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Overview of caNanoLab

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The cancer Nanotechnology Laboratory portal (caNanoLab) is a web-based 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 physico-chemical and in vitro nanoparticle assays and the sharing of these characterizations and associated nanotechnology protocols in a secure fashion.

Project Collaboration

caNanoLab is a collaboration between the
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titleKeeping Up With caNanoLab Documentation
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titleNanotechnology CDE and Terminology Development
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For information about this caNanoLab release:

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titleAt a Glance Details
  • Version Number: 3.1.14
  • Release Date: February 14, 2024
  • Primary audience: Investigators and researchers interested in information about the characterizations of nanomaterials used in biomedical research.
  • The new release 3.1 has been moved to deploy on the Google Cloud App Engine Flex system. For now, use the 3.0 release for local installations.
  • Installation Level (for 3.0): Intermediate - technical assistance may be required, download may require supporting infrastructure or software.
  • System Requirements (for 3.0): This is a web-based application that can be accessed through an industry standard browser. Installation requires:
    • Memory 1GB or more (Linux, Solaris, or Windows)
    • Disk storage 36 GB (minimum)
    • Database Server: MySQL v 5.5.x
    • JBoss Wildfly, 8
    • Java 1.8

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Tool Overview

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Introduction
Introduction

caNanoLab provides access to information on:

  • Nanotechnology protocols in biomedicine
  • Composition of nanomaterials
  • Functions of nanomaterials (for example, therapeutic, targeting, diagnostic imaging)
  • Physico-chemical characterizations including size, molecular weight, shape, physical state, surface chemistry, purity, solubility, and relaxivity
  • In Vitro characterizations such as cytotoxicity, blood contact properties, oxidative stress, and immune cell functions
  • Publications and reports from nanotechnology studies in biomedicine

caNanoLab was developed as a collaboration between the NCI Center for Biomedical Informatics and Information Technology (CBIIT),

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the NCI Nanotechnology Characterization Laboratory (NCL), and

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the NCI

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caNanoLab Users Group

caNanoLab is currently deployed at the NCL, Washington University, Stanford, and George Tech. Future caNanoLab feature requests are obtained by working with the nanotechnology community through the caNanoLab Users Group and the caBIG Integrative Cancer Research (ICR) Nanotechnology (Nano) Working Group. The caBIG ICR Nano Working group is aimed at developing a vision for nanoinformatics and is composed of members from the NCL, CCNEs, and other members of the nanoinformatics community.

caNanoLab Users Group meetings occur the 3rd Friday of every month from 1:30PM-2:30PM EST. caNanoLab Users Group Presentations are available on the caNanoLab Project Site. To become a caNanoLab Users Group member, please subscribe via the caNanoLab Users Listserv.

caNanoLab In Vivo Characterizations Discussion Group

In vivo characterizations are performed on nanoparticles to determine the safety, efficacy, and toxicokinetic properties of nanoparticles in animal models so that these particles can be transitioned for use in clinical applications. Similar to the in vivo characterizations required for drugs and other medical devices, nanoparticles and their functionalizing entities need to undergo rigorous testing to determine particle toxicity and PK/ADME properties.

The primary goal of the caNanoLab In Vivo Characterization Discussion Group is to develop a robust information model in support of nanotechnology in vivo characterizations that leverages and extends existing concepts from in vivo characterizations performed on small molecules and biomedical devices.

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Discussion group objectives include:

  • Assist in the collaborative design of a robust information (object) model supporting nanotechnology in vivo characterizations
  • Assist in the collaborative annotation and review of controlled terminology for in vivo characterization model class names and attributes
  • Assist in the collaborative design and review of the DRAFT caNanoLab User Interface supporting in vivo characterizations

To become a caNanoLab In Vivo Characterization Discussion Group Member please subscribe via the Nanotechnology In Vivo Characterization Listserv. Artifacts from the discussion group are maintained on the caNanoLab project site:

Common Data Element (CDE) and Terminology Development

caNanoLab is engineered for caBIG compliance in support of semantic interoperability across centers performing nanoparticle characterization studies. caNanoLab is based on an initial object model representing nanoparticles and their physical and in vitro characterization. All classes and attributes within the model are maintained in the NCI's cancer Data Standards Repository (caDSR) and Enterprise Vocabulary Services (EVS). The NCI's EVS team provides assistance in curating concept definitions with the community. These concept definitions are available in the NCI Thesaurus and a glossary of these terms is provided within caNanoLab application. EVS also provides the Biomedical Grid Terminology (BiomedGT) Collaborative Ontology Development Wiki, a tool enabling open collaborative terminology development. The BiomedGT Wiki includes terminology in the nanotechnology domain.

The caNanoLab information model also leverages concepts from the Nanoparticle Ontology (NPO) developed by Washington University which is made available via the NCI BioPortal.

CDE and terminology development is an ongoing process within caNanoLab as standards supporting nanotechnology in biomedicine are emerging. CDE and terminology development that is currently ongoing in discussion with the community includes:

  • Physico-Chemical and In Vitro Characterization Assays - Physico-Chemical and In Vitro Characterization assays performed on nanoparticles including assay conditions and endpoints. Physico-Chemical characterizations focus on the nanoparticle physical (size, molecular weight) and chemical (surface chemistry) properities. In Vitro characterizations assess a nanoparticle interaction with cellular components and include cytotoxicy and blood contact properties.
  • In Vivo Characterization Concepts - Characterizations performed on nanoparticles to determine the safety, efficacy, and toxicokinetic properties of nanoparticles in animal models so that these particles can be transitioned for use in clinical applications.
  • Instruments and Techniques - Instruments and techniques leveraged in performing nanoparticle characterizations.

The focus of CDE and terminology development is re-use of existing biomedical standards maintained in the NCI's EVS and the creation of new concepts, when needed, via interaction with the community and other standards organizations.

If you would like to participate in discussions regarding the identification and development of biomedical nanotechnology concepts, please contact the caNanoLab Users Group via the caNanoLab Users Listserv.

Data Curation

Data curation is a key component for ensuring that data is appropriately annotated to facilitate data sharing in a semantically interoperable fashion. 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, please contact Washington University (Nathan Baker).

Using the caNanoLab Wiki

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Office of Cancer Nanotechnology Research (OCNR).

Data Curation

Data curation is a key component for ensuring that data is appropriately annotated to facilitate data sharing in a semantically interoperable fashion. Data curation activities on caNanoLab are currently performed by the NCI Alliance for Nanotechnology in Cancer Data Coordinators and the NCI data curator. 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 submitting your data into caNanoLab, contact caNanoLab-Support@ISB-CGC.org.

Detailed data curation steps are explained in the Curation of Biomedical Data into ISA-TAB-Nano and caNanoLab Standard Operating Procedure.

Installation and Downloads

caNanoLab 3.1.14 Artifacts

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caNanoLab 2.4.1 Artifacts

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Forum and Support

Presentations, Demos and Other Materials

The caNanoLab Data Submission Video and accompanying transcript is available to assist people in submitting data in caNanoLab. 

Note: Materials for previous caNanoLab releases are available from the caNanoLab Presentations, Demos and Other Materials archive. 

Documentation and Training

To access online help in the application, click the Help button.

Note: Documents for previous caNanoLab releases are available from the caNanoLab Presentations, Demos and Other Materials Archive and the Docs Archive Page - calab. 

Related Tools and Terminology

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