Integrate JBrowse REST API Framework with Adama Federation Architecture
Download as PPTX, PDF
0 likes529 views
This presentation describes the work done to integrate the JBrowse REST API Framework with the Araport.org-developed Adama Federation Architecture, enabling community developers to package their published datasets and expose them in a manner which is compatible with JBrowse.
Integrate JBrowse REST API Framework with Adama Federation Architecture
- 1. araport.org@araport Integrate JBrowse REST API with ADAMA Vivek Krishnakumar 12/03/2015
- 2. araport.org@araport Outline JBrowse REST API spec ADAMA endpoints Mapping JBrowse to ADAMA endpoints Extending JBrowse REST feature store Handling Auth in JBrowse 1.x Use Case Integrate Chromatin States data into JBrowse via ADAMA Summary Challenges
- 3. araport.org@araport JBrowse REST API spec Javascript based portable genome browser tool developed by GMOD community Ships with REST feature and names store adapter REST feature store requires access to following endpoints via HTTP GET: (base)/stats/global (base)/stats/region/(refseq)?start=123&end=456 (base)/stats/regionFeatureDensities/(refseq)?start=123&end=456&basesP erBin=20000 (base)/features/(refseq)?start=234&end=5678 Can provide feature, sequence, and quantitative data for display Accepted response type: application/json http://gmod.org/wiki/JBrowse_Configuration_Guide#Writing_JBrowse-compatible_Web_Services
- 4. araport.org@araport ADAMA endpoints Araport Data And Microservices API Developed by WalterM and MattV Encapsulates python code into reusable docker containers Exposes internal logic as API endpoints: query, generic adapters via HTTP GET (base)/search (base)/list passthrough adapters via HTTP GET and POST (base)/access Implements token based Auth via iPlant OAuth2 https://github.com/Arabidopsis-Information-Portal/adama
- 5. araport.org@araport Mapping JBrowse to ADAMA endpoints ADAMA (currently) doesnt allow defining custom endpoints So, we have to map the 4 JBrowse endpoints to the 2 ADAMA endpoints Proposed endpoint mapping: JBrowse ADAMA (base)/stats/global (base)/search?q=global (base)/stats/region (base)/search?q=region (base)/stats/regionFeatureDensities (base)/search?q=regionFeatureDensities (base)/features (base)/search?q=features (base)/list?q=makeTrackListJson
- 6. araport.org@araport Extending JBrowse REST feature store JBrowse/Store/SeqFeature/REST handles requests from the browser to the configured API service Understands the 4 pre-defined endpoints REST feature store extended based on proposed endpoint mapping Utilize JBrowse Plugin architecture to develop Araport plugin: Araport/Store/SeqFeature/REST http://gmod.org/wiki/JBrowse_Configuration_Guide#Writing_JBrowse_Plugins
- 7. araport.org@araport Handling Auth in JBrowse 1.x ADAMA (currently) requires all requests to be accompanied by an Authorization Bearer $TOKEN JBrowse 1.x does not support OAuth2 implicit flow, thus cannot generate tokens Solution: OAuth2 $TOKEN created with unlimited validity (-1) $TOKEN generated by Araport anonymous user $TOKEN scope limited to ADAMA services Araport/Store/SeqFeature/RESTAuth hard codes $TOKEN Araport/Store/SeqFeature/REST inherits from RESTAuth
- 8. araport.org@araport Use Case Integrate Chromatin States data into JBrowse via ADAMA Published dataset representing a landscape of Arabidopsis thaliana chromatin states using 16 features, including DNA sequence, CG methylation, histone variants, and modifications Data represents chromosomal regions (start/stop coordinates) corresponding with 9 distinct chromatin states Published with manuscript as supplementary dataset (in XLS format)Sequeira-Mendes, J., Arag端ez, I., Peir坦, R., Mendez-Giraldez, R., Zhang, X., Jacobsen, S. E., ... & Gutierrez, C. (2014). The functional topography of the Arabidopsis genome is organized in a reduced number of linear motifs of chromatin states. The Plant Cell, 26(6), 2351-2366.
- 9. araport.org@araport Develop ADAMA adapter to dynamically query data from desired region and represent as JBrowse compatible JSON Code: https://github.com/Arabidopsis-Information- Portal/chromatin_states_to_jbrowse Implementation logic: Data transformed from 9 XLS worksheets into individual GFF3 files Pythonic parser developed using gffutils, allowing range querying (via intermediary sqlite database) ADAMA metadata.yml written which describes dependencies, endpoints and provenance Data hosted with code (due to small size, well within GitHub file size limits) ADAMA namespace created and adapter registered Available in API explorer (search for chromatin) Use Case Integrate Chromatin States data into JBrowse via ADAMA https://jira.araport.org/browse/MINE-1078
- 10. araport.org@araport Integrate Chromatin States data into JBrowse via ADAMA JBrowse tracks configured to talk to registered ADAMA endpoint End result visible in screenshot above Live view: https://apps.araport.org/jbrowse/?data=arabidopsis&loc=Chr3:11355449..11407858&tracks=chromatin_state_1,chr omatin_state_2,chromatin_state_3,chromatin_state_4,chromatin_state_5,chromatin_state_6,chromatin_state_7,chr omatin_state_8,chromatin_state_9,Araport11_gene_models
- 11. araport.org@araport Summary Extended JBrowse to integrate with ADAMA endpoints Exposed a published community dataset via ADAMA as an API Exposed track configuration via ADAMA API Visualized dataset in JBrowse via ADAMA API
- 12. araport.org@araport Challenges Making web service calls to ADAMA requires Authorization $TOKEN JBrowse needs to hard code the Authorization $TOKEN Track configuration needs to be manually added to JBrowse Scaling to larger datasets not feasible via GitHub route
- 13. araport.org@araport Acknowledgements JCVI Araport Team Chia-Yi Cheng Agnes Chan Chris Town TACC Araport Team Walter Moreira Matthew Vaughn Prof. Crisanto Gutierrez (CBMSO)