The undersigned acknowledge that they have reviewed the Curation of Biomedical Data into ISA-TAB-Nano and caNanoLab SOP and agree with the information presented within this document. Changes to this Curation of Biomedical Data into ISA-TAB-Nano and caNanoLab SOP will be coordinated with and approved by the undersigned or their designated representatives.
Released by / Effective Date:
Written by | ||
---|---|---|
Name | Title | Date |
Michal Lijowski | Curator |
Approved by | ||
---|---|---|
Name | Title | Date |
Kanakadurga Addepalli |
Version Number | Implemented By | Revision Date | Description of Change |
---|---|---|---|
0.5 | Michal Lijowski | 10/29/2012 | Initial draft of "Nanotechnology Biomedical Data Curation Standard Operating Procedure" |
0.6 | Michal Lijowski | 11/07/2012 | Updated based on feedback |
1.0 | Sharon Gaheen | 12/14/2012 | Updated based on NCI feedback and re-formatted document in new template |
2.0 | Michal Lijowski and Carolyn Klinger | August 4, 2021 | Renamed as "Curation of Biomedical Data into ISA-TAB-Nano and caNanoLab Standard Operating Procedure," updated all procedures, and converted to NCI wiki. |
This Standard Operating Procedure (SOP) explains how to curate biomedical data into ISA-TAB-Nano and caNanoLab.
The following table summarizes the documents referenced in this document.
Document Name | Location | |
---|---|---|
ISA-TAB-Nano Information | Information about ISA-TAB-Nano, an extension of ISA-TAB, an existing specification developed by the ISA-community | |
Specification Documentation, ISA-TAB 1.0, Release Candidate 1 | Guidelines on the format of ISA-TAB | |
caNanoLab User's Guide | Procedures for using caNanoLab | |
caNanoLab Website | caNanoLab application | |
BioPortal Website | Detailed description of ontologies, as well as forms associated with a publication or an investigation. |
It is the responsibility of the Curation Subject Matter Expert (SME) to perform the steps summarized in Data Curation and detailed throughout this guide.
It is the responsibility of the NCI collaborator to provide a list of publications suggested for curation and contact investigators.
It is the responsibility of the Government Sponsor to supervise the technical and budgetary aspects.
It is the responsibility of the Project Officer to review the monthly report.
It is the responsibility of the Leidos Technical Project Manager to coordinate technical and budgetary aspects.
The following table provides definitions and explanations for terms and acronyms relevant to the content presented within this document.
Term | Definition |
---|---|
ISA-TAB | Investigation Study Assay Tab delimited file format |
ISA-TAB-Nano | ISA-TAB-Nano extends ISA-TAB, an existing specification developed by the ISA-community. Refer to the ISA-TAB Specification for guidelines on the format of ISA-TAB. The ISA-TAB-Nano wiki page provides additional information. |
NPO | Nanoparticle Ontology |
Curation of biomedical information is accomplished by selecting relevant publications, extracting reported text and data, submitting extracted information to ISA-TAB-Nano and caNanoLab, and keeping track of performed activities.
caNanoLab and ISA-TAB-Nano have differences in nomenclature, structure, and the way information is stored.
Data curation is performed by following the steps below.
The Curation SME performs the following data extraction steps.
Establish definitions 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, for example, in targeting functionalized entity, a new target, such as a gene.
If the information provided by the publication, such as the name of an instrument or a chemical compound, does not agree with the information provided somewhere else, such as manufacturer catalog, retain the information provided by the publication for curation. Record the discrepancy for correspondence with authors in a file in the subfolder comprising all files comprising information to be submitted to caNanoLab and ISA-TAB-Nano that contains a request for the numerical data that were used to generate the figures.
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 8 biopolymer (chitosan) fluorescent 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 |
Submit the extracted information and reported numerical data into caNanoLab following the procedures in the caNanoLab User Guide, which is accessible by selecting caNanoLab FAQ or Online Help buttons (Figure 2).
If you submit a new term in any field in caNanoLab, use all lowercase.
If a Composing Element having an Inherent Function is associated with another Composing Element, make a Composing Element with an Inherent Function as a Functionalized Entity. In most cases, select “small molecule” as the Functionalizing Entity Type, and submit additional information (Figure 8, Figure 9).
Select the Chemical Association tab, then click Add and select an Association Type from the drop-down menu. Add information about the association in the Description field. Select the Functionalized Element in the Element field on the left side and select the corresponding Composing Element on the right side in the Element field (Figure 10).
A Curation queue comprises Samples, Publications, and Protocols submitted by users without Curator privileges. In order to make a Sample public, each section must have complete information. The sample Name must indicate the name of an institution that represents the origin of a sample. It should comprise other identifiable information that distinguishes it from other samples.
The General Info section should provide the name, postal address, and email address of an investigator or a person responsible for sample submission into caNanoLab. The sample must have its Composition and Characterizations details submitted as mentioned in caNanoLab Data Submission and be machine-readable, searchable, and comply with established standards.
If a new version of a protocol is submitted to the caNanoLab curation queue, then the old version of the protocol must be assigned a version number, and the new version of the protocol must be assigned a different version number.
At the time this document was published, the curation in ISA-TAB-Nano follows the ISA-TAB-Nano 1.3 Release. More detailed information is provided in the ISA-TAB-Nano wiki. The filenames of the ISA-TAB-Nano forms consist of a prefix corresponding to a specific form, that is, i_ for an investigation form, s_ for a study form, a_ for an assay form, m_ for a material form, a custom abbreviation of institution(s) names, a name of the first author (first name abbreviation, full last name), a custom abbreviation of journal title and a year of publication; for example, i_USC_UV-JCrecente-CampoJCR2019. A suffix for Study indicates a study type e.g. physicochemical, in_vitro. A suffix for an Assay file and the type of Study it is related to includes a name of the assay; for example, size, zeta potential.
For example:
a_ USC_UV-JCrecente-CampoJCR2019-physicochemical-size-DLS
The first lines of the Investigation form (Figure 13) are dedicated to names of ontologies from Bioportal (http://bioportal.bioontology.org). The information about ontologies is added while creating the ISA-TAB-Nano Investigation form and selecting the appropriate annotation from Bioportal for terms, which are entered into ISA-TAB-Nano forms. In case a term exists in multiple ontologies, select the most in depth annotation.
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.
ONTOLOGY SOURCE REFERENCE | |
---|---|
Term Source Name | EFO |
Term Source File | |
Term Source Version | 3.29.0 |
Term Source Description | Experimental Factor Ontology |
Enter the Investigation information into the Investigation form.
INVESTIGATION | |
---|---|
Investigation Identifier | USC_UV-JCrecente0CampoJCR2019 |
Investigation Title | Dependence of interaction with macrophages and biodistribution in zebrafish on size and composition of polymeric nanocapsules |
Investigation Description | This work aimed to understand |
Investigation Submission Date | |
Investigation Public Release Date | |
Investigation Disease | |
Investigation Disease Term Accession Number | |
Investigation Disease Term Source REF | |
Investigation Outcome | The in vitro results showed that small nanocapsules interacted more efficiently with macrophages than their larger counterparts. Inulin nanocapsules were significantly less toxic than chitosan nanocapsules. Finally, following in vivo administration (intravenous/intramuscular) to zebrafish, small nanocapsules, regardless of their composition, disseminated considerably faster and further than their medium size counterparts. These results emphasize how small changes in the nanometric range can lead to a remarkably different interaction with the immune cells and biodistribution profile. |
Based on information obtained earlier and related to sample characterizations, identify studies and assays, which are common to a specific study.
Study Identifier | USC_UV-JCrecente0CampoJCR2019-physicochemical |
---|---|
Study Title | size |
Study Description | The particle size and polydispersity index (PDI) were measured by a dynamic light scattering using a Zetasizer Nano S (Malvern) at 25 C with a detection angle 173 degrees and in distilled water. |
Study Submission Date | |
Study Public Release Date | |
Study Disease | |
Study Disease Term Accession Number | |
Study Disease Term Source REF | |
Study Outcome | |
Study File Name | s_USC_UV-JCrecente-CampoJCR2019-physicochemical.ods |
Enter into a Study section of the Investigation form the following.
INVESTIGATION PUBLICATIONS | |
---|---|
Investigation PubMed ID | 31306677 |
Investigation Publication DOI | 10.1016/j.jconrel.2019.07.011 |
Investigation Publication Author List | Jose Crecente-Campo;Jorge Guerra-Varela;Mercedes Peleteiro;Carlha Gutierrez-Lovera;Iago Fernandez-Marino; Andrea Dieguez-Docampo;Africa Gonzalez-Fernandez;Laura Sanchez;Maria Jose Alonso |
Investigation Publication Title | The size and composition of polymeric nanocapsules dictate their interaction with macrophages and biodistribution in zebrafish |
Investigation Publication Status | published |
Investigation Publication Status Term Accession Number | |
Investigation Publication Status Term Source REF | EFO |
Identify factors, that is, 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.
STUDY FACTORS | ||
---|---|---|
Study Factor Name | nanoparticle sample | sample number |
Study Factor Type | nanoparticle sample | sample number |
Study Factor Type Term Accession Number | ||
Study Factor Type Term Source REF | NPO | MS |
Enter into a Study Assay section the following (Figure 18) Study Assay Measurement Type, e.g. hydrodynamic size, corresponding Term Accession Number, Term Source REF, Study Assay Technology Type, for example, dynamic light scattering, corresponding Term Accession Number, Term Source REF.
STUDY ASSAYS | |
---|---|
Study Assay Measurement Type | hydrodynamic size |
Study Assay Measurement Term Accession Number | |
Study Assay Measurement Term Source REF | NPO |
Study Assay Technology Type | dynamic light scattering |
Study Assay Technology Type Term Accession Number | |
Study Assay Technology Type Term Source REF | NPO |
Study Assay Technology Platform | Zetasizer Nano S (Malvern) |
Study Assay Measurement Name | hydrodynamic diameter; polydispersity index |
Study Assay Measurement Name Term Accession Number | http://purl.bioontology.org/ontology/npo#NPO_1915;http://purl.bioontology.org/ontology/npo#NPO_1155 |
Study Assay Measurement Name Term Source REF | NPO;NPO |
Study Assay File Name | a_USC_UV-JCrecente-CampoJCR2019-physicochemical-size_DLS.ods |
In case, a protocol is provided (Figure 19), then enter the following.
STUDY PROTOCOLS | |
---|---|
Study Protocol Name | dynamic light scattering |
Study Protocol Type | dynamic light scattering |
Study Protocol Type Term Accession Number | |
Study Protocol Type Term Source REF | NPO |
Study Protocol Description | |
Study Protocol URI | |
Study Protocol Version | |
Study Protocol Parameters Name | medium; temperature; detection angle |
Study Protocol Parameters Name Term Accession Number | |
Study Protocol Parameters Name Term Source REF | NPO;PATO; |
Study Protocol Components Name | distilled water;Zetasizer Nano S (Malvern) |
Study Protocol Components Type | medium; dynamic light scattering instrument |
Study Protocol Components Type Term Accession Number | |
Study Protocol Components Type Term Source REF | NPO;NPO |
Enter into Study Contacts section information from a contact person.
STUDY CONTACTS | |
---|---|
Study Person Last Name | Sanchez |
Study Person First Name | Laura |
Study Person Mid Initials | |
Study Person Email | lauraelena.sanchez@usc.es |
Study Person Phone | |
Study Person Fax | |
Study Person Address | Department of Zoology, Genetics & Physical Anthropology Universidade de Santiago de Compostela |
Study Person Affiliation | |
Study Person Roles | investigator |
Study Person Roles Term Accession Number | |
Study Person Roles Term Source REF | NCIT |
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.
In the first line of Material form enter the information about a sample.
The number of created Study forms should be equal to the number of Study sections in the Investigation form. In the case of imaging studies, create corresponding Study and Assay forms, when images are available without any restriction. Then enter the name of the file containing the image into the Image File field of a corresponding Assay 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.
For each study, create a number of Assays forms corresponding to assays in the Study Assay subsection of the Study section in the Investigation form, in case corresponding numerical data are readily available. Enter the following into an Assay form (Figure 19).
Sample Name | Protocol REF | Assay Name | Measurement Value[mean(hydrodynamic diameter)] | Unit | Term Accession Number | Term Source REF |
---|---|---|---|---|---|---|
USC_UV-JCrecente-CampoJCR2019-01-physicochem-DLS-size | dynamic light scattering | hydrodynamic diameter measurement | 69 | nm | UO | |
USC_UV-JCrecente-CampoJCR2019-02-physicochem-DLS-size | dynamic light scattering | hydrodynamic diameter measurement | 246 | nm | UO |
Convert all files to csv format. This step can be performed in macOS and Linux platforms using the unoconv script. Run this script from the ISA-TAB-Nano folder in a terminal window.unoconv -e FilterOptions=9/32,,9 -f csv -o ../ISA-TAB-Nano_csv
*.xlsx
Use *.xlsx if ISA-TAB-Nano forms were created using Excel.
The abbreviations below are suggested for use during caNanoLab curation.
Journal Title | Custom Abbreviation |
---|---|
AAPS J | AAPSJ |
ACS Nano | ACSNano |
Adv Func Mater | AFM |
Adv Mater | AM |
Advanced Healthcare Materials | AHM |
Anal Chem | AC |
Angew Chem Int Ed Engl | ACIEE |
Anticancer Drugs | AD |
Arterioscler Thromb Vasc Biol | ATVB |
Bioconjug Chem | BC |
Biomacromolecules | BM |
Biomaterials | Bmat |
Cancer Lett | CL |
Cancer Res | CR |
Chem Commun | CCR |
Chem Res Toxicol | CRT |
ChemBioChem | CBC |
Clin Cancer Res | CCR |
Environ Health Perspect | EHP |
Environ Mol Mutagen | EMM |
Eur J Pharm Sci | EJPS |
Faseb J | FJ |
IEEE Ultrasonics Symposium | IEEEUS |
Int J Cancer | IJC |
Int J Nanomedicine | IJN |
Int J Pharm | IJP |
Integr Biol | IR |
Invest Radiol | IR |
J Agric Food Chem | JAFC |
J Am Chem Soc | JACS |
J Clin Invest | JCI |
J Control Release | JCR |
J Drug Target | JDT |
J Mater Chem | JMC |
J Nanobiotechnology | JNBT |
J Nucl Med | JNM |
J Pharm Sci | JPS |
Langmuir | LGMR |
Magn Reson Med | MRM |
Mater Sci Eng C | MSEC |
Mol Pharm | MP |
Mol Ther | MT |
Nano Lett | NL |
Nanomedicine (London) | Nanomed |
Nanomedicine: Nanotechnology, Biology and Medicine | NNBM |
Nanoscale | Nanoscale |
Nanotechnology | NT |
Nanotoxicology | NTX |
Nature | Nature |
Nature Medicine | NatMed |
Nature Nanotechnol | NatNano |
Nature Biotechnol | NatBiotech |
Nature Commun | NatComm |
Nature Materials | NatMat |
Nucleic Acid Res | NAR |
Pharm Res | PR |
Photochem Photobiol | PhPh |
Proc Natl Acad Sci U S A | PNAS |
Radiology | Radiol |
Scanning | Sc |
Sci Transl Med | STM |
Science | Science |
Scientific Reports | SR |
Small | Small |
Toxicol Appl Pharmacol | TAP |
Toxicol Lett | TL |
Toxicol Sc | TS |
Ultrasound Med Biol | UMB |