semCDI: A Query Formulation for Semantic Data Integration in caBIG
To develop mechanisms to formulate queries over the semantic representation of cancer-related data services available through the cancer Biomedical Informatics Grid (caBIG). The semCDI query formulation uses a view of caBIG semantic concepts, metadata, and data as an ontology, and defines a methodol...
Gespeichert in:
| Veröffentlicht in: | Journal of the American Medical Informatics Association : JAMIA 2008-07, Vol.15 (4), p.559-568 |
|---|---|
| Hauptverfasser: | , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 568 |
|---|---|
| container_issue | 4 |
| container_start_page | 559 |
| container_title | Journal of the American Medical Informatics Association : JAMIA |
| container_volume | 15 |
| creator | Shironoshita, E. Patrick Jean-Mary, Yves R. Bradley, Ray M. Kabuka, Mansur R. |
| description | To develop mechanisms to formulate queries over the semantic representation of cancer-related data services available through the cancer Biomedical Informatics Grid (caBIG).
The semCDI query formulation uses a view of caBIG semantic concepts, metadata, and data as an ontology, and defines a methodology to specify queries using the SPARQL query language, extended with Horn rules. semCDI enables the joining of data that represent different concepts through associations modeled as object properties, and the merging of data representing the same concept in different sources through Common Data Elements (CDE) modeled as datatype properties, using Horn rules to specify additional semantics indicating conditions for merging data.
In order to validate this formulation, a prototype has been constructed, and two queries have been executed against currently available caBIG data services.
The semCDI query formulation uses the rich semantic metadata available in caBIG to build queries and integrate data from multiple sources. Its promise will be further enhanced as more data services are registered in caBIG, and as more linkages can be achieved between the knowledge contained within caBIG's NCI Thesaurus and the data contained in the Data Services.
semCDI provides a formulation for the creation of queries on the semantic representation of caBIG. This constitutes the foundation to build a semantic data integration system for more efficient and effective querying and exploratory searching of cancer-related data. |
| doi_str_mv | 10.1197/jamia.M2732 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_2442262</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><els_id>S1067502708000637</els_id><sourcerecordid>69279602</sourcerecordid><originalsourceid>FETCH-LOGICAL-c456t-e3099116ad655cb96aa7b55a6d23f90c5846cfd17dacb1e50fd549a0501bc5a63</originalsourceid><addsrcrecordid>eNqFkc1L7TAQxYM88ePqyv2jq7eRapI2SeNC0OvXBUVEBXdhmk59kbbRpBX8763eix8guJqB8-MwZw4hW4zuMKbV7gO0DnYuuMr4ElljgqtUq_zuz7hTqVJBuVol6zE-UMokz8QKWWVFnslCqzVyGLGdHs32koPkasDwkpz40A4N9M53Se1Dco0tdL2zyRH0kMy6Hu_DXHVdYuFwdrpBlmtoIm4u5oTcnhzfTM_S88vT2fTgPLW5kH2KGdWaMQmVFMKWWgKoUgiQFc9qTa0ocmnriqkKbMlQ0LoSuQYqKCvtiGUTsj_3fRzKFiuLXR-gMY_BtRBejAdnviud-2_u_bPhec75mHxC_i0Mgn8aMPamddFi00CHfohGaq60pL-DnKpCFSwbwe05aIOPMWD9cQ2j5q0c816OeS9npP9-DfDJLtoYATEHcHzjs8NgonXYWaxcQNubyrsfjV8B6jydwg</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>20787813</pqid></control><display><type>article</type><title>semCDI: A Query Formulation for Semantic Data Integration in caBIG</title><source>Oxford University Press Journals All Titles (1996-Current)</source><source>MEDLINE</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><creator>Shironoshita, E. Patrick ; Jean-Mary, Yves R. ; Bradley, Ray M. ; Kabuka, Mansur R.</creator><creatorcontrib>Shironoshita, E. Patrick ; Jean-Mary, Yves R. ; Bradley, Ray M. ; Kabuka, Mansur R.</creatorcontrib><description>To develop mechanisms to formulate queries over the semantic representation of cancer-related data services available through the cancer Biomedical Informatics Grid (caBIG).
The semCDI query formulation uses a view of caBIG semantic concepts, metadata, and data as an ontology, and defines a methodology to specify queries using the SPARQL query language, extended with Horn rules. semCDI enables the joining of data that represent different concepts through associations modeled as object properties, and the merging of data representing the same concept in different sources through Common Data Elements (CDE) modeled as datatype properties, using Horn rules to specify additional semantics indicating conditions for merging data.
In order to validate this formulation, a prototype has been constructed, and two queries have been executed against currently available caBIG data services.
The semCDI query formulation uses the rich semantic metadata available in caBIG to build queries and integrate data from multiple sources. Its promise will be further enhanced as more data services are registered in caBIG, and as more linkages can be achieved between the knowledge contained within caBIG's NCI Thesaurus and the data contained in the Data Services.
semCDI provides a formulation for the creation of queries on the semantic representation of caBIG. This constitutes the foundation to build a semantic data integration system for more efficient and effective querying and exploratory searching of cancer-related data.</description><identifier>ISSN: 1067-5027</identifier><identifier>EISSN: 1527-974X</identifier><identifier>DOI: 10.1197/jamia.M2732</identifier><identifier>PMID: 18436897</identifier><language>eng</language><publisher>England: Elsevier Inc</publisher><subject>Biomedical Research - organization & administration ; Cancer Care Facilities - organization & administration ; Computational Biology ; Humans ; Information Management - methods ; Information Storage and Retrieval - methods ; Information Systems - organization & administration ; Internet ; Medical Oncology - organization & administration ; Model Formulation ; Semantics ; Vocabulary, Controlled</subject><ispartof>Journal of the American Medical Informatics Association : JAMIA, 2008-07, Vol.15 (4), p.559-568</ispartof><rights>2008 J Am Med Inform Assoc.</rights><rights>Copyright © 2008, American Medical Informatics Association 2008</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c456t-e3099116ad655cb96aa7b55a6d23f90c5846cfd17dacb1e50fd549a0501bc5a63</citedby><cites>FETCH-LOGICAL-c456t-e3099116ad655cb96aa7b55a6d23f90c5846cfd17dacb1e50fd549a0501bc5a63</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2442262/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2442262/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18436897$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Shironoshita, E. Patrick</creatorcontrib><creatorcontrib>Jean-Mary, Yves R.</creatorcontrib><creatorcontrib>Bradley, Ray M.</creatorcontrib><creatorcontrib>Kabuka, Mansur R.</creatorcontrib><title>semCDI: A Query Formulation for Semantic Data Integration in caBIG</title><title>Journal of the American Medical Informatics Association : JAMIA</title><addtitle>J Am Med Inform Assoc</addtitle><description>To develop mechanisms to formulate queries over the semantic representation of cancer-related data services available through the cancer Biomedical Informatics Grid (caBIG).
The semCDI query formulation uses a view of caBIG semantic concepts, metadata, and data as an ontology, and defines a methodology to specify queries using the SPARQL query language, extended with Horn rules. semCDI enables the joining of data that represent different concepts through associations modeled as object properties, and the merging of data representing the same concept in different sources through Common Data Elements (CDE) modeled as datatype properties, using Horn rules to specify additional semantics indicating conditions for merging data.
In order to validate this formulation, a prototype has been constructed, and two queries have been executed against currently available caBIG data services.
The semCDI query formulation uses the rich semantic metadata available in caBIG to build queries and integrate data from multiple sources. Its promise will be further enhanced as more data services are registered in caBIG, and as more linkages can be achieved between the knowledge contained within caBIG's NCI Thesaurus and the data contained in the Data Services.
semCDI provides a formulation for the creation of queries on the semantic representation of caBIG. This constitutes the foundation to build a semantic data integration system for more efficient and effective querying and exploratory searching of cancer-related data.</description><subject>Biomedical Research - organization & administration</subject><subject>Cancer Care Facilities - organization & administration</subject><subject>Computational Biology</subject><subject>Humans</subject><subject>Information Management - methods</subject><subject>Information Storage and Retrieval - methods</subject><subject>Information Systems - organization & administration</subject><subject>Internet</subject><subject>Medical Oncology - organization & administration</subject><subject>Model Formulation</subject><subject>Semantics</subject><subject>Vocabulary, Controlled</subject><issn>1067-5027</issn><issn>1527-974X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkc1L7TAQxYM88ePqyv2jq7eRapI2SeNC0OvXBUVEBXdhmk59kbbRpBX8763eix8guJqB8-MwZw4hW4zuMKbV7gO0DnYuuMr4ElljgqtUq_zuz7hTqVJBuVol6zE-UMokz8QKWWVFnslCqzVyGLGdHs32koPkasDwkpz40A4N9M53Se1Dco0tdL2zyRH0kMy6Hu_DXHVdYuFwdrpBlmtoIm4u5oTcnhzfTM_S88vT2fTgPLW5kH2KGdWaMQmVFMKWWgKoUgiQFc9qTa0ocmnriqkKbMlQ0LoSuQYqKCvtiGUTsj_3fRzKFiuLXR-gMY_BtRBejAdnviud-2_u_bPhec75mHxC_i0Mgn8aMPamddFi00CHfohGaq60pL-DnKpCFSwbwe05aIOPMWD9cQ2j5q0c816OeS9npP9-DfDJLtoYATEHcHzjs8NgonXYWaxcQNubyrsfjV8B6jydwg</recordid><startdate>20080701</startdate><enddate>20080701</enddate><creator>Shironoshita, E. Patrick</creator><creator>Jean-Mary, Yves R.</creator><creator>Bradley, Ray M.</creator><creator>Kabuka, Mansur R.</creator><general>Elsevier Inc</general><general>American Medical Informatics Association</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20080701</creationdate><title>semCDI: A Query Formulation for Semantic Data Integration in caBIG</title><author>Shironoshita, E. Patrick ; Jean-Mary, Yves R. ; Bradley, Ray M. ; Kabuka, Mansur R.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c456t-e3099116ad655cb96aa7b55a6d23f90c5846cfd17dacb1e50fd549a0501bc5a63</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>Biomedical Research - organization & administration</topic><topic>Cancer Care Facilities - organization & administration</topic><topic>Computational Biology</topic><topic>Humans</topic><topic>Information Management - methods</topic><topic>Information Storage and Retrieval - methods</topic><topic>Information Systems - organization & administration</topic><topic>Internet</topic><topic>Medical Oncology - organization & administration</topic><topic>Model Formulation</topic><topic>Semantics</topic><topic>Vocabulary, Controlled</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Shironoshita, E. Patrick</creatorcontrib><creatorcontrib>Jean-Mary, Yves R.</creatorcontrib><creatorcontrib>Bradley, Ray M.</creatorcontrib><creatorcontrib>Kabuka, Mansur R.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Journal of the American Medical Informatics Association : JAMIA</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Shironoshita, E. Patrick</au><au>Jean-Mary, Yves R.</au><au>Bradley, Ray M.</au><au>Kabuka, Mansur R.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>semCDI: A Query Formulation for Semantic Data Integration in caBIG</atitle><jtitle>Journal of the American Medical Informatics Association : JAMIA</jtitle><addtitle>J Am Med Inform Assoc</addtitle><date>2008-07-01</date><risdate>2008</risdate><volume>15</volume><issue>4</issue><spage>559</spage><epage>568</epage><pages>559-568</pages><issn>1067-5027</issn><eissn>1527-974X</eissn><abstract>To develop mechanisms to formulate queries over the semantic representation of cancer-related data services available through the cancer Biomedical Informatics Grid (caBIG).
The semCDI query formulation uses a view of caBIG semantic concepts, metadata, and data as an ontology, and defines a methodology to specify queries using the SPARQL query language, extended with Horn rules. semCDI enables the joining of data that represent different concepts through associations modeled as object properties, and the merging of data representing the same concept in different sources through Common Data Elements (CDE) modeled as datatype properties, using Horn rules to specify additional semantics indicating conditions for merging data.
In order to validate this formulation, a prototype has been constructed, and two queries have been executed against currently available caBIG data services.
The semCDI query formulation uses the rich semantic metadata available in caBIG to build queries and integrate data from multiple sources. Its promise will be further enhanced as more data services are registered in caBIG, and as more linkages can be achieved between the knowledge contained within caBIG's NCI Thesaurus and the data contained in the Data Services.
semCDI provides a formulation for the creation of queries on the semantic representation of caBIG. This constitutes the foundation to build a semantic data integration system for more efficient and effective querying and exploratory searching of cancer-related data.</abstract><cop>England</cop><pub>Elsevier Inc</pub><pmid>18436897</pmid><doi>10.1197/jamia.M2732</doi><tpages>10</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1067-5027 |
| ispartof | Journal of the American Medical Informatics Association : JAMIA, 2008-07, Vol.15 (4), p.559-568 |
| issn | 1067-5027 1527-974X |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_2442262 |
| source | Oxford University Press Journals All Titles (1996-Current); MEDLINE; EZB-FREE-00999 freely available EZB journals; PubMed Central |
| subjects | Biomedical Research - organization & administration Cancer Care Facilities - organization & administration Computational Biology Humans Information Management - methods Information Storage and Retrieval - methods Information Systems - organization & administration Internet Medical Oncology - organization & administration Model Formulation Semantics Vocabulary, Controlled |
| title | semCDI: A Query Formulation for Semantic Data Integration in caBIG |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-30T08%3A31%3A28IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=semCDI:%20A%20Query%20Formulation%20for%20Semantic%20Data%20Integration%20in%20caBIG&rft.jtitle=Journal%20of%20the%20American%20Medical%20Informatics%20Association%20:%20JAMIA&rft.au=Shironoshita,%20E.%20Patrick&rft.date=2008-07-01&rft.volume=15&rft.issue=4&rft.spage=559&rft.epage=568&rft.pages=559-568&rft.issn=1067-5027&rft.eissn=1527-974X&rft_id=info:doi/10.1197/jamia.M2732&rft_dat=%3Cproquest_pubme%3E69279602%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=20787813&rft_id=info:pmid/18436897&rft_els_id=S1067502708000637&rfr_iscdi=true |