ASTM E2909-2013 Standard Guide for Investigation Study Assay Tab-Delimited Format for Nanotechnologies (ISA-TAB-Nano) Standard File Format for the Submission and Exchange of Data o.pdf

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1、Designation: E2909 13Standard Guide forInvestigation/Study/Assay Tab-Delimited Format forNanotechnologies (ISA-TAB-Nano): Standard File Format forthe Submission and Exchange of Data on Nanomaterialsand Characterizations1This standard is issued under the fixed designation E2909; the number immediatel

2、y following the designation indicates the year oforiginal adoption or, in the case of revision, the year of last revision. A number in parentheses indicates the year of last reapproval. Asuperscript epsilon () indicates an editorial change since the last revision or reapproval.1. Scope1.1 This guide

3、 (ISA-TAB-Nano) specifies the format forrepresenting and sharing information about nanomaterials,small molecules and biological specimens along with theirassay characterization data (including metadata, and summarydata) using spreadsheet or TAB-delimited files.1.2 The Appendices Sections contain a d

4、etailed listing ofISA-TAB-Nano fields (Appendix X1), a practical example(Appendix X2), a discussion of optional files (Appendix X3),and summary of background (Appendix X4).1.3 The values stated in SI units are to be regarded asstandard. No other units of measurement are included in thisstandard.1.4

5、This standard does not purport to address all of thesafety concerns, if any, associated with its use. It is theresponsibility of the user of this standard to establish appro-priate safety and health practices and determine the applica-bility of regulatory limitations prior to use.2. Referenced Docum

6、ents2.1 ISA-TAB Format Specification:2ISA-TAB Release Candidate 1.0 ISA-TAB 1.02.2 Assay Protocol Documents from NCL:3NCL Method GTA-1 (Version 1.1) LLC-PK1 Kidney Cyto-toxicity Assay2.3 Reports from NCL:4NCL200612A Dendrimer-Based MRI Contrast Agents, Pre-pared for Dendritic Nanotechnologies, Inc.

7、December20063. Significance and Use3.1 This guide is intended to facilitate the meaningfulsubmission and exchange of nanomaterial descriptions andcharacterization data (metadata and summary data) along withthe other files (raw/derived data files, image files, protocoldocuments, etc.) among individua

8、l researchers and to or fromnanotechnology resources. This guide also serves to empowerorganizations to adopt standard methods for representing datain nanotechnology publications; and to provide researcherswith guidelines for representing nanomaterials and character-izations to achieve cross-materia

9、l comparison. This guideencourages standardization in the field of informatics, whereadherence ISA-TAB-Nano concepts nanotechnology to abroader and established bioinformatics community.3.2 The format of this guide is of a file structure thatcontains four primary filesinvestigation, study, assay (ISA

10、),and material files.3.2.1 In addition, raw or derived data files and any otherfiles (for example, image files, protocol documents) specific toeach assay can be shared along with the four primary ISA-TAB-Nano files if the data files are referenced in the primaryISA-TAB-Nano files. The specification

11、does not provide for-mat specification for files other than the four primary files:investigation, study, assay, and material files. The ISA-TAB-Nano investigation file is used for three purposes: (1) to recordall declarative information referenced in other files; (2)to1This guide is under the jurisd

12、iction of ASTM Committee E56 on Nanotech-nology and is the direct responsibility of Subcommittee E56.01 on Informatics andTerminology.Current edition approved Feb. 1, 2013. Published April 2013. DOI: 10.1520/E2909-13.2Available from ISAtools, http:/isa-tools.org.3Available from Nanotechnology Charac

13、terization Laboratory (NCL), FrederickNational Laboratory for Cancer Research, SAIC-Frederick, Inc., P.O. Box B,Frederick, MD 21702-1201, http:/ncl.cancer.gov.4Available from Nanotechnology Characterization Laboratory (NCL), FrederickNational Laboratory for Cancer Research, SAIC-Frederick, Inc., P.O

14、. Box B,Frederick, MD 21702-1201, http:/ncl.cancer.gov. Download available from http:/ncl.cancer.gov/120406.pdf.Copyright ASTM International, 100 Barr Harbor Drive, PO Box C700, West Conshohocken, PA 19428-2959. United States1relate assay files to study files; and (3) to group multiple studyfiles th

15、at are part of the same investigation. The ISA-TAB-Nano study file is used to record information about the source,sampling methodology, treatment, preparation, and character-istics of the subjects (biospecimens) studied using one or moreassays under an investigation. The ISA-TAB-Nano assay filerecor

16、ds the assay protocol names, endpoint measurements andreferences to image/data files; and the material file is used torepresent the composition and characteristics of nanoparticleformulations and small molecules.3.2.2 Use of Ontologies and Standard Terminologies inISA-TAB-Nano:3.2.2.1 ISA-TAB-Nano p

17、rovides fields for entering andreferencing terms selected from ontologies and standard termi-nologies. The ontologies are available at BioPortal,5which ismaintained by the National Center for Biomedical Ontologies.Though the investigator may use alternative ontology andvocabulary sources, the abilit

18、y to evaluate and share datarequire that all parties have access to those being used (theyshould be available to the investigators). All terms and fieldsused in this guide utilize the NCI EVS and NanoparticleOntology elements. The NanoParticle Ontology (NPO)6pro-vides a subset of the terms and relat

19、ionships for the descriptionand characterization of nanomaterials in the ISA-TAB-Nanofile format.3.2.2.2 Distinction Between Biological and Non-BiologicalSamplesIn nanotechnology, samples from biological andnon-biological sources can be the primary subjects of a study.Therefore, in ISA-TAB-Nano, sam

20、ples derived from biologicalsources are called biological specimens or biospecimens (forexample, cell line, body fluids, organs, etc.). Whereas, samplesderived from non-biological sources are simply called materialsamples (for example, nanomaterials, nanoparticleformulations, small molecules). For p

21、hysico-chemical charac-terizations of nanomaterials, the sample is the nanomaterial.For in-vitro and in-vivo characterizations, the sample is thebiological specimen (cell line, animal, and so forth). Hence, inISA-TAB-Nano, the concept of a sample is defined to includeboth biological specimens and ma

22、terial samples. The ISA-TAB-Nano study file can only be used to record the source andcharacteristics of biospecimens studied in an assay and cannotsupport the representation of materials. Therefore, in ISA-TAB-Nano, the material file is used to describe materialsamples, while the study file is used

23、to describe biospecimens.3.2.2.3 ISA-TAB-Nano File NamesISA-TAB-Nano filenames may end in either .txt or .xls extensions. The ISA-TAB-Nano files used as examples in this document were prepared inexcel spreadsheets, and so their filenames have the .xlsextension.4. ISA-TAB-Nano Release Candidate 1.0 F

24、iles and Struc-ture4.1 ISA-TAB-Nano File Structure:4.1.1 ISA-TAB-Nano uses four primary files investigationfile, study file, assay file and material file (Fig. 1). Other filessuch as raw/derived data files, image files, protocol documents,etc., referenced in the ISA-TAB-Nano files have to be shareda

25、long with the ISA-TAB-Nano files.4.1.2 When sharing primary ISA-TAB-Nano files, otherfiles referenced in these files have to be shared along with theprimary files.4.2 ISA-TAB-Nano File Development Process:4.2.1 In Fig. 2, the ISA-TAB-Nano file development processis described. Typically, the investig

26、ation file is developed firstand describes the overall investigation, associated studies andassays. The investigation file is a text file with a namingconvention of “i_xxx.txt” or “i_xxx.xls,” in which xxx can beany name provided by the investigator. Once the investigationfile has been completed, on

27、e or more study files (following theconvention “s_xxx.txt” or “s_xxx.xls”) can be created.Similarly, one or more material files can be created. Thematerial file describes the nanomaterial (or small molecule)and its components including structural information and fol-lows the naming convention “m_xxx

28、.txt” or “m_xxx.xls”.Assay files (following the convention “a_xxx.txt” or “a_xxx.xls”) are created for all assays performed. Each assay isdefined by the endpoint measured and the technique used tomeasure that endpoint. Data files (raw or derived) specific toeach type of assay can be associated to th

29、e respective assayfiles by referencing the names of the data files in the assay files.5Available from BioPortal, The National Center for Biomedical Ontology,Stanford Biomedical Informatics Research, Medical School Office Building X-215,1265 Welch Road, Stanford, CA 94305-5479, http:/www.bioontology.

30、org.6Thomas, D.G., Pappu, R.V., and Baker, N.A., “Nanoparticle Ontology forCancer Nanotechnology Research,” Journal of Biomedical Informatics, Vol 44, No.1, 2011, pp. 5974, http:/www.nano-ontology.org.FIG. 1 ISA-TAB-Nano File StructureE2909 1324.3 Once the ISA-TAB-Nano files have been created, thefi

31、les can be validated and submitted into nanotechnologyresources that support the ISA-TAB-Nano specification.4.4 ISA-TAB-Nano File Descriptions4.4.1 Investigation File:4.4.1.1 Description:(1) The ISA-TAB-Nano investigation allows for the de-scription of the primary investigation and associated studie

32、sincluding assays and protocols. An investigation can have oneor more studies. For example, an investigation titled“Dendrimer-Based MRI Contrast Agents” may have two stud-ies titled as “Characterizing the Size of Dendrimer based MRIContrast Agents” and “Determining the cytotoxicity propertyof Dendri

33、mer based MRI Contrast Agents in porcine proximaltubule cells.” Each study can have one or more assaysdepending on the endpoint measured and the technique used.For example, a cytotoxicity study may be conducted using anMTT assay and a LDH release assay. A size characterizationstudy can include two t

34、ypes of assays based on the techniqueused one using DLS and the other using AFM.(2) The ISA-TAB-Nano guide provides flexibility in rep-resenting the level of granularity in information associated witha study; however, the level of granularity should factor in theeffective representation of assays an

35、d protocols in conformancewith the specification. For example, a study focusing on “SizeCharacterizations” will have multiple size measurements (forexample, Z-average size, hydrodynamic size) and may involvethe use of multiple techniques (for example, size by DLS, sizeby AFM). These can be represent

36、ed effectively in the ISA-TAB-Nano file structure.(3) The investigation file provides descriptive informationabout studies including design descriptors, publications,factors, assays, protocols, and contacts. This descriptive infor-mation lays the foundation for other ISA-TAB-Nano files. Forexample,

37、Table 1 shows a subset of the Investigation File,which is the study factors section of the investigation file. Thissection provides the names of factors (for example,temperature, solvent medium) used in the study and theirassociated units of measurement (if the factors are quantita-tive). The values

38、 of these factors (for example, PBS, 25Celsius) are specified either in the study or the assay file.4.4.1.2 File FormatThe ISA-TAB-Nano investigation fileis a vertical-based spreadsheet format with row headers in thefirst column, as shown in Table 1. The fields are divided intosections, therefore, t

39、he field values in the investigation file areentered in column order. For instance, in Table 1, Column Aindicates the field names and Columns B and C contain thefield values.4.4.2 Study File:4.4.2.1 DescriptionThe ISA-TAB-Nano study file pro-vides a mapping between the samples (biospecimens andmater

40、ial samples) and processing events (occurs whenever aprotocol is applied) associated with a study. It is also used toprovide values for the parameters and factors associated withan assay of the sample. In ISA-TAB-Nano, factors can beeither entered in the study file or in the assay file. Forphysico-c

41、hemical characterizations of nanomaterials, thesample is the nanomaterial. For in-vitro and in-vivocharacterizations, the sample is the biological specimen (cellFIG. 2 ISA-TAB-Nano File Development ProcessTABLE 1 Example Subset of the Investigation File FormatABCSTUDY FACTORSStudy Factor Name temper

42、ature solvent mediumTerm AccessionNumberPATO_0000146 NPO_1855Term Source REF PATO NPOStudy Factor Type condition conditionTerm AccessionNumberTerm Source REFTABLE 2 Extensions and Constraints Applied to the ISA-TABInvestigation File in Support of ISA-TAB-NanoSection Field ChangeField Status(if appli

43、cable)INVESTIGATION InvestigationdiseaseAddition OptionalINVESTIGATION InvestigationoutcomeAddition OptionalSTUDY Study disease Addition OptionalSTUDY Study outcome Addition OptionalSTUDY ASSAYS Study assaymeasurementnameAddition OptionalE2909 133line, animal, and so forth). The nanomaterial applied

44、 to abiospecimen in an in-vitro or in-vivo assay is considered as astudy factor along with other factors that vary in the experi-ment (for example, dose). The study file is required as itfunctions as the primary mapping file between the samples andthe assay. For studies involving nanomaterials (also

45、 applies tosmall molecules), the material file allows for a detaileddescription of the composition and characteristics of thenanomaterial, and the ISA-TAB-Nano material file name isreferenced as a qualifier for the source sample (nanomaterial)in the study file.4.4.2.2 File FormatThe ISA-TAB-Nano stu

46、dy file is ahorizontal-based spreadsheet format with column headers inthe first row. An example subset of this format is provided inTable 3. Please note, the concept specified within the bracket “” is a variable depending on the type of sample.4.4.3 Material File:4.4.3.1 Description:(1) The material

47、 file describes the composition of thematerial formulation. The material file is an important file thatis designed to allow for nanomaterial comparison acrossnanotechnology resources.(2) An investigation typically involves the preparation ofmultiple materials that are tested. These materials could b

48、e ofthe same chemical composition (same type and amount ofchemical components in the sample) or different chemicalcompositions. Materials having the same chemical composi-tion should be described using one material file. Materials ofdifferent chemical composition should be described separatelyusing

49、multiple materials files.4.4.3.2 File FormatThe material file format leverages ahorizontal-based spreadsheet format with rows representingmultiple values. Table 4 shows an example subset of thematerial file.4.4.4 Assay File:4.4.4.1 DescriptionThe assay file provides references toassay results including measurements, raw data files, deriveddata files, image files, and other file types. There can bemultiple assay files per study.4.4.4.2 File FormatThe ISA-TAB-Nano assay file is ahorizontal-based spreadsheet format with column headers androw values. An example subset