caNanoLab Documentation
caNanoLab Overview
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 nanomaterials in biomedicine. caNanoLab provides support for the annotation of nanomaterials with characterizations resulting from physico-chemical and in vitro nanomaterial assays and the sharing of these characterizations and associated nanotechnology protocols in a secure fashion.
caNanoLab is a collaboration between 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 and Standards Development
The caNanoLab project is actively involved in a variety of efforts supporting the development of standards for representing nanomaterials and their characterizations as applied to the field of nanomedicine. The caNanoLab project participates in the caBIG® Integrative Cancer Research (ICR) Nanotechnology Working Group (Nano WG) which is chartered to integrate nanotechnology information and tools to aid discovery and clinical translation in the cancer research community leveraging caBIG infrastructure components. The primary objectives of the caBIG ICR Nano WG are to:
- Define and prioritize development and governance needs for the cancer nanotechnology ontology
- Adopt and collect data sharing standards and protocols for cancer nanotechnology data
- Develop a vision for nanoinformatics enabling information exchange with nanotechnology resources leveraging data standards
The caNanoLab project participates in working group objectives by assisting in the development of nanotechnology standards and the application of these standards in the caNanoLab nanotechnology resource. Information on caBIG ICR Nano WG standards leveraged by caNanoLab is provided in the subsections below.
Nanotechnology Data Sharing Standards
The caNanoLab project worked with the caBIG ICR Nano WG to develop a Nanotechnology Data Sharing Standards document which identifies common data elements leveraged across nanotechnology resources.
Nanotechnology Data Sharing Standards includes support for:
- Nanomaterials and their Composition - Nanomaterials (e.g. dendrimer) and their associated properties (e.g. branch, generation) and composing elements (e.g. core). Includes functionalizing entities (e.g. small molecule, antibodies) associated with the nanomaterial that allow the material to function as a targeting, therapeutic, and/or diagnostic agent.
- Physico-Chemical Characterizations - Assay conditions and measurements associated with the physical (e.g. size, molecular weight) and chemical (e.g. surface chemistry) properties of nanomaterials.
- In Vitro Characterizations - Assay conditions and measurements that assess a nanomaterial's interaction with cellular components including cytotoxicity and blood contact properties.
- In Vivo Characterizations - Characterizations performed on nanomaterials to determine the safety, efficacy, pharmacokinetics, and toxicology properties of nanomaterials in animal models so that nanomaterials can be transitioned for use in clinical applications.
NanoParticle Ontology
caNanoLab consumes of and contributes to the NanoParticle Ontology (NPO) developed by Washington University. Information on the NPO is available on the caBIG ICR Nano WG Ontology Development and Governance Site.
nano-TAB
nano-TAB is a tab-delimited spreadsheet type of format facilitating the submission and exchange of data pertaining to nanomaterial composition and their characterizations. The caNanoLab project participates on the caBIG ICR Nano WG sub-group supporting the development of nano-TAB which leverages and extends the ISA-TAB standard.
To become a member of the nano-TAB sub-group, please subscribe to the nano-TAB Listserv. Artifacts from the sub-group are available on the nano-TAB project site:
LS DAM Nano Sub-Domain
caNanoLab has been working with the caBIG Life Sciences Domain Analysis Modeling (LS DAM) team to develop a nano sub-domain. The nano sub-domain is based on the caNanoLab object model (nano-OM) extended to support existing LS DAM concepts. The caNanoLab project aims to develop future services leveraging the NCI's Enterprise Compliance and Conformance Framework (ECCF).
caNanoLab Users Group
caNanoLab hosts data from a variety of organizations conducting nanomaterial characterizations. caNanoLab feature requests are obtained by working with the nanotechnology community through the caNanoLab Users Group and the caBIG ICR Nano WG.
caNanoLab Users Group meetings occur the 3rd Friday of every month from 1:30PM-2:30PM ET. 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.
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 submitting your data into caNanoLab, please contact the caNanoLab Users Listserv.
caNanoLab Architecture
caNanoLab leverages the caCORE SDK and caGrid technologies to develop, deploy, and advertise common services for nanomaterials and characterizations. caNanoLab grid services are available through caB2B and other caBIG resources consuming of caGrid services.
Using the caNanoLab Wiki
This is the wiki home page of caNanoLab. Collaborators may edit this page and add more pages. If you can see the link at the bottom of the page, you may add comments.
