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Table 1 Comparison of existing platforms and systems that provide and apply life science ontologies

From: GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution

 

OLS

OBO

BioPortal

GOMMA

SAMBO

Description

Service to query, browse and navigate biomedical ontologies

Collaborative platform having shared principles to govern and coordinate ontology development

System to access and share ontologies that are actively used in biomedical communities

Infrastructure to manage, analyze and match ontologies taking their evolution into account

System for aligning and merging biomedical ontologies

Supported ontology formats

OBO

OBO, OWL

OBO, OWL, RDF, RRF, ...

OBO, OWL, RDF, ... (extensible via flexible importers)

OWL

Ontology mappings

-

x

x

x

x

Versioning support

- (only latest versions are accessible)

x (downloadable versions via CVS repository)

x (access and download of ontology versions)

x (efficient versioning of ontologies in a repository)

- (no explicit ontology versioning possible)

Evolution mappings

     

1) change log

-

x (information about changes via newsletters)

-

- (version comparison to detect changes)

-

2) complex diff

-

-

-

x

-

Match support/functionality

-

-

-

x (metadata, external knowledge, instances)

x (metadata, external knowledge, documents, learner)

Search, navigation

ontologies

ontologies

ontologies and mappings

ontologies, ontology evolution

-

"Special Functionalities"

auto completion, term hierarchies via graphs

discussion lists and wiki to support collaborative development

automatic text annotation

enhanced Diff, annotation migration

merging, user interaction

Availability and Access

     

1) download (ontologies, mappings)

x

x

x

-

-

2) visualization/GUI

x (web application))

- (infrastructure to share the ontologies)

x (web portal)

x (web application OnEX)

x (desktop GUI)

3) API/web service

x (web service: Ontology QueryService

-

x (web service to access and query available on tologies)

x (query ontology and mapping versions, statistics, diff, match via API)

unknown

  1. The table provides a comparative overview of platforms that provide and apply life science ontologies. The systems are compared by different characteristics such as versioning support or search/navigation facilities.