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1. Create a The caNanoLabData folder on a system or server that gets backup regularly. The caNanoLabData folder contains folders, named after institution or collaboration, e.g. USC_UV which contain additional subfolders. These subfolders, e.g., are named after first author of a publication, publication abbreviation, and publication year, e.g. , JCrecente-CampoJCR2019 contain an individual publication, i.e. PDF file and any supplemental data associated with a publication, extracted data, and supplemental data provided by an author. The caNanoLabData folder contains all auxiliary files, e.g. a list of cell lines, a list of all curated publications, a list of chemical compounds, a list of new terms, and recently added list of Bioportal terms.
2. Create a subfolder in caNanoLab folder to store the publication and extracted data. A subfolder name comprises first author name, journal name, and year of publication. Additional subfolder within this subfolder is created to store ISA-TAB-Nano forms.

Data Extraction

1. Establish a number of samples, which have different composition or properties, and a number of characterizations using information provided in text, tables, figures, and figures' captions in curated publication.
2. Establish sample names, following the pattern: abbreviation(s) of institution names, name of the first author (without middle name), custom abbreviation of journal title, year of publication, and sample sequential number, e.g. USC_UV-JCrecente-CampoJCR2019-01.
3. Associate samples with characterizations based on information provided in text, tables, figures, and figures’ captions. This information is kept in a text file listing all samples and associated characterizations (Figure 1).

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1. Establish definition for new terms used in the publication, which are not in the caNanoLab glossary or Bioportal, but in other sources, like Wikipedia, and references therein, Encyclopedic Dictionary of Genetics, Genomics, and Proteomics. Record this definition or term, in a designated text file or if possible enter into caNanoLab, e.g. in targeting functionalized entity, a new target, i.e. gene.
2. If information provided by the publication on e.g. name of an instrument or a chemical compound does not agree with information provided somewhere else, like manufacturer catalog, retain for curation information provided by the publication and record a discrepancy for a correspondence with authors, in a file, which contains a request for numerical data which were used to generate Figures.

caNanoLab Data Submission

 Submit extracted information and reported numerical data into caNanoLab following online caNanoLab User Guide, which is accessible by selecting caNanoLab FAQ or Online Help buttons  (Figure 2). If submitting a new term in any field in caNanoLab use lower case.

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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.

Figure 13. An Ontology Source Reference section in Investigation form.

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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.

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

Figure 15.  A Study Information subsection of a Study Section.

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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.

Figure 16. A Study Publication 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.

Figure 17. A Study Factors section with two factors

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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.

Figure 18  A Study Assays section.

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

Figure 19. A Study Contacts section.

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• 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.

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