHEBI CHEBI:46195 12.5 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 3.0 Prepare test concentrations C3-plate3
45
+ cell culture paracetamol CHEBI CHEBI:46195 25.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 3.0 Prepare test concentrations C4-plate3
46
+ cell culture paracetamol CHEBI CHEBI:46195 50.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 3.0 Prepare test concentrations C5-plate3
47
+ cell culture paracetamol CHEBI CHEBI:46195 100.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 3.0 Prepare test concentrations C6-plate3
48
+ cell culture paracetamol CHEBI CHEBI:46195 200.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 3.0 Prepare test concentrations C7-plate3
49
+ cell culture paracetamol CHEBI CHEBI:46195 250.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 3.0 Prepare test concentrations C8-plate3
50
+ cell culture Vehicle 0.0 mg/L UO 273.0 blank 3.0 Prepare test concentrations VCb-plate3
51
+ cell culture paracetamol CHEBI CHEBI:46195 2.5 mg/L UO 273.0 blank 3.0 Prepare test concentrations C1b-plate3
52
+ cell culture paracetamol CHEBI CHEBI:46195 5.0 mg/L UO 273.0 blank 3.0 Prepare test concentrations C2b-plate3
53
+ cell culture paracetamol CHEBI CHEBI:46195 12.5 mg/L UO 273.0 blank 3.0 Prepare test concentrations C3b-plate3
54
+ cell culture paracetamol CHEBI CHEBI:46195 25.0 mg/L UO 273.0 blank 3.0 Prepare test concentrations C4b-plate3
55
+ cell culture paracetamol CHEBI CHEBI:46195 50.0 mg/L UO 273.0 blank 3.0 Prepare test concentrations C5b-plate3
56
+ cell culture paracetamol CHEBI CHEBI:46195 100.0 mg/L UO 273.0 blank 3.0 Prepare test concentrations C6b-plate3
57
+ cell culture paracetamol CHEBI CHEBI:46195 200.0 mg/L UO 273.0 blank 3.0 Prepare test concentrations C7b-plate3
58
+ cell culture paracetamol CHEBI CHEBI:46195 250.0 mg/L UO 273.0 blank 3.0 Prepare test concentrations C8b-plate3