What is caNanoLab?
- What functionality does caNanoLab support?
- How do you enter nanoparticle characterizations?
The cancer Nanotechnology Laboratory portal (caNanoLab) is a portal designed to facilitate data sharing in the research community to expedite and validate the use of nanoparticles in biomedicine. caNanoLab provides support for the annotation of nanoparticles with characterizations resulting from physical and in vitro nanoparticle assays and the sharing of these characterizations and associated nanotechnology protocols in a secure fashion. Additional information on caNanoLab is available on the caNanoLab Wiki.
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Additional information on caNanoLab is available on the caNanoLab Wiki Home page.
If you do not have a caNanoLab login account and want to save items in caNanoLab, you must register for an account first. Contact caNanoLab-Support@ISB-CGC.org. You will be assigned a user role which affects what actions you can perform in caNanoLab.
If you forget your password or need to reset your caNanoLab password, contact caNanoLab-Support@ISB-CGC.org.
To request a caNanoLab user account to login, contact caNanoLab-Support@ISB-CGC.org.
caNanoLab was developed as a collaboration between the NCI CSSI Office of Cancer Nanotechnology Research and the NCI Center for Biomedical Informatics and Information Technology (CBIIT), the NCI Nanotechnology Characterization Laboratory (NCL), and the NCI Cancer Centers of Nanotechnology Excellence (CCNEs). CCNEs actively involved in the caNanoLab effort include Washington University, Stanford, Emory/Georgia Tech, and MIT.
caNanoLab was designed to operate in a standalone and federated environment. Organizations deploying caNanoLab install caNanoLab locally and connect to the caBIG grid (caGrid) for information sharing across the research community. Organizations that do not have local facilities can contact NCI CBIIT Application Support to request access to the NCI caNanoLab system for data submission and retrieval.
Does caNanoLab leverage any existing standards for describing nanoparticles and associated characterizations?
Standards supporting nanotechnology in the biomedical domain are emerging and under continuous development. caNanoLab leverages and extends concepts from existing standards developed by the biomedical and nanotechnology community. caNanoLab leverages biomedical and nanotechnology concepts from the NCI's Enterprise Vocabulary Services (EVS) and the Nanoparticle Ontology (NPO) developed by Washington University. The caNanoLab team works with the biomedical nanotechnology community to identify and define concepts identified during use case analysis. New concepts are maintained in the NCI Thesaurus.
Definitions to caNanoLab concepts are available in the caNanoLab User's Guide, caNanoLab glossary, and through the NCI Thesaurus. The caNanoLab glossary is included in the download package and made available to users through the caNanoLab portal.
caNanoLab is open source software developed under the NCI caBIG initiative and open source license. caNanoLab is available for download via the caNanoLab Project Site.________________________________________
It is the policy of NIH that the results of research accomplished through Federal support should be made available to the public. To meet this requirement, NIH applicants are required to provide a Data Sharing Plan (Resource Sharing Plan), as described in the NIH Data Sharing Policy and SF424 (R&R) Application Guide. If you are applying for nanotechnology-based research funding that requires a data sharing or data management plan, you may find useful information in the document caNanoLab & Data Sharing that can be used in your research proposal. The suggested text is based on the requirements for NIH Data Sharing Plans, but you can modify this text to fit the needs of your proposed research. For additional information about caNanoLab or to reference caNanoLab, refer to Gaheen et al., 2013, caNanoLab: data sharing to expedite the use of nanotechnology in biomedicine. Comput. Sci. Discov. 6 014010 doi:10.1088/1749-4699/6/1/014010.
Authors who use caNanoLab should acknowledge caNanoLab in their work by properly referencing samples. The majority of caNanoLab sample record information is curated from publications. For these, acknowledge the associated publication and caNanoLab either by citation or in the acknowledgements section of your publication.
Alert us by email of any publications that cite or acknowledge the use of caNanoLab to enable us to highlight it on our website. Below are options for including caNanoLab use in publications.
- Example acknowledgement: "The results <published or shown> here are in whole or partly based upon data made available through caNanoLab: https://cananolab.cancer.gov. For questions, contact the NCI Center for Biomedical Informatics and Information Technology (CBIIT)."
- General caNanoLab citation: Cite the caNanoLab publication available at either Comput Sci Discover or Beilstein J Nanotechnol.
- Citing published caNanoLab data: Cite the associated publication when using information from a sample record in caNanoLab. Publication information can be found under the Publication Tab on the left-hand side Navigation Tree for each sample.
- Citing unpublished caNanoLab data (no associated publication record): Cite the caNanoLab sample page using the following format –Sample Name, caNanoLab Data Portal, National Cancer Institute, Bethesda, Maryland. World Wide Web (URL: https://cananolab.cancer.gov). [Date data retrieved (month, year)].
What functionality does caNanoLab Support?
caNanoLab allows researchers to submit and retrieve information on nanoparticles and associated information including:
- The composition of the particle including nanoparticle entities (e.g. dendrimers, carbon nanotubes, quantum dots, etc.), functionalizing entities (therapeutic, targeting, and diagnostics entities), and chemical associations (chemical associations, attachments, or encapsulations between nanoparticle entities or functionalizing entities).
- Physical characterizations performed on a nanoparticle including size, molecular weight, shape, purity, etc.
- In vitro characterizations performed on a nanoparticle including cytotoxicity, immunotoxicity, and general toxicity characterization results.
- Protocols for characterizations performed on nanoparticles or general nanotechnology protocols from biomedical nanotechnology studies.
- Publications from biomedical nanotechnology studies.
caNanoLab provides secure access to data and requires authentication and authorization for access to non-public data.
How do you enter nanoparticle characterizations?
caNanoLab allows users to upload characterization files and submit data values through controlled metadata as well as uncontrolled metadata. All data values are entered as derived datum.
For example, to submit a Z-Average Size of 120 nm for a nanoparticle, the user would:
- Submit the nanoparticle sample
- Select to add the Size characterization from the Physical Characterization Navigation Tree item
- Complete required summary fields including characterization source and descriptive title
- Select to add Derived Bioassay Data (optional)
- Select to upload a file (optional)
- Select to add Derived Datum (optional)
- Select Z-Average Size from the Derived Data Name
- Select Mean from the Value Type
- Enter the Value of 120 in the Value field
- Select nm in the Unit pull down list
- Add a description (optional)
Uncontrolled metadata can be submitted by selecting Other in any of the pull-down lists and entering the new term in the popup window.
Note, a user must have privileges to submit data to see the Add feature. Detailed information on submitting characterization data is available from the caNanoLab portal via the caNanoLab help link. Return to top of page
In order to save a protocol, sample, or publication in caNanoLab, you must have an account belonging to the Data Curator group. To register for a login account, contact caNanoLab-Support@ISB-CGC.org. Once you have an account, you can log into caNanoLab and create an item and assign access to users and collaboration groups. If you are a Data Curator, you can make the item publicly-accessible. If not, you must submit the item for review, and when the Data Curator approves the item, it will be public.
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What types of data can I submit into caNanoLab?
caNanoLab provides support for a variety of different types of data including:
- Nanomaterials and their composition
- Nanomaterial Characterizations from physico-chemical characterizations
- Nanomaterial Characterizations from in vitro characterizations
- Nanotechnology protocols
- Nanotechnology publication
caNanoLab supports the submission of publication information and the association of caNanoLab data with publications. To submit publication information, complete the web-based submit publication form. If the publication is available in PubMed, provide the PubMed ID and caNanoLab will auto-populate the publication information. When submitting publication information, select the caNanoLab samples associated with the publication. This will associate the publication with caNanoLab data available for the sample.
In addition to associating samples with publication information stored in the the caNanoLab Data Portal, caNanoLab has established a direct reciprocal link between datasets and associated research articles published by Elsevier. When a user performs an Elsevier search, caNanoLab now returns a caNanoLab logo if the publication has linked samples in the caNanoLab database. If not, caNanoLab sends a transparent one pixel image.
The following is the URL format that searches caNanoLab for a DOI ID.
The current list of Elsevier journals that offer reciprocal linking as well as the future list are available on the caNanoLab Integration with Elsevier web page.
Who can I contact to save data into caNanoLab?
A data curator is available to assist in curating data from nanotechnology characterizations in biomedicine. Data curation activities on caNanoLab are currently performed by nanotechnology data scientists at Washington University and the Nanotechnology Characterization Laboratory (NCL). Data curators assist in extracting data from publications and nanotechnology experiments, annotating extracted data, and providing overall data quality control.
If you are interested in depositing your data into caNanoLab, contact NCIcaNanoLab@mail.nih.gov.