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a_ USC_UV-JCrecente-CampoJCR2019-physicochemical-size-DLS.

Investigation

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Form

The very first lines of Investigation form (Figure 13) are dedicated to names of ontologies from Bioportal (http://bioportal.bioontology.org). The information about ontologies is added, while creating ISA-TAB-Nano Investigation form and selecting appropriate annotation from Bioportal for terms, which are entered into ISA-TAB-Nano forms. In case, a term exists in multiple ontologies, then the most in depth annotation is selected.

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The most applicable ontologies are NanoParticle Ontology (NPO, https://bioportal.bioontology.org/ontologies/NPO), NCI Thesaurus (NCIT, https://bioportal.bioontology.org/ontologies/NCIT),  Eagle-I Research Resource Ontology (ERO, https://bioportal.bioontology.org/ontologies/ERO), Ontology for Biomedical Investigations (OBI, https://bioportal.bioontology.org/ontologies/OBI) Experimental Factor Ontology (EFO, https://bioportal.bioontology.org/ontologies/EFO), Phenotypic Quality Ontology (PATO, https://bioportal.bioontology.org/ontologies/PATO), and BioAssay Ontology (BAO, https://bioportal.bioontology.org/ontologies/BAO). If it is necessary to annotate entries in Material, Study, and Assay files with terms from Ontologies which are not in Ontology Source Reference section than one should enter these Ontologies into this section.

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• Investigation Identifier, in most cases, comprising institution names, first author, journal title, and publication year.
• Custom investigation title, e.g. a rephrased publication title.
• Custom investigation description, e.g. an abbreviated abstract.
• Custom investigation outcome.
• PubMed ID.
• Publication DOI.
• Author list.
• Publication title.
• Publication status (published, submitted, in press, in preparation).

Figure 14. A general information section of Investigation form.

Study Section of Investigation

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Form

Based on information obtained earlier and related to sample characterizations, identify studies and assays, which are common to a specific study.

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• Study Identifier, which can comprise Investigation Identifier and study name, e.g. size.
• Custom Study Title.
• Custom Study Description – this may include a short description of all assays, which are included in the study, in case, when several assays are included in a single study.
• Study Disease, if is available, corresponding Term Accession Number from the Bioportal Ontology. (http://bioportal.bioontology.org) and Term Source REF, i.e. a name of a corresponding ontology.
• Custom Study Outcome.
• A Study Filename and its Description are entered after a corresponding Study form is created.
• Study Publication section is left blank, since there is no other publication related to this study besides a publication listed in the Investigation Publications section.

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Identify Factors, i.e., independent variables manipulated by the investigator with the intention to affect biological systems in a way that they can be measured by an assay. Enter them into Study Factor section (Figure 14). One factor per cell/column e.g. temperature, corresponding Accession Number and Term Source REF from Bioportal, Study Factor Type, its Accession Number, Term Source REF from Bioportal.

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• Study Assay Technology Platform, i.e., instrument name, e.g. Zetasizer Nano ZS (Malvern), corresponding Term Accession Number, and Term Source REF.
• Study Assay Measurement Name, outputs from assay measurements e.g. hydrodynamic diameter, corresponding Term Accession Number, Term Source REF.
• Study Assay Filename, which is entered after creating corresponding Assay form.

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• Study Protocol Name.
• Study Study Protocol Type and its corresponding Term Accession Number and Term Source REF from Bioportal.
• Study Protocol Description.
• Study Protocol Parameter Name, names of measurable quantities, which remain constant as part of assay, separated by semicolons.
• Study Protocol Components Name, names of instruments, software, reagents etc., which are part of assay, separated by semicolon. Manufacturer names are entered next to the Component Name in parentheses.
• Study Protocol Components Type, an instrument type, e.g. a flow cytometer, separated by semicolon, corresponding Term Accession Numbers from a Bioportal separated by semicolon into Term Accession Number field, Term Source REF, and Term Accession Number. In empty columns to the right of protocols enter Study Protocol Names as preparations for the actual Protocols. This Protocol Names should be enter to Protocol REF field in the Study file (Figure 21B).

Figure 18A   A Study Protocols section

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Figure 18B   A Study Protocols section.

 Enter Enter into Study Contacts section information from about a person who is a Contact person.

Figure 19. A Study Contacts section.

Material

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Form

 Create a number of Material forms corresponding to a number of identified samples. In addition to identified samples, which are submitted into caNanoLab, one can create Material forms for substances, like sucrose, saline, or drugs, which are used as control materials.

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• Enter into Characteristics fields additional information this particular constituent of sample, like amount, functionality, or molecular formula
• If amount of constituent is specified, enter unit into Unit field and corresponding Term Accession Number from Bioportal and Term Source REF.
• If any two or more components of sample are linked, then in the very first line of Material form, enter Material Names of components, which are linked, into Material Part Name, and add information about a type of association into Material Linkage Type. Enter Term Accession Number corresponding to Material Linkage Type, and its Term Source REF (Figure 20). Repeat this step if the additional components are linked.

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Figure 20. Part of Material form showing a linkage subsection. 

Study and Assay Forms

A number of created Study forms should be equal to a number of Study sections in Investigation form. In case of imaging studies, create corresponding Study and Assay forms, when images are available without any restriction. Then, a name of file containing image is entered into an Image File field of a corresponding Assay form. 

Study Form

The number of fields in a Study form and which fields are in this form depends on the number of Study Factors, which are entered in the Investigation form for this particular Study. The common fields in Study form are in all types of Studies are Source Name, Sample Name, Factor and Parameter Values (Figure 18), if both latter are specified in the Investigation form.

• Enter into Source Name, either Material Source Identifier in case of physicochemical Study e.g. USC_UV-JCrecente-CampoJCR2019-04, cell line in case of in vitro characterization e.g. H-1650, or animal name e.g mice in case of in vivo
• Enter material type, either as a free-text description or as a term from Bioportal, its Term Accession Number, and Term Source REF.
• Enter into Characteristics field cell type and cell line in case of in vitro Study or animal type in case of in vivo
• Enter Factor Value, e.g. Material Source Identifier in case, in which an experiment involved only different samples, or entered multiple Factor values. In Sample Name field, enter either name of nanomaterial sample in case, there no Factors, or a name, which includes a combination of sample name, factors numerical values, cell name, and/or animal name. Number of lines in Study form depends on number of Factor Values and numerical Factor Values. 
• Enter protocol name from the corresponding Study Section in the Investigation form into Protocol REF field.
• Enter Study filename into the corresponding Study File Name field in the Investigation form.

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Figure 21A. Part of a Study form showing primary entries in this form for in vitro assay.

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Figure 21B. Part of a Study form showing entries in this form for in physicochemical assay. 

Assay

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Form

For each study, create a number of Assays forms corresponding to assays in Study Assay subsection of Study section in the Investigation form, in case corresponding numerical data are readily available. Enter the following into an Assay form (Figure 19).

• Enter sample names created, while generating corresponding Study form into Sample Name fields.
• Enter protocol name from the corresponding field in the Investigation form into Protocol REF field.
• Enter assay name into Assay Name fields.
• In Measurement Value field replace “measurement term” with appropriate term.
• Enter respective data into Measurement Value fields.  Specify statistic, i.e. mean, standard deviation, and number of replicates in Statistic fields.
• If numerical data possess units, then enter units for mean and standard deviation into Unit field, enter corresponding Term Accession Number and Term Source REF.

Figure 22. Part of Assay form showing important entries.

Final steps

• Complete the Information form by entering Material File Names, Material Source Name, Study File Names, and Assay File Names.
• Convert all files into csv format. This step can be performed in macos and Linux platforms using the unoconv script

unoconv   -e FilterOptions=9/32,,9 -f csv   -o ../ISA-TAB-Nano_csv  *.xlsx if ISA-TAB-Nano forms were created using the Excel.

          Before using this script create the ISA-TAB-Nano_csv folder and run this         script from the ISA-TAB-Nano folder in a terminal window.

• In the Information form replace all extensions e.g. xlsx with csv using a text editor or a script.
• Compress all forms and associated information into a single compressed file and post the file into the caNanoLab Data Curation Project Wiki under ISA-TAB-Nano Curated Examples including a citation of the publication.
• Update caNanoLab/ISA-TAB-Nano curation status in the caNanoLab Data Curation Project Status file.
• After completing caNanoLab curation provide NCI collaborator with explicit list and description of data needed from investigators to complete curation task.
• Submit to the NCI JIRA tracker reports regarding defects encountered in caNanoLab and requests for improvements.
• Prepare and disseminate weekly reporte to the Government Sponsor, Project Officer, Leidos Technical Project Manager (COB Friday), and ESI Manager.
• Attend weekly teleconference.
• Prepare and disseminate the monthly report.