Structured Literature Image Finder: Parsing Text and Figures in Biomedical Literature
Identifieur interne : 000599 ( Main/Exploration ); précédent : 000598; suivant : 000600Structured Literature Image Finder: Parsing Text and Figures in Biomedical Literature
Auteurs : Amr Ahmed [États-Unis] ; Andrew Arnold [États-Unis] ; Luis Pedro Coelho [États-Unis] ; Joshua Kangas [États-Unis] ; Abdul-Saboor Sheikh [États-Unis] ; Eric Xing [États-Unis] ; William Cohen [États-Unis] ; Robert F. Murphy [États-Unis]Source :
- Web semantics (Online) [ 1570-8268 ] ; 2010.
Abstract
The SLIF project combines text-mining and image processing to extract structured information from biomedical literature.
SLIF extracts images and their captions from published papers. The captions are automatically parsed for relevant biological entities (protein and cell type names), while the images are classified according to their type (e.g., micrograph or gel). Fluorescence microscopy images are further processed and classified according to the depicted subcellular localization.
The results of this process can be queried online using either a user-friendly web-interface or an XML-based web-service. As an alternative to the targeted query paradigm, SLIF also supports browsing the collection based on latent topic models which are derived from both the annotated text and the image data.
The SLIF web application, as well as labeled datasets used for training system components, is publicly available at
Url:
DOI: 10.1016/j.websem.2010.04.002
PubMed: 24991197
PubMed Central: 4075770
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000137
- to stream Pmc, to step Curation: 000137
- to stream Pmc, to step Checkpoint: 000141
- to stream Ncbi, to step Merge: 000198
- to stream Ncbi, to step Curation: 000198
- to stream Ncbi, to step Checkpoint: 000198
- to stream Main, to step Merge: 000604
- to stream Main, to step Curation: 000599
Le document en format XML
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last="Ahmed">Amr Ahmed</name><affiliation wicri:level="4"><nlm:aff id="A1">Machine Learning Department, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation><affiliation wicri:level="4"><nlm:aff id="A2">Language Technologies Institute, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation></author><author><name sortKey="Arnold, Andrew" sort="Arnold, Andrew" uniqKey="Arnold A" first="Andrew" last="Arnold">Andrew Arnold</name><affiliation wicri:level="4"><nlm:aff id="A1">Machine Learning Department, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation></author><author><name sortKey="Coelho, Luis Pedro" sort="Coelho, Luis Pedro" uniqKey="Coelho L" first="Luis Pedro" last="Coelho">Luis Pedro Coelho</name><affiliation><nlm:aff id="A3">Joint Carnegie Mellon University–University of Pittsburgh Ph.D. Program in Computational Biology</nlm:aff></affiliation><affiliation wicri:level="4"><nlm:aff id="A4">Center for Bioimage Informatics, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation><affiliation wicri:level="4"><nlm:aff id="A5">Lane Center for Computational Biology, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation></author><author><name sortKey="Kangas, Joshua" sort="Kangas, Joshua" uniqKey="Kangas J" first="Joshua" last="Kangas">Joshua Kangas</name><affiliation><nlm:aff id="A3">Joint Carnegie Mellon University–University of Pittsburgh Ph.D. Program in Computational Biology</nlm:aff></affiliation><affiliation wicri:level="4"><nlm:aff id="A4">Center for Bioimage Informatics, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation><affiliation wicri:level="4"><nlm:aff id="A5">Lane Center for Computational Biology, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation></author><author><name sortKey="Sheikh, Abdul Saboor" sort="Sheikh, Abdul Saboor" uniqKey="Sheikh A" first="Abdul-Saboor" last="Sheikh">Abdul-Saboor Sheikh</name><affiliation wicri:level="4"><nlm:aff id="A4">Center for Bioimage Informatics, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation></author><author><name sortKey="Xing, Eric" sort="Xing, Eric" uniqKey="Xing E" first="Eric" last="Xing">Eric Xing</name><affiliation wicri:level="4"><nlm:aff id="A1">Machine Learning Department, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation><affiliation wicri:level="4"><nlm:aff id="A2">Language Technologies Institute, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation><affiliation><nlm:aff id="A3">Joint Carnegie Mellon University–University of Pittsburgh Ph.D. Program in Computational Biology</nlm:aff></affiliation><affiliation wicri:level="4"><nlm:aff id="A4">Center for Bioimage Informatics, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation><affiliation wicri:level="4"><nlm:aff id="A5">Lane Center for Computational Biology, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation><affiliation wicri:level="4"><nlm:aff id="A6">Department of Biological Sciences, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation></author><author><name sortKey="Cohen, William" sort="Cohen, William" uniqKey="Cohen W" first="William" last="Cohen">William Cohen</name><affiliation wicri:level="4"><nlm:aff id="A1">Machine Learning Department, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation><affiliation wicri:level="4"><nlm:aff id="A2">Language Technologies Institute, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation><affiliation><nlm:aff id="A3">Joint Carnegie Mellon University–University of Pittsburgh Ph.D. Program in Computational Biology</nlm:aff></affiliation><affiliation wicri:level="4"><nlm:aff id="A4">Center for Bioimage Informatics, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation><affiliation wicri:level="4"><nlm:aff id="A5">Lane Center for Computational Biology, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation></author><author><name sortKey="Murphy, Robert F" sort="Murphy, Robert F" uniqKey="Murphy R" first="Robert F." last="Murphy">Robert F. Murphy</name><affiliation wicri:level="4"><nlm:aff id="A1">Machine Learning Department, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation><affiliation><nlm:aff id="A3">Joint Carnegie Mellon University–University of Pittsburgh Ph.D. Program in Computational Biology</nlm:aff></affiliation><affiliation wicri:level="4"><nlm:aff id="A4">Center for Bioimage Informatics, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation><affiliation wicri:level="4"><nlm:aff id="A5">Lane Center for Computational Biology, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation><affiliation wicri:level="4"><nlm:aff id="A6">Department of Biological Sciences, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation><affiliation wicri:level="4"><nlm:aff id="A7">Department of Biomedical Engineering, Carnegie Mellon University</nlm:aff><country>États-Unis</country><placeName><settlement type="city">Pittsburgh</settlement><region type="state">Pennsylvanie</region></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation></author></analytic><series><title level="j">Web semantics (Online)</title><idno type="ISSN">1570-8268</idno><idno type="eISSN">1873-7749</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P1">The SLIF project combines text-mining and image processing to extract structured information from biomedical literature.</p><p id="P2">SLIF extracts images and their captions from published papers. The captions are automatically parsed for relevant biological entities (protein and cell type names), while the images are classified according to their type (e.g., micrograph or gel). Fluorescence microscopy images are further processed and classified according to the depicted subcellular localization.</p><p id="P3">The results of this process can be queried online using either a user-friendly web-interface or an XML-based web-service. As an alternative to the targeted query paradigm, SLIF also supports browsing the collection based on latent topic models which are derived from both the annotated text and the image data.</p><p id="P4">The SLIF web application, as well as labeled datasets used for training system components, is publicly available at <ext-link ext-link-type="uri" xlink:href="http://slif.cbi.cmu.edu">http://slif.cbi.cmu.edu</ext-link>.</p></div></front></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Pennsylvanie</li></region><settlement><li>Pittsburgh</li></settlement><orgName><li>Université Carnegie-Mellon</li></orgName></list><tree><country name="États-Unis"><region name="Pennsylvanie"><name sortKey="Ahmed, Amr" sort="Ahmed, Amr" uniqKey="Ahmed A" first="Amr" last="Ahmed">Amr Ahmed</name></region><name sortKey="Ahmed, Amr" sort="Ahmed, Amr" uniqKey="Ahmed A" first="Amr" last="Ahmed">Amr Ahmed</name><name sortKey="Arnold, Andrew" sort="Arnold, Andrew" uniqKey="Arnold A" first="Andrew" last="Arnold">Andrew Arnold</name><name sortKey="Coelho, Luis Pedro" sort="Coelho, Luis Pedro" uniqKey="Coelho L" first="Luis Pedro" last="Coelho">Luis Pedro Coelho</name><name sortKey="Coelho, Luis Pedro" sort="Coelho, Luis Pedro" uniqKey="Coelho L" first="Luis Pedro" last="Coelho">Luis Pedro Coelho</name><name sortKey="Cohen, William" sort="Cohen, William" uniqKey="Cohen W" first="William" last="Cohen">William Cohen</name><name sortKey="Cohen, William" sort="Cohen, William" uniqKey="Cohen W" first="William" last="Cohen">William Cohen</name><name sortKey="Cohen, William" sort="Cohen, William" uniqKey="Cohen W" first="William" last="Cohen">William Cohen</name><name sortKey="Cohen, William" sort="Cohen, William" uniqKey="Cohen W" first="William" last="Cohen">William Cohen</name><name sortKey="Kangas, Joshua" sort="Kangas, Joshua" uniqKey="Kangas J" first="Joshua" last="Kangas">Joshua Kangas</name><name sortKey="Kangas, Joshua" sort="Kangas, Joshua" uniqKey="Kangas J" first="Joshua" last="Kangas">Joshua Kangas</name><name sortKey="Murphy, Robert F" sort="Murphy, Robert F" uniqKey="Murphy R" first="Robert F." last="Murphy">Robert F. Murphy</name><name sortKey="Murphy, Robert F" sort="Murphy, Robert F" uniqKey="Murphy R" first="Robert F." last="Murphy">Robert F. Murphy</name><name sortKey="Murphy, Robert F" sort="Murphy, Robert F" uniqKey="Murphy R" first="Robert F." last="Murphy">Robert F. Murphy</name><name sortKey="Murphy, Robert F" sort="Murphy, Robert F" uniqKey="Murphy R" first="Robert F." last="Murphy">Robert F. Murphy</name><name sortKey="Murphy, Robert F" sort="Murphy, Robert F" uniqKey="Murphy R" first="Robert F." last="Murphy">Robert F. Murphy</name><name sortKey="Sheikh, Abdul Saboor" sort="Sheikh, Abdul Saboor" uniqKey="Sheikh A" first="Abdul-Saboor" last="Sheikh">Abdul-Saboor Sheikh</name><name sortKey="Xing, Eric" sort="Xing, Eric" uniqKey="Xing E" first="Eric" last="Xing">Eric Xing</name><name sortKey="Xing, Eric" sort="Xing, Eric" uniqKey="Xing E" first="Eric" last="Xing">Eric Xing</name><name sortKey="Xing, Eric" sort="Xing, Eric" uniqKey="Xing E" first="Eric" last="Xing">Eric Xing</name><name sortKey="Xing, Eric" sort="Xing, Eric" uniqKey="Xing E" first="Eric" last="Xing">Eric Xing</name><name sortKey="Xing, Eric" sort="Xing, Eric" uniqKey="Xing E" first="Eric" last="Xing">Eric Xing</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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