From 339db385cb5fa30b99ed0cddf3e5051a230fb284 Mon Sep 17 00:00:00 2001 From: Philippe Rocca-Serra Date: Mon, 5 Aug 2024 10:29:59 +0100 Subject: [PATCH 1/3] adjusting bh23 workbook, and model class --- ...i-programmatic-BH2023-multiomics-isa.ipynb | 217 ++++++------------ ...-api-programmatic-rebuild-of-BII-S-3.ipynb | 58 ++--- isatools/model/utils.py | 13 +- .../core/comment_schema.json | 2 +- 4 files changed, 86 insertions(+), 204 deletions(-) diff --git a/isa-cookbook/content/notebooks/isa-api-programmatic-BH2023-multiomics-isa.ipynb b/isa-cookbook/content/notebooks/isa-api-programmatic-BH2023-multiomics-isa.ipynb index c57f3188..095c7e48 100644 --- a/isa-cookbook/content/notebooks/isa-api-programmatic-BH2023-multiomics-isa.ipynb +++ b/isa-cookbook/content/notebooks/isa-api-programmatic-BH2023-multiomics-isa.ipynb @@ -32,7 +32,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": { "scrolled": true }, @@ -150,7 +150,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": { "scrolled": true }, @@ -184,7 +184,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -201,7 +201,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": { "scrolled": true }, @@ -287,7 +287,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": { "scrolled": true }, @@ -313,7 +313,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": { "scrolled": true }, @@ -345,7 +345,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": { "scrolled": true }, @@ -534,7 +534,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": { "scrolled": true }, @@ -642,22 +642,22 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "metadata": { "scrolled": true }, "outputs": [], "source": [ "#Starting by declaring the 2 types of assays used in BII-S-3 as coded with ISAcreator tool\n", - "assay = Assay(filename=\"a_\"+ study.identifier + \"-isotopologue-ms-assay.txt\")\n", - "assay.measurement_type = OntologyAnnotation(term=\"isotopologue distribution analysis\",term_accession=\"http://purl.obolibrary.org/obo/msio.owl#mass_isotopologue_distribution_analysis\", term_source=msio)\n", - "assay.technology_type = OntologyAnnotation(term=\"mass spectrometry\", term_accession=\"http://purl.obolibrary.org/obo/CHMO_0000470\", term_source=msio)\n", - "assay.comments.append(Comment(name=\"target repository\", value=\"metabolights\"))\n", - "\n", - "assay_nmr_topo = Assay(filename=\"a_\"+ study.identifier + \"-isotopomer-nmr-assay.txt\")\n", - "assay_nmr_topo.measurement_type = OntologyAnnotation(term=\"isotopomer analysis\",term_accession=\"http://purl.obolibrary.org/obo/msio.owl#isotopomer_analysis\", term_source=msio)\n", - "assay_nmr_topo.technology_type = OntologyAnnotation(term=\"NMR spectroscopy\",term_accession=\"http://purl.obolibrary.org/obo/CHMO_0000591\", term_source=msio)\n", - "assay_nmr_topo.comments.append(Comment(name=\"target repository\", value=\"metabolights\"))\n", + "# assay = Assay(filename=\"a_\"+ study.identifier + \"-isotopologue-ms-assay.txt\")\n", + "# assay.measurement_type = OntologyAnnotation(term=\"isotopologue distribution analysis\",term_accession=\"http://purl.obolibrary.org/obo/msio.owl#mass_isotopologue_distribution_analysis\", term_source=msio)\n", + "# assay.technology_type = OntologyAnnotation(term=\"mass spectrometry\", term_accession=\"http://purl.obolibrary.org/obo/CHMO_0000470\", term_source=msio)\n", + "# assay.comments.append(Comment(name=\"target repository\", value=\"metabolights\"))\n", + "\n", + "# assay_nmr_topo = Assay(filename=\"a_\"+ study.identifier + \"-isotopomer-nmr-assay.txt\")\n", + "# assay_nmr_topo.measurement_type = OntologyAnnotation(term=\"isotopomer analysis\",term_accession=\"http://purl.obolibrary.org/obo/msio.owl#isotopomer_analysis\", term_source=msio)\n", + "# assay_nmr_topo.technology_type = OntologyAnnotation(term=\"NMR spectroscopy\",term_accession=\"http://purl.obolibrary.org/obo/CHMO_0000591\", term_source=msio)\n", + "# assay_nmr_topo.comments.append(Comment(name=\"target repository\", value=\"metabolights\"))\n", "#\n", "assay_nmr_metpro = Assay(filename=\"a_\"+ study.identifier + \"-metabolite-profiling-nmr-assay.txt\")\n", "assay_nmr_metpro.measurement_type = OntologyAnnotation(term=\"metabolite profiling\",term_accession=\"http://purl.obolibrary.org/obo/MSIO_0000101\", term_source=msio)\n", @@ -696,7 +696,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -721,7 +721,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": { "scrolled": true }, @@ -797,9 +797,9 @@ " assay_nmr_metpro.process_sequence.append(metpro_process)\n", " assay_nmr_metpro.process_sequence.append(nmr_da_process) \n", "\n", - " plink(sample_collection_mbx, extraction_process_nmr_metpro)\n", - " plink(extraction_process_nmr_metpro, metpro_process)\n", - " plink(metpro_process, nmr_da_process)\n", + " # plink(sample_collection_mbx, extraction_process_nmr_metpro)\n", + " # plink(extraction_process_nmr_metpro, metpro_process)\n", + " # # plink(metpro_process, nmr_da_process)\n", "# make sure the extract, data file, and the processes are attached to the assay\n", "\n", "\n", @@ -816,7 +816,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "metadata": { "scrolled": true }, @@ -918,7 +918,7 @@ " rnaseq_drvdf = DataFile(filename=\"rna-seq-DEA.txt\", label=\"Derived Data File\")\n", " dvf=open(os.path.join(main_path,\"rna-seq-DEA.txt\"),\"w+\")\n", " dvf.write(\"rna-seq-DEA.txt\")\n", - " # dvf.close\n", + " dvf.close\n", " \n", "\n", " rna_drvdata_comment = Comment(name=\"export\", value=\"yes\")\n", @@ -939,10 +939,10 @@ " assay_rna_seq.process_sequence.append(rna_seq_process)\n", " assay_rna_seq.process_sequence.append(rna_da_process)\n", " \n", - " plink(sample_collection_gtx, extraction_process_rna_seq)\n", - " plink(extraction_process_rna_seq, rna_lib_process)\n", - " plink(rna_lib_process, rna_seq_process)\n", - " plink(rna_seq_process, rna_da_process)\n", + " # plink(sample_collection_gtx, extraction_process_rna_seq)\n", + " # plink(extraction_process_rna_seq, rna_lib_process)\n", + " # plink(rna_lib_process, rna_seq_process)\n", + " # plink(rna_seq_process, rna_da_process)\n", "\n", " \n", "assay_rna_seq.characteristic_categories.append(char_ext_rna_seq.category)\n" @@ -957,26 +957,11 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "metadata": { "scrolled": true }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Stuff Type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='gDNA', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/OBOfoundry/obi:123414', comments=[]), unit=None, comments=[])]\n", - "[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Stuff Type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='gDNA', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/OBOfoundry/obi:123414', comments=[]), unit=None, comments=[])]\n", - "[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Stuff Type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='gDNA', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/OBOfoundry/obi:123414', comments=[]), unit=None, comments=[])]\n", - "[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Stuff Type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='gDNA', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/OBOfoundry/obi:123414', comments=[]), unit=None, comments=[])]\n", - "[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Stuff Type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='gDNA', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/OBOfoundry/obi:123414', comments=[]), unit=None, comments=[])]\n", - "[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Stuff Type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='gDNA', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/OBOfoundry/obi:123414', comments=[]), unit=None, comments=[])]\n", - "[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Stuff Type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='gDNA', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/OBOfoundry/obi:123414', comments=[]), unit=None, comments=[])]\n", - "[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Stuff Type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='gDNA', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/OBOfoundry/obi:123414', comments=[]), unit=None, comments=[])]\n" - ] - } - ], + "outputs": [], "source": [ "char_ext_cnv_seq = Characteristic(category=OntologyAnnotation(term=\"Stuff Type\", term_source=\"\", term_accession=\"\"),\n", " value=OntologyAnnotation(term=\"gDNA\", term_source=obi, term_accession=\"https://purl.org/OBOfoundry/obi:123414\"))\n", @@ -1063,10 +1048,10 @@ " # dvf.close\n", " \n", " \n", - " # cnvseq_drvdf = DataFile(filename=\"cnv-seq-data-{}.vcf\".format(i), label=\"Derived Data File\")\n", - " # dvf=open(os.path.join(main_path,\"cnv-seq-data-{}.vcf\".format(i)),\"w+\")\n", - " # dvf.write(\"cnv-seq-data-{}.vcf\".format(i))\n", - " # dvf.close\n", + " cnvseq_drvdf = DataFile(filename=\"cnv-seq-data-{}.vcf\".format(i), label=\"Derived Data File\")\n", + " dvf=open(os.path.join(main_path,\"cnv-seq-data-{}.vcf\".format(i)),\"w+\")\n", + " dvf.write(\"cnv-seq-data-{}.vcf\".format(i))\n", + " dvf.close\n", " \n", "\n", " cnv_drvdata_comment = Comment(name=\"export\",value=\"yes\") \n", @@ -1089,10 +1074,10 @@ " assay_cnv_seq.process_sequence.append(cnv_seq_process)\n", " assay_cnv_seq.process_sequence.append(cnv_da_process)\n", " \n", - " plink(sample_collection_gtx, extraction_process_cnv_seq)\n", - " plink(extraction_process_cnv_seq, cnv_lib_process)\n", - " plink(cnv_lib_process, cnv_seq_process)\n", - " plink(cnv_seq_process, cnv_da_process)\n", + " # plink(sample_collection_gtx, extraction_process_cnv_seq)\n", + " # plink(extraction_process_cnv_seq, cnv_lib_process)\n", + " # plink(cnv_lib_process, cnv_seq_process)\n", + " # plink(cnv_seq_process, cnv_da_process)\n", "#\n", "assay_cnv_seq.characteristic_categories.append(char_ext_cnv_seq.category)\n", "# print(assay_cnv_seq.other_material[0].characteristics[0].value.term)" @@ -1107,7 +1092,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": null, "metadata": { "scrolled": true }, @@ -1129,7 +1114,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": null, "metadata": { "scrolled": true }, @@ -1146,8 +1131,8 @@ " ])\n", "study.protocols.append(workflow_ref)\n", "\n", - "# print(investigation.ontology_source_references[4].comments[0])\n", - "# print(study.assays[3].comments[0])" + "print(investigation.ontology_source_references[4].comments[0])\n", + "print(study.assays[0].comments[0])" ] }, { @@ -1159,25 +1144,16 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": null, "metadata": { "scrolled": true }, - "outputs": [ - { - "data": { - "text/plain": "isatools.model.Investigation(identifier='', filename='', title='', submission_date='', public_release_date='', ontology_source_references=[isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), isatools.model.OntologySource(name='MSIO', file='', version='', 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isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/647a7452-01f5-4d9f-8932-679276554275\". name=\"assay-name-nmr-metpro-CPMG-3\", executes_protocol=Protocol(\n\tname=1D 13C NMR spectroscopy for metabolite profiling\n\tprotocol_type=NMR spectroscopy\n\turi=\n\tversion=\n\tparameters=3 ProtocolParameter objects\n\tcomponents=0 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isatools.model.DataFile(filename='nmr-data-metpro-CPMG-3.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-4.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-5.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-6.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-7.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-8.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[])], outputs=[isatools.model.DataFile(filename='metpro-analysis.txt', label='Derived Spectral Data File', generated_from=[], comments=[])]), 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isatools.model.DataFile(filename='nmr-data-metpro-CPMG-8.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[])], outputs=[isatools.model.DataFile(filename='metpro-analysis.txt', label='Derived Spectral Data File', generated_from=[], comments=[])]), isatools.model.process.Process(id=\"#process/68993726-e121-4c07-ae79-d025efdef7dd\". name=\"extract-process-4\", executes_protocol=Protocol(\n\tname=intracellular metabolite extraction\n\tprotocol_type=extraction\n\turi=\n\tversion=\n\tparameters=0 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', 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isatools.model.DataFile(filename='nmr-data-metpro-CPMG-6.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-7.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-8.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[])], outputs=[isatools.model.DataFile(filename='metpro-analysis.txt', label='Derived Spectral Data File', generated_from=[], comments=[])]), isatools.model.process.Process(id=\"#process/ee677866-1f66-4386-beff-dc01cc309f4a\". name=\"extract-process-5\", executes_protocol=Protocol(\n\tname=intracellular metabolite extraction\n\tprotocol_type=extraction\n\turi=\n\tversion=\n\tparameters=0 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-2', 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isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/3607d945-5b30-441f-90bc-e8f8ce07cbf1\". name=\"assay-name-nmr-metpro-CPMG-7\", executes_protocol=Protocol(\n\tname=1D 13C NMR spectroscopy for metabolite profiling\n\tprotocol_type=NMR spectroscopy\n\turi=\n\tversion=\n\tparameters=3 ProtocolParameter objects\n\tcomponents=0 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isatools.model.DataFile(filename='nmr-data-metpro-CPMG-8.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[])], outputs=[isatools.model.DataFile(filename='metpro-analysis.txt', label='Derived Spectral Data File', generated_from=[], comments=[])])], other_material=[, , , , , , , ], characteristic_categories=[], comments=[isatools.model.Comment(name='target repository', value='metabolights')], units=[isatools.model.OntologyAnnotation(term='Tesla', term_source=isatools.model.OntologySource(name='UO', file='', version='', description='Unit Ontology', comments=[]), term_accession='https://purl.org/', comments=[])]), isatools.model.Assay(measurement_type=isatools.model.OntologyAnnotation(term='transcription profiling', term_source=isatools.model.OntologySource(name='MSIO', file='', version='', description='Metabolomics Standards Initiative Ontology', comments=[]), term_accession='https://purl.org', comments=[]), 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characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', 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description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/8d92e3c9-1a25-4ee9-8067-e357f1fd4fa2\". name=\"cnv-library-name-2\", executes_protocol=Protocol(\n\tname=gDNA library preparation\n\tprotocol_type=library construction\n\turi=\n\tversion=\n\tparameters=4 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/ec062370-3210-406a-b244-91aefce60269\". name=\"assay-name-cnv-seq-2\", 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inputs=[isatools.model.DataFile(filename='cnv-seq-data-2.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])], outputs=[isatools.model.DataFile(filename='cnv-seq-derived-data.vcf', label='Derived Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='623e79888c6e3125283423d2df36e2fb'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/b32470f2-f66b-4e51-b957-c71b949394ec\". name=\"extract-process-cnv-seq-3\", executes_protocol=Protocol(\n\tname=gDNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=0 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/cc8cab19-bc78-4702-9ad9-625295f31a8d\". name=\"cnv-library-name-3\", executes_protocol=Protocol(\n\tname=gDNA library preparation\n\tprotocol_type=library construction\n\turi=\n\tversion=\n\tparameters=4 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/d3276f10-0c48-4dda-9598-a2748336171e\". name=\"assay-name-cnv-seq-3\", executes_protocol=Protocol(\n\tname=nucleic acid sequencing\n\tprotocol_type=nucleic acid sequencing\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='cnv-seq-data-3.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/234b01b9-a061-4cb6-8f08-6fbaa598cf46\". name=\"VCF-DT\", executes_protocol=Protocol(\n\tname=CNV analysis\n\tprotocol_type=data transformation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='cnv-seq-data-3.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])], outputs=[isatools.model.DataFile(filename='cnv-seq-derived-data.vcf', label='Derived Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='623e79888c6e3125283423d2df36e2fb'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/5426bf58-522e-4c38-8ad7-4db53648aaed\". name=\"extract-process-cnv-seq-4\", executes_protocol=Protocol(\n\tname=gDNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=0 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/9f226150-c935-4fcd-8f07-57f9a211283c\". name=\"cnv-library-name-4\", executes_protocol=Protocol(\n\tname=gDNA library preparation\n\tprotocol_type=library construction\n\turi=\n\tversion=\n\tparameters=4 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/55a69430-76a7-49c2-9848-09c1c77ad04c\". name=\"assay-name-cnv-seq-4\", executes_protocol=Protocol(\n\tname=nucleic acid sequencing\n\tprotocol_type=nucleic acid sequencing\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='cnv-seq-data-4.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/24eafb9d-0891-4ac7-90cf-2425bba17cac\". name=\"VCF-DT\", executes_protocol=Protocol(\n\tname=CNV analysis\n\tprotocol_type=data transformation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='cnv-seq-data-4.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])], outputs=[isatools.model.DataFile(filename='cnv-seq-derived-data.vcf', label='Derived Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='623e79888c6e3125283423d2df36e2fb'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/716ef59c-5a08-4e59-89b2-1d22e7284714\". name=\"extract-process-cnv-seq-5\", executes_protocol=Protocol(\n\tname=gDNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=0 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/8388804b-70f3-4803-bf45-2e71a78f63c4\". name=\"cnv-library-name-5\", executes_protocol=Protocol(\n\tname=gDNA library preparation\n\tprotocol_type=library construction\n\turi=\n\tversion=\n\tparameters=4 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/18a7e197-6303-48d9-9d78-1601df67e725\". name=\"assay-name-cnv-seq-5\", executes_protocol=Protocol(\n\tname=nucleic acid sequencing\n\tprotocol_type=nucleic acid sequencing\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='cnv-seq-data-5.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/bcb49eb0-0b99-458b-afa1-9848060482eb\". name=\"VCF-DT\", executes_protocol=Protocol(\n\tname=CNV analysis\n\tprotocol_type=data transformation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='cnv-seq-data-5.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])], outputs=[isatools.model.DataFile(filename='cnv-seq-derived-data.vcf', label='Derived Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='623e79888c6e3125283423d2df36e2fb'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/8f083d02-a6b9-48cd-9a11-f35452ba9be3\". name=\"extract-process-cnv-seq-6\", executes_protocol=Protocol(\n\tname=gDNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=0 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', 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unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[]), isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[]), isatools.model.Sample(name='culture-2-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], process_sequence=[isatools.model.process.Process(id=\"#process/58a400cc-d853-48df-823f-2925b3aa1bbe\". name=\"sample-collection-process-mbx\", executes_protocol=Protocol(\n\tname=cell culture and isotopic labeling\n\tprotocol_type=sample collection\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='culture-1-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[]), isatools.model.Sample(name='culture-1-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[]), isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[]), isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])]), isatools.model.process.Process(id=\"#process/baa11002-9a1e-4378-81ba-3e14e8879f6d\". name=\"sample-collection-process-gtx\", executes_protocol=Protocol(\n\tname=cell culture and isotopic labeling\n\tprotocol_type=sample collection\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[]), isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[]), isatools.model.Sample(name='culture-2-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[]), isatools.model.Sample(name='culture-2-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])])], other_material=[], characteristic_categories=[isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[])], comments=[isatools.model.Comment(name='EMBL Broker Name', value='OXFORD'), isatools.model.Comment(name='EMBL Center Name', value='OXFORD'), isatools.model.Comment(name='EMBL Center Project Name', value='OXFORD'), isatools.model.Comment(name='EMBL Lab Name', value='Oxford e-Research Centre'), isatools.model.Comment(name='EMBL Submission Action', value='ADD'), isatools.model.Comment(name='Study Funding Agency', value=''), isatools.model.Comment(name='Study Grant Number', value='')], units=[])], comments=[])" - }, - "execution_count": 16, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "from isatools.isatab import dump\n", "\n", "# note the use of the flag for explicit serialization on factor values on assay tables\n", - "dump(investigation, os.path.join(main_path,'TAB'), write_factor_values_in_assay_table=False)" + "dump(investigation, os.path.join(main_path,'TAB'), write_factor_values_in_assay_table=True)" ] }, { @@ -1189,18 +1165,9 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": 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isatools.model.OntologySource(name='UO', file='', version='', description='Unit Ontology', comments=[])], publications=[], contacts=[], studies=[isatools.model.Study(filename='s_BH2023-study.txt', identifier='BH2023', title='[U-13C6]-D-glucose labeling experiment in MCF7 cancer cell line', description='Probing cancer pathways of MCF7 cell line using 13C stable isotope resolved metabolomics study using isotopologue distribution analysis with mass spectrometry and isotopomer analysis by 1D 1H NMR.', submission_date='2021-08-15', public_release_date='2021-08-15', contacts=[isatools.model.Person(last_name='Min', first_name='Weng', mid_initials='', email='weng.min@bim.edu.cn', phone='', fax='', address='Prospect Street, Beijing, People's Republic of China', affiliation='Beijing Institute of Metabolism', roles=[isatools.model.OntologyAnnotation(term='principal investigator role', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='SRA Inform On Status', 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term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/f8defc15-5712-4116-93d7-fa544a5a5b70\". name=\"process-1-intracellular metabolite extraction\", executes_protocol=Protocol(\n\tname=intracellular metabolite extraction\n\tprotocol_type=extraction\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', 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term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/68378a26-f521-4cb9-adf9-cbd22d2a3363\". name=\"process-2-intracellular metabolite extraction\", executes_protocol=Protocol(\n\tname=intracellular metabolite extraction\n\tprotocol_type=extraction\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical 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comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/dc3441a6-f82a-48d3-b536-b2c921c75e6b\". name=\"process-3-intracellular metabolite extraction\", executes_protocol=Protocol(\n\tname=intracellular metabolite extraction\n\tprotocol_type=extraction\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], 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value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/19c6eaae-bf11-42b7-89bb-b7f32dbe9a28\". name=\"process-4-intracellular metabolite extraction\", executes_protocol=Protocol(\n\tname=intracellular metabolite extraction\n\tprotocol_type=extraction\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', 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term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/89ddda6c-72e6-4a02-b9a5-98b3fc9ead01\". name=\"process-5-intracellular metabolite extraction\", executes_protocol=Protocol(\n\tname=intracellular metabolite extraction\n\tprotocol_type=extraction\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', 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value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', 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term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/734ee247-9a25-4c24-a1f9-92137cfdffa8\". name=\"process-7-intracellular metabolite extraction\", executes_protocol=Protocol(\n\tname=intracellular metabolite extraction\n\tprotocol_type=extraction\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 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term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/44b8f636-9b99-4363-872a-79fbfac15f43\". name=\"assay-name-nmr-metpro-CPMG-1\", executes_protocol=Protocol(\n\tname=1D 13C NMR spectroscopy for metabolite profiling\n\tprotocol_type=NMR spectroscopy\n\turi=\n\tversion=\n\tparameters=3 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-1.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/99e21933-bf22-494f-aa2f-af27d77f29ce\". name=\"assay-name-nmr-metpro-CPMG-3\", executes_protocol=Protocol(\n\tname=1D 13C NMR spectroscopy for metabolite profiling\n\tprotocol_type=NMR spectroscopy\n\turi=\n\tversion=\n\tparameters=3 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-3.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/3f14e789-f458-4825-a88a-6fb5ab07e336\". name=\"assay-name-nmr-metpro-CPMG-5\", executes_protocol=Protocol(\n\tname=1D 13C NMR spectroscopy for metabolite profiling\n\tprotocol_type=NMR spectroscopy\n\turi=\n\tversion=\n\tparameters=3 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-5.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/70271b13-7b5c-4386-b981-500f19518fb3\". name=\"assay-name-nmr-metpro-CPMG-7\", executes_protocol=Protocol(\n\tname=1D 13C NMR spectroscopy for metabolite profiling\n\tprotocol_type=NMR spectroscopy\n\turi=\n\tversion=\n\tparameters=3 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-7.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/10ee62c7-e399-448a-8b03-f99662361a48\". name=\"assay-name-nmr-metpro-CPMG-2\", executes_protocol=Protocol(\n\tname=1D 13C NMR spectroscopy for metabolite profiling\n\tprotocol_type=NMR spectroscopy\n\turi=\n\tversion=\n\tparameters=3 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-2.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/9740a4c9-d09b-49a1-a15f-65d68ad8f73e\". name=\"assay-name-nmr-metpro-CPMG-4\", executes_protocol=Protocol(\n\tname=1D 13C NMR spectroscopy for metabolite profiling\n\tprotocol_type=NMR 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term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/626f1236-b8eb-4632-bdcb-53606323596e\". name=\"assay-name-nmr-metpro-CPMG-6\", executes_protocol=Protocol(\n\tname=1D 13C NMR spectroscopy for metabolite profiling\n\tprotocol_type=NMR spectroscopy\n\turi=\n\tversion=\n\tparameters=3 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-6.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-2-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/50172d83-1807-4e67-89c4-24e157de7f6d\". name=\"assay-name-nmr-metpro-CPMG-8\", executes_protocol=Protocol(\n\tname=1D 13C NMR spectroscopy for metabolite profiling\n\tprotocol_type=NMR 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term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/ec7fcbe4-a100-452d-a38f-256a025c0b0c\". name=\"NMR-metpro-DT-ident\", executes_protocol=Protocol(\n\tname=NMR metabolite identification\n\tprotocol_type=data transformation\n\turi=https://doi.org/10.1021/acs.analchem.1c01064\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-1.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', 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isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/0553e069-08ca-48d4-9fc2-b792b01bd3b3\". name=\"process-2-mRNA extraction\", executes_protocol=Protocol(\n\tname=mRNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/b99f9eab-cbcb-4f7d-ae54-69d09973658a\". name=\"process-3-mRNA extraction\", executes_protocol=Protocol(\n\tname=mRNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/48175220-5d68-4e50-823e-32b660525b27\". name=\"process-4-mRNA extraction\", executes_protocol=Protocol(\n\tname=mRNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/bafbe5a4-76c1-4178-aad1-01396d77a866\". name=\"process-5-mRNA extraction\", executes_protocol=Protocol(\n\tname=mRNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/47950561-b99f-41f9-9226-dcd71024cc93\". name=\"process-6-mRNA extraction\", executes_protocol=Protocol(\n\tname=mRNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical 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value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', 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factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/4d8eaf67-8daa-4179-9354-191b9a15a427\". name=\"process-2-gDNA extraction\", executes_protocol=Protocol(\n\tname=gDNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/d0d2a5fc-09a2-4f73-9bd1-9bb234cac7f9\". name=\"process-3-gDNA extraction\", executes_protocol=Protocol(\n\tname=gDNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/41680259-fef6-4413-ba7a-d22066acb53d\". name=\"process-4-gDNA extraction\", executes_protocol=Protocol(\n\tname=gDNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/44554a3e-58f7-4a72-8f31-8d44f5c7aef1\". name=\"process-5-gDNA extraction\", executes_protocol=Protocol(\n\tname=gDNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/ddc57cc8-edc8-43f9-be23-4e005081c30c\". name=\"process-6-gDNA extraction\", executes_protocol=Protocol(\n\tname=gDNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', 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value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', 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isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', 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isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', 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characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], process_sequence=[isatools.model.process.Process(id=\"#process/737f363b-7c43-4e6b-956a-8a761917125b\". name=\"process-0-cell culture and isotopic labeling\", executes_protocol=Protocol(\n\tname=cell culture and isotopic labeling\n\tprotocol_type=sample collection\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='culture-1-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-1-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/05a5ac0f-b3a7-4b1b-8aeb-225085e10d2f\". name=\"process-4-cell culture and isotopic labeling\", executes_protocol=Protocol(\n\tname=cell culture and isotopic labeling\n\tprotocol_type=sample collection\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-2-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-2-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])])], other_material=[], characteristic_categories=[isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[])], comments=[isatools.model.Comment(name='EMBL Broker Name', value='OXFORD'), isatools.model.Comment(name='EMBL Center Name', value='OXFORD'), isatools.model.Comment(name='EMBL Center Project Name', value='OXFORD'), isatools.model.Comment(name='EMBL Lab Name', value='Oxford e-Research Centre'), isatools.model.Comment(name='EMBL Submission Action', value='ADD'), isatools.model.Comment(name='Study Funding Agency', value=''), isatools.model.Comment(name='Study Grant Number', value='')], units=[])], comments=[])" - }, - "execution_count": 17, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "from isatools.isatab import load\n", "with open(os.path.join(main_path,\"TAB\", \"i_investigation.txt\")) as isa_sirm_test:\n", @@ -1220,17 +1187,9 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "./output/ISA-BH2023-ALL/\n" - ] - } - ], + "outputs": [], "source": [ "from isatools.isajson.dump import ISAJSONEncoder\n", "from json import dumps, loads\n", @@ -1251,17 +1210,9 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "free variable 'spl' referenced before assignment in enclosing scope\n" - ] - } - ], + "outputs": [], "source": [ "from isatools import isatab\n", "\n", @@ -1270,20 +1221,11 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": null, "metadata": { "scrolled": true }, - "outputs": [ - { - "data": { - "text/plain": "[]" - }, - "execution_count": 20, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "my_json_report_isa_flux[\"errors\"]" ] @@ -1304,7 +1246,7 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": null, "metadata": { "scrolled": true }, @@ -1317,21 +1259,9 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "free variable 'spl' referenced before assignment in enclosing scope\n", - "NMR spectroscopy\n", - "assay-name-nmr-metpro-CPMG-5\n", - "['process-0-intracellular metabolite extraction', 'process-1-intracellular metabolite extraction', 'process-2-intracellular metabolite extraction', 'process-3-intracellular metabolite extraction', 'process-4-intracellular metabolite extraction', 'process-5-intracellular metabolite extraction', 'process-6-intracellular metabolite extraction', 'process-7-intracellular metabolite extraction', 'assay-name-nmr-metpro-CPMG-1', 'assay-name-nmr-metpro-CPMG-3', 'assay-name-nmr-metpro-CPMG-5', 'assay-name-nmr-metpro-CPMG-7', 'assay-name-nmr-metpro-CPMG-2', 'assay-name-nmr-metpro-CPMG-4', 'assay-name-nmr-metpro-CPMG-6', 'assay-name-nmr-metpro-CPMG-8', 'NMR-metpro-DT-ident']\n", - "Process(name=process-0-mRNA extraction)\n" - ] - } - ], + "outputs": [], "source": [ "from isatools.convert import isatab2json\n", "import json\n", @@ -1351,7 +1281,7 @@ " new_investigation_dict = json.loads(out_fp.read())\n", " new_investigation = Investigation()\n", " new_investigation.from_dict(new_investigation_dict)\n", - " print(new_investigation.studies[0].assays[1].process_sequence[0])\n" + " print(new_investigation.studies[0].assays[0].process_sequence[0])\n" ] }, { @@ -1363,18 +1293,9 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "./output/ISA-BH2023-ALL/JSON\\BH23-ISATAB_FROM_JSON\n", - "CONFIG at: F:\\Work\\isa-api\\isatools\\isajson\\..\\resources\\config\\json\\default\n" - ] - } - ], + "outputs": [], "source": [ "from isatools.convert import json2isatab\n", "with open(os.path.join(main_path,'JSON','isa-bh2023-t2j.json')) as in_fp:\n", @@ -1393,17 +1314,9 @@ }, { "cell_type": "code", - "execution_count": 24, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CONFIG at: F:\\Work\\isa-api\\isatools\\isajson\\..\\resources\\config\\json\\default\n" - ] - } - ], + "outputs": [], "source": [ "from isatools.convert import json2isatab\n", "with open(os.path.join(main_path, 'isa-v2.json')) as in_fp:\n", @@ -1425,7 +1338,7 @@ }, { "cell_type": "code", - "execution_count": 24, + "execution_count": null, "metadata": {}, "outputs": [], "source": [] @@ -1447,9 +1360,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.7" + "version": "3.12.4" } }, "nbformat": 4, "nbformat_minor": 4 -} \ No newline at end of file +} diff --git a/isa-cookbook/content/notebooks/isa-api-programmatic-rebuild-of-BII-S-3.ipynb b/isa-cookbook/content/notebooks/isa-api-programmatic-rebuild-of-BII-S-3.ipynb index c0257776..64f2268e 100644 --- a/isa-cookbook/content/notebooks/isa-api-programmatic-rebuild-of-BII-S-3.ipynb +++ b/isa-cookbook/content/notebooks/isa-api-programmatic-rebuild-of-BII-S-3.ipynb @@ -4,15 +4,13 @@ "cell_type": "markdown", "metadata": {}, "source": [ - " ### Loading the ISA-API" + "### Loading the ISA-API" ] }, { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "from isatools.model import (\n", @@ -53,9 +51,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "investigation = Investigation()\n", @@ -223,9 +219,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "study.sources = [Source(name=\"GSM255770\"), Source(name=\"GSM255771\"),Source(name=\"GSM255772\"),Source(name=\"GSM255773\")]\n", @@ -268,9 +262,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "# Starting by declaring the 2 types of assays used in BII-S-3 as coded with ISAcreator tool\n", @@ -308,9 +300,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "\n", @@ -435,9 +425,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "study.assays.append(assay)\n", @@ -447,9 +435,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "# assay_g = investigation.studies[0].assays[1]\n", @@ -506,9 +492,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "from isatools.isatab import dump\n", @@ -527,9 +511,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "from isatools.isatab import load\n", @@ -581,9 +563,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "# import hashlib\n", @@ -594,9 +574,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "import filecmp\n", @@ -607,9 +585,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "filecmp.cmp('./output/BII-S-3-synth/s_BII-S-3-synthesis.txt', './notebook-output/BII-S-3-roundtrip/s_BII-S-3-synthesis.txt')" @@ -618,9 +594,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "filecmp.cmp('./output/BII-S-3-synth/a_gilbert-assay-Gx.txt', './notebook-output/BII-S-3-roundtrip/a_gilbert-assay-Gx.txt')" @@ -629,9 +603,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [], "source": [ "filecmp.cmp('./output/BII-S-3-synth/a_gilbert-assay-Tx.txt', './notebook-output/BII-S-3-roundtrip/a_gilbert-assay-Tx.txt')" diff --git a/isatools/model/utils.py b/isatools/model/utils.py index 46032580..058c25e5 100644 --- a/isatools/model/utils.py +++ b/isatools/model/utils.py @@ -1,7 +1,5 @@ import itertools - import networkx as nx -import os from isatools.model.datafile import DataFile from isatools.model.process import Process @@ -60,7 +58,6 @@ def _expand_path(path, identifiers_to_objects, dead_end_outputs): path_modified = False for i, identifier in enumerate(path): node = identifiers_to_objects[identifier] - # If the node is a process at beginning of the path, add a path for each of its inputs. if i == 0 and isinstance(node, Process): identifier_list = [input_.sequence_identifier for input_ in node.inputs] @@ -90,7 +87,7 @@ def _expand_path(path, identifiers_to_objects, dead_end_outputs): output_sequence_identifiers = {output.sequence_identifier for output in node.outputs} input_sequence_identifiers = {input_.sequence_identifier for input_ in identifiers_to_objects[path[i + 1]].inputs} - identifier_intersection = output_sequence_identifiers.intersection(input_sequence_identifiers) + identifier_intersection = list(output_sequence_identifiers.intersection(input_sequence_identifiers)) combinations = _compute_combinations(identifier_intersection, identifiers_to_objects) for combo in combinations: @@ -206,6 +203,7 @@ def _build_paths_and_indexes(process_sequence=None): return paths, identifiers_to_objects + def _build_assay_graph(process_sequence=None): """:obj:`networkx.DiGraph` Returns a directed graph object based on a given ISA process sequence.""" @@ -289,7 +287,7 @@ def batch_create_assays(*args, n=1): from a prototype sequence (currently works only as flat end-to-end processes of Material->Process->Material->...) - :param *args: An argument list representing the process sequence prototype + # :param *args: An argument list representing the process sequence prototype :param n: Number of process sequences to create in the batch :returns: List of process sequences replicating the prototype sequence @@ -376,13 +374,13 @@ def batch_create_assays(*args, n=1): if isinstance(material_a, list): process.inputs = material_a else: - process.inputs.append(material_a) + process.inputs = [material_a] # /.append(material_a) if isinstance(material_b, list): process.outputs = material_b for material in material_b: material.derives_from = [material_a] else: - process.outputs.append(material_b) + process.outputs = [material_b] # .append(material_b) material_b.derives_from = [material_a] process_sequence.append(process) material_a = material_b @@ -402,4 +400,3 @@ def _deep_copy(isa_object): if isinstance(isa_object, ProcessSequenceNode): new_obj.assign_identifier() return new_obj - diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json index 43689513..a0684dd1 100644 --- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json +++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json @@ -1,4 +1,4 @@ -{ + { "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json", "$schema": "https://json-schema.org/draft/2020-12/schema", "title": "ISA Comment schema - it corresponds to ISA Comment[] construct", From 95a788c50a0b908118c2d16ad342478d3f5ef064 Mon Sep 17 00:00:00 2001 From: Philippe Rocca-Serra Date: Mon, 9 Sep 2024 09:33:37 +0100 Subject: [PATCH 2/3] fixes #569 --- isatools/isatab/__init__.py | 3 ++ isatools/isatab/dump/__init__.py | 2 +- isatools/isatab/dump/write.py | 28 +++++++++++++------ isatools/isatab/utils.py | 9 ++++-- isatools/model/parameter_value.py | 2 +- isatools/net/mw2isa/__init__.py | 2 +- .../core/comment_schema.json | 2 +- tests/isatab/test_isatab.py | 22 ++++++++++++++- tests/model/test_parameter_value.py | 2 +- 9 files changed, 56 insertions(+), 16 deletions(-) diff --git a/isatools/isatab/__init__.py b/isatools/isatab/__init__.py index a5ba1139..c370f1b7 100644 --- a/isatools/isatab/__init__.py +++ b/isatools/isatab/__init__.py @@ -4,6 +4,8 @@ write_study_table_files, write_assay_table_files, write_value_columns, + flatten, + dump_tables_to_dataframes ) from isatools.isatab.load import ( @@ -18,3 +20,4 @@ from isatools.isatab.defaults import default_config_dir from isatools.isatab.utils import IsaTabDataFrame, TransposedTabParser from isatools.isatab.validate import validate, batch_validate + diff --git a/isatools/isatab/dump/__init__.py b/isatools/isatab/dump/__init__.py index a5e987e2..6fc25e1d 100644 --- a/isatools/isatab/dump/__init__.py +++ b/isatools/isatab/dump/__init__.py @@ -1,2 +1,2 @@ from isatools.isatab.dump.core import dump, dumps, dump_tables_to_dataframes -from isatools.isatab.dump.write import write_study_table_files, write_assay_table_files, write_value_columns +from isatools.isatab.dump.write import write_study_table_files, write_assay_table_files, write_value_columns, flatten diff --git a/isatools/isatab/dump/write.py b/isatools/isatab/dump/write.py index 3d707c9e..bce3c2fb 100644 --- a/isatools/isatab/dump/write.py +++ b/isatools/isatab/dump/write.py @@ -26,6 +26,26 @@ ) +def flatten(current_list) -> list: + """ + :rtype: object + :param current_list: List + :return: flattened_listL: List + """ + flattened_list = [] + if current_list is not None: + + for sublist in current_list: + if sublist is not None: + for item in sublist: + flattened_list.append(item) + else: + raise ValueError + else: + raise ValueError + return flattened_list + + def write_study_table_files(inv_obj, output_dir): """Writes out study table files according to pattern defined by @@ -49,10 +69,6 @@ def write_study_table_files(inv_obj, output_dir): break protrefcount = 0 protnames = dict() - - def flatten(current_list): - return [item for sublist in current_list for item in sublist] - columns = [] # start_nodes, end_nodes = _get_start_end_nodes(s_graph) @@ -255,10 +271,6 @@ def write_assay_table_files(inv_obj, output_dir, write_factor_values=False): break protrefcount = 0 protnames = dict() - - def flatten(current_list): - return [item for sublist in current_list for item in sublist] - columns = [] paths, indexes = _build_paths_and_indexes(assay_obj.process_sequence) diff --git a/isatools/isatab/utils.py b/isatools/isatab/utils.py index 807436f8..fa6bedb4 100644 --- a/isatools/isatab/utils.py +++ b/isatools/isatab/utils.py @@ -388,10 +388,15 @@ def get_pv_columns(label, pv): """ columns = None try: - columns = ["{0}.Parameter Value[{1}]".format(label, pv.category.parameter_name.term)] + if pv.category is not None: + columns = ["{0}.Parameter Value[{1}]".format(label, pv.category.parameter_name.term)] + print(columns) + else: + raise ValueError except AttributeError: log.fatal(label, pv) - columns.extend(get_value_columns(columns[0], pv)) + if columns is not None: + columns.extend(get_value_columns(columns[0], pv)) return columns diff --git a/isatools/model/parameter_value.py b/isatools/model/parameter_value.py index d4a8219e..202e8b55 100644 --- a/isatools/model/parameter_value.py +++ b/isatools/model/parameter_value.py @@ -27,7 +27,7 @@ def __init__(self, category=None, value=None, unit=None, comments=None): # Shouldn't this be in the setter to avoid manually setting a non-numerical value when a unit is supplied ? if not isinstance(value, Number) and unit: - raise ValueError("ParameterValue value mus be quantitative (i.e. numeric) if a unit is supplied") + raise ValueError("ParameterValue value must be quantitative (i.e. numeric) if a unit is supplied") self.value = value self.unit = unit diff --git a/isatools/net/mw2isa/__init__.py b/isatools/net/mw2isa/__init__.py index f794b3e5..d47b43c8 100644 --- a/isatools/net/mw2isa/__init__.py +++ b/isatools/net/mw2isa/__init__.py @@ -60,7 +60,7 @@ def getblock(container, start_marker, end_marker): def get_archived_file(mw_study_id): - """A method of download Metabolomics Workbench archived data from their anonymous FTP site input: a valid Metabolomics + """ A method of download Metabolomics Workbench archived data from their anonymous FTP site input: a valid Metabolomics Workbench study accession number that should follow this pattern ^ST\d+[6] :param mw_study_id -> str :return: success -> boolean diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json index a0684dd1..43689513 100644 --- a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json +++ b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json @@ -1,4 +1,4 @@ - { +{ "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json", "$schema": "https://json-schema.org/draft/2020-12/schema", "title": "ISA Comment schema - it corresponds to ISA Comment[] construct", diff --git a/tests/isatab/test_isatab.py b/tests/isatab/test_isatab.py index 0488f6bf..b7bef7c5 100644 --- a/tests/isatab/test_isatab.py +++ b/tests/isatab/test_isatab.py @@ -18,8 +18,12 @@ ) from isatools.tests.utils import assert_tab_content_equal from isatools.tests import utils -from isatools.isatab import IsaTabDataFrame +from isatools.isatab import IsaTabDataFrame, flatten +from isatools.isatab.utils import ( + get_comment_column, + get_pv_columns +) def setUpModule(): if not os.path.exists(utils.DATA_DIR): @@ -94,6 +98,22 @@ def setUp(self): def tearDown(self): shutil.rmtree(self._tmp_dir) + def test_isatab_flatten(self): + test_list = None + with self.assertRaises(ValueError): + flatten(test_list) + + def test_isatab_get_pv_columns(self): + columns = [] + pp = ProtocolParameter(parameter_name="test_parameter_name") + with self.assertRaises(AttributeError): + pv = ParameterValue(category="test_parameter_name", value=3) + get_pv_columns("Protocol REF", pv) + + with self.assertRaises(AttributeError): + pv = ParameterValue(category=pp.parameter_name, value=3) + get_pv_columns("Protocol REF", pv) + def test_isatab_bad_i_file_name(self): with self.assertRaises(NameError): isatab.dump(Investigation(), self._tmp_dir, i_file_name='investigation.txt') diff --git a/tests/model/test_parameter_value.py b/tests/model/test_parameter_value.py index 8c8bcb12..3f06898c 100644 --- a/tests/model/test_parameter_value.py +++ b/tests/model/test_parameter_value.py @@ -18,7 +18,7 @@ def test_init(self): with self.assertRaises(ValueError) as context: ParameterValue(unit=OntologyAnnotation()) self.assertEqual(str(context.exception), - "ParameterValue value mus be quantitative (i.e. numeric) if a unit is supplied") + "ParameterValue value must be quantitative (i.e. numeric) if a unit is supplied") def test_category(self): self.assertIsNone(self.parameter.category) From 5a693575bd33a87f7c04585c436e934143fdcf47 Mon Sep 17 00:00:00 2001 From: Philippe Rocca-Serra Date: Mon, 9 Sep 2024 15:01:39 +0100 Subject: [PATCH 3/3] adding a check on parameter values in write_study and write_assay methods --- isatools/isatab/dump/write.py | 15 ++++--- tests/isatab/test_isatab.py | 77 +++++++++++++++++++++++++++++++++++ 2 files changed, 87 insertions(+), 5 deletions(-) diff --git a/isatools/isatab/dump/write.py b/isatools/isatab/dump/write.py index bce3c2fb..51d7cbd3 100644 --- a/isatools/isatab/dump/write.py +++ b/isatools/isatab/dump/write.py @@ -151,9 +151,11 @@ def write_study_table_files(inv_obj, output_dir): protocol_in_path_count += 1 df_dict[olabel][-1] = node.executes_protocol.name for pv in node.parameter_values: - pvlabel = "{0}.Parameter Value[{1}]".format( - olabel, pv.category.parameter_name.term) - write_value_columns(df_dict, pvlabel, pv) + if pv.category: + pvlabel = "{0}.Parameter Value[{1}]".format(olabel, pv.category.parameter_name.term) + write_value_columns(df_dict, pvlabel, pv) + else: + raise(ValueError, "Protocol Value has no valid parameter_name") if node.date is not None: df_dict[olabel + ".Date"][-1] = node.date if node.performer is not None: @@ -405,8 +407,11 @@ def pbar(x): if node.performer is not None: df_dict[olabel + ".Performer"][-1] = node.performer for pv in node.parameter_values: - pvlabel = "{0}.Parameter Value[{1}]".format(olabel, pv.category.parameter_name.term) - write_value_columns(df_dict, pvlabel, pv) + if pv.category: + pvlabel = "{0}.Parameter Value[{1}]".format(olabel, pv.category.parameter_name.term) + write_value_columns(df_dict, pvlabel, pv) + else: + raise(ValueError, "Protocol Value has no valid parameter_name") for co in node.comments: colabel = "{0}.Comment[{1}]".format(olabel, co.name) df_dict[colabel][-1] = co.value diff --git a/tests/isatab/test_isatab.py b/tests/isatab/test_isatab.py index b7bef7c5..1e83d03e 100644 --- a/tests/isatab/test_isatab.py +++ b/tests/isatab/test_isatab.py @@ -512,6 +512,83 @@ def test_simple_investigation(self): self.assertEqual(i2.studies[0].samples[0].characteristics[0].value, investigation.studies[0].samples[0].characteristics[0].value) + def test_simple_investigation_protocol_well_formed_parameter_value_use(self): + unit_source = OntologySource(name='UO', description='Unit Ontology') + investigation = Investigation(ontology_source_references=[unit_source]) + unit = OntologyAnnotation(term='mg', term_source=unit_source) + concentration_category = OntologyAnnotation(term='concentration', term_source=unit_source) + concentration = Characteristic( + value=500, + unit=unit, + category=concentration_category + ) + protocol = Protocol(name="protest", protocol_type=OntologyAnnotation(term="extraction")) + parameter = ProtocolParameter(parameter_name="param_test") + protocol.parameters.append(parameter) + source = Source(name="source_1", id_="#isatest/source_1") + sample = Sample( + name='sample1', + id_="#isatest/sample1", + characteristics=[concentration] + ) + pv = ParameterValue(category=parameter, value="T4") + ps1 = Process(executes_protocol=protocol, parameter_values=[pv], inputs=[source], outputs=[sample]) + study = Study( + title='study1', + sources=[source], + samples=[sample], + units=[unit], + characteristic_categories=[concentration_category], + protocols=[protocol], + process_sequence=[ps1] + ) + investigation.studies = [study] + i_dict = investigation.to_dict() + + i2 = Investigation() + i2.from_dict(i_dict) + self.assertEqual(i2.studies[0].samples[0].characteristics[0].value, + investigation.studies[0].samples[0].characteristics[0].value) + self.assertEqual(i2.studies[0].process_sequence[0].parameter_values[0].value.term, "T4") + + + def test_simple_investigation_protocol_badly_formed_parameter_value_use(self): + unit_source = OntologySource(name='UO', description='Unit Ontology') + investigation = Investigation(ontology_source_references=[unit_source]) + unit = OntologyAnnotation(term='mg', term_source=unit_source) + concentration_category = OntologyAnnotation(term='concentration', term_source=unit_source) + concentration = Characteristic( + value=500, + unit=unit, + category=concentration_category + ) + protocol = Protocol(name="protest", protocol_type=OntologyAnnotation(term="extraction")) + parameter = ProtocolParameter(parameter_name="param_test") + protocol.parameters.append(parameter) + source = Source(name="source_1", id_="#isatest/source_1") + sample = Sample( + name='sample1', + id_="#isatest/sample1", + characteristics=[concentration] + ) + pv = ParameterValue(value="T4") # declaration of a parameter value without a catogory + ps1 = Process(executes_protocol=protocol, parameter_values=[pv], inputs=[source], outputs=[sample]) + study = Study( + title='study1', + sources=[source], + samples=[sample], + units=[unit], + characteristic_categories=[concentration_category], + protocols=[protocol], + process_sequence=[ps1] + ) + investigation.studies = [study] + + with self.assertRaises(ValueError): + isatab.dump(investigation, self._tmp_dir, i_file_name='i_investigation.txt') + # my_json_report_isa_flux = isatab.validate(open(os.path.join(self._tab_data_dir, "issue-569", "i_investigation.txt"))) + # print(my_json_report_isa_flux) + def test_isatab_dump_investigation_with_assay(self): # Create an empty Investigation object and set some values to the # instance variables.