PhenoImageShare: An image annotation and query infrastructure

Albert Georg Burger; Richard Baldock; Solomon Adebayo; Ilinca Tudose; Kenneth McLeod; David Osumi-Sutherland; Helen Parkinson; Tony Burdett

doi:10.1186/s13326-016-0072-2

PhenoImageShare: An image annotation and query infrastructure

Albert Georg Burger, Richard Baldock, Solomon Adebayo, Ilinca Tudose, Kenneth McLeod, David Osumi-Sutherland, Helen Parkinson, Tony Burdett

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Abstract

Background: High throughput imaging is now available to many groups and it is possible to generate a large quantity of high quality images quickly. Managing this data, consistently annotating it, or making it available to the community are all challenges that come with these methods.

Results: PhenoImageShare provides an ontology-enabled lightweight image data query, annotation service and a single point of access backed by a Solr server for programmatic access to an integrated image collection enabling improved community access. PhenoImageShare also provides an easy to use online image annotation tool with functionality to draw regions of interest on images and to annotate them with terms from an autosuggest-enabled ontology-lookup widget. The provenance of each image, and annotation, is kept and links to original resources are provided. The semantic and intuitive search interface is species and imaging technology neutral. PhenoImageShare now provides access to annotation for over 100,000 images for 2 species.

Conclusion: The PhenoImageShare platform provides underlying infrastructure for both programmatic access and user-facing tools for biologists enabling the query and annotation of federated images. PhenoImageShare is accessible online at http://www.phenoimageshare.org.

Original language	English
Article number	35
Journal	Journal of Biomedical Semantics
Volume	7
DOIs	https://doi.org/10.1186/s13326-016-0072-2
Publication status	Published - 7 Jun 2016

Keywords

Phenotype description
Infrastructure
semantic interoperability
image annotation
semantic annotation
genotype-phenotype associations

ASJC Scopus subject areas

Computer Science (miscellaneous)
Developmental Biology
Animal Science and Zoology

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Albert Georg Burger
- A.G.Burgerhw.acuk
- School of Mathematical & Computer Sciences - Professor
- School of Mathematical & Computer Sciences, Computer Science - Professor
Person: Academic (Research & Teaching)

Cite this

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title = "PhenoImageShare: An image annotation and query infrastructure",

abstract = "Background: High throughput imaging is now available to many groups and it is possible to generate a large quantity of high quality images quickly. Managing this data, consistently annotating it, or making it available to the community are all challenges that come with these methods.Results: PhenoImageShare provides an ontology-enabled lightweight image data query, annotation service and a single point of access backed by a Solr server for programmatic access to an integrated image collection enabling improved community access. PhenoImageShare also provides an easy to use online image annotation tool with functionality to draw regions of interest on images and to annotate them with terms from an autosuggest-enabled ontology-lookup widget. The provenance of each image, and annotation, is kept and links to original resources are provided. The semantic and intuitive search interface is species and imaging technology neutral. PhenoImageShare now provides access to annotation for over 100,000 images for 2 species. Conclusion: The PhenoImageShare platform provides underlying infrastructure for both programmatic access and user-facing tools for biologists enabling the query and annotation of federated images. PhenoImageShare is accessible online at http://www.phenoimageshare.org. ",

keywords = "Phenotype description, Infrastructure, semantic interoperability, image annotation, semantic annotation, genotype-phenotype associations",

author = "Burger, {Albert Georg} and Richard Baldock and Solomon Adebayo and Ilinca Tudose and Kenneth McLeod and David Osumi-Sutherland and Helen Parkinson and Tony Burdett",

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doi = "10.1186/s13326-016-0072-2",

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AU - Burger, Albert Georg

AU - Baldock, Richard

AU - Adebayo, Solomon

AU - Tudose, Ilinca

AU - McLeod, Kenneth

AU - Osumi-Sutherland, David

AU - Parkinson, Helen

AU - Burdett, Tony

PY - 2016/6/7

Y1 - 2016/6/7

N2 - Background: High throughput imaging is now available to many groups and it is possible to generate a large quantity of high quality images quickly. Managing this data, consistently annotating it, or making it available to the community are all challenges that come with these methods.Results: PhenoImageShare provides an ontology-enabled lightweight image data query, annotation service and a single point of access backed by a Solr server for programmatic access to an integrated image collection enabling improved community access. PhenoImageShare also provides an easy to use online image annotation tool with functionality to draw regions of interest on images and to annotate them with terms from an autosuggest-enabled ontology-lookup widget. The provenance of each image, and annotation, is kept and links to original resources are provided. The semantic and intuitive search interface is species and imaging technology neutral. PhenoImageShare now provides access to annotation for over 100,000 images for 2 species. Conclusion: The PhenoImageShare platform provides underlying infrastructure for both programmatic access and user-facing tools for biologists enabling the query and annotation of federated images. PhenoImageShare is accessible online at http://www.phenoimageshare.org.

AB - Background: High throughput imaging is now available to many groups and it is possible to generate a large quantity of high quality images quickly. Managing this data, consistently annotating it, or making it available to the community are all challenges that come with these methods.Results: PhenoImageShare provides an ontology-enabled lightweight image data query, annotation service and a single point of access backed by a Solr server for programmatic access to an integrated image collection enabling improved community access. PhenoImageShare also provides an easy to use online image annotation tool with functionality to draw regions of interest on images and to annotate them with terms from an autosuggest-enabled ontology-lookup widget. The provenance of each image, and annotation, is kept and links to original resources are provided. The semantic and intuitive search interface is species and imaging technology neutral. PhenoImageShare now provides access to annotation for over 100,000 images for 2 species. Conclusion: The PhenoImageShare platform provides underlying infrastructure for both programmatic access and user-facing tools for biologists enabling the query and annotation of federated images. PhenoImageShare is accessible online at http://www.phenoimageshare.org.

KW - Phenotype description

KW - Infrastructure

KW - semantic interoperability

KW - image annotation

KW - semantic annotation

KW - genotype-phenotype associations

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DO - 10.1186/s13326-016-0072-2

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VL - 7

JO - Journal of Biomedical Semantics

JF - Journal of Biomedical Semantics

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ER -

PhenoImageShare: An image annotation and query infrastructure

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Keywords

ASJC Scopus subject areas

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Albert Georg Burger

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