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1. The NCI collaborator provides a list of publications suggested for curation.
2. Publications are evaluated whether they are curable, i.e. comprise information relavant for curation in caNanoLab.
3. Data extraction from the publication.
4. Submission of extracted data into caNanoLab and into ISA-TAB-Nano forms.
5. Information submitted into caNanoLab must be machine-readable, searchable and comply with the established standards.
6. Sending to authors of a publication, a request for additional data and submission of provided additional data into caNanoLab and ISA-TAB-Nano forms.

Initial Steps

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.

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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).

Crecente-Campo J, Guerra-Varela J, Peleteiro M, Gutierrez-Lovera C, Fernandez-Marino I, Dieguez-Docampo A, Gonzalez-Fernandez A, Sanchez L, Alonso MJ. The size and composition of polymeric nanocapsules dictate their interaction with macrophages and biodistribution in zebrafish. J Control Release. 308:98-108 (2019).

 1  biopolymer (inulin) small nanocapsule

  physicochemical  size  zeta potential  Figure 1

 in vitro cytotoxicity Figure 2

 in vivo stability Figure S1 toxicity Figure 4  survival Table S1 Table S2 Table S3

2 biopolymer (inulin) medium nanocapsule

physicochemical size  zeta potential  Figure 1

in vitro cytotoxicity Figure 2

in vivo stability Figure S1  toxicity Figure 4  survival Table S1 Table S2 Table S3

3  biopolymer (chitosan) small nanocapsule

physicochemical size  zeta potential Figure 1

in vitro cytotoxicity Figure 2

in vivo stability Figure S1 toxicity Figure 4 survival Table S1 Table S2 Table S3

4 biopolymer (chitosan) medium nanocapsule

physicochemical size  zeta potential Figure 1

in vitro cytotoxicity Figure 2

in vivo stability Figure S1 toxicity Figure 4 survival Table S1 Table S2 Table S3

5 biopolymer (inulin) fluorescent small nanocapsule

 in vitro targeting cell internalization Figure 3

 in vivo biodistribution Figure 5 biodistribution Figure 6 biodistribution Figure S3   biodistribution Figure S4 biodistribution Figure S5

6 biopolymer (inulin) fluorescent small nanocapsule

 in vitro targeting cell internalization Figure 3

 in vivo biodistribution Figure 5 biodistribution Figure 6 biodistribution Figure S3   biodistribution Figure S4 biodistribution Figure S5

7 biopolymer (chitosan) fluorescent small nanocapsule

 in vitro targeting cell internalization Figure 3

 in vivo biodistribution Figure 5 biodistribution Figure 6 biodistribution Figure S3   biodistribution Figure S4 biodistribution Figure S5

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1. Extract information on composition, physicochemical, in vitro, and in vivo characterizations, numerical data for each individual sample into corresponding text file. Replace Greek fonts with English equivalents e.g. α replace with alpha. Check extracted text for nonstandard hyphens. Remove references to Figures and to publications. Rephrase active sentences to passive. For example “We synthesized the previously reported nMOF, Hf-DBA (DBA = 2,5-di(p-benzoato)aniline), and used it as a control.” replace with “The previously synthesized and reported nMOF, Hf-DBA (DBA = 2,5-di(p-benzoato)aniline), was used as a control”.

2. 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.

3. 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.

   Info
   icon false
   Crecente-Campo J, Guerra-Varela J, Peleteiro M, Gutierrez-Lovera C, Fernandez-Marino I, Dieguez-Docampo A, Gonzalez-Fernandez A, Sanchez L, Alonso MJ. The size and composition of polymeric nanocapsules dictate their interaction with macrophages and biodistribution in zebrafish. J Control Release. 308:98-108 (2019). 1  biopolymer (inulin) small nanocapsule   physicochemical  size  zeta potential  Figure 1  in vitro cytotoxicity Figure 2  in vivo stability Figure S1 toxicity Figure 4  survival Table S1 Table S2 Table S3 2 biopolymer (inulin) medium nanocapsule physicochemical size  zeta potential  Figure 1 in vitro cytotoxicity Figure 2 in vivo stability Figure S1  toxicity Figure 4  survival Table S1 Table S2 Table S3 3  biopolymer (chitosan) small nanocapsule physicochemical size  zeta potential Figure 1 in vitro cytotoxicity Figure 2 in vivo stability Figure S1 toxicity Figure 4 survival Table S1 Table S2 Table S3 4 biopolymer (chitosan) medium nanocapsule physicochemical size  zeta potential Figure 1 in vitro cytotoxicity Figure 2 in vivo stability Figure S1 toxicity Figure 4 survival Table S1 Table S2 Table S3 5 biopolymer (inulin) fluorescent small nanocapsule  in vitro targeting cell internalization Figure 3  in vivo biodistribution Figure 5 biodistribution Figure 6 biodistribution Figure S3   biodistribution Figure S4 biodistribution Figure S5

Figure 1. A typical text showing associations between samples and characterizations.

1. Extract information on composition, physicochemical, in vitro, and in vivo characterizations, numerical data for each individual sample into corresponding text file. Replace Greek fonts with English equivalents e.g. α replace with alpha.

Check extracted text for nonstandard hyphens. Remove references to Figures and to publications. Rephrase active sentences to passive. For example “We synthesized the previously reported nMOF, Hf-DBA (DBA = 2,5-di(p-benzoato)aniline), and used it as a control.” replace with “The previously synthesized and reported nMOF, Hf-DBA (DBA = 2,5-di(p-benzoato)aniline), was

used as a control”.

1. 6 biopolymer (inulin) fluorescent small nanocapsule  in vitro targeting cell internalization Figure 3  in vivo biodistribution Figure 5 biodistribution Figure 6 biodistribution Figure S3   biodistribution Figure S4 biodistribution Figure S5 7 biopolymer (chitosan) fluorescent small nanocapsule  in vitro targeting cell internalization Figure 3  in vivo biodistribution Figure 5 biodistribution Figure 6 biodistribution Figure S3   biodistribution Figure S4 biodistribution Figure S5 8 biopolymer (chitosan)  fluorecent medium nanocapsule  in vitro targeting cell internalization Figure 3  in vivo biodistribution Figure 5 biodistribution Figure 6 biodistribution Figure S3   biodistribution Figure S4 biodistribution Figure S5

   Figure 1. A typical text showing associations between samples and characterizations

2. 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.
3. 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

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