Image Driven Ontology Editing - University of Texas at Austin · 2009. 11. 5. · OBO Triple Store...
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OBO Triple Store OBO Triple Store Image Driven Ontology Editing Timothy Rowe°, Julian Humphries°, Daniel P. Miranker ! , Syed Hamid Tirmizi ! , Kerin M. Claeson°, Juan F. Sequeda ! , Willard S. Willard ! , Ferner Cilloniz-Bicchi ! , Nirav Savjani ! . Department of Geological Sciences°, Department of Computer Sciences ! . The University of Texas at Austin Triple Store Triple Store SPARQL / Jena API SPARQL / Jena API Interface Interface OBO/OWL OBO/OWL Roundtrip Roundtrip Transformation Transformation Image Driven Ontology Tools Image Driven Ontology Tools OntoIllustrator OntoIllustrator, , OntoBrowser OntoBrowser etc. etc. OBO Foundry ontologies are downloaded in OBO Flat File format from their source The triple store is a Semantic Web enabled ontology store accessible through W3C recommended SPARQL interface, and Jena API Common Common Anatomy Anatomy Reference Reference (CARO) (CARO) Zebrafish Zebrafish Anatomy (ZFIN) Anatomy (ZFIN) Gene Gene Ontology Ontology (GO) (GO) Phenotypic Phenotypic Quality Ontology Quality Ontology (PATO) (PATO) By developing a lossless roundtrip transformation mechanism between OBO and By developing a lossless roundtrip transformation mechanism between OBO and Semantic Web (OWL) Semantic Web (OWL) ontologies ontologies, we , we have opened the Semantic Web infrastructure for biomedical have opened the Semantic Web infrastructure for biomedical ontologies ontologies. As a result, we have successfully deployed a . As a result, we have successfully deployed a triple-store backend for OBO triple-store backend for OBO ontologies ontologies, powered by an engine for W3C recommended SPARQL language and Jena API. , powered by an engine for W3C recommended SPARQL language and Jena API. sharp tooth cranium cranium neurocranium neurocranium pharyngeal arch skeleton pharyngeal arch skeleton jaw jaw chondrocranium chondrocranium tooth shape tooth shape tooth tooth blunt blunt sharp sharp part_of part_of part_of part_of part_of part_of is_a is_a part_of part_of image_of image_of appears_in appears_in appears_in appears_in character_ character_ of of state_of state_of state_of state_of Anatomy Term Anatomy Term Character Character Character State Character State Standard Standard Image related Image related Character/state related Character/state related Concept shapes Concept shapes Property types Property types Legend: Legend: It It’ s All An Ontology s All An Ontology Timothy Rowe: Timothy Rowe: [email protected] Julian Humphries: Julian Humphries: [email protected] Daniel Daniel Miranker Miranker: : [email protected] [email protected] Syed Syed Hamid Hamid Tirmizi: Tirmizi: hamid@cs hamid@cs.utexas utexas.edu edu Contact Information Contact Information Introduction Introduction In near term, our tools will support comprehensive morphology studies of various kinds by providing support for character/state definitions and matrix management. We aim to organize and facilitate these studies through ontology driven matrix management. We aim to provide integrated LSID tagging with Nexus files to enable exports to Treebase II (pending APIs) and Mesquite project. TAPIR Portals Specimen search and data import from GBIF and TDWG TAPIR portals will be enabled in later versions. In the future: In the future: Morphbank & other Image Services A screenshot of ontology driven image annotation interface. Terms from ontologies can be dragged and dropped on to the images as labels. The connection between ontology terms and labels is stored, and can be used to search for images that contain a particular label. Labeled images and associated metadata can be stored in repositories provided by Morphbank and other services. Effort is underway where an illustrated ontology can be used as a query-by-example method for retrieving related imagery from Morphbank. We are working on: We are working on: A screenshot of OntoIllustrator showing illustration of an ontology by attaching images to corresponding ontology terms through a drag and drop mechanism. Images can be filtered and sorted in a number of ways. As shown in the screenshot, multiple ontologies can be illustrated with images simultaneously. Illustrated ontologies can be quickly exported to OntoBrowser. The results of OntoIllustrator can be exported directly to OntoBrowser. Ontobrowser is a web application making illustrated ontologies browsable from any machine on the Internet. Large illustrated ontologies can be browsed quickly using the dynamic tree view. The image thumbnail strip can be used to browse through a list of images. Export Nomina Nomina Anatomica Anatomica Image Driven Ontology Tools Image Driven Ontology Tools Images Images Taxa Input OntoIllustrator projects use standard ontologies, images, and taxon information imported using integrated search and format translation methods. Our 3D Phyloinformatics project concerns distributed data integration, data provenance and morphological image data management. The larger context is the uniting of information standards across the NSF grand challenge to assemble the tree of life (AToL), NIH model organism efforts (e.g. ZFIN), and global biodiversity information efforts (GBIF, TDWG). Our targeted effort is the creation of a productivity tool for systematic biologists. The tool enables users to create, organize and annotate an image database of morphological characters and features. Resulting illustrated ontologies may be published on the Web. The interface metaphor is succinctly described as image-driven ontology editing. Users may import annotation vocabulary from diverse externally defined ontologies and extend those ontologies as needed. We have: We have: Our Our OntoIllustrator OntoIllustrator tool is capable of illustrating OBO and OWL tool is capable of illustrating OBO and OWL ontologies ontologies with images. It is powered by a triple store, an image database and an integrated with images. It is powered by a triple store, an image database and an integrated search and retrieval of search and retrieval of taxa taxa from from uBio uBio. We have . We have successfully tested successfully tested ontologies ontologies including including Nomina Anatomica Nomina Anatomica: anatomical is-part-of : anatomical is-part-of ontologies ontologies for both fish and mouse, for both fish and mouse, emerging vocabularies for comparing anatomies, CARO, and describing phenotypes, PATO. We have also deployed some illustrated emerging vocabularies for comparing anatomies, CARO, and describing phenotypes, PATO. We have also deployed some illustrated ontologies ontologies for browsing through our for browsing through our OntoBrowser OntoBrowser. Import Export
Transcript of Image Driven Ontology Editing - University of Texas at Austin · 2009. 11. 5. · OBO Triple Store...
OBO Triple StoreOBO Triple Store
Image Driven Ontology EditingTimothy Rowe°, Julian Humphries°, Daniel P. Miranker!, Syed Hamid Tirmizi!, Kerin M. Claeson°,
Juan F. Sequeda!, Willard S. Willard!, Ferner Cilloniz-Bicchi!, Nirav Savjani!.Department of Geological Sciences°, Department of Computer Sciences!. The University of Texas at Austin
Triple StoreTriple Store
SPARQL / Jena APISPARQL / Jena APIInterfaceInterface
OBO/OWLOBO/OWLRoundtripRoundtrip
TransformationTransformation
Image Driven Ontology ToolsImage Driven Ontology Tools
OntoIllustratorOntoIllustrator, , OntoBrowserOntoBrowseretc.etc.
OBO Foundry ontologies are downloadedin OBO Flat File format from their source
The triple store is a Semantic Web enabled ontologystore accessible through W3C recommendedSPARQL interface, and Jena API
CommonCommonAnatomyAnatomy
ReferenceReference(CARO)(CARO)
ZebrafishZebrafishAnatomy (ZFIN)Anatomy (ZFIN)
GeneGene OntologyOntology(GO)(GO)
PhenotypicPhenotypicQuality OntologyQuality Ontology
(PATO)(PATO)
By developing a lossless roundtrip transformation mechanism between OBO andBy developing a lossless roundtrip transformation mechanism between OBO and Semantic Web (OWL) Semantic Web (OWL) ontologiesontologies, we, wehave opened the Semantic Web infrastructure for biomedical have opened the Semantic Web infrastructure for biomedical ontologiesontologies. As a result, we have successfully deployed a. As a result, we have successfully deployed atriple-store backend for OBO triple-store backend for OBO ontologiesontologies, powered by an engine for W3C recommended SPARQL language and Jena API., powered by an engine for W3C recommended SPARQL language and Jena API.
sharp tooth
craniumcranium
neurocraniumneurocranium
pharyngeal arch skeletonpharyngeal arch skeleton
jawjaw
chondrocraniumchondrocranium
tooth shapetooth shape
toothtooth
bluntblunt sharpsharp
part_ofpart_of
part_ofpart_of
part_ofpart_of
is_ais_a
part_ofpart_of
image_ofimage_of
appears_inappears_in
appears_inappears_incharacter_character_ofof
state_ofstate_of state_ofstate_ofAnatomy TermAnatomy Term
CharacterCharacter
Character StateCharacter State
StandardStandard
Image relatedImage related
Character/state relatedCharacter/state related
Concept shapesConcept shapes Property typesProperty types
Legend:Legend:
ItIt’’s All An Ontologys All An Ontology
Timothy Rowe: Timothy Rowe: [email protected] Julian Humphries: Julian Humphries: [email protected] Daniel MirankerMiranker: : [email protected]@cs.utexas.edu Syed Syed Hamid Hamid Tirmizi: Tirmizi: hamid@[email protected]
Contact InformationContact Information
IntroductionIntroduction
In near term, our tools will support comprehensive morphologystudies of various kinds by providing support for character/statedefinitions and matrix management. We aim to organize and facilitatethese studies through ontology driven matrix management.
We aim to provide integrated LSID taggingwith Nexus files to enable exports toTreebase II (pending APIs) and Mesquiteproject.
TAPIRPortals
Specimen search and data importfrom GBIF and TDWG TAPIR portalswill be enabled in later versions.
In the future:In the future:
Morphbank
&
other Image Services
A screenshot of ontology driven image annotation interface. Terms fromontologies can be dragged and dropped on to the images as labels. Theconnection between ontology terms and labels is stored, and can be used tosearch for images that contain a particular label.
Labeled images and associated metadata can bestored in repositories provided by Morphbank andother services. Effort is underway where an illustratedontology can be used as a query-by-example methodfor retrieving related imagery from Morphbank.
We are working on:We are working on:
A screenshot of OntoIllustrator showing illustration of an ontology byattaching images to corresponding ontology terms through a drag and dropmechanism. Images can be filtered and sorted in a number of ways. Asshown in the screenshot, multiple ontologies can be illustrated with imagessimultaneously. Illustrated ontologies can be quickly exported toOntoBrowser.
The results of OntoIllustrator can be exported directly toOntoBrowser. Ontobrowser is a web application makingillustrated ontologies browsable from any machine on theInternet. Large illustrated ontologies can be browsed quicklyusing the dynamic tree view. The image thumbnail strip can beused to browse through a list of images.
Export
NominaNominaAnatomicaAnatomica
Image Driven Ontology ToolsImage Driven Ontology Tools
ImagesImages
Taxa
Input
OntoIllustrator projects usestandard ontologies, images, andtaxon information imported usingintegrated search and formattranslation methods.
Our 3D Phyloinformatics project concerns distributed data integration, data provenance and morphological image data management. The larger
context is the uniting of information standards across the NSF grand challenge to assemble the tree of life (AToL), NIH model organism efforts (e.g.
ZFIN), and global biodiversity information efforts (GBIF, TDWG). Our targeted effort is the creation of a productivity tool for systematic biologists. The
tool enables users to create, organize and annotate an image database of morphological characters and features. Resulting illustrated ontologies may
be published on the Web. The interface metaphor is succinctly described as image-driven ontology editing. Users may import annotation vocabulary
from diverse externally defined ontologies and extend those ontologies as needed.
We have: We have: Our Our OntoIllustrator OntoIllustrator tool is capable of illustrating OBO and OWL tool is capable of illustrating OBO and OWL ontologies ontologies with images. It is powered by a triple store, an image database and an integratedwith images. It is powered by a triple store, an image database and an integrated
search and retrieval of search and retrieval of taxa taxa fromfrom uBiouBio. We have . We have successfully tested successfully tested ontologies ontologies including including Nomina AnatomicaNomina Anatomica: anatomical is-part-of : anatomical is-part-of ontologies ontologies for both fish and mouse,for both fish and mouse,emerging vocabularies for comparing anatomies, CARO, and describing phenotypes, PATO. We have also deployed some illustrated emerging vocabularies for comparing anatomies, CARO, and describing phenotypes, PATO. We have also deployed some illustrated ontologies ontologies for browsing through ourfor browsing through ourOntoBrowserOntoBrowser..
ImportExport
