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ISA-TAB and ISA-TAB-Nano overview
ISA-TAB and ISA-TAB-Nano overview
ISA-TAB and ISA-TAB-Nano overview
ISA-TAB and ISA-TAB-Nano overview
ISA-TAB and ISA-TAB-Nano overview
ISA-TAB and ISA-TAB-Nano overview
ISA-TAB and ISA-TAB-Nano overview
ISA-TAB and ISA-TAB-Nano overview
ISA-TAB and ISA-TAB-Nano overview
ISA-TAB and ISA-TAB-Nano overview
ISA-TAB and ISA-TAB-Nano overview
ISA-TAB and ISA-TAB-Nano overview
ISA-TAB and ISA-TAB-Nano overview
ISA-TAB and ISA-TAB-Nano overview
ISA-TAB and ISA-TAB-Nano overview
ISA-TAB and ISA-TAB-Nano overview
ISA-TAB and ISA-TAB-Nano overview
ISA-TAB and ISA-TAB-Nano overview
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ISA-TAB and ISA-TAB-Nano overview

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  • 1. NINA JELIAZKOVA IdeaConsult Ltd. Sofia, Bulgaria www.ideaconsult.net
  • 2. Why I got interested in ISA-TAB • FP7 ToxBank project (2011-2015) http://toxbank.net/ • Database support for http://www.seurat-1.eu/ (highly heterogeneous biological experiments ) • ISA-TAB identified and accepted as a solution I D E A C O N S U L T L T D . 2 ISA-TAB http://www.isa-tools.org/
  • 3. The open source ISA metadata tracking tools help to manage an increasingly diverse set of life science, environmental and biomedical experiments that employing one or a combination of technologies. Built around the ‘Investigation’ (the project context), ‘Study’ (a unit of research) ‘Assay’ (analytical measurement) general-purpose Tabular format, the ISA tools helps you to provide rich description of the experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to- data relationships) so that the resulting data and discoveries are reproducible and reusable. I D E A C O N S U L T L T D . 3 HTTP://WWW.ISA-TOOLS.ORG
  • 4. ISA-TAB - NAMED NODES AND PROTOCOLS STUDY DESCRIPTION Source Name Characteristic s [organism] Characteristi cs [strain] Protocol REF Sampl e Name Factor Value [limiting nutrient] Factor Value [rate] Unit culture1 Saccharomyce s cerevisiae FY1679 growth protocol C-0.07- aliquot1 carbon 0.07 l/hour culture4 Saccharomyce s cerevisiae FY1679 growth protocol N-0.07- aliquot1 nitrogen 0.07 l/hour culture5 Saccharomyce s cerevisiae FY1679 growth protocol N-0.1- aliquot1 nitrogen 0.1 l/hour Source name Sample Name Protocol REF Characteristics [organism] Processed by Characteristics [strain] Factor Value [limiting nutrient] Factor Value [rate] Unit Protocol Parameter
  • 5. ISA-TAB - NAMED NODES AND PROTOCOLS ASSAY DESCRIPTION (BII-S-1 EXAMPLE) Sample name Extract Name Protocol REF Processed by Protocol REF Processed by Labeled Extract Name Protocol REF Processed by Hybridi zation Assay Name
  • 6. ISACREATOR CONFIGURATOR WWW.ISA-TOOLS.ORG 6
  • 7. ISACONFIGURATOR: SIZE MEASUREMENT / DLS 7
  • 8. DEFINE ONTOLOGY SOURCE 8
  • 9. ISACREATOR: ADD ASSAY 9
  • 10. 10 STUDY FILE ASSAY FILE DATA FILE
  • 11. ISA-TAB-NANO • ISA-TAB-Nano site https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano • ISA-TAB-Nano templates to create ISA-TAB-Nano files • Template glossary for definitions • Example files • Publications • BMC Biotechnology 2013, 13:2 http://www.biomedcentral.com/1472-6750/13/2/abstract • Commentary Nature Nanotechnology 2013, 8, 73-74 http://www.nature.com/nnano/journal/v8/n2/full/nnano.2013.12.html • NanoParticle ontology http://purl.bioontology.org/ontology/NPO • EC FP7 eNanoMapper project considers using ISA-TAB-Nano http://enanomapper.net/
  • 12. ISA-TAB-NANO EXAMPLE EMORY_ONT-GLEEACSNANO2013 12https://cananolab.nci.nih.gov/caNanoLab/characterization.do?dispatch=summaryView&sampleId=40566787&pag e=0&tab=ALL Assay files Material files Study files Investigation file https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano+Curated+Examples
  • 13. I_EMORY_ONT-GLEEACSNANO2013.TXT (INVESTIGATION) • s_EMORY_ONT-GleeACSNano2013-phys_chem.txt  a_EMORY_ONT-GleeACSNano2013-physchem_size_DLS.txt  a_EMORY_ONT-GleeACSNano2013-physchem_stability.txt  a_EMORY_ONT-GleeACSNano2013-physchem_TEM.txt  a_EMORY_ONT-GleeACSNano2013-physchem_drug_content.txt  a_EMORY_ONT-GleeACSNano2013-physchem_drug_release.txt  a_EMORY_ONT-GleeACSNano2013-physchem_protein_assay.txt  a_EMORY_ONT-GleeACSNano2013-physchem_relaxivity.txt • s_EMORY_ONT-GleeACSNano2013-in_vitro.txt  a_EMORY_ONT-GleeACSNano2013-in_vitro_cell_viability.txt  a_EMORY_ONT-GleeACSNano2013-in_vitro_targeting.txt  a_EMORY_ONT-GleeACSNano2013-in_vitro_stability.txt • s_EMORY_ONT-GleeACSNano2013-in_vivo.txt  a_EMORY_ONT-GleeACSNano2013-in_vivo_health_status.txt  a_EMORY_ONT-GleeACSNano2013-in_vivo_histology.txt  a_EMORY_ONT-GleeACSNano2013-in_vivo_therapeutic_efficacy01.txt  a_EMORY_ONT-GleeACSNano2013-in_vivo_therapeutic_efficacy02.txt 13 … and 6 m_* (Material) files
  • 14. 14 STUDY FILE ASSAY FILE MATERIAL FILE
  • 15. Material Source Name Material Name Manufacturer Lot Identifier Material Description Material Synthesis Material Design Rationale Material Intended Application Term Accession Number Term Source REF Material Type Term Accession Number Term Source REF Material Chemical Name Term Accession Number Term Source REF Characteristics[size] Unit Term Accession Number Term Source REF Material Constituent Material Linkage (removed in 1.2) Material Linkage Type Term Accession Number Term Source REF Material Data File Material Data File Type Term Accession Number Term Source REF Material Data File Description I D E A C O N S U L T L T D . 15 ISA-TAB-NANO 1.1 MATERIAL TEMPLATE FIELDS
  • 16. ISA-TAB-NANO 1.2 RELEASE NOTES Modified the ISA-TAB-Nano 1.1 version to address user comments. • Removed the Material Linkage column from the Material File. The Material Constituent column identifies the materials that are linked if the Material Linkage Type is specified. • Modified the Material Linkage Type description to indicate that if the linkage type is an entrapment or encapsulation, the Material Type column can specify whether the constituent is entrapped or encapsulated. • Rephrased Material File instructions as follows: "Materials of different chemical composition or physical characteristics should be described in separate Material files." • Enhanced the definition of material Characteristics to indicate that nominal particle characteristics (or vendor supplied) should be included in the Material File as characteristics. Experimentally determined characteristics should be included in the Assay File. I D E A C O N S U L T L T D . 16 https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano+1.2+Release+Notes
  • 17. DISCUSSION (+/-) What is the best approach describe nano materials in ISA-TAB? Sample identifiers in ISA-TAB are in principle not restricted to biological samples Biological samples characterisation are described in ISA-TAB without any extension ISA-TAB practice to describing chemical compounds = ontology entry. What if – no proper ontology entry; or batch identifier / composition (impurities, additivies) are important? (Ideas)  Chemical or material composition can be described without introducing ISA- TAB extensions  Generic types of materials could be defined in an ontology and used for annotation  similar to ChEBI ;  or The OpenTox compound service plugin for ISACreator https://github.com/ToxBank/toxbank-isa-plugin  Material samples can follow the usual ISA-TAB rules I D E A C O N S U L T L T D . 17
  • 18. CONCLUSIONS ISA-TAB • (+)Very powerful and flexible data model • (describes the experimental graph) • (+)Ontology definition and annotation of all entities • (-)Metadata only; data files not standardized • (+)But we have experience in ToxBank in standardizing data files (and converting to RDF) https://github.com/ToxBank/isa2rdf • (-)Data preparation time consuming, requires knowledge of both data modelling and biological assays. Need of tools hiding the complexity. ISA-TAB-Nano • (+)Extends ISA-TAB • (+/-)Is this the best approach describe NM in ISA-TAB? • (-)Under development • Tools not available, examples under development I D E A C O N S U L T L T D . 18

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