Plant ontology web services on Araport

+

Old Wine in New Bottles Give existing web services new

life and new audiences in Araport Justin Preece Oregon State University

+I work on these projects:

! Plant Ontology - PO ! cont. in Planteome

! Planteome !  started Dec 2014 !  A.K.A. “Common Reference Ontologies for

Plants (cROP) and Tools for Integrative Plant Genomics”

!  Will carry Plant Ontology development forward, along with several other ontologies and related data annotation and analysis tools

! Plant Reactome ! Part of the Gramene project

(NSF #1127112)

(NSF #1340112)

(NSF #0822201)

+Plant Ontology * Describes plant anatomy, morphology and stages of development for all plants.

* Now dual-hosted on project servers and iPlant.

+I set up these PO web services several years ago…

Plant Ontology Term Search Plant Ontology Term Details

+I use them in other software projects.

Planteome Annotation Wiki (prototype)

AISO: Annotating Images with Ontologies

+ They’re also publicly accessible and documented.

+The ontology data itself is used heavily, but the web services…not so much. ! Many groups have collaborated with us on annotating

their data with PO terms.

! Most of those projects were facilitated by direct interaction with the PO group.

! We would like to see more developers and researchers make independent use of this ontology data, via programmatic interfaces.

How can I extend the reach of these web services?

+…enter AIP and Araport.

! Araport offers tutorials, registration and hosting infrastructure for developing community APIs ! Wrap and register our existing services in an Araport

API ! Position our services for authenticated access and use

by a new community of researchers and developers.

! Araport also provides a bootstrap environment for developing client-side applications using these APIs. ! Use JavaScript frameworks to build and publish apps

that use our web services via the Araport API. Other developers can also make apps that use our services.

! Bonus: Have immediate access to a fresh UI

+…enter AIP and Araport.

+1. Clone and checkout an Araport/Adama API template from GitHub.

Creating and registering a “generic” API

+ Creating and registering a “generic” API 2. Edit the main Python script and config file to interact with your web service.

+ Creating and registering a “generic” API 3. Test and register your service with Adama (well-documented cmd- line steps).

+ Creating and deploying my own PO Term Lookup app This uses my freshly wrapped “PO term search” web service, via the API. 1. Clone and checkout an Araport Science App template from GitHub.

+ Creating and deploying my own PO Term Lookup app This uses my freshly wrapped “PO term search” web service, via the API. 2. Modify the HTML and JavaScript to use your web service.

+

3. Test your app in your local browser. (Yeah!)

Creating and deploying my own PO Term Lookup app This uses my freshly wrapped “PO term search” web service, via the API.

+ Creating and deploying my own PO Term Lookup app This uses my freshly wrapped “PO term search” web service, via the API. 4. Check in your app and add it to your workspace on the Araport Dev site.

+AIP Plant Ontology Lookup Service Here’s the resulting app, deployed and running in the Araport development environment.

+AIP Plant Ontology Lookup Service Results are displayed in a data table.

+AIP Plant Ontology Lookup Service Multi-column sorting and pagination…

+AIP Plant Ontology Lookup Service

This prototype – service API and app – took ~7 hrs.

Result filtering…

This prototype – service API and app – took ~7 hrs.

+What next? Extend this PO services prototype. !  Expose all available term search web service parameters to

the API and the app:

!  Add the PO term details web service and modal dialog to the app. Translation: A pop-up window with a term definition, synonyms, and other details.

+What could other developers do with the PO web services in Araport? !  Add a widget version of the PO term lookup service to an

Araport-hosted Arabidopsis gene annotation app

!  Use the PO term details service to enrich any display of data annotated with Plant Ontology terms

+Future plans: Planteome + AIP collaboration Implement AIP wrappers for new web services coming from the Planteome project.

Planteome Common Reference Ontologies for Plants (cROP) and Tools for Integrative Plant Genomics

!  Centralized platform where reference ontologies for plants will be developed and hosted, along with crop-specific application ontologies and analysis tools.

!  Reference and crop ontologies will be used for integration and annotation of genetic, genomic and germplasm data sets, collected and managed by collaborative national and international projects.

(NSF #1340112)

+Common Reference Ontologies for Plants (cROP)

Plant Ontology (PO) Plant Trait Ontology (TO) Plant Stress Ontology (PSO) Plant Experimental Conditions Ontology (PECO/EO) Gene Ontology (plants) Phenotypic Qualities Ontology (PATO) Cell Type Ontology (CL) Environment Ontology (ENVO) Chemicals (ChEBI) Protein Ontology (PRO)

+The Planteome Informatics Portal and Data Store

! Online informatics portal for ontology-based, annotated data for plant germplasm, gene expression, and non-model genomes

! Semantic data query, analysis, visualization and community-based annotation and curation tools

+ Other plans: Plant Reactome service integration

"  Wrap the new Plant Reactome RESTful web services in Araport.

"  Develop Araport apps that use this data to draw HTML5 diagrams, develop overlays of data from other Araport APIs (e.g. A.th. gene info from Thalemine superimposed on pathway gene products).

(NSF #1127112)

+ Other plans: Plant Reactome service integration

+Thanks! !  Jaiswal Lab, Oregon State Univ.

!  Laurel Cooper !  Justin Elser !  Vindhya Amarasinghe !  Shushma Naithani !  Pankaj Jaiswal (Planteome,

Gramene)

!  JCVI !  Jason Miller (AIP, Co-PI) !  Erik Ferlanti !  Vivek Krishnakumar !  Chris Town (AIP)

!  TACC !  Matt Vaughn (AIP, Co-PI)

!  Matt Hanlon

!  Steve Mock

!  Walter Moreira

!  CSHL !  Kapeel Chougule

!  Andrew Olson

!  Doreen Ware (Gramene)