My Bioportal, Slices - NCI Wiki

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THE NATIONAL CENTER FOR

BIOMEDICAL ONTOLOGY

BioPortal Updates and

Planned Features

Trish Whetzel

May 3, 2012

New Functionality in Last Year


Allow BioPortal configuration


My Bioportal, Slices


Improved support for Notes


Provisional ids for new terms, archiving, email notification


Allow private and licensed ontologies


Flag obsolete terms


“Productionized” Ontology Recommender


Automated handling of OWL2 ontologies


Created beta version of triple
-
store architecture

Systemic Improvements


Solidified core system


M
onthly release schedule


Many long
-
standing bugs fixed


Established regular VM release cycle (3x/year)


Reworked entire UI to be simpler and more consistent


Improved Annotator performance by 5
-
10x


Improved user
-
tracking with API Key mechanism



Home
Page

Recommender Tab

Browse Page

Custom display of

selected ontologies

Search

Ontology Recommender

Annotator

Slice

Resource Index

ODiSSea


Elsevier SciVerse


Who is using our Web services?


Who is using our Web services?

Technical Aims

1.
Develop, enhance, and deploy software services and
tools that allow investigators to use ontologies.


2.
Integrate ontology publishing and peer review with
ontology authoring.


3.
Create a comprehensive ontology
-
based index for
publicly available biomedical resources.


4.
Develop analytic methods to summarize and profile
biomedical data sets
.

Plans for Coming Year


Move RDF triple
-
store from beta to production release*


Synchronize Annotator and Mappings to ontology submission
and update


Re
-
implement
Annotator and Resource Index
to
be more
reliable, better performing, and more scalable


Add additional
resources in Resource Index


Provide improved
support for projects and views


Implement CTS2
API for
BioPortal*


Replace FlexViz Ontology Visualization with
BioMixer*

* Beta version of feature

BioPortal Architecture Updates

RDF

LexEVS

Protégé DB

Hibernate ORM

Spring Framework

Restlet

Tomcat

OWL

RDF

Protégé frames

Ruby on Rails

OBO format

UMLS RRF

LexGrid XML


Transform

Server

CTS2

BioPortal

SPARQL Endpoint

http://sparql.bioontology.org/

Concluded Driving Biological Projects



Candidate Gene Discovery through Ontological Indexing


Medical College of Wisconsin; Simon Twigger




Annotation of Biomedical Data in CVRG


Johns Hopkins; Rai Winslow




Cancer Nanotechnology Knowledge Base


Stanford/PNNL; David Paik & Nathan Baker

New Driving Biological Projects



Ontology
-
driven analysis of high
-
throughput data


European Bioinformatics Institute;

Helen Parkinson




Using ontologies and data fusion approaches to understand
organismal aging


Buck Institute for Research on Aging;

Sean Mooney



Synapse: A precondition space for integrative genomics


Sage Bionetworks; Michael Kellen

Collaborative R01 Projects


Active


Integrative Tools for Protozoan Parasite
Research
-

Chris
Stoeckert,
UPenn


Completed (2011
-
2012)


Reference
Ontologies for the Semantic
Web
-

Jim
Brinkley, University
of
Washington


Neuroscience
Information
Framework
-

Maryann
Martone, UCSD


Ontologies and Biomedical Language
Processing
-

Larry
Hunter,
University of
Colorado


Ontology
Development Information
Extraction
-

Rebecca
Crowley,
University of Pittsburgh


Context
-
based Ontology
Integration
-

Gil
Alterovitz, Brigham and
Women’s
Hospital


Semantics
and Services Enabled Problem Solving Environment for
T.
cruzi
-

Amit
Sheth, Wright
State

Other NCBO collaborations


Informatics for Integrating Biology and the
Bedside (i2b2)


BioSitemaps


UCSF Clinical and Translational Sciences
Institute


BioSharing (including Minimal Information for
Biological and Biomedical Investigations)


BioDBCore initiative of the

International Society for Biocuration


Links of Interest


Web
service
documentation

http://www.bioontology.org/wiki/index.php/
NCBO_R
EST_services


Release
Notes


http://www.bioontology.org/wiki/index.php/
BioPortal_Rel
ease_Notes



Software questions


Software support:
support
@bioontology.org



Social media


Twitter
: @bioontology


Facebook:
http://on.fb.me/
bioontology



LinkedIn:
http://linkd.in/ncbo
-
group