Structured Literature Image Finder: Parsing Text and Figures in Biomedical Literature
Identifieur interne : 000198 ( Ncbi/Merge ); précédent : 000197; suivant : 000199Structured 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
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
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PMC:4075770Le document en format XML
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<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>
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<title-group><article-title>Structured Literature Image Finder: Parsing Text and Figures in Biomedical Literature</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Ahmed</surname>
<given-names>Amr</given-names>
</name>
<xref ref-type="aff" rid="A1">a</xref>
<xref ref-type="aff" rid="A2">b</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Arnold</surname>
<given-names>Andrew</given-names>
</name>
<xref ref-type="aff" rid="A1">a</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Coelho</surname>
<given-names>Luis Pedro</given-names>
</name>
<xref ref-type="aff" rid="A3">c</xref>
<xref ref-type="aff" rid="A4">d</xref>
<xref ref-type="aff" rid="A5">e</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kangas</surname>
<given-names>Joshua</given-names>
</name>
<xref ref-type="aff" rid="A3">c</xref>
<xref ref-type="aff" rid="A4">d</xref>
<xref ref-type="aff" rid="A5">e</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Sheikh</surname>
<given-names>Abdul-Saboor</given-names>
</name>
<xref ref-type="aff" rid="A4">d</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Xing</surname>
<given-names>Eric</given-names>
</name>
<xref ref-type="aff" rid="A1">a</xref>
<xref ref-type="aff" rid="A2">b</xref>
<xref ref-type="aff" rid="A3">c</xref>
<xref ref-type="aff" rid="A4">d</xref>
<xref ref-type="aff" rid="A5">e</xref>
<xref ref-type="aff" rid="A6">f</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Cohen</surname>
<given-names>William</given-names>
</name>
<xref ref-type="aff" rid="A1">a</xref>
<xref ref-type="aff" rid="A2">b</xref>
<xref ref-type="aff" rid="A3">c</xref>
<xref ref-type="aff" rid="A4">d</xref>
<xref ref-type="aff" rid="A5">e</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Murphy</surname>
<given-names>Robert F.</given-names>
</name>
<xref ref-type="aff" rid="A1">a</xref>
<xref ref-type="aff" rid="A3">c</xref>
<xref ref-type="aff" rid="A4">d</xref>
<xref ref-type="aff" rid="A5">e</xref>
<xref ref-type="aff" rid="A6">f</xref>
<xref ref-type="aff" rid="A7">g</xref>
</contrib>
</contrib-group>
<aff id="A1"><label>a</label>
Machine Learning Department, Carnegie Mellon University</aff>
<aff id="A2"><label>b</label>
Language Technologies Institute, Carnegie Mellon University</aff>
<aff id="A3"><label>c</label>
Joint Carnegie Mellon University–University of Pittsburgh Ph.D. Program in Computational Biology</aff>
<aff id="A4"><label>d</label>
Center for Bioimage Informatics, Carnegie Mellon University</aff>
<aff id="A5"><label>e</label>
Lane Center for Computational Biology, Carnegie Mellon University</aff>
<aff id="A6"><label>f</label>
Department of Biological Sciences, Carnegie Mellon University</aff>
<aff id="A7"><label>g</label>
Department of Biomedical Engineering, Carnegie Mellon University</aff>
<pub-date pub-type="nihms-submitted"><day>19</day>
<month>7</month>
<year>2013</year>
</pub-date>
<pub-date pub-type="ppub"><day>1</day>
<month>7</month>
<year>2010</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>30</day>
<month>6</month>
<year>2014</year>
</pub-date>
<volume>8</volume>
<issue>2-3</issue>
<fpage>151</fpage>
<lpage>154</lpage>
<pmc-comment>elocation-id from pubmed: 10.1016/j.websem.2010.04.002</pmc-comment>
<abstract><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>
</abstract>
</article-meta>
</front>
</pmc>
<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>
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