toxbank-investigation 0.0.1pre-x86-linux
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/.gitignore +11 -0
- data/Gemfile +7 -0
- data/Gemfile.lock +101 -0
- data/LICENSE +674 -0
- data/README +14 -0
- data/Rakefile +31 -0
- data/application.rb +246 -0
- data/bin/toxbank-investigation-install +76 -0
- data/config/production.rb +9 -0
- data/config.ru +5 -0
- data/java/config/isa_configurator/cellcount_flowcytometry.xml +1 -0
- data/java/config/isa_configurator/cellsorting_flowcyt.xml +5 -0
- data/java/config/isa_configurator/clinical_chemistry.xml +1 -0
- data/java/config/isa_configurator/copynumvariation_micro.xml +1 -0
- data/java/config/isa_configurator/dnamethylation_micro.xml +1 -0
- data/java/config/isa_configurator/dnamethylation_seq.xml +1 -0
- data/java/config/isa_configurator/envgen_survey_seq.xml +1 -0
- data/java/config/isa_configurator/genome_seq.xml +1 -0
- data/java/config/isa_configurator/hematology.xml +1 -0
- data/java/config/isa_configurator/heterozygosity_micro.xml +1 -0
- data/java/config/isa_configurator/histology.xml +1 -0
- data/java/config/isa_configurator/histonemodification_seq.xml +1 -0
- data/java/config/isa_configurator/metaboliteprofiling_ms.xml +114 -0
- data/java/config/isa_configurator/metaboliteprofiling_nmr.xml +114 -0
- data/java/config/isa_configurator/metagenome_seq.xml +1 -0
- data/java/config/isa_configurator/nru_assay.xml +8 -0
- data/java/config/isa_configurator/ppi_detection_micro.xml +1 -0
- data/java/config/isa_configurator/protein_dna_binding_ident_micro.xml +1 -0
- data/java/config/isa_configurator/protein_dna_binding_ident_seq.xml +1 -0
- data/java/config/isa_configurator/protein_expression_ge.xml +101 -0
- data/java/config/isa_configurator/protein_expression_micro.xml +1 -0
- data/java/config/isa_configurator/protein_expression_ms.xml +1 -0
- data/java/config/isa_configurator/proteinident_ms.xml +1 -0
- data/java/config/isa_configurator/snpanalysis_micro.xml +1 -0
- data/java/config/isa_configurator/studySample.xml +1 -0
- data/java/config/isa_configurator/tfbsident_micro.xml +1 -0
- data/java/config/isa_configurator/tfbsident_seq.xml +1 -0
- data/java/config/isa_configurator/transcription_micro.xml +1 -0
- data/java/config/isa_configurator/transcription_rtpcr.xml +1 -0
- data/java/config/isa_configurator/transcription_seq.xml +6 -0
- data/test/Rakefile +48 -0
- data/test/all.rb +3 -0
- data/test/authorization.rb +112 -0
- data/test/basic_rest.rb +98 -0
- data/test/data/invalid/BII-invalid.n3 +19641 -0
- data/test/data/invalid/a_TB-ACCUTOX-plate1.txt +97 -0
- data/test/data/invalid/a_TB-ACCUTOX-plate2.txt +97 -0
- data/test/data/invalid/a_TB-ACCUTOX-plate3.txt +97 -0
- data/test/data/invalid/acetaminophen-plate1-data.txt +97 -0
- data/test/data/invalid/acetaminophen-plate2-data.txt +97 -0
- data/test/data/invalid/acetaminophen-plate3-data.txt +97 -0
- data/test/data/invalid/i_Investigation.txt +156 -0
- data/test/data/invalid/ic50.txt +20 -0
- data/test/data/invalid/isa_TB_ACCUTOX.xls +0 -0
- data/test/data/invalid/isa_TB_ACCUTOX.zip +0 -0
- data/test/data/invalid/s_TB-ACCUTOX-acetaminophen.txt +58 -0
- data/test/data/valid/BII-I-1.n3 +19648 -0
- data/test/data/valid/BII-I-1.rdf +19648 -0
- data/test/data/valid/BII-I-1.zip +0 -0
- data/test/data/valid/isa-tab-renamed.zip +0 -0
- data/test/data/valid/isa_TB_BII.xls +0 -0
- data/test/httpd.rb +69 -0
- data/test/querytest.rb +42 -0
- data/test/upload.rb +152 -0
- data/test/xls_upload.rb +60 -0
- data/toxbank-investigation.gemspec +29 -0
- metadata +133 -0
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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 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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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 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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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
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Study PubMed ID
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Study Publication DOI
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Study Publication Author List
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Study Publication Title
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Study Publication Status
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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
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Study Factor Type compound dose cell_line repeat
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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-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
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Study Protocol Type Prepare concentrations Neutral Red Uptake (NRU) Cytotoxicity Test dose response curve
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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 Address
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Study Person Affiliation
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Study Person Roles Term Source REF
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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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Binary file
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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
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cell culture KKKK123 Vehicle 0.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 1.0 Prepare test concentrations VC1-plate1
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cell culture Solvent 0.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 1.0 Prepare test concentrations VC2-plate1
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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
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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
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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
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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
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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
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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
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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
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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
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cell culture Vehicle 0.0 mg/L UO 273.0 blank 1.0 Prepare test concentrations VCb-plate1
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cell culture paracetamol CHEBI CHEBI:46195 2.5 mg/L UO 273.0 blank 1.0 Prepare test concentrations C1b-plate1
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cell culture paracetamol CHEBI CHEBI:46195 5.0 mg/L UO 273.0 blank 1.0 Prepare test concentrations C2b-plate1
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cell culture paracetamol CHEBI CHEBI:46195 12.5 mg/L UO 273.0 blank 1.0 Prepare test concentrations C3b-plate1
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cell culture paracetamol CHEBI CHEBI:46195 25.0 mg/L UO 273.0 blank 1.0 Prepare test concentrations C4b-plate1
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cell culture paracetamol CHEBI CHEBI:46195 50.0 mg/L UO 273.0 blank 1.0 Prepare test concentrations C5b-plate1
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cell culture paracetamol CHEBI CHEBI:46195 100.0 mg/L UO 273.0 blank 1.0 Prepare test concentrations C6b-plate1
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cell culture paracetamol CHEBI CHEBI:46195 200.0 mg/L UO 273.0 blank 1.0 Prepare test concentrations C7b-plate1
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cell culture paracetamol CHEBI CHEBI:46195 250.0 mg/L UO 273.0 blank 1.0 Prepare test concentrations C8b-plate1
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cell culture Vehicle 0.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 2.0 Prepare test concentrations VC1-plate2
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cell culture Solvent 0.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 2.0 Prepare test concentrations VC2-plate2
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cell culture paracetamol CHEBI CHEBI:46195 2.5 mg/l UO 273.0 BTO BTO 218.0 2.0 Prepare test concentrations C1-plate2
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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
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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
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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
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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
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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
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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
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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
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cell culture Vehicle 0.0 mg/L UO 273.0 blank 2.0 Prepare test concentrations VCb-plate2
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cell culture paracetamol CHEBI CHEBI:46195 2.5 mg/L UO 273.0 blank 2.0 Prepare test concentrations C1b-plate2
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cell culture paracetamol CHEBI CHEBI:46195 5.0 mg/L UO 273.0 blank 2.0 Prepare test concentrations C2b-plate2
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cell culture paracetamol CHEBI CHEBI:46195 12.5 mg/L UO 273.0 blank 2.0 Prepare test concentrations C3b-plate2
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cell culture paracetamol CHEBI CHEBI:46195 25.0 mg/L UO 273.0 blank 2.0 Prepare test concentrations C4b-plate2
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cell culture paracetamol CHEBI CHEBI:46195 50.0 mg/L UO 273.0 blank 2.0 Prepare test concentrations C5b-plate2
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cell culture paracetamol CHEBI CHEBI:46195 100.0 mg/L UO 273.0 blank 2.0 Prepare test concentrations C6b-plate2
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cell culture paracetamol CHEBI CHEBI:46195 200.0 mg/L UO 273.0 blank 2.0 Prepare test concentrations C7b-plate2
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cell culture paracetamol CHEBI CHEBI:46195 250.0 mg/L UO 273.0 blank 2.0 Prepare test concentrations C8b-plate2
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cell culture Vehicle 0.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 3.0 Prepare test concentrations VC1-plate3
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cell culture Solvent 0.0 mg/L UO 273.0 BALB/3T3 cell BTO 218.0 3.0 Prepare test concentrations VC2-plate3
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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
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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
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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
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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
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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
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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
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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
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+
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
|