Merge pull request #514 from ISA-tools/issue-511

Issue 511
ISA-tools · Jul 15, 2024 · 9d0063b · 9d0063b
2 parents 68e8619 + 66e0aca
commit 9d0063b
Show file tree

Hide file tree

Showing 113 changed files with 26,901 additions and 2,112 deletions.
diff --git a/isa-cookbook/content/notebooks/ISA-json to ISA-Tab and back to ISA-json - roundtrip.ipynb b/isa-cookbook/content/notebooks/ISA-json to ISA-Tab and back to ISA-json - roundtrip.ipynb
diff --git a/...nt/notebooks/MTBLS2746-QuickFix/a_MTBLS2746_LC-MS_negative_hilic_metabolite_profiling.txt b/...nt/notebooks/MTBLS2746-QuickFix/a_MTBLS2746_LC-MS_negative_hilic_metabolite_profiling.txt
diff --git a/...ooks/MTBLS2746-QuickFix/a_MTBLS2746_LC-MS_negative_reverse-phase_metabolite_profiling.txt b/...ooks/MTBLS2746-QuickFix/a_MTBLS2746_LC-MS_negative_reverse-phase_metabolite_profiling.txt
diff --git a/...nt/notebooks/MTBLS2746-QuickFix/a_MTBLS2746_LC-MS_positive_hilic_metabolite_profiling.txt b/...nt/notebooks/MTBLS2746-QuickFix/a_MTBLS2746_LC-MS_positive_hilic_metabolite_profiling.txt
diff --git a/...ooks/MTBLS2746-QuickFix/a_MTBLS2746_LC-MS_positive_reverse-phase_metabolite_profiling.txt b/...ooks/MTBLS2746-QuickFix/a_MTBLS2746_LC-MS_positive_reverse-phase_metabolite_profiling.txt
diff --git a/isa-cookbook/content/notebooks/MTBLS2746-QuickFix/i_Investigation.txt b/isa-cookbook/content/notebooks/MTBLS2746-QuickFix/i_Investigation.txt
diff --git a/...books/MTBLS2746-QuickFix/m_MTBLS2746_LC-MS_negative_hilic_metabolite_profiling_v2_maf.tsv b/...books/MTBLS2746-QuickFix/m_MTBLS2746_LC-MS_negative_hilic_metabolite_profiling_v2_maf.tsv
@@ -0,0 +1,2 @@
+database_identifier	chemical_formula	smiles	inchi	metabolite_identification	mass_to_charge	fragmentation	modifications	charge	retention_time	taxid	species	database	database_version	reliability	uri	search_engine	search_engine_score	smallmolecule_abundance_sub	smallmolecule_abundance_stdev_sub	smallmolecule_abundance_std_error_sub
+0																				
diff --git a/...BLS2746-QuickFix/m_MTBLS2746_LC-MS_negative_reverse-phase_metabolite_profiling_v2_maf.tsv b/...BLS2746-QuickFix/m_MTBLS2746_LC-MS_negative_reverse-phase_metabolite_profiling_v2_maf.tsv
@@ -0,0 +1,2 @@
+database_identifier	chemical_formula	smiles	inchi	metabolite_identification	mass_to_charge	fragmentation	modifications	charge	retention_time	taxid	species	database	database_version	reliability	uri	search_engine	search_engine_score	smallmolecule_abundance_sub	smallmolecule_abundance_stdev_sub	smallmolecule_abundance_std_error_sub
+0																				
diff --git a/...books/MTBLS2746-QuickFix/m_MTBLS2746_LC-MS_positive_hilic_metabolite_profiling_v2_maf.tsv b/...books/MTBLS2746-QuickFix/m_MTBLS2746_LC-MS_positive_hilic_metabolite_profiling_v2_maf.tsv
@@ -0,0 +1,2 @@
+database_identifier	chemical_formula	smiles	inchi	metabolite_identification	mass_to_charge	fragmentation	modifications	charge	retention_time	taxid	species	database	database_version	reliability	uri	search_engine	search_engine_score	smallmolecule_abundance_sub	smallmolecule_abundance_stdev_sub	smallmolecule_abundance_std_error_sub
+0																				
diff --git a/...BLS2746-QuickFix/m_MTBLS2746_LC-MS_positive_reverse-phase_metabolite_profiling_v2_maf.tsv b/...BLS2746-QuickFix/m_MTBLS2746_LC-MS_positive_reverse-phase_metabolite_profiling_v2_maf.tsv
@@ -0,0 +1,2 @@
+database_identifier	chemical_formula	smiles	inchi	metabolite_identification	mass_to_charge	fragmentation	modifications	charge	retention_time	taxid	species	database	database_version	reliability	uri	search_engine	search_engine_score	smallmolecule_abundance_sub	smallmolecule_abundance_stdev_sub	smallmolecule_abundance_std_error_sub
+0																				
diff --git a/isa-cookbook/content/notebooks/MTBLS2746-QuickFix/s_MTBLS2746.txt b/isa-cookbook/content/notebooks/MTBLS2746-QuickFix/s_MTBLS2746.txt
diff --git a/...estigation-from-datascriptor-config-observational-variables-and-ontology-annotation.ipynb b/...estigation-from-datascriptor-config-observational-variables-and-ontology-annotation.ipynb
@@ -364,7 +364,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -378,7 +378,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.1"
+   "version": "3.9.0"
   }
  },
  "nbformat": 4,
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		database_identifier chemical_formula smiles inchi metabolite_identification mass_to_charge fragmentation modifications charge retention_time taxid species database database_version reliability uri search_engine search_engine_score smallmolecule_abundance_sub smallmolecule_abundance_stdev_sub smallmolecule_abundance_std_error_sub
		0