CAIRR: A pipeline to submit AIRR data to the NCBI through the CEDAR Workbench
0 likes140 views
CAIRR is a pipeline that allows users to submit AIRR data to NCBI through the CEDAR Workbench. It addresses issues with the current direct NCBI submission process such as a lack of metadata standardization and error-prone data entry. CAIRR streamlines the submission process into three simple steps - finding a template, adding standardized metadata by mapping attributes to ontologies, and uploading and submitting the data. This helps ensure metadata is complete and consistent compared to direct submission to NCBI.
CAIRR: A pipeline to submit AIRR data to the NCBI through the CEDAR Workbench
- 1. CAIRR: A pipeline to submit AIRR data to the NCBI through the CEDAR Workbench Syed Ahmad Chan Bukhari, Martin J. O'Connor, Marcos Martínez-Romero, Attila L. Egyedi, Debra Willrett, John Graybeal , Mark A. Musen, Florian Rubelt, Steven H. Kleinstein , Kei-Hoi Cheung
- 2. AIRR Community defined MiAIRR and implemented with NCBI
- 3. NCBI is an important resource to archive biomedical data ● NCBI hosts a collection of biomedical databases and provide long-term support. ○ BioProject, BioSample, SRA, GenBank, GEO etc. ● Minimal use of standard terminologies to define the necessary metadata ○ Ontologies recommended for some data elements (Not implemented) ● NCBI metadata are often described using inconsistent terminologies ○ Limit our ability to access, find, interoperate and reuse the data sets
- 4. What are the issues with the current NCBI submission process? ● Rapid growth ● Lack of metadata standardization ● Error prone data entry ● Lack of community-specific metadata (e.g., AIRR)
- 5. CEDAR for AIRR Submit your AIRR metadata to NCBI, faster and better. Organism NCBITAXON Disease/Diagnosis DOID Tissue BTO Cell Subset CL Example of Ontological Mapping
- 7. Three simple steps to deposit AIRR data to the NCBI Find template by typing MiAIRR
- 8. Three simple steps to deposit AIRR data to the NCBI Add metadata
- 9. Three simple steps to deposit AIRR data to the NCBI Upload and Submit
- 10. Why use CAIRR instead of direct submission? 1. Just one simple form (with tool tips!) to fill out, instead of multiple NCBI templates. 2. Make your metadata right the first time with auto-completion, suggestions, and validation. 3. Exact answers—Your metadata attributes and values come from unique ontology concepts, so they are unambiguous and fully described. 4. Better feedback during the submission process. 5. CEDAR is faster and easier!