from bcbio import isatab
#rec= isatab.parse('/Users/abhishek/Downloads/isa_7283/')
rec= isatab.parse('/Users/abhishek/projects/isa_tab/data/ISA-tab_Munoz-Heck_July26')
#rec = isatab.parse('/Users/abhishek/projects/isa_tab/data/BII-S-3')
print rec.studies
[<bcbio.isatab.parser.ISATabStudyRecord instance at 0x1036399e0>]
print 'ISA-TAB Summary'
print '#studies %d' % len(rec.studies)
print '#assays %d' % sum([len(study.assays) for study in rec.studies])
ISA-TAB Summary #studies 1 #assays 2
for study in rec.studies:
print 'Study:---------------'
print dir(study)
"""
for assay in study.assays:
print assay.metadata
"""
Study:--------------- ['__doc__', '__init__', '__module__', '__str__', 'assays', 'contacts', 'design_descriptors', 'factors', 'metadata', 'nodes', 'protocols', 'publications']
study.contacts
[{'# Investigation File generated for Scientific Data with Investigation File Authoring Tool version 0.1.0 on 26/07/2013': '', 'Comment [Funder Term Accession Number]': '', 'Comment [Funder Term Source REF]': '', 'Comment [Funder]': '', 'Comment [Grant Identifier]': '', 'Comment [Study Person ORCID]': '', 'Study Person Address': '', 'Study Person Affiliation': 'Netherlands Proteomics Centre, Padualaan 8, Utrecht, 3584 CH, Netherlands', 'Study Person Email': 'A.J.R.Heck@uu.nl', 'Study Person Fax': '', 'Study Person First Name': 'Albert', 'Study Person Last Name': 'Heck', 'Study Person Mid Initials': '', 'Study Person Phone': '', 'Study Person Roles': '', 'Study Person Roles Term Accession Number': '', 'Study Person Roles Term Source REF': ''}, {'# Investigation File generated for Scientific Data with Investigation File Authoring Tool version 0.1.0 on 26/07/2013': '', 'Comment [Funder Term Accession Number]': '', 'Comment [Funder Term Source REF]': '', 'Comment [Funder]': '', 'Comment [Grant Identifier]': '', 'Comment [Study Person ORCID]': '', 'Study Person Address': '', 'Study Person Affiliation': 'Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht, 3584 CH, Netherlands', 'Study Person Email': '', 'Study Person Fax': '', 'Study Person First Name': 'Javier', 'Study Person Last Name': 'Munoz', 'Study Person Mid Initials': '', 'Study Person Phone': '', 'Study Person Roles': '', 'Study Person Roles Term Accession Number': '', 'Study Person Roles Term Source REF': ''}]
# Study Tite
print 'Study Title %s \n\n' % study.metadata['Study Title']
#Study Description
print 'Study Description %s \n\n' % study.metadata['Study Description']
#study submission date
print 'Study Submission Date %s \n\n ' % study.metadata['Study Submission Date']
#study public release date
print 'Study Public Release Date %s ' % study.metadata['Study Public Release Date']
Study Title Proteomic Profiles of Human Embryonic Stem Cells, Induced-Pluripotent Stem Cells and Precursor Fibroblasts Study Description Study Submission Date Study Public Release Date
#1. Study Design Type
' '.join([ descp['Study Design Type'] for descp in study.design_descriptors ])
'cell type comparison design growth condition intervention design'
dir(study)
['__doc__', '__init__', '__module__', '__str__', 'assays', 'contacts', 'design_descriptors', 'factors', 'metadata', 'nodes', 'protocols', 'publications']
#contacts
#working on following structure
'''
{'Study Person Address': 'Prospect Place, Plymouth, United Kingdom',
'Study Person Affiliation': 'Plymouth Marine Laboratory',
'Study Person Email': 'jagi@pml.ac.uk',
'Study Person Fax': '',
'Study Person First Name': 'Jack',
'Study Person Last Name': 'Gilbert',
'Study Person Mid Initials': 'A',
'Study Person Phone': '',
'Study Person Roles': 'principal investigator role',
'Study Person Roles Term Accession Number': '103',
'Study Person Roles Term Source REF': 'OBI'},
'''
full_names = []
for contact in study.contacts:
full_name = '%s %s %s' % ( contact.get('Study Person First Name','NA'),
contact.get('Study Person Mid Initials','NA'),
contact.get('Study Person Last Name'))
full_names.append(full_name)
print ', '.join(full_names)
Albert Heck, Javier Munoz
study.publications
[{'Study PubMed ID': 'PMID: 22108792', 'Study Publication Author List': 'Munoz J, Low TY, Kok YJ, Chin A, Frese CK, Ding V, Choo A, Heck AJ', 'Study Publication DOI': 'doi: 10.1038/msb.2011.84', 'Study Publication Status': 'published', 'Study Publication Status Term Accession Number': '', 'Study Publication Status Term Source REF': '', 'Study Publication Title': 'The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells'}]
#publications
publications_line = ''
for publication in study.publications:
publications_line += publication['Study Publication Author list'] + '\n'
publications_line += publication['Study Publication Title']
publications_line += '[Pubmed](http://www.ncbi.nlm.nih.gov/pubmed/%s) \n\n' % publication.get('Study PubMed ID','NA')
print publications_line
--------------------------------------------------------------------------- KeyError Traceback (most recent call last) <ipython-input-14-7f32aac0de91> in <module>() 2 publications_line = '' 3 for publication in study.publications: ----> 4 publications_line += publication['Study Publication Author list'] + '\n' 5 publications_line += publication['Study Publication Title'] 6 publications_line += '[Pubmed](http://www.ncbi.nlm.nih.gov/pubmed/%s) \n\n' % publication.get('Study PubMed ID','NA') KeyError: 'Study Publication Author list'
for protocol in study.protocols:
print protocol.get('Study Protocol Name','NA')
print '%s' % protocol.get('Study Protocol Description', 'NA')
Cell Culture Flow cytometry analysis (FACS) Staining of hESC for markers Karyotypic stability In-vivo differentiation assay, SCID mice model and teratoma analysis Sample preparation for MS Mass spectrometric analysis Data processing RNA isolation Transcriptome analysis Microarray data analysis
for assay in study.assays:
print dir(assay)
for key,val in assay.nodes.iteritems():
print key
print '----------'
['__doc__', '__init__', '__module__', '__str__', 'metadata', 'nodes'] ftp://ftp.pride.ebi.ac.uk/2013/02/PXD000134/OR1_091015_Javier_iPS_Singapore_Mix1_BigSCX*.raw ftp://ftp.pride.ebi.ac.uk/2013/02/PXD000134/4Skin_Mix2_SCX*.raw ftp://ftp.pride.ebi.ac.uk/2013/02/PXD000134/4Skin_Mix1_SCX*.raw ftp://ftp.pride.ebi.ac.uk/2013/02/PXD000134/OR1_091015_Javier_iPS_Singapore_Mix2_BigSCX*.raw ---------- ['__doc__', '__init__', '__module__', '__str__', 'metadata', 'nodes'] http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649323&format=file&file=GSM649323%2ECEL%2Egz http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649336&format=file&file=GSM649336%2ECEL%2Egz http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649335&format=file&file=GSM649335%2ECEL%2Egz http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649337&format=file&file=GSM649337%2ECEL%2Egz http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649332&format=file&file=GSM649332%2ECEL%2Egz http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649324&format=file&file=GSM649324%2ECEL%2Egz http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649321&format=file&file=GSM649321%2ECEL%2Egz http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649333&format=file&file=GSM649333%2ECEL%2Egz http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649320&format=file&file=GSM649320%2ECEL%2Egz http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649319&format=file&file=GSM649319%2ECEL%2Egz http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649322&format=file&file=GSM649322%2ECEL%2Egz http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649334&format=file&file=GSM649334%2ECEL%2Egz ----------
print assay
* Assay metadata: {'Study Assay File Name': 'a_assay_SCIDATA-example1-2.txt', 'Study Assay Measurement Type': 'transcription profiling', 'Study Assay Measurement Type Term Accession Number': '', 'Study Assay Measurement Type Term Source REF': '', 'Study Assay Technology Platform': 'Affymetrix U133 Plus 2.0 GeneChip Microarrays', 'Study Assay Technology Type': 'DNA microarray', 'Study Assay Technology Type Term Accession Number': '', 'Study Assay Technology Type Term Source REF': ''} nodes: * Node http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649323&format=file&file=GSM649323%2ECEL%2Egz Raw Data File metadata: {'Data Record Accession': [Attrs(Data_Record_Accession='GSE26451'), Attrs(Data_Record_Accession='')], 'Data Repository': [Attrs(Data_Repository=''), Attrs(Data_Repository='Gene Expression Omnibus')], 'Derived Data File': [''], 'Label': [Attrs(Label='')], 'Labeled Extract Name': [Attrs(Labeled_Extract_Name='')], 'Protocol REF': [Attrs(Protocol_REF='Microarray data analysis'), Attrs(Protocol_REF=''), Attrs(Protocol_REF='Transcriptome analysis'), Attrs(Protocol_REF='RNA isolation')], 'Raw Data File': ['http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649323&format=file&file=GSM649323%2ECEL%2Egz'], 'Sample Name': ['4Skin_Fibro_1']} * Node http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649336&format=file&file=GSM649336%2ECEL%2Egz Raw Data File metadata: {'Data Record Accession': [Attrs(Data_Record_Accession='GSE26453'), Attrs(Data_Record_Accession='')], 'Data Repository': [Attrs(Data_Repository=''), Attrs(Data_Repository='Gene Expression Omnibus')], 'Derived Data File': [''], 'Label': [Attrs(Label='')], 'Labeled Extract Name': [Attrs(Labeled_Extract_Name='')], 'Protocol REF': [Attrs(Protocol_REF='Microarray data analysis'), Attrs(Protocol_REF=''), Attrs(Protocol_REF='Transcriptome analysis'), Attrs(Protocol_REF='RNA isolation')], 'Raw Data File': ['http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649336&format=file&file=GSM649336%2ECEL%2Egz'], 'Sample Name': ['IMR90_Fibro_1']} * Node http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649335&format=file&file=GSM649335%2ECEL%2Egz Raw Data File metadata: {'Data Record Accession': [Attrs(Data_Record_Accession='GSE26453'), Attrs(Data_Record_Accession='')], 'Data Repository': [Attrs(Data_Repository=''), Attrs(Data_Repository='Gene Expression Omnibus')], 'Derived Data File': [''], 'Label': [Attrs(Label='')], 'Labeled Extract Name': [Attrs(Labeled_Extract_Name='')], 'Protocol REF': [Attrs(Protocol_REF='Microarray data analysis'), Attrs(Protocol_REF=''), Attrs(Protocol_REF='Transcriptome analysis'), Attrs(Protocol_REF='RNA isolation')], 'Raw Data File': ['http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649335&format=file&file=GSM649335%2ECEL%2Egz'], 'Sample Name': ['HES-3_2']} * Node http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649337&format=file&file=GSM649337%2ECEL%2Egz Raw Data File metadata: {'Data Record Accession': [Attrs(Data_Record_Accession='GSE26453'), Attrs(Data_Record_Accession='')], 'Data Repository': [Attrs(Data_Repository=''), Attrs(Data_Repository='Gene Expression Omnibus')], 'Derived Data File': [''], 'Label': [Attrs(Label='')], 'Labeled Extract Name': [Attrs(Labeled_Extract_Name='')], 'Protocol REF': [Attrs(Protocol_REF='Microarray data analysis'), Attrs(Protocol_REF=''), Attrs(Protocol_REF='Transcriptome analysis'), Attrs(Protocol_REF='RNA isolation')], 'Raw Data File': ['http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649337&format=file&file=GSM649337%2ECEL%2Egz'], 'Sample Name': ['IMR90_Fibro_2']} * Node http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649332&format=file&file=GSM649332%2ECEL%2Egz Raw Data File metadata: {'Data Record Accession': [Attrs(Data_Record_Accession='GSE26453'), Attrs(Data_Record_Accession='')], 'Data Repository': [Attrs(Data_Repository=''), Attrs(Data_Repository='Gene Expression Omnibus')], 'Derived Data File': [''], 'Label': [Attrs(Label='')], 'Labeled Extract Name': [Attrs(Labeled_Extract_Name='')], 'Protocol REF': [Attrs(Protocol_REF='Microarray data analysis'), Attrs(Protocol_REF=''), Attrs(Protocol_REF='Transcriptome analysis'), Attrs(Protocol_REF='RNA isolation')], 'Raw Data File': ['http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649332&format=file&file=GSM649332%2ECEL%2Egz'], 'Sample Name': ['IMR90_iPS_1']} * Node http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649324&format=file&file=GSM649324%2ECEL%2Egz Raw Data File metadata: {'Data Record Accession': [Attrs(Data_Record_Accession='GSE26451'), Attrs(Data_Record_Accession='')], 'Data Repository': [Attrs(Data_Repository=''), Attrs(Data_Repository='Gene Expression Omnibus')], 'Derived Data File': [''], 'Label': [Attrs(Label='')], 'Labeled Extract Name': [Attrs(Labeled_Extract_Name='')], 'Protocol REF': [Attrs(Protocol_REF='Microarray data analysis'), Attrs(Protocol_REF=''), Attrs(Protocol_REF='Transcriptome analysis'), Attrs(Protocol_REF='RNA isolation')], 'Raw Data File': ['http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649324&format=file&file=GSM649324%2ECEL%2Egz'], 'Sample Name': ['4Skin_Fibro_2']} * Node http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649321&format=file&file=GSM649321%2ECEL%2Egz Raw Data File metadata: {'Data Record Accession': [Attrs(Data_Record_Accession='GSE26451'), Attrs(Data_Record_Accession='')], 'Data Repository': [Attrs(Data_Repository=''), Attrs(Data_Repository='Gene Expression Omnibus')], 'Derived Data File': [''], 'Label': [Attrs(Label='')], 'Labeled Extract Name': [Attrs(Labeled_Extract_Name='')], 'Protocol REF': [Attrs(Protocol_REF='Microarray data analysis'), Attrs(Protocol_REF=''), Attrs(Protocol_REF='Transcriptome analysis'), Attrs(Protocol_REF='RNA isolation')], 'Raw Data File': ['http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649321&format=file&file=GSM649321%2ECEL%2Egz'], 'Sample Name': ['HES-3_3']} * Node http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649333&format=file&file=GSM649333%2ECEL%2Egz Raw Data File metadata: {'Data Record Accession': [Attrs(Data_Record_Accession='GSE26453'), Attrs(Data_Record_Accession='')], 'Data Repository': [Attrs(Data_Repository=''), Attrs(Data_Repository='Gene Expression Omnibus')], 'Derived Data File': [''], 'Label': [Attrs(Label='')], 'Labeled Extract Name': [Attrs(Labeled_Extract_Name='')], 'Protocol REF': [Attrs(Protocol_REF='Microarray data analysis'), Attrs(Protocol_REF=''), Attrs(Protocol_REF='Transcriptome analysis'), Attrs(Protocol_REF='RNA isolation')], 'Raw Data File': ['http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649333&format=file&file=GSM649333%2ECEL%2Egz'], 'Sample Name': ['IMR90_iPS_2']} * Node http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649320&format=file&file=GSM649320%2ECEL%2Egz Raw Data File metadata: {'Data Record Accession': [Attrs(Data_Record_Accession='GSE26451'), Attrs(Data_Record_Accession='')], 'Data Repository': [Attrs(Data_Repository=''), Attrs(Data_Repository='Gene Expression Omnibus')], 'Derived Data File': [''], 'Label': [Attrs(Label='')], 'Labeled Extract Name': [Attrs(Labeled_Extract_Name='')], 'Protocol REF': [Attrs(Protocol_REF='Microarray data analysis'), Attrs(Protocol_REF=''), Attrs(Protocol_REF='Transcriptome analysis'), Attrs(Protocol_REF='RNA isolation')], 'Raw Data File': ['http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649320&format=file&file=GSM649320%2ECEL%2Egz'], 'Sample Name': ['4Skin_iPS_2']} * Node http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649319&format=file&file=GSM649319%2ECEL%2Egz Raw Data File metadata: {'Data Record Accession': [Attrs(Data_Record_Accession='GSE26451'), Attrs(Data_Record_Accession='')], 'Data Repository': [Attrs(Data_Repository=''), Attrs(Data_Repository='Gene Expression Omnibus')], 'Derived Data File': [''], 'Label': [Attrs(Label='')], 'Labeled Extract Name': [Attrs(Labeled_Extract_Name='')], 'Protocol REF': [Attrs(Protocol_REF='Microarray data analysis'), Attrs(Protocol_REF=''), Attrs(Protocol_REF='Transcriptome analysis'), Attrs(Protocol_REF='RNA isolation')], 'Raw Data File': ['http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649319&format=file&file=GSM649319%2ECEL%2Egz'], 'Sample Name': ['4Skin_iPS_1']} * Node http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649322&format=file&file=GSM649322%2ECEL%2Egz Raw Data File metadata: {'Data Record Accession': [Attrs(Data_Record_Accession='GSE26451'), Attrs(Data_Record_Accession='')], 'Data Repository': [Attrs(Data_Repository=''), Attrs(Data_Repository='Gene Expression Omnibus')], 'Derived Data File': [''], 'Label': [Attrs(Label='')], 'Labeled Extract Name': [Attrs(Labeled_Extract_Name='')], 'Protocol REF': [Attrs(Protocol_REF='Microarray data analysis'), Attrs(Protocol_REF=''), Attrs(Protocol_REF='Transcriptome analysis'), Attrs(Protocol_REF='RNA isolation')], 'Raw Data File': ['http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649322&format=file&file=GSM649322%2ECEL%2Egz'], 'Sample Name': ['HES-3_4']} * Node http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649334&format=file&file=GSM649334%2ECEL%2Egz Raw Data File metadata: {'Data Record Accession': [Attrs(Data_Record_Accession='GSE26453'), Attrs(Data_Record_Accession='')], 'Data Repository': [Attrs(Data_Repository=''), Attrs(Data_Repository='Gene Expression Omnibus')], 'Derived Data File': [''], 'Label': [Attrs(Label='')], 'Labeled Extract Name': [Attrs(Labeled_Extract_Name='')], 'Protocol REF': [Attrs(Protocol_REF='Microarray data analysis'), Attrs(Protocol_REF=''), Attrs(Protocol_REF='Transcriptome analysis'), Attrs(Protocol_REF='RNA isolation')], 'Raw Data File': ['http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM649334&format=file&file=GSM649334%2ECEL%2Egz'], 'Sample Name': ['HES-3_1']}
dir(assay)
['__doc__', '__init__', '__module__', '__str__', 'metadata', 'nodes']
assay.metadata
{'Study Assay File Name': 'a_gilbert-assay-Tx.txt', 'Study Assay Measurement Type': 'transcription profiling', 'Study Assay Measurement Type Term Accession Number': '424', 'Study Assay Measurement Type Term Source REF': 'OBI', 'Study Assay Technology Platform': '454 Genome Sequencer FS', 'Study Assay Technology Type': 'nucleotide sequencing', 'Study Assay Technology Type Term Accession Number': '', 'Study Assay Technology Type Term Source REF': 'OBI'}
for node in assay.nodes:
print assay.nodes.get(node,'NA')
* Node EVHINN104.sff Raw Data File metadata: {'Derived Data File': ['GSE10119_series_matrix.txt'], 'Material Type': [Attrs(Material_Type='mRNA', Term_Source_REF='CHEBI', Term_Accession_Number='16991')], 'Protocol REF': [Attrs(Protocol_REF='mRNA extraction - standard procedure 3'), Attrs(Protocol_REF='nucleic acid extraction - standard procedure 2'), Attrs(Protocol_REF='library construction'), Attrs(Protocol_REF='sequence analysis - standard procedure 7'), Attrs(Protocol_REF='reverse transcription - standard procedure 5'), Attrs(Protocol_REF='pyrosequencing - standard procedure 6')], 'Raw Data File': ['EVHINN104.sff'], 'Sample Name': ['GSM255770']} * Node EVHINN115.sff Raw Data File metadata: {'Derived Data File': ['GSE10119_series_matrix.txt'], 'Material Type': [Attrs(Material_Type='mRNA', Term_Source_REF='CHEBI', Term_Accession_Number='16991')], 'Protocol REF': [Attrs(Protocol_REF='mRNA extraction - standard procedure 3'), Attrs(Protocol_REF='nucleic acid extraction - standard procedure 2'), Attrs(Protocol_REF='library construction'), Attrs(Protocol_REF='sequence analysis - standard procedure 7'), Attrs(Protocol_REF='reverse transcription - standard procedure 5'), Attrs(Protocol_REF='pyrosequencing - standard procedure 6')], 'Raw Data File': ['EVHINN115.sff'], 'Sample Name': ['GSM255773']} * Node EVHINN105.sff Raw Data File metadata: {'Derived Data File': ['GSE10119_series_matrix.txt'], 'Material Type': [Attrs(Material_Type='mRNA', Term_Source_REF='CHEBI', Term_Accession_Number='16991')], 'Protocol REF': [Attrs(Protocol_REF='mRNA extraction - standard procedure 3'), Attrs(Protocol_REF='nucleic acid extraction - standard procedure 2'), Attrs(Protocol_REF='library construction'), Attrs(Protocol_REF='sequence analysis - standard procedure 7'), Attrs(Protocol_REF='reverse transcription - standard procedure 5'), Attrs(Protocol_REF='pyrosequencing - standard procedure 6')], 'Raw Data File': ['EVHINN105.sff'], 'Sample Name': ['GSM255771']} * Node EVNG8PH03.sff Raw Data File metadata: {'Derived Data File': ['GSE10119_series_matrix.txt'], 'Material Type': [Attrs(Material_Type='mRNA', Term_Source_REF='CHEBI', Term_Accession_Number='16991')], 'Protocol REF': [Attrs(Protocol_REF='mRNA extraction - standard procedure 3'), Attrs(Protocol_REF='nucleic acid extraction - standard procedure 2'), Attrs(Protocol_REF='library construction'), Attrs(Protocol_REF='sequence analysis - standard procedure 7'), Attrs(Protocol_REF='reverse transcription - standard procedure 5'), Attrs(Protocol_REF='pyrosequencing - standard procedure 6')], 'Raw Data File': ['EVNG8PH03.sff'], 'Sample Name': ['GSM255772']} * Node EVUSNDQ01.sff Raw Data File metadata: {'Derived Data File': ['GSE10119_series_matrix.txt'], 'Material Type': [Attrs(Material_Type='mRNA', Term_Source_REF='CHEBI', Term_Accession_Number='16991')], 'Protocol REF': [Attrs(Protocol_REF='mRNA extraction - standard procedure 3'), Attrs(Protocol_REF='nucleic acid extraction - standard procedure 2'), Attrs(Protocol_REF='library construction'), Attrs(Protocol_REF='sequence analysis - standard procedure 7'), Attrs(Protocol_REF='reverse transcription - standard procedure 5'), Attrs(Protocol_REF='pyrosequencing - standard procedure 6')], 'Raw Data File': ['EVUSNDQ01.sff'], 'Sample Name': ['GSM255770']} * Node EVHINN101.sff Raw Data File metadata: {'Derived Data File': ['GSE10119_series_matrix.txt'], 'Material Type': [Attrs(Material_Type='mRNA', Term_Source_REF='CHEBI', Term_Accession_Number='16991')], 'Protocol REF': [Attrs(Protocol_REF='mRNA extraction - standard procedure 3'), Attrs(Protocol_REF='nucleic acid extraction - standard procedure 2'), Attrs(Protocol_REF='library construction'), Attrs(Protocol_REF='sequence analysis - standard procedure 7'), Attrs(Protocol_REF='reverse transcription - standard procedure 5'), Attrs(Protocol_REF='pyrosequencing - standard procedure 6')], 'Raw Data File': ['EVHINN101.sff'], 'Sample Name': ['GSM255770']} * Node EVHINN108.sff Raw Data File metadata: {'Derived Data File': ['GSE10119_series_matrix.txt'], 'Material Type': [Attrs(Material_Type='mRNA', Term_Source_REF='CHEBI', Term_Accession_Number='16991')], 'Protocol REF': [Attrs(Protocol_REF='mRNA extraction - standard procedure 3'), Attrs(Protocol_REF='nucleic acid extraction - standard procedure 2'), Attrs(Protocol_REF='library construction'), Attrs(Protocol_REF='sequence analysis - standard procedure 7'), Attrs(Protocol_REF='reverse transcription - standard procedure 5'), Attrs(Protocol_REF='pyrosequencing - standard procedure 6')], 'Raw Data File': ['EVHINN108.sff'], 'Sample Name': ['GSM255771']} * Node EVHINN103.sff Raw Data File metadata: {'Derived Data File': ['GSE10119_series_matrix.txt'], 'Material Type': [Attrs(Material_Type='mRNA', Term_Source_REF='CHEBI', Term_Accession_Number='16991')], 'Protocol REF': [Attrs(Protocol_REF='mRNA extraction - standard procedure 3'), Attrs(Protocol_REF='nucleic acid extraction - standard procedure 2'), Attrs(Protocol_REF='library construction'), Attrs(Protocol_REF='sequence analysis - standard procedure 7'), Attrs(Protocol_REF='reverse transcription - standard procedure 5'), Attrs(Protocol_REF='pyrosequencing - standard procedure 6')], 'Raw Data File': ['EVHINN103.sff'], 'Sample Name': ['GSM255770']} * Node EVNG8PH02.sff Raw Data File metadata: {'Derived Data File': ['GSE10119_series_matrix.txt'], 'Material Type': [Attrs(Material_Type='mRNA', Term_Source_REF='CHEBI', Term_Accession_Number='16991')], 'Protocol REF': [Attrs(Protocol_REF='mRNA extraction - standard procedure 3'), Attrs(Protocol_REF='nucleic acid extraction - standard procedure 2'), Attrs(Protocol_REF='library construction'), Attrs(Protocol_REF='sequence analysis - standard procedure 7'), Attrs(Protocol_REF='reverse transcription - standard procedure 5'), Attrs(Protocol_REF='pyrosequencing - standard procedure 6')], 'Raw Data File': ['EVNG8PH02.sff'], 'Sample Name': ['GSM255771']} * Node EVHINN111.sff Raw Data File metadata: {'Derived Data File': ['GSE10119_series_matrix.txt'], 'Material Type': [Attrs(Material_Type='mRNA', Term_Source_REF='CHEBI', Term_Accession_Number='16991')], 'Protocol REF': [Attrs(Protocol_REF='mRNA extraction - 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