https://wiki.wormbase.org/index.php?title=Lexicon_Development_Tool&feed=atom&action=historyLexicon Development Tool - Revision history2024-03-29T11:59:26ZRevision history for this page on the wikiMediaWiki 1.33.0https://wiki.wormbase.org/index.php?title=Lexicon_Development_Tool&diff=6012&oldid=prevCgrove at 23:46, 13 August 20102010-08-13T23:46:41Z<p></p>
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</table>Cgrovehttps://wiki.wormbase.org/index.php?title=Lexicon_Development_Tool&diff=2023&oldid=prevRfang at 09:28, 19 May 20092009-05-19T09:28:34Z<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 09:28, 19 May 2009</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div class="Section1"></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div class="Section1"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><span style="mso-spacerun: yes"></span>Lexicon Development Tool (LDT) is built on top of existing <span class="SpellE">Textpresso</span> search functionalities. <span style="mso-spacerun: yes"></span>It employed a three-tier architecture using CGI in Perl for the front end web interface, middle tier functional process logic and <span class="SpellE">Postgres</span> relational database for backend data storage. <span style="mso-spacerun: yes"></span>Briefly, it allows a curator to login (see screenshot 1_CE_Login), setup a project (see screenshot 2_CE_Project) and submit <span class="SpellE">Textpresso</span> search (see screenshot 3_CE_Search), and the search results (sentences) are stored in the back end database. <span style="mso-spacerun: yes"></span>These sentences can be retrieved by the curator and displayed on web page. <span style="mso-spacerun: yes"></span>Curator can then select sentences of interest to make categories based on word frequency or save words/phrases based on the context in the sentence to include in appropriate categories or exclusion list (see screenshot 4_CE_SentenceAnnotation). <span style="mso-spacerun: yes"></span><span style="mso-spacerun: yes"></span>These newly made categories can be included in a new round of search and this process can thus go on iteratively.<span style="mso-spacerun: yes"></span></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><span style="mso-spacerun: yes"></span>Lexicon Development Tool (LDT) is built on top of existing <span class="SpellE">Textpresso</span> search functionalities. <ins class="diffchange diffchange-inline"> </ins><span style="mso-spacerun: yes"></span>It employed a three-tier architecture using CGI in Perl for the front end web interface, middle tier functional process logic and <span class="SpellE">Postgres</span> relational database for backend data storage. <ins class="diffchange diffchange-inline"> </ins><span style="mso-spacerun: yes"></span>Briefly, it allows a curator to login (see <ins class="diffchange diffchange-inline"><span class="GramE"></ins>screenshot <ins class="diffchange diffchange-inline"><span style="mso-spacerun: yes"></span></span>[http://caprica.caltech.edu/celegans/LDT/1_CE_Login.JPG </ins>1_CE_Login<ins class="diffchange diffchange-inline">]</ins>), setup a project (see screenshot <ins class="diffchange diffchange-inline">[http://caprica.caltech.edu/celegans/LDT/</ins>2_CE_Project<ins class="diffchange diffchange-inline">.JPG 2_CE_Project.JPG]</ins>) and submit <span class="SpellE">Textpresso</span> search (see screenshot <ins class="diffchange diffchange-inline">[http://caprica.caltech.edu/celegans/LDT/</ins>3_CE_Search<ins class="diffchange diffchange-inline">.JPG 3_CE_Search.JPG]</ins>), and the search results (sentences) are stored in the back end database. <ins class="diffchange diffchange-inline"> </ins><span style="mso-spacerun: yes"></span>These sentences can be retrieved by the curator and displayed on web page. <ins class="diffchange diffchange-inline"> </ins><span style="mso-spacerun: yes"> </span>Curator can then select sentences of interest to make categories based on word frequency or save words/phrases based on the context in the sentence to include in appropriate categories or exclusion list (see screenshot <ins class="diffchange diffchange-inline">[http://caprica.caltech.edu/celegans/LDT/4_CE_SentenceAnnotation.JPG </ins>4_CE_SentenceAnnotation<ins class="diffchange diffchange-inline">.JPG]</ins>). <ins class="diffchange diffchange-inline"> </ins><span style="mso-spacerun: yes"></span><span style="mso-spacerun: yes"></span>These newly made categories can be included in a new round of search and this process can thus go on iteratively.<span style="mso-spacerun: yes"></span></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><span style="mso-spacerun: yes"></span>This utility can be applied in both <span class="SpellE">datatype</span> identification and automatic extraction of text for <span class="SpellE">curation</span>. <span style="mso-spacerun: yes"></span>In <span class="SpellE">datatype</span> identification, curator can upload a small training set containing 50 <span class="SpellE">positiveID</span> and <span class="SpellE">negativeID</span> of a <span class="SpellE">datatype</span> into LDT and optimize search query based on recall and precision measurement. <span style="mso-spacerun: yes"></span>Once satisfying recall and precision values are obtained, the batch mode version of LDT (e.g. the search module) can be run in the automatic pipeline using the search query optimized on new <span class="SpellE">paperIDs</span> and those IDs identified as positive for the <span class="SpellE">datatype</span> can be deposited into the tracking database.<span style="mso-spacerun: yes"></span><span style="mso-spacerun: yes"></span></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><span style="mso-spacerun: yes"></span>This utility can be applied in both <span class="SpellE">datatype</span> identification and automatic extraction of text for <span class="SpellE">curation</span>. <ins class="diffchange diffchange-inline"> </ins><span style="mso-spacerun: yes"></span>In <span class="SpellE">datatype</span> identification, curator can upload a small training set containing 50 <span class="SpellE">positiveID</span> and <span class="SpellE">negativeID</span> of a <span class="SpellE">datatype</span> into LDT and optimize search query based on recall and precision measurement. <ins class="diffchange diffchange-inline"> </ins><span style="mso-spacerun: yes"></span>Once satisfying recall and precision values are obtained, the batch mode version of LDT (e.g. the search module) can be run in the automatic pipeline using the search query optimized on new <span class="SpellE">paperIDs</span> and those IDs identified as positive for the <span class="SpellE">datatype</span> can be deposited into the tracking database.<span style="mso-spacerun: yes"></span><span style="mso-spacerun: yes"></span></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><span style="mso-spacerun: yes"></span>In automatic extraction of text for <span class="SpellE">curation</span>, curator can upload a single article of a <span class="SpellE">datatype</span> and conduct the same iterative process of Search-Making Category-Search until the search query is so specific that only those sentences containing relevant <span class="SpellE">curation</span> information are returned. <span style="mso-spacerun: yes"></span>The same search query can then be applied to all the other papers of the <span class="SpellE">datatype</span> need to be <span class="SpellE">curated</span>. <span style="mso-spacerun: yes"></span>These selected sentences can then be exported into a <span class="SpellE">textfile</span> in the user's folder (see screenshot 5_CE_Results) in the format which can then be directly imported into a <span class="SpellE">curation</span> tool such as <span class="SpellE">Phenote</span> for further <span class="SpellE">curation</span>.<span style="mso-spacerun: yes"></span></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><span style="mso-spacerun: yes"></span>In automatic extraction of text for <span class="SpellE">curation</span>, curator can upload a single article of a <span class="SpellE">datatype</span> and conduct the same iterative process of Search-Making Category-Search until the search query is so specific that only those sentences containing relevant <span class="SpellE">curation</span> information are returned. <ins class="diffchange diffchange-inline"> </ins><span style="mso-spacerun: yes"></span>The same search query can then be applied to all the other papers of the <span class="SpellE">datatype</span> need to be <span class="SpellE">curated</span>. <ins class="diffchange diffchange-inline"> </ins><span style="mso-spacerun: yes"></span>These selected sentences can then be exported into a <span class="SpellE">textfile</span> in the user's folder (see screenshot <ins class="diffchange diffchange-inline">[http://caprica.caltech.edu/celegans/LDT/</ins>5_CE_Results<ins class="diffchange diffchange-inline">.JPG 5_CE_Results.JPG]</ins>) in the format which can then be directly imported into a <span class="SpellE">curation</span> tool such as <span class="SpellE">Phenote</span> for further <span class="SpellE">curation</span>.<span style="mso-spacerun: yes"></span></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></td></tr>
</table>Rfanghttps://wiki.wormbase.org/index.php?title=Lexicon_Development_Tool&diff=2020&oldid=prevRfang at 08:53, 19 May 20092009-05-19T08:53:39Z<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 08:53, 19 May 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div class="Section1"></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div class="Section1"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><span style="mso-spacerun: yes"></span>Lexicon Development Tool (LDT) is built on top of existing <span class="SpellE">Textpresso</span> search functionalities. <span style="mso-spacerun: yes"></span>It employed a three-tier architecture using CGI in Perl for the front end web interface, middle tier functional process logic and <span class="SpellE">Postgres</span> relational database for backend data storage.<span style="mso-spacerun: yes"></span>Briefly, it allows a curator to login (see screenshot 1_CE_Login), setup a project (see screenshot 2_CE_Project) and submit <span class="SpellE">Textpresso</span> search (see screenshot 3_CE_Search), and the search results (sentences) are stored in the back end database.<span style="mso-spacerun: yes"></span>These sentences can be retrieved by the curator and displayed on web page.<span style="mso-spacerun: yes"></span>Curator can then select sentences of interest to make categories based on word frequency or save words/phrases based on the context in the sentence to include in appropriate categories or exclusion list (see screenshot 4_CE_SentenceAnnotation).<span style="mso-spacerun: yes"></span><span style="mso-spacerun: yes"></span>These newly made categories can be included in a new round of search and this process can thus go on iteratively.<span style="mso-spacerun: yes"></span></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><span style="mso-spacerun: yes"></span>Lexicon Development Tool (LDT) is built on top of existing <span class="SpellE">Textpresso</span> search functionalities. <span style="mso-spacerun: yes"></span>It employed a three-tier architecture using CGI in Perl for the front end web interface, middle tier functional process logic and <span class="SpellE">Postgres</span> relational database for backend data storage. <span style="mso-spacerun: yes"></span>Briefly, it allows a curator to login (see screenshot 1_CE_Login), setup a project (see screenshot 2_CE_Project) and submit <span class="SpellE">Textpresso</span> search (see screenshot 3_CE_Search), and the search results (sentences) are stored in the back end database. <span style="mso-spacerun: yes"></span>These sentences can be retrieved by the curator and displayed on web page. <span style="mso-spacerun: yes"></span>Curator can then select sentences of interest to make categories based on word frequency or save words/phrases based on the context in the sentence to include in appropriate categories or exclusion list (see screenshot 4_CE_SentenceAnnotation). <span style="mso-spacerun: yes"></span><span style="mso-spacerun: yes"></span>These newly made categories can be included in a new round of search and this process can thus go on iteratively.<span style="mso-spacerun: yes"></span></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><span style="mso-spacerun: yes"></span>This utility can be applied in both <span class="SpellE">datatype</span> identification and automatic extraction of text for <span class="SpellE">curation</span>.<span style="mso-spacerun: yes"></span>In <span class="SpellE">datatype</span> identification, curator can upload a small training set containing 50 <span class="SpellE">positiveID</span> and <span class="SpellE">negativeID</span> of a <span class="SpellE">datatype</span> into LDT and optimize search query based on recall and precision measurement.<span style="mso-spacerun: yes"></span>Once satisfying recall and precision values are obtained, the batch mode version of LDT (e.g. the search module) can be run in the automatic pipeline using the search query optimized on new <span class="SpellE">paperIDs</span> and those IDs identified as positive for the <span class="SpellE">datatype</span> can be deposited into the tracking database.<span style="mso-spacerun: yes"></span><span style="mso-spacerun: yes"></span></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><span style="mso-spacerun: yes"></span>This utility can be applied in both <span class="SpellE">datatype</span> identification and automatic extraction of text for <span class="SpellE">curation</span>. <span style="mso-spacerun: yes"></span>In <span class="SpellE">datatype</span> identification, curator can upload a small training set containing 50 <span class="SpellE">positiveID</span> and <span class="SpellE">negativeID</span> of a <span class="SpellE">datatype</span> into LDT and optimize search query based on recall and precision measurement. <span style="mso-spacerun: yes"></span>Once satisfying recall and precision values are obtained, the batch mode version of LDT (e.g. the search module) can be run in the automatic pipeline using the search query optimized on new <span class="SpellE">paperIDs</span> and those IDs identified as positive for the <span class="SpellE">datatype</span> can be deposited into the tracking database.<span style="mso-spacerun: yes"></span><span style="mso-spacerun: yes"></span></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><span style="mso-spacerun: yes"></span>In automatic extraction of text for <span class="SpellE">curation</span>, curator can upload a single article of a <span class="SpellE">datatype</span> and conduct the same iterative process of Search-Making Category-Search until the search query is so specific that only those sentences containing relevant <span class="SpellE">curation</span> information are returned.<span style="mso-spacerun: yes"></span>The same search query can then be applied to all the other papers of the <span class="SpellE">datatype</span> need to be <span class="SpellE">curated</span>.<span style="mso-spacerun: yes"></span>These selected sentences can then be exported into a <span class="SpellE">textfile</span> in the user's folder (see screenshot 5_CE_Results) in the format which can then be directly imported into a <span class="SpellE">curation</span> tool such as <span class="SpellE">Phenote</span> for further <span class="SpellE">curation</span>.<span style="mso-spacerun: yes"></span></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><span style="mso-spacerun: yes"></span>In automatic extraction of text for <span class="SpellE">curation</span>, curator can upload a single article of a <span class="SpellE">datatype</span> and conduct the same iterative process of Search-Making Category-Search until the search query is so specific that only those sentences containing relevant <span class="SpellE">curation</span> information are returned. <span style="mso-spacerun: yes"></span>The same search query can then be applied to all the other papers of the <span class="SpellE">datatype</span> need to be <span class="SpellE">curated</span>. <span style="mso-spacerun: yes"></span>These selected sentences can then be exported into a <span class="SpellE">textfile</span> in the user's folder (see screenshot 5_CE_Results) in the format which can then be directly imported into a <span class="SpellE">curation</span> tool such as <span class="SpellE">Phenote</span> for further <span class="SpellE">curation</span>.<span style="mso-spacerun: yes"></span></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></td></tr>
</table>Rfanghttps://wiki.wormbase.org/index.php?title=Lexicon_Development_Tool&diff=2019&oldid=prevRfang at 08:51, 19 May 20092009-05-19T08:51:15Z<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 08:51, 19 May 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div class="Section1"></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div class="Section1"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><span style="mso-spacerun: yes"><del class="diffchange diffchange-inline">??? </del></span>Lexicon Development Tool (LDT) is built on top of existing <span class="SpellE">Textpresso</span> search functionalities.<span style="mso-spacerun: yes"><del class="diffchange diffchange-inline">? </del></span>It employed a three-tier architecture using CGI in Perl for the front end web interface, middle tier functional process logic and <span class="SpellE">Postgres</span> relational database for backend data storage.<span style="mso-spacerun: yes"><del class="diffchange diffchange-inline">? </del></span>Briefly, it allows a curator to login (see screenshot 1_CE_Login), setup a project (see screenshot 2_CE_Project) and submit <span class="SpellE">Textpresso</span> search (see screenshot 3_CE_Search), and the search results (sentences) are stored in the back end database.<span style="mso-spacerun: yes"><del class="diffchange diffchange-inline">? </del></span>These sentences can be retrieved by the curator and displayed on web page.<span style="mso-spacerun: yes"><del class="diffchange diffchange-inline">? </del></span>Curator can then select sentences of interest to make categories based on word frequency or save words/phrases based on the context in the sentence to include in appropriate categories or exclusion list (see screenshot 4_CE_SentenceAnnotation).<span style="mso-spacerun: yes"><del class="diffchange diffchange-inline">? </del></span><span style="mso-spacerun: yes"><del class="diffchange diffchange-inline">?</del></span>These newly made categories can be included in a new round of search and this process can thus go on iteratively.<span style="mso-spacerun: yes"><del class="diffchange diffchange-inline">?? </del></span></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><span style="mso-spacerun: yes"></span>Lexicon Development Tool (LDT) is built on top of existing <span class="SpellE">Textpresso</span> search functionalities. <span style="mso-spacerun: yes"></span>It employed a three-tier architecture using CGI in Perl for the front end web interface, middle tier functional process logic and <span class="SpellE">Postgres</span> relational database for backend data storage.<span style="mso-spacerun: yes"></span>Briefly, it allows a curator to login (see screenshot 1_CE_Login), setup a project (see screenshot 2_CE_Project) and submit <span class="SpellE">Textpresso</span> search (see screenshot 3_CE_Search), and the search results (sentences) are stored in the back end database.<span style="mso-spacerun: yes"></span>These sentences can be retrieved by the curator and displayed on web page.<span style="mso-spacerun: yes"></span>Curator can then select sentences of interest to make categories based on word frequency or save words/phrases based on the context in the sentence to include in appropriate categories or exclusion list (see screenshot 4_CE_SentenceAnnotation).<span style="mso-spacerun: yes"></span><span style="mso-spacerun: yes"></span>These newly made categories can be included in a new round of search and this process can thus go on iteratively.<span style="mso-spacerun: yes"></span></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><span style="mso-spacerun: yes"><del class="diffchange diffchange-inline">??? </del></span>This utility can be applied in both <span class="SpellE">datatype</span> identification and automatic extraction of text for <span class="SpellE">curation</span>.<span style="mso-spacerun: yes"><del class="diffchange diffchange-inline">? </del></span>In <span class="SpellE">datatype</span> identification, curator can upload a small training set containing 50 <span class="SpellE">positiveID</span> and <span class="SpellE">negativeID</span> of a <span class="SpellE">datatype</span> into LDT and optimize search query based on recall and precision measurement.<span style="mso-spacerun: yes"><del class="diffchange diffchange-inline">? </del></span>Once satisfying recall and precision values are obtained, the batch mode version of LDT (e.g. the search module) can be run in the automatic pipeline using the search query optimized on new <span class="SpellE">paperIDs</span> and those IDs identified as positive for the <span class="SpellE">datatype</span> can be deposited into the tracking database.<span style="mso-spacerun: yes"><del class="diffchange diffchange-inline">? </del></span><span style="mso-spacerun: yes"><del class="diffchange diffchange-inline">?</del></span></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><span style="mso-spacerun: yes"></span>This utility can be applied in both <span class="SpellE">datatype</span> identification and automatic extraction of text for <span class="SpellE">curation</span>.<span style="mso-spacerun: yes"></span>In <span class="SpellE">datatype</span> identification, curator can upload a small training set containing 50 <span class="SpellE">positiveID</span> and <span class="SpellE">negativeID</span> of a <span class="SpellE">datatype</span> into LDT and optimize search query based on recall and precision measurement.<span style="mso-spacerun: yes"></span>Once satisfying recall and precision values are obtained, the batch mode version of LDT (e.g. the search module) can be run in the automatic pipeline using the search query optimized on new <span class="SpellE">paperIDs</span> and those IDs identified as positive for the <span class="SpellE">datatype</span> can be deposited into the tracking database.<span style="mso-spacerun: yes"></span><span style="mso-spacerun: yes"></span></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><span style="mso-spacerun: yes"><del class="diffchange diffchange-inline">??? </del></span>In automatic extraction of text for <span class="SpellE">curation</span>, curator can upload a single article of a <span class="SpellE">datatype</span> and conduct the same iterative process of Search<del class="diffchange diffchange-inline">?CMaking </del>Category-Search until the search query is so specific that only those sentences containing relevant <span class="SpellE">curation</span> information are returned.<span style="mso-spacerun: yes"><del class="diffchange diffchange-inline">? </del></span>The same search query can then be applied to all the other papers of the <span class="SpellE">datatype</span> need to be <span class="SpellE">curated</span>.<span style="mso-spacerun: yes"><del class="diffchange diffchange-inline">?? </del></span>These selected sentences can then be exported into a <span class="SpellE">textfile</span> in the user<del class="diffchange diffchange-inline">??</del>s folder (see screenshot 5_CE_Results) in the format which can then be directly imported into a <span class="SpellE">curation</span> tool such as <span class="SpellE">Phenote</span> for further <span class="SpellE">curation</span>.<span style="mso-spacerun: yes"><del class="diffchange diffchange-inline">? </del></span></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><span style="mso-spacerun: yes"></span>In automatic extraction of text for <span class="SpellE">curation</span>, curator can upload a single article of a <span class="SpellE">datatype</span> and conduct the same iterative process of Search<ins class="diffchange diffchange-inline">-Making </ins>Category-Search until the search query is so specific that only those sentences containing relevant <span class="SpellE">curation</span> information are returned.<span style="mso-spacerun: yes"></span>The same search query can then be applied to all the other papers of the <span class="SpellE">datatype</span> need to be <span class="SpellE">curated</span>.<span style="mso-spacerun: yes"></span>These selected sentences can then be exported into a <span class="SpellE">textfile</span> in the user<ins class="diffchange diffchange-inline">'</ins>s folder (see screenshot 5_CE_Results) in the format which can then be directly imported into a <span class="SpellE">curation</span> tool such as <span class="SpellE">Phenote</span> for further <span class="SpellE">curation</span>.<span style="mso-spacerun: yes"></span></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></td></tr>
</table>Rfanghttps://wiki.wormbase.org/index.php?title=Lexicon_Development_Tool&diff=2017&oldid=prevRfang at 08:43, 19 May 20092009-05-19T08:43:02Z<p></p>
<a href="https://wiki.wormbase.org/index.php?title=Lexicon_Development_Tool&diff=2017&oldid=2016">Show changes</a>Rfanghttps://wiki.wormbase.org/index.php?title=Lexicon_Development_Tool&diff=2016&oldid=prevRfang: New page: <html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns="http://www.w3.org/TR/REC-html40"> <head> <meta http-equiv=Content-Type conte...2009-05-19T08:37:20Z<p>New page: <html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns="http://www.w3.org/TR/REC-html40"> <head> <meta http-equiv=Content-Type conte...</p>
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<p class=MsoNormal><span style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp; </span>Lexicon<br />
Development Tool (LDT) is built on top of existing <span class=SpellE>Textpresso</span><br />
search functionalities.<span style='mso-spacerun:yes'>&nbsp; </span>It employed<br />
a three-tier architecture using CGI in Perl for the front end web interface,<br />
middle tier functional process logic and <span class=SpellE>Postgres</span><br />
relational database for backend data storage.<span<br />
style='mso-spacerun:yes'>&nbsp; </span>Briefly, it allows a curator to login<br />
(see screenshot 1_CE_Login), setup a project (see screenshot 2_CE_Project) and submit<br />
<span class=SpellE>Textpresso</span> search (see screenshot 3_CE_Search), and<br />
the search results (sentences) are stored in the back end database.<span<br />
style='mso-spacerun:yes'>&nbsp; </span>These sentences can be retrieved by the<br />
curator and displayed on web page.<span style='mso-spacerun:yes'>&nbsp;<br />
</span>Curator can then select sentences of interest to make categories based on<br />
word frequency or save words/phrases based on the context in the sentence to<br />
include in appropriate categories or exclusion list (see screenshot<br />
4_CE_SentenceAnnotation).<span style='mso-spacerun:yes'>&nbsp; </span><span<br />
style='mso-spacerun:yes'>&nbsp;</span>These newly made categories can be<br />
included in a new round of search and this process can thus go on iteratively.<span<br />
style='mso-spacerun:yes'>&nbsp;&nbsp; </span></p><br />
<br />
<p class=MsoNormal><span style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp; </span>This<br />
utility can be applied in both <span class=SpellE>datatype</span> identification<br />
and automatic extraction of text for <span class=SpellE>curation</span>.<span<br />
style='mso-spacerun:yes'>&nbsp; </span>In <span class=SpellE>datatype</span><br />
identification, curator can upload a small training set containing 50 <span<br />
class=SpellE>positiveID</span> and <span class=SpellE>negativeID</span> of a <span<br />
class=SpellE>datatype</span> into LDT and optimize search query based on recall<br />
and precision measurement.<span style='mso-spacerun:yes'>&nbsp; </span>Once satisfying<br />
recall and precision values are obtained, the batch mode version of LDT (e.g.<br />
the search module) can be run in the automatic pipeline using the search query<br />
optimized on new <span class=SpellE>paperIDs</span> and those IDs identified as<br />
positive for the <span class=SpellE>datatype</span> can be deposited into the<br />
tracking database.<span style='mso-spacerun:yes'>&nbsp; </span><span<br />
style='mso-spacerun:yes'>&nbsp;</span></p><br />
<br />
<p class=MsoNormal><span style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp; </span>In<br />
automatic extraction of text for <span class=SpellE>curation</span>, curator<br />
can upload a single article of a <span class=SpellE>datatype</span> and conduct<br />
the same iterative process of Search¨CMaking Category-Search until the search<br />
query is so specific that only those sentences containing relevant <span<br />
class=SpellE>curation</span> information are returned.<span<br />
style='mso-spacerun:yes'>&nbsp; </span>The same search query can then be<br />
applied to all the other papers of the <span class=SpellE>datatype</span> need to<br />
be <span class=SpellE>curated</span>.<span<br />
style='mso-spacerun:yes'>&nbsp;&nbsp; </span>These selected sentences can then<br />
be exported into a <span class=SpellE>textfile</span> in the user¡¯s folder (see<br />
screenshot 5_CE_Results) in the format which can then be directly imported into<br />
a <span class=SpellE>curation</span> tool such as <span class=SpellE>Phenote</span><br />
for further <span class=SpellE>curation</span>.<span<br />
style='mso-spacerun:yes'>&nbsp; </span></p><br />
<br />
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