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.

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) doesn’t 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., Aragüez, I., Peiró, 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)