caNanoLab Users Group

February 2012

Use of Informatics to Expedite and Validate the Application of

Nanotechnology in Biomedicine

Agenda

• Current Release Overview• Planned Release Overview• Future Features Discussion

Current Release: caNanoLab 1.5.2

https://cananolab.nci.nih.gov/caNanoLab/https://cananolab.nci.nih.gov/caNanoLab/

caNanoLab 1.5.2 Features

• Support for private data submission by individual researchers and processing of requests for public submission by the data curator

• Support for collaboration groups and group data access• Support for data availability metrics against the caNanoLab model and the

MinChar standard• Support for data ownership transfer• Migration to LDAP-based user authentication• Resolution of reported defects

Planned Release: caNanoLab 1.5.3

• Release Features:

• Various upgrades to meet technical and compliance requirements • Section 508 compliance• Technology stack upgrades• Security compliance upgrades

• Release Timeline:

• June 2012

Future Features (1 of 3)

JIRA # Feature/Description Priority (1=High, 2=Med, 3=Low)

caNanoLab-2 Feature: Provide support for in vivo characterization data

Description: Support the NCI Alliance use case for understanding the effects of nanomaterial size and shape on biodistribution. Requires support for studies, animal and treatment information, pharmacokinetics, and toxicology.

caNanoLab-19 Feature: Provide support for the ISA-TAB-Nano standard

Description: Support the validation, import, and export of ISA-TAB-Nano files. Leverage existing ISA-Tools where possible. Requires support for studies.

caNanoLab-20 Feature: Provide a Java and SOAP API, including RESTful services for accessing caNanoLab data

Description: Expose the caCORE SDK generated APIs and add the security filter

Animal/Treatment Information ExampleNCL In Vivo Study

Pharmacokinetics Data ExampleNCL In Vivo Study

PK Parameters

Plasma vs. Time Graphs

Tissue Distribution Data ExampleNCL In Vivo Study

Tissue Distribution

Toxicology Data Example NCL In Vivo Study

Hematology

Clinical Chemistry

Organ Body Weight

Gross Pathology Histopathology

ISA-TAB-Nano

http://isatab.sourceforge.net/tools.htmlhttp://isatab.sourceforge.net/tools.html

• Explore the use of ISA-Tools

• Use and extension of isaValidator for validating ISA-TAB-Nano files prior to submission into caNanoLab

• Import of validated ISA-TAB-Nano files into caNanoLab

• Export of validated ISA-TAB-Nano files in support of data sharing

• Requires extensions to caNanoLab to support ISA-TAB concepts (Investigation, Study, etc.)

Future Features (2 of 3)

JIRA # Feature/Description Priority (1=High, 2=Med, 3=Low)

caNanoLab-21 Feature: Interface with analysis and visualization tools such as GenePattern

Description: Allow users to view data queried from caNanoLab in GenePattern (e.g. heatmap displaying particle size vs. toxicity)

caNanoLab-22 Feature: Interface with the National Biomedical Imaging Archive (NBIA) and the Molecular Imaging and Contrast Agent Database (MICAD) database in support of nanomaterial images

Description: Allow users to upload biomedical images into NBIA and link caNanoLab to NBIA. Provide links from nanomaterials used as image contrast agents to MICAD

caNanoLab-23 Feature: Interface with the cancer Models Organism Database (caMOD) in support of animal models used in nanomaterial characterizations

Description: Provide links from nanomaterial characterizations to animal models

caNanoLab Interfaces

• Interface with GenePattern

• Allow user to display nanomaterial characterizations in a heatmap view

• Interface with NBIA and MICAD

• Allow users to upload images in NBIA and agents in MICAD and make accessible via caNanoLab

• Interface with caMOD

• Allow users to upload animal models in caMOD and link to caNanoLab

GenePattern NBIA caMOD

Future Features (3 of 3)

JIRA # Feature/Description Priority (1=High, 2=Med, 3=Low)

caNanoLab-24 Feature: Add support for Structure-Activity-Relationships (SARs)

Description: Interface with the Collaboratory for Structural Nanotechnology (CSN)

caNanoLab-25 Feature: Integrate with the Nanoparticle Ontology (NPO)

Description: Allow users to submit and browse caNanoLab terms leveraging the NPO

caNanoLab-26 Feature: Provide support for automatic report generation

Description: Allow researchers to export data in a customized report leveraging a report template

caNanoLab-27 Feature: Add Google-like Search

Description: Add capability to perform freestyle search

caNanoLab-28 Feature: Provide links to clinically validated biomarkers in support of nanomaterial design

Description: Provide links to biomarker repositories

Collaboratory for Structural Nanobiology

• The Collaboratory for Structural Nanobiology (CSN) provides access to caNanoLab for shared nanomaterials

• Implement an interface from caNanoLab to the CSN

CSN

Other Features?

Next Steps

• Continue supporting caNanoLab 1.5.3

• Continue participating in ISA-TAB-Nano discussions

• Review prioritized features

• Host next caNanoLab Users Group Meeting:

• Users Group: April 5, 2012 1:00 PM EST

caNanoLab Team

• NCI Project Sponsor – Juli Klemm

• NCI Project Officer - JJ Pan

• SAIC-F COTR – Deb Hope

• SAIC Project Manager – Sharon Gaheen

• SAIC Technical Lead – Sue Pan

• NCI Quality Assurance – Quy Phung

References

• caNanoLab Portal

• http://cananolab.nci.nih.gov

• caNanoLab Wiki

• https://wiki.nci.nih.gov/display/caNanoLab/caNanoLab+Wiki+Home+Page

• ISA-TAB-Nano Data Standard

• https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano

• ISA-TAB

• http://isatab.sourceforge.net/

• NBIA

• https://imaging.nci.nih.gov/ncia/login.jsf

• caMOD

• https://cancermodels.nci.nih.gov/camod/

• CSN

• http://csn.ncifcrf.gov/csn/index2.php