tag:blogger.com,1999:blog-67922339553500264482023-11-16T21:08:04.249+02:00 Environments-EOLA project aiming at processing the <a href="http://eol.org">Encyclopedia of Life</a>'s (EOL) Taxon pages to extract descriptions of their environmental context. Such input will subsequently employed to answer integrative large-scale biological questions (Funded by the <a href="http://eol.org/info/52">EOL Rubenstein Fellows Program</a>)
evangeloshttp://www.blogger.com/profile/03781515992542140689noreply@blogger.comBlogger13125tag:blogger.com,1999:blog-6792233955350026448.post-42338502487581483182014-10-03T18:36:00.000+03:002014-10-03T18:36:04.216+03:00September 22 -25 2014: "SEQenvIII: From Signals to Environmentally Tagged Sequences III" Hackathon, HCMR, Crete, Creece<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhROym3p6MTOPLIjxUxKKcGBC0YHs68Rt36vP_4z8mKKGBU9flURFl1YQYB19663ErM0nFJvfbP4SyTiQ3VqEsXPvy_M8JQ2YXvs6Z9jDnUKwTEVww-KkQlp_JQ-kamcQEqbnHkY4_oK5yf/s1600/20140925-DSC_3681.jpg" imageanchor="1" style="clear: left; display: inline !important; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhROym3p6MTOPLIjxUxKKcGBC0YHs68Rt36vP_4z8mKKGBU9flURFl1YQYB19663ErM0nFJvfbP4SyTiQ3VqEsXPvy_M8JQ2YXvs6Z9jDnUKwTEVww-KkQlp_JQ-kamcQEqbnHkY4_oK5yf/s320/20140925-DSC_3681.jpg" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><div style="text-align: left;">
Participants: From left to right: Christina Pavloudi, <br />
Anastasis Oulas, Lex Overmars, Conor Meehan, Lars Juhl<br />
Jensen, Tomas Flouri, Tomas Vetrovsky, Chris Quince, Lucas<br />
Sinclair. Not shown: Umer Ijaz (via Skype), Evangelos Pafilis </div>
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<a href="http://environments.hcmr.gr/seqenv.html" target="_blank">SEQenv</a>, is a sister project of ENVIRONMENTS-EOL, addressing the microbial realm and bringing together the worlds of text mining, sequence analysis, statistics and vizualization through the prism of microbial ecology.<br />
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In particular, SEQenv is a pipeline aiming at annotating 16S rRNA and metagenomics microbial sequences based on environment descriptive terms.
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Sequence similarity searches against public databases and the recognition of terms such as “glacier, pelagic, forest, lagoon” (i.e. <a href="http://environmentontology.org/" target="_blank">Environment Ontology</a> terms identified by the <a href="http://environments.hcmr.gr/" target="_blank">ENVIRONMENTS tagger</a>) within Genbank records (e.g. “isolation source" field) and/or in the relevant literature (PubMed abstracts) are being employed to characterize novel microbial sequences.
Subsequently, a range of visualizations, such as tag clouds, heatmaps, are generated to describe OTUs and samples.<br />
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Built incrementally, in three hackathons since September 2012, several features were added to SEQenv. e.g. starting from 16S rRNA sequences the pipeline now may be invoked either a. for DNA sequences or b. for protein sequences.<br />
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This year, it was time to clean up the code and package it in a language that would be easy to distribute. Moreover, speed performance was optimized and novel forms of visualization were explored. The core modules were rewritten in Python, speed-ups, e.g. by optimizing the sequence similarity searches were implemented, and interactive HTML/Javascript vizualizations started replacing R-generated static diagrams. In addition, integrating SEQenv-derived annotations with phylogenetic information and text-mining module extensions were investigated.<br />
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The effort and devotion of all participants (see image above) was the driving force overcoming the long-hours and any technical difficulties that arose. A big thank you from the organizers (without forgetting the SEQenvI and SEQenvII participants).<br />
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<span style="font-family: inherit;">All three SEQenv hackathons have been funded by the <a href="http://www.cost.eu/domains_actions/essem/Actions/ES1103" target="_blank">EU COST ES 1103 Action</a> on "<a href="http://www.cost.eu/domains_actions/essem/Actions/ES1103" target="_blank">Microbial ecology & the earth system: collaborating for insight and success with the new generation of sequencing tools</a>". </span><br />
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<span style="font-family: inherit;"><span style="font-size: 15px; vertical-align: baseline; white-space: pre-wrap;">Besides the EU </span><span style="font-size: 17px; line-height: 1.15; text-align: justify; white-space: pre-wrap;">COST ES1103 Action t</span><span style="font-size: 15px; vertical-align: baseline; white-space: pre-wrap;">he organizers would like to thank the <a href="http://www.lifewatchgreece.eu/" target="_blank">LifeWatchGreece</a> project </span><span style="font-size: 15px; vertical-align: baseline; white-space: pre-wrap;">for additional local support. </span></span><br />
<span style="font-family: inherit;">Any software <span style="background-color: transparent; color: black; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">produced during the hackathon will be made available as open source.</span></span></div>
evangeloshttp://www.blogger.com/profile/03781515992542140689noreply@blogger.com0tag:blogger.com,1999:blog-6792233955350026448.post-26575185641202252562014-03-07T12:35:00.001+02:002014-03-26T18:00:35.327+02:00November 2013 - February 2014: EOL/Traitbank Integration, On-going Benchmark, Exploratory Visualizations<span style="font-family: Arial, Helvetica, sans-serif;">Unlike the silence of this blog, progress has occurred in all fronts of the ENVIRONMENTS-EOL project. Many sub-parts of which are now either finished, or nearing completion.</span><br />
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<span style="font-family: Arial, Helvetica, sans-serif;"><b>Have you seen <span style="line-height: 18.399999618530273px;">ENVIRONMENTS-EOL predictions in the Encyclopedia of Life?</span></b></span><br />
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<span style="font-family: Arial, Helvetica, sans-serif; text-align: center;">Early in 2014 the </span><span style="font-family: Arial, Helvetica, sans-serif; text-align: center;"><a href="http://eol.org/" target="_blank">Encyclopedia of Life (EOL)</a></span><span style="font-family: Arial, Helvetica, sans-serif; text-align: center;"> released its </span><span style="font-family: Arial, Helvetica, sans-serif; text-align: center;"><a href="http://blog.eol.org/post/74751984298/announcing-traitbank" target="_blank">new version</a></span><span style="font-family: Arial, Helvetica, sans-serif; text-align: center;">, along with </span><span style="font-family: Arial, Helvetica, sans-serif; text-align: center;"><a href="http://eol.org/info/516" target="_blank">Traitbank</a>,</span><b style="font-family: Arial, Helvetica, sans-serif; text-align: center;"> </b><span style="font-family: Arial, Helvetica, sans-serif; text-align: center;">its novel data search facility. </span><span style="font-family: Arial, Helvetica, sans-serif;">Among other <a href="http://blog.eol.org/post/74761217387/traitbank-release-notes" target="_blank">innovative biodiversity research features</a>, </span><span style="font-family: Arial, Helvetica, sans-serif;"><a href="http://eol.org/users/20470" target="_blank">Jennifer Hammock</a>, <a href="http://eol.org/users/13" target="_blank">Patrick Leary</a></span><span style="font-family: Arial, Helvetica, sans-serif;">, <a href="http://eol.org/users/35200" target="_blank">Katja Schulz</a></span><span style="font-family: Arial, Helvetica, sans-serif;">, <a href="http://eol.org/users/25567" target="_blank">Cyndy Parr</a></span><b style="font-family: Arial, Helvetica, sans-serif;"> </b><span style="font-family: Arial, Helvetica, sans-serif;">(and anyone else I may be omitting) have incorporated ENVIRONMENTS-EOL predictions into the EOL system.</span><br />
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<a href="http://eol.org/pages/212027" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiAjGIBO4uVQ741nVkDrzHpGf4J2KUTNu-_OC3SCN8-YFC7D0OpzvzgRq6j2NdXn8nE_luMuRewjBvKvX7qt3jWhmhsxcg31N74tTOOxk3pn0doDmXISw-GtkQR-K-tafXk8cQuTYE7vIWp/s1600/QuickFacts.tiff" height="186" width="320" /></a><a href="http://eol.org/pages/212027/data" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;" target="blank"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiX-YGBbrLwzhdGBMPCXd5zaAwjgPMNzyRqmvqso02GRBlw1DXE7Cj1fRYhvtGv6FuWJ9utWAfMfZhURBMU2ZwVmgWnH1CPcFXo8FYTOps7pHpKRwuSPvndXzWk9T1tGVqcJ_N8bKxMwXbN/s1600/DataTab.tiff" height="212" width="320" /></a><span style="font-family: Arial, Helvetica, sans-serif;">As shown on the left <a href="http://environmentontology.org/" target="_blank">Environment Ontology (ENVO)</a><b> </b>descriptive terms associated with a taxon (in this example: <i>Hexanchus griseus</i>, the Bluntnose Six-gill Shark), can be seen both in the <a href="http://eol.org/pages/212027/overview" target="_blank">Overview, Quick Facts</a><b> </b>(short list, upper-right part of the figure), and under the <a href="http://eol.org/pages/212027/data" target="_blank">Data Tab</a> (extended list, lower-right part of the figure).</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Such features render the ENVIRONMENTS-EOL predictions accessible for all EOL users indifferent of the Information Technology skills.</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Due to </span><span style="font-family: Arial, Helvetica, sans-serif;">natural language</span><span style="font-family: Arial, Helvetica, sans-serif;"> intricacies, such as the <a href="http://en.wikipedia.org/wiki/Polysemy" target="_blank">multiple meanings a word may have</a>, erroneous predictions will occur. As described in previous posts (<a href="http://environments-eol.blogspot.gr/2013/08/july-2013-first-deliverables-tagger.html" target="_blank">April</a>,<b> </b><a href="http://environments-eol.blogspot.gr/2013/05/nice-days-during-visit-in-copenhagen-1.html" target="_blank">July 2013</a>), ENVIRONMENTS-EOL has been developed in iterative cycles aiming to identify and handle the most prominent of such errors.</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">An improved version of the ENVIRONMENTS tagger is now ready and the release of a new ENVIRONMENTS-EOL annotation dataset is in preparation.</span></div>
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<b><span style="font-family: Arial, Helvetica, sans-serif;">Named Entity Recognition (NER) Evaluation</span></b></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">In a text-mining point-of-view, </span><span style="font-family: Arial, Helvetica, sans-serif;">the work on the </span><span style="font-family: Arial, Helvetica, sans-serif;"><a href="http://environments-eol.blogspot.gr/2013/09/august-2013-e600-curation-month.html" target="_blank">ENVIRONMENTS-600 corpus</a></span><b style="font-family: Arial, Helvetica, sans-serif;"> </b><span style="font-family: Arial, Helvetica, sans-serif;">has been concluded; the </span><span style="font-family: Arial, Helvetica, sans-serif;"><a href="http://en.wikipedia.org/wiki/Cohen's_kappa" target="_blank">Inter Annotator Agreement</a></span><span style="font-family: Arial, Helvetica, sans-serif;"> having been the last step of the process.</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">The tagger evaluation in terms of <a href="http://en.wikipedia.org/wiki/Precision_and_recall" target="_blank">precision and recall</a> is nearly complete. Points of particular interest were:</span></div>
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<li><span style="font-family: Arial, Helvetica, sans-serif;">the handling of multiple EnvO identifiers having been mapped to a term by the curators, and/or being returned by the tagger</span></li>
<li><span style="font-family: Arial, Helvetica, sans-serif;">the hierarchical relationship of curated/predicted terms according to EnvO</span></li>
<li><span style="font-family: Arial, Helvetica, sans-serif;">the NER evaluation for distinct EnvO sub-graphs only (e.g. only for environmental features, or habitats, or environmental materials)</span></li>
<li><span style="font-family: Arial, Helvetica, sans-serif;">the NER evaluation for the different <a href="http://eol.org/info/toc_subjects" target="_blank">EOL Species page sections</a> (e.g. only for "Habitat", or "Distribution", or "Taxon Biology")</span></li>
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<span style="font-family: Arial, Helvetica, sans-serif;">The analysis of the NER performance is on-going.</span></div>
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<b><span style="font-family: Arial, Helvetica, sans-serif;">North, South America bird habitat associations and vizualisations</span></b></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Early in February 2014, the </span><span style="font-family: Arial, Helvetica, sans-serif;"><a href="http://eol.org/info/nescent_EOL_BHL" target="_blank">NESCent EOL-BHL Research Sprint</a> </span><span style="font-family: Arial, Helvetica, sans-serif;">(</span><span class="s1" style="font-family: Arial, Helvetica, sans-serif;">Durham, North Carolina) </span><span style="font-family: Arial, Helvetica, sans-serif;">event gave ENVIRONMENTS-EOL a unique opportunity to explore concrete biological questions based on its machinery.</span><br />
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<span style="font-family: Arial, Helvetica, sans-serif;">Interdisciplinary collaboration was the at very center of the event; Biologists were teamed with Information Technology reseachers to tackle open biodiversity research questions <span class="s1">based on <a href="http://eol.org/" target="_blank">EOL/</a><a href="http://eol.org/info/516" target="_blank">TraitBank</a>, and <a href="http://www.biodiversitylibrary.org/" target="_blank">Biodiversity Heritage Library (BHL)</a> data.</span></span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><a href="https://docs.google.com/document/d/1ajW50BkXjSJe7qOt8WBrX8Pvt-A7A6yK6kw6YHYCaaY/edit#heading=h.p54hewsa3lqf" target="_blank">NoPlaceLikeHome</a><b>, </b>a project initiated and driven by <a href="http://www.umb.edu/academics/csm/faculty_staff/robert_stevenson" target="_blank">Prof. Rob Stevenson, U Mass, Boston</a>,<b> </b>aimed at exploring species - habitat associations. Significant contribution was received by the local collaborator </span><span style="font-family: Arial, Helvetica, sans-serif;"><a href="http://www.linkedin.com/pub/carl-nordman/13/a17/579" target="_blank">Dr. Carl Nordman</a>,</span><b style="font-family: Arial, Helvetica, sans-serif;"> </b><span style="font-family: Arial, Helvetica, sans-serif;"><a href="http://www.natureserve.org/" target="_blank">NatureServe</a></span><span style="font-family: Arial, Helvetica, sans-serif;">.</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">In this context ENVIRONMENTS was used to annotate in-house North and South America Bird (Aves) information such as ecology, habitat, migration descriptions and others. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Heatmaps and tagclouds (see below) were </span><span style="font-family: Arial, Helvetica, sans-serif;">generated to visualise the text mining results: species - EnvO term associations based on simple term counts.</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">The visualisation scripts have been developed as part of the <a href="http://environments.hcmr.gr/seqenv.html" target="_blank">SEQenv</a> sister project to characterize microbial sample sequences, according to the environment from which they derive. </span><br />
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<span style="font-family: Arial, Helvetica, sans-serif;">Employed in a higher eukaryote context, the same tools can still support knowledge exploration e.g. by highlighting </span><span style="font-family: Arial, Helvetica, sans-serif;">rare/frequent habitats, species habitat breadth, and intra-taxon environment association differences.</span><br />
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<span style="font-family: Arial, Helvetica, sans-serif;">An even user-friendlier, interactive version of the graphicsis under way in collaboration with <a href="http://userweb.eng.gla.ac.uk/umer.ijaz/" target="_blank">Dr. Umer Ijaz, Uni. of Glasgow</a>. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">The image shown below is a compilation of the project outputs by <a href="http://eol.org/users/25567" target="_blank">Cyndy Parr</a>, as found in the <a href="http://blog.eol.org/" target="_blank">EOL Blog</a> (among other reports from the <a href="http://eol.org/info/nescent_EOL_BHL" target="_blank">NESCent EOL-BHL Research Sprint</a> and EOL News). Quoting Cyndy's to-the-point legend: "Species are on the X axis and the Environment Ontology (EnvO) habitat term associations on the Y axis, with the redness (or size in the inset Wordle) based on simple term counts." </span><span style="font-family: Arial, Helvetica, sans-serif;"> </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>evangeloshttp://www.blogger.com/profile/03781515992542140689noreply@blogger.com0tag:blogger.com,1999:blog-6792233955350026448.post-86760910573615526892013-10-29T11:40:00.000+02:002013-10-29T11:40:03.077+02:00September – October 2013: ENVIRONMENTS-EOL Outreach (BioCreative IV, TDWG 2013), E600 Housekeeping <br />
Outreach activities have been the main focal point so far in Autumn 2013.<br />
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ENVIRONMENTS, ENVIRONMENTS-EOL, and the sister project <a href="http://species.hcmr.gr/" target="_blank">SPECIES</a> have been presented at an invited talk at the <a href="http://www.biocreative.org/events/biocreative-iv/workshop/" target="_blank">BioCreative IV</a> workshop (7 - 9 October, Washington DC, US) as part of a <a href="http://energy.gov/" target="_blank">DOE</a>-funded Discussion Panel on Metagenomics.<br />
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Bridging the metagenomics and text mining communities e.g. by employing text mining techniques to support <a href="http://gensc.org/" target="_blank">standards</a>-compliant sequence metadata annotation was one of the main discussion points.<br />
The Biocreative IV workshop proceedings including opinions on the previous point are available <a href="http://www.biocreative.org/resources/publications/biocreative-iv-proceedings/" target="_blank">here</a> (see Volume 1, pages 279-291).<br />
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On behalf of the ENVIRONMENTS-EOL team a big thank you to the BioCreative organizers.<br />
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At the time of writing, the <a href="http://www.tdwg.org/conference2013" target="_blank">Biodiversity Information Standards Conference</a> (<a href="http://www.tdwg.org/conference2013" target="_blank">TDWG 2013</a>, 28 Oct - 1 Nov, Firenze), is on-going.<br />
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ENVIRONMENTS-EOL will be be presented this Friday (1st Nov, 11:20) in the "Interoperability with genomic and ecological semantics" session of the <a href="http://semantics4biodiversity.nceas.ucsb.edu/" target="_blank">Semantics for Biodiversity Symposium</a> of <a href="http://www.tdwg.org/conference2013" target="_blank">TDWG2013</a> (Travel made possible thanks to <a href="http://eol.org/info/52" target="_blank">EOL Rubenstein Fellows Program</a>'s funding).<br />
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In parallel and while the benchmarking algorithms are being prepared, the ENVIRONMENTS-600 (E600) corpus returned by the curators (see August's <a href="http://environments-eol.blogspot.com/2013/09/august-2013-e600-curation-month.html" target="_blank">post</a>) underwent housekeeping processing e.g. by removing any errors that had been introduced during the manual curation such as missing tabs in the annotation items, flag misspellings and others.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjKqWcYHtzWdRuQITfczAEePp_DuIOVOxKItj8XKWOTo4vBmkIhd11Ygkou272ab-5cd8HzwuE9B_B9QQSTbt-iPY1dxH9VBhKlR_c427FmO0fXPtp6mzYDhOawH9G6bXyZrmAa13eqEYpK/s1600/Dolomites.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="138" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjKqWcYHtzWdRuQITfczAEePp_DuIOVOxKItj8XKWOTo4vBmkIhd11Ygkou272ab-5cd8HzwuE9B_B9QQSTbt-iPY1dxH9VBhKlR_c427FmO0fXPtp6mzYDhOawH9G6bXyZrmAa13eqEYpK/s320/Dolomites.jpg" width="320" /></a>A mountain range (ENVO:00000080) as seen on board a flight from Münich, Germany to Florence, Italy to attend TDWG2013. Could it be the Dolomite mountain range?<br />
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<br />evangeloshttp://www.blogger.com/profile/03781515992542140689noreply@blogger.com0tag:blogger.com,1999:blog-6792233955350026448.post-31571518724792420382013-09-14T11:35:00.000+03:002013-09-14T13:07:31.281+03:00August 2013: The E600 curation month<div>
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<span style="color: black; font-family: Calibri; font-size: 11.0pt;">Amid
July – August high temperatures for some of the team members, visits in
associate labs for some others, and as a side-activity to normal lab/office
work for the rest, the most tedious and time-consuming part of this
project has now been completed.<o:p></o:p></span></div>
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<br /></div>
<div style="margin-bottom: .0001pt; margin: 0cm; text-align: justify; text-justify: inter-ideograph;">
<span style="font-family: Calibri; font-size: 11pt;">Environments-600
(E600), a corpus comprising 600 EOL Taxa pages was evenly and randomly
distributed among the 6 curators (4 graduate students, 2 postdocs, see <a href="http://environments-eol.blogspot.gr/2013/07/june-2013-dry-run-curation-month.html" target="_blank"><span style="color: blue;">June’s post</span></a>). <o:p></o:p></span></div>
<div style="margin-bottom: .0001pt; margin: 0cm; text-align: justify; text-justify: inter-ideograph;">
<br /></div>
<div style="margin-bottom: .0001pt; margin: 0cm; text-align: justify; text-justify: inter-ideograph;">
<span style="color: black; font-family: Calibri; font-size: 11.0pt;">To
maximize environment type coverage the 600 EOL documents were species pages randomly
picked from the following eight taxonomic taxa: Actinopterygii, Annelida,
Arthropoda, Aves, Chlorophyta, Mammalia, Mollusca, Streptophyta. These are taxa
either associated with different environments to each other, or known to exist
in a diverse range of environments.<o:p></o:p></span></div>
<div style="margin-bottom: .0001pt; margin: 0cm; text-align: justify; text-justify: inter-ideograph;">
<br /></div>
<div style="margin-bottom: .0001pt; margin: 0cm; text-align: justify; text-justify: inter-ideograph;">
<span style="font-family: Calibri; font-size: 11pt;">Each
curator had 45 days to annotate 120 documents (ie. their part of the corpus:
600/6 = 100 documents each, plus 20 documents (ie. 20% of 100) that are common
with other curators. The ‘20% overlap’ is an important part of the curation process.
It supports the calculation of the Inter-annotator agreement (IAA, based on
pairwise calculations of the <a href="http://en.wikipedia.org/wiki/Cohen's_kappa"><span style="color: blue;">Cohen's kappa coefficient</span></a>.
<o:p></o:p></span></div>
<div style="margin-bottom: .0001pt; margin: 0cm; text-align: justify; text-justify: inter-ideograph;">
<br /></div>
<div style="margin-bottom: .0001pt; margin: 0cm; text-align: justify; text-justify: inter-ideograph;">
<span style="color: black; font-family: Calibri; font-size: 11.0pt;">Each
curator had access to his/her own documents only. No information on the shared
documents had been disclosed.<o:p></o:p></span></div>
<div style="margin-bottom: .0001pt; margin: 0cm; text-align: justify; text-justify: inter-ideograph;">
<br /></div>
<div style="margin-bottom: .0001pt; margin: 0cm; text-align: justify; text-justify: inter-ideograph;">
<span style="color: black; font-family: Calibri; font-size: 11.0pt;">All
curators were instructed to evaluate all document substrings and map the
recognized environment descriptors to the corresponding EnvO terms.<o:p></o:p></span></div>
<div style="margin-bottom: .0001pt; margin: 0cm; text-align: justify; text-justify: inter-ideograph;">
<br /></div>
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<span style="color: black; font-family: Calibri; font-size: 11.0pt;">Reflecting on the EnvO, </span><span style="font-family: Calibri; font-size: 11.0pt; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman";"><a href="http://purl.obolibrary.org/obo/subsets/envo-basic.obo"><span style="background-color: white; background-position: initial initial; background-repeat: initial initial;"><span style="color: blue;">envo-basic.obo</span></span></a></span><span style="background: white; color: #222222; font-family: Calibri; font-size: 11.0pt; mso-bidi-font-family: Arial; mso-fareast-font-family: "Times New Roman";">, version-date: 14th June 2013,
such environment descriptors included:</span><span style="color: black; font-family: Calibri; font-size: 11.0pt;"> habitats, biomes, enviromental
features, conditions and materials (EnvO high level terms:<span style="mso-spacerun: yes;"> </span>00002036, 00000428, 00002297, 01000203, 00010483
respectively)<o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: Calibri; font-size: 11pt;">All recognized mentions should be listed (including repetitions)
in the order of appearance in text. To facilitate EnvO term search and ontology
browsing <a href="http://oboedit.org/"><span style="color: blue;">OBO-Edit</span></a> has been employed.<o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div style="margin-bottom: .0001pt; margin: 0cm; text-align: justify; text-justify: inter-ideograph;">
<span style="color: black; font-family: Calibri; font-size: 11.0pt;">When
an environment descriptor could refer to more than one EnvO terms multiple
mappings were allowed (e.g. mapping “forest” to ENVO:00000111, “forest”
(environmental feature), and<span style="mso-spacerun: yes;"> </span>01000174,
“forest biome”).<o:p></o:p></span></div>
<div style="margin-bottom: .0001pt; margin: 0cm; text-align: justify; text-justify: inter-ideograph;">
<br /></div>
<div style="margin-bottom: .0001pt; margin: 0cm; text-align: justify; text-justify: inter-ideograph;">
<span style="color: black; font-family: Calibri; font-size: 11.0pt;">In
the case of “nested” environment descriptors, a “left-longest most”-like
matching approach applied. If for example “sandy sediment” is met in text, it
will be mapped to ENVO:</span> <span style="color: black; font-family: Calibri; font-size: 11.0pt;">01000118, “sandy sediment” (and not to the nested terms: sand,
sediment).<o:p></o:p></span></div>
<div style="margin-bottom: .0001pt; margin: 0cm; text-align: justify; text-justify: inter-ideograph;">
<br /></div>
<div style="margin-bottom: .0001pt; margin: 0cm; text-align: justify; text-justify: inter-ideograph;">
<span style="color: black; font-family: Calibri; font-size: 11.0pt;">During
the curation a range of special cases were encountered. Cases like
misspellings, EnvO term missing synonyms and enumerations were indicated as
such. Environment descriptors that did not correspond to an existing EnvO term
were also marked as such. <o:p></o:p></span></div>
<div style="margin-bottom: .0001pt; margin: 0cm; text-align: justify; text-justify: inter-ideograph;">
<br /></div>
<div style="margin-bottom: .0001pt; margin: 0cm; text-align: justify; text-justify: inter-ideograph;">
<span style="font-family: Calibri; font-size: 11pt;">Finally,
when environment descriptive terms where part of geographical locations and/or
common taxon names (e.g. Steppe Eagle, <i><a href="http://eol.org/pages/914512/overview"><span style="color: blue;">Aquila nipalensis</span></a>, </i>shown in
the Figure) were flagged as such to allow for downstream analysis.<o:p></o:p></span></div>
<div style="margin-bottom: .0001pt; margin: 0cm; text-align: justify; text-justify: inter-ideograph;">
<br /></div>
<div style="margin-bottom: .0001pt; margin: 0cm; text-align: justify; text-justify: inter-ideograph;">
<span style="color: black; font-family: Calibri; font-size: 11.0pt;">Calculating
the IAA, merging the annotated document in a single corpus are now ongoing,
paving the ground for the ENVIRONMENT’s accuracy benchmark. Stay tuned!<o:p></o:p></span></div>
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<span style="font-family: Calibri; font-size: 11pt;">Steppe Eagle, <a href="http://eol.org/pages/914512/overview"><i><span style="color: blue;">Aquila
nipalensis</span></i></a>, a common species name including a reference to an
environment. Such cases occurred during the curation have been flagged for
follow-up analysis (Image License: CC BY NC SA, © Tarique Sani, </span><span style="background: white; color: #394651; font-family: Calibri; font-size: 11.0pt; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman";">Source: </span><span style="font-family: Calibri; font-size: 11.0pt; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman";"><a href="http://www.flickr.com/photos/tariquesani/4318013600/"><span style="background-color: white; background-position: initial initial; background-repeat: initial initial;"><span style="color: blue;">Flickr: EOL Images</span></span></a>)<i> </i></span><span style="font-family: Calibri; font-size: 11.0pt;"> </span><span style="font-family: Calibri; font-size: 11.0pt; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman";"><o:p></o:p></span></div>
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evangeloshttp://www.blogger.com/profile/03781515992542140689noreply@blogger.com0tag:blogger.com,1999:blog-6792233955350026448.post-71370209972955695492013-08-09T15:15:00.000+03:002013-08-14T16:03:36.587+03:00July 2013: First Deliverables: Tagger, Dictionary, Stopword-list: v1.0 Ready!<div class="MsoNormal">
<span lang="EN-US">July 2013 has been a highly active month. </span></div>
<div class="MsoNormal">
<span lang="EN-US"><br /></span></div>
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<span lang="EN-US">A visit of <a href="http://www.cpr.ku.dk/staff/staff_all/?id=343848&vis=medarbejder" target="_blank">Dr. Lars Juhl Jensen</a> in <a href="http://www.hcmr.gr/en/" target="_blank">HCMR </a>(Hellenic Center for Marine Research),</span><span lang="EN-US"> Crete followed
up on last April’s ENVIRONMENTS software developments (see <a href="http://environments-eol.blogspot.gr/2013/05/nice-days-during-visit-in-copenhagen-1.html" target="_blank">post</a></span><span lang="EN-US">).<o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US"><br /></span></div>
<div class="MsoNormal">
<span lang="EN-US">The main focus was on updating the dictionary and the stopword-list
according to the information contained in a <a href="http://environmentontology.org/downloads" target="_blank">recent Environmental Ontology version</a> (<a href="http://purl.obolibrary.org/obo/subsets/envo-basic.obo">envo-basic.obo</a>, date: 14 June 2013)<o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US"><br /></span></div>
<div class="MsoNormal">
<span lang="EN-US">The Environmental Ontology updates including an improved coverage of terrestrial
biomes (see<a href="http://environmentontology.org/home/news/terrestrialbiomesupdate" target="_blank"> EnvO News post</a>) were the main reason for such an update.<o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US"><br /></span></div>
<div class="MsoNormal">
<span lang="EN-US" style="line-height: 115%;">As a result, the v1.0 ENVIRONMENTS
tagger is now ready and has been delivered to EOL (including the latest dictionary
of environment descriptive terms and the relevant stopword-list). All these software components are open source and will be made available at due time.<o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US" style="line-height: 115%;"><br /></span></div>
<div class="MsoNormal">
<span lang="EN-US" style="line-height: 115%;">An annotation of all
EOL-Taxon pages using the v1.0 tagger, along with a precision analysis of the different EOL page section annotation have been completed.<o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US" style="line-height: 115%;"><br /></span></div>
<div class="MsoNormal">
<span lang="EN-US" style="color: #222222; line-height: 115%;">The gold
standard corpus curation and the analysis of ENVIRONMENTS’ accuracy based on
that corpus are now the main focus.</span><span style="color: #222222; line-height: 115%;"> </span><span style="color: #222222; line-height: 115%;">600 EOL
species pages (from eight taxonomic taxa: Actinopterygii, Annelida, Arthropoda,
Aves, Chlorophyta, Mammalia, Mollusca, Streptophyta – to maximize environment
diversity) have now been shared among the curators and the manual annotation is
ongoing.</span></div>
<br />
<div class="MsoNormal">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEicqqFcqM8_nH0AgnA1JhTSbeCRSWB2pVOmz8jiobHDitqrxUpnxBPzHPFkga67bSPry3PUGEwJUDTRnGte3_s4I4yhBh5MCXLrIx4x_m9aLcykSSJM66utHvOw8BVJ_RFM4v4DmZgnK_95/s1600/Falasarna_sunset.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="209" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEicqqFcqM8_nH0AgnA1JhTSbeCRSWB2pVOmz8jiobHDitqrxUpnxBPzHPFkga67bSPry3PUGEwJUDTRnGte3_s4I4yhBh5MCXLrIx4x_m9aLcykSSJM66utHvOw8BVJ_RFM4v4DmZgnK_95/s320/Falasarna_sunset.jpg" width="320" /></a><span lang="EN-US" style="color: #222222; line-height: 115%;">At the mean time
brief holiday opportunities arise :) (Picture taken at Ancient Falasarna, Chania,
Crete, Early August 2013, CC BY-NC-SA)<span style="font-size: small;"><o:p></o:p></span></span></div>
evangeloshttp://www.blogger.com/profile/03781515992542140689noreply@blogger.com0tag:blogger.com,1999:blog-6792233955350026448.post-43092181722881370072013-07-04T16:12:00.002+03:002013-07-04T16:12:30.809+03:00June 2013: The “dry-run” curation month<div class="MsoNormal">
A gold
standard corpus generation comprises steps such as: document collection/selection,
manual document annotation, annotation result collection and statistical
analysis.</div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US">The first
and last steps can be computationally assisted and partially automated. However,
this is not the case for the manual document annotation. Also called “curation”,
the manual document annotation comprises the manual scanning of the document
text to identify environment descriptive terms and map them to unique
identifiers according to a community resource (the <a href="http://environmentontology.org/" target="_blank">Environment Ontology</a> (EnvO)
in this case).<o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US"><br /></span></div>
<div class="MsoNormal">
<span lang="EN-US">The tediousness
and time-demands of such process call for collaborative effort. Aa international
group of six researchers: <a href="http://www.marbigen.org/users/lucia-fanini" target="_blank">Lucia Fanini</a>, <a href="http://www.marbigen.org/users/sarah-faulwetter" target="_blank">Sarah Faulwetter</a>, <a href="http://epafilis.info/" target="_blank">Evangelos Pafilis</a>, <a href="http://www.marbigen.org/users/christina-pavloudi" target="_blank">Christina Pavloudi</a>, <a href="http://www.mpi-bremen.de/en/Page6679.html" target="_blank">Julia Schnetzer</a>, <a href="http://www.marbigen.org/users/katerina-vasileiadou" target="_blank">Katerina Vasileiadou</a> (in alphabetical order) have
undertaken this task. </span></div>
<div class="MsoNormal">
<span lang="EN-US"><br /></span></div>
<div class="MsoNormal">
Coming from a diverse range of scientific background (such
as ecology, computational biology, molecular biology, and systematic) they
represent different mindsets upon scanning pieces of text, in a way
representing different EOL readers.</div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
Such
pluralism is a desired feature for the corpus curation, however a common
understanding among team members has to be established.</div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US">This was
one of the main aims of the test curation (“dry run”) that took place during
June 2013. A small set of documents (Text sections from EOL species pages, see <a href="http://environments-eol.blogspot.gr/2013/05/nice-days-during-visit-in-copenhagen-1.html" target="_blank">post</a></span><span lang="EN-US">) were delivered to all curators. Upon manually annotating these
documents curators collected as many
questions as possible around unclear and/or problematic annotation cases. Some
examples of the latter are: terms and/or synonyms missing from EnvO, words that
could be mapped to multiple EnvO terms, location names, nested environment
descriptive terms.</span></div>
<br />
<div class="MsoNormal">
<span lang="EN-US">A strategy employing
a set of flags to indicate such cases is now in place. The previously generated
the curation guideline document (see <a href="http://environments-eol.blogspot.gr/2013/03/march-2013-paving-ground-on-several.html" target="_blank">post</a>)</span> has been updated
accordingly and the production-level curation may now start.</div>
evangeloshttp://www.blogger.com/profile/03781515992542140689noreply@blogger.com0tag:blogger.com,1999:blog-6792233955350026448.post-13256225717704202382013-07-04T15:08:00.000+03:002013-07-04T15:08:31.103+03:00The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text @ PLOS ONE <div class="MsoNormal">
<span lang="EN-US">The sister
projects of <a href="http://species.jensenlab.org/" target="_blank">SPECIES </a>and <a href="http://organisms.jensenlab.org/" target="_blank">ORGANISMS</a> now published at <a href="http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0065390" target="_blank">PLOS ONE</a>, part of the <a href="http://www.ploscollections.org/article/browseIssue.action?issue=info:doi/10.1371/issue.pcol.v01.i14" target="_blank">PLOS Text Mining Collection</a>.<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US"><i>The SPECIES
and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names
in Text</i>. Pafilis E, Frankild SP, Fanini L, Faulwetter S, Pavloudi C, et al.
(2013) PLoS ONE 8(6): e65390. doi:10.1371/journal.pone.0065390<br />
</span><a href="http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0065390"><span lang="EN-US">http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0065390</span></a><span lang="EN-US"><o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US"><br /></span></div>
<div class="MsoNormal">
<span lang="EN-US">The
knowledge, skills and know-how gained through this work paved the ground for
ENVIRONMENTS. <o:p></o:p></span></div>
<br />
<div class="MsoNormal">
<span lang="EN-US">A big thank
you to the team, Evangelos<o:p></o:p></span></div>
evangeloshttp://www.blogger.com/profile/03781515992542140689noreply@blogger.com0tag:blogger.com,1999:blog-6792233955350026448.post-9033935551161996182013-06-03T13:08:00.001+03:002013-06-03T13:08:47.351+03:00May 2013: gearing up the corpus curation, mining names and synonyms from EOL content, following closing EnvO developments<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjY0w8SwVQGUN5aKojvV2l3YWtQvIXb0iEH-Ow3BXMpNUJuOFiKjRzXOGtxYFPTrdITxZxjQAK7U2aUhSn9HFp46hqhh3iucy-5VoXpQ8l1OfSc91b0hJ4BwuMNKyFgPCWEVRJas31_ygFc/s1600/ready-DSC_3349_AC.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="210" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjY0w8SwVQGUN5aKojvV2l3YWtQvIXb0iEH-Ow3BXMpNUJuOFiKjRzXOGtxYFPTrdITxZxjQAK7U2aUhSn9HFp46hqhh3iucy-5VoXpQ8l1OfSc91b0hJ4BwuMNKyFgPCWEVRJas31_ygFc/s320/ready-DSC_3349_AC.jpg" width="320" /></a></div>
A “beach sand” (ENVO:00002138) picture taken at the island of <a href="http://en.wikipedia.org/wiki/Chrysi_(island)" target="_blank">Chrisi</a>, a Natura 2000 site south-east of Crete, Greece. “Coarse beach sand” (ENVO:00002148) can be observed along with shells forming a “biogenous sediment” (ENVO:01000082); a unique feature of this island. Besides the “Coarse beach sand” are all types of sand included in the <a href="http://environmentontology.org/" target="_blank">Environment Ontology</a>? Can the Environments-EOL project assist in proposing terms, names and synonyms? (Image: CC BY-NC-SA)<br />
<br />
<div class="MsoNormal" style="text-align: justify;">
<span lang="EN-US">The Environments-EOL project is nearing its
main stages (corpus creation, tagger bench-marking, EOL annotation and taxa
characterization, to take place in Summer 2013). To this end a range of
preparatory tasks are being/have been conducted.<o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span lang="EN-US"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span lang="EN-US">May 2013 has seen a “dry-run” curation being
setup. A small set of document is being used for a trial curation (ongoing).
The manual and lengthy nature of a corpus generation dictates tests take place
before the main body of work commences. Via such a “dry-run” curators are
getting familiarized with the Environment Ontology as well as with relevant
browsing and searching tools. Additionally, questions are being raised and
discussions invoked on the exact context of terms to be annotated by the Environments-EOL
project.<o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span lang="EN-US"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span lang="EN-US">In parallel: early tests showed that the manual
addition of synonyms in the dictionary (see “Dictionary Generation in previous
<a href="http://environments-eol.blogspot.gr/2013/05/nice-days-during-visit-in-copenhagen-1.html" target="_blank">post</a>”) could improve the tagger performance. To facilitate such task
specialized EOL sections (e.g. <i>Habitat</i>)
have been analyzed (counting word frequency in non-tagged text segments). A priority list of terms to be considered was
derived. After manual inspection environment related words have been mapped to
EnvO terms and can now be added in the dictionary. The EOL records involved in
this training step have been excluded from the corpus generation (and
subsequently the software evaluation).<o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<span lang="EN-US">Last but not least: Environments-EOL is a project
tightly bound to the <a href="http://environmentontology.org/" target="_blank">Environment Ontology</a> community resource. Highlighting this
connection as well the projects’ dynamic nature: a thank you for the EnvO team’s
prompt and timely response in updating the "terrestrial biome"
hierarchy, comprising now more compact and fine grained terms (see <a href="http://environmentontology.org/home/news/terrestrialbiomesupdate" target="_blank">EnvO News Post</a>)<o:p></o:p></span></div>
evangeloshttp://www.blogger.com/profile/03781515992542140689noreply@blogger.com0tag:blogger.com,1999:blog-6792233955350026448.post-45315497215168096522013-05-03T10:45:00.001+03:002013-05-03T10:48:50.812+03:00April 2013: Visit to NNFCPR, Copenhagen, Denmark. Implementing main ENVIRONMENTS components<div class="" style="clear: both; text-align: left;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3ZtLnwElmNiGBaBdUpRish_DkGvtbwPd5qBrgI9AVQYJNtZYPuCIoxpMFSuFdRDLQ8MIoYRwaIgpTyASlzPUSSiBv6M7RO4zsjJ12vgmSIcyF2r4Tf0OQGO53NEfPiT-xIGupnoBkbPn9/s1600/ready-DSC_1835-6-cropped.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="193" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3ZtLnwElmNiGBaBdUpRish_DkGvtbwPd5qBrgI9AVQYJNtZYPuCIoxpMFSuFdRDLQ8MIoYRwaIgpTyASlzPUSSiBv6M7RO4zsjJ12vgmSIcyF2r4Tf0OQGO53NEfPiT-xIGupnoBkbPn9/s320/ready-DSC_1835-6-cropped.jpg" width="320" /></a>Nice days during the visit in Copenhagen (1-13 April 2013); while working on ENVIRONMENTS balloons showed up in the "air"(ENVO:00002005) (image taken at Frederiksberg, Copenhagen; <span style="background-color: white; color: #222222; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; line-height: 18px;">CC BY-NC-SA</span>)</div>
<div style="text-align: left;">
<br /></div>
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<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<span style="line-height: 115%;"><br /></span></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<span style="line-height: 115%;"><br /></span></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<span style="line-height: 115%;"><br /></span></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<span style="line-height: 115%;"><br /></span></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<span style="line-height: 115%;"><br /></span></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<span style="line-height: 115%;">April 2013 has been
mainly a travelling month. Besides the presentation of ENVIRONMENTS at GSC 15
(see <a href="http://environments-eol.blogspot.gr/2013/05/environmentsgsc15-april-22-24-nih.html" target="_blank">previous post</a>) a 2-week visit (made possible via the <a href="http://eol.org/info/52" target="_blank">EOL-RubensteinFellowship</a> support) at <a href="http://www.cpr.ku.dk/staff/staff_all/?id=343848&vis=medarbejder" target="_blank">Dr. Lars Juhl Jensen</a> and <a href="http://www.cpr.ku.dk/staff/385200/?id=276685&vis=medarbejder" target="_blank">Dr. Sune Frankild</a> premises
(<a href="http://www.cpr.ku.dk/" target="_blank">NNF-CPR</a>, Denmark) has resulted in the implementation of series of critical
tasks.<o:p></o:p></span></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<br /></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<b><span style="line-height: 115%;">ENVIRONMENTS Software Development: Dictionary generation<o:p></o:p></span></b></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<span style="line-height: 115%;">The name and synonym
information in the <a href="http://environmentontology.org/" target="_blank">Environment Ontology</a> (EnvO) resource has been assessed.
Based on them a dictionary has been generated mapping environment descriptive
terms to EnvO identifiers.<o:p></o:p></span></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<span style="line-height: 115%;"><br />
Where necessary, extra synonyms were generated capturing the variable ways EnvO
terms may be written in text. As an extension to previous work (see <a href="http://environments-eol.blogspot.gr/2013/03/march-2013-paving-ground-on-several.html" target="_blank">post</a>) the generation
of adjectives (e.g. coast – coastal) or plural forms (e.g. brackish water – brackish
waters) has been included.<o:p></o:p></span></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<br /></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<span style="line-height: 115%;">Species names and
anatomy terms present in EnvO, also described in other taxonomies/ontologies,
were not included in the dictionary. Moreover food names were excluded as they
may give rise to out-of-context text mining results.<o:p></o:p></span></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<br /></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<b><span style="line-height: 115%;">Encyclopedia of Life textual component retrieval and processing<o:p></o:p></span></b></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<span style="line-height: 115%;">The EOL API has been
used to retrieve sections (“subjects” in the EOL terminology) for every taxon
such as: <i>TaxonBiology</i>, <i>Description</i>, <i>Biology</i>, <i>Distribution</i>,
<i>Habitat</i> and more)<o:p></o:p></span></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<br /></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<span style="line-height: 115%;">The EOL Taxa text
components have been downloaded in the JSON format. A parser has been
development that collected the selected sections only and converts the text in
a ENVIRONMENTS compatible format (e.g. removes HTML tags and convers UTF8
characters to ASCII)<o:p></o:p></span></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<br /></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<b><span style="line-height: 115%;">ENVIRONMENTS Software Development: Stopword curation<o:p></o:p></span></b></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<span style="line-height: 115%;">Local text
repositories of PubMed and EOL were processed with ENVIRONMENTS (using an
early-version dictionary). The most frequently tagged terms were inspected
manually in-text. Those that were found, most of the times, in a context other
than describing an environment were added in a “stopword” list. “well”,
“sping”, “range” are a few such examples. Such terms would have caused a high number
of false positive matches. This “stopword” list is a mechanism against such
phenomenon; its terms will be excluded from the analysis.<o:p></o:p></span></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<br /></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<b><span style="line-height: 115%;">ENVIRONMENTS corpus preparation<o:p></o:p></span></b></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<span style="line-height: 115%;">A major component of
this project is the creation of a manually annotated corpus (gold standard).<o:p></o:p></span></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<span style="line-height: 115%;">Such a corpus
comprises a set of documents in which environment descriptors have been
manually identified and mapped to unique identifiers in community resources
(e.g. the Environment Ontology terms). By comparing the manual annotations with
software predicted tags the accuracy of environment descriptive term
identification software can be evaluated.<o:p></o:p></span></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<br /></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<span style="line-height: 115%;">Two basic requirements
that such a corpus must meet is:<o:p></o:p></span></div>
<div class="MsoNormal" style="line-height: 115%; margin-left: 54.0pt; mso-list: l0 level1 lfo1; mso-outline-level: 1; text-align: justify; text-indent: -18.0pt; text-justify: inter-ideograph;">
<!--[if !supportLists]--><span style="line-height: 115%;">a.<span style="font-family: 'Times New Roman'; line-height: normal;">
</span></span><!--[endif]--><span style="line-height: 115%;">to be comprehensive i.e. to
contain text that refer to diverse types of environments<o:p></o:p></span></div>
<div class="MsoNormal" style="line-height: 115%; margin-left: 54.0pt; mso-list: l0 level1 lfo1; mso-outline-level: 1; text-align: justify; text-indent: -18.0pt; text-justify: inter-ideograph;">
<!--[if !supportLists]--><span style="line-height: 115%;">b.<span style="font-family: 'Times New Roman'; line-height: normal;"> </span></span><span style="line-height: 115%;">to contain a minimum number
of terms per document that would make the manual annotation feasible in a
pragmatic time frame<o:p></o:p></span></div>
<div class="MsoNormal" style="line-height: 115%; mso-outline-level: 1; text-align: justify; text-justify: inter-ideograph;">
<br /></div>
<span style="font-family: 'Times New Roman';">Having such criteria on mind several <i>in silico</i> experiments were
conducted to collect documents from EOL. The basic components of a pipeline
have been implemented to randomly select EOL pages of species belonging to
certain higher-level taxa for the corpus generation. The next step is to
further define such higher-level taxa. Could randomly picking bird species
EOL-Pages (members of class Aves) result in a set of documents mentioning
different types of environments ? </span><!--EndFragment--><br />
<div style="text-align: left;">
<br /></div>
<div style="text-align: left;">
<br /></div>
evangeloshttp://www.blogger.com/profile/03781515992542140689noreply@blogger.com0tag:blogger.com,1999:blog-6792233955350026448.post-48929166438667270702013-05-02T14:26:00.000+03:002013-05-02T14:26:48.551+03:00ENVIRONMENTS@GSC15, April 22-24, NIH, Washington DC<div class="" style="clear: both; text-align: left;">
<span style="font-family: Times, Times New Roman, serif;">ENVIRONMENTS was presented (talk, poster) last week (April 22-24), at the <a href="http://15th%20genomic%20standards%20consortium%20meeting%20%28gsc15%29/" target="_blank">15th Genomic Standards Consortium meeting (GSC15)</a> (NIH, Washington DC). Very good and creative feedback was received. A PDF version of the poster is available <a href="http://epafilis.info/posters/2013-04-ENVIRONMENTS-GSC15-Pafilis.pdf" target="_blank">here</a> (15MB). <span style="background-color: white; line-height: 16px;">A special edition of the Standards in Genomic Sciences (SIGS) Journal with all the accepted abstract of the meeting can be found</span> <a href="http://www.standardsingenomics.org/index.php/sigen/article/view/sigs.4167847/pdf" target="_blank">in this link</a>.</span></div>
<div class="" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjncezQlWgAS2Kvt9dMc_89K9ttzGLAp9yNQ2eQURdHoUtwHqQiC2XRiCTlQO_emcMr96G0StmSkSLGctTX698BV8klXF3FuvB-fsqECo3kGhXQowjcFmNFGyDvZvwiI59diZOcAxb8gBgJ/s1600/ready-DSC_2131.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="209" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjncezQlWgAS2Kvt9dMc_89K9ttzGLAp9yNQ2eQURdHoUtwHqQiC2XRiCTlQO_emcMr96G0StmSkSLGctTX698BV8klXF3FuvB-fsqECo3kGhXQowjcFmNFGyDvZvwiI59diZOcAxb8gBgJ/s320/ready-DSC_2131.jpg" width="320" /></a></div>
"River bank" (ENVO:00000143) of the Potomac River. Picture taken from a location <a href="https://maps.google.com/maps?q=38.885822,-77.049136&z=15" target="_blank">close to the Lincoln Memorial</a> (CC BY-NC-SA).evangeloshttp://www.blogger.com/profile/03781515992542140689noreply@blogger.com0tag:blogger.com,1999:blog-6792233955350026448.post-52356062063577581462013-03-30T18:01:00.003+02:002013-03-30T18:01:39.735+02:00March 2013: paving the ground on several project aspects
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<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;">March 2013 has
largely been a preparatory month paving the ground for follow-up tasks. <o:p></o:p></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;"><br /></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;">The main task of
ENVIRONMENTS-EOL is the<b> identification of environment descriptive terms</b>, such
as <i>terrestrial</i>, <i>aquatic</i>, <i>lagoon</i>, <i>coral reef</i>, <b>in EOL Pages</b>. <o:p></o:p></span></span></div>
<div class="MsoNormal" style="text-align: justify; text-indent: -0.55pt;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;"><br /></span></span></div>
<div class="MsoNormal" style="text-align: justify; text-indent: -0.55pt;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;">To materialize this aim one needs: on the one hand to
collect the text bits of the EOL Taxon Pages containing environmental context
information that could be mined, and on the other hand a piece of software
capable of identifying environment descriptors in these text bits.<o:p></o:p></span></span></div>
<div class="MsoNormal" style="text-align: justify; text-indent: -0.55pt;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;"><br /></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;">For the former
scripts have been written employing the <a href="http://eol.org/api/" target="_blank">EOL API</a> to
retrieve sections (“subjects” in the <a href="http://eol.org/info/98" target="_blank">EOL terminology</a>) of
every taxon such as: <i>TaxonBiology</i>, <i>Description</i>, <i>Biology</i>, <i>Distribution</i>, <i>Habitat</i> and more. EOL’s adherence to the
standards (e.g. to the <a href="http://wiki.tdwg.org/twiki/bin/view/SPM/WebHome" target="_blank">Species Profile Model</a>)
has significantly assisted such procedure. In active collaboration with the EOL
Developer Team the text retrieval will be optimized further.<o:p></o:p></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;"><br /></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;">For the latter a
prototype tagger, ENVIRONMENTS, has been compiled. ENVIRONMENTS is based on
<a href="http://species.jensenlab.org/" target="_blank">SPECIES</a>,
a tagger capable of identifying organism names in text using a dictionary-based
approach (Main developers: <a href="http://larsjuhljensen.wordpress.com/about/" target="_blank">Lars</a>, <a href="http://www.linkedin.com/pub/sune-pletscher-frankild/1/35b/5a3" target="_blank">Sune</a>). <o:p></o:p></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;"><br /></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;">ENVIRONMENTS is
capable of identifying environment descriptive terms by looking up words in the
text against a dictionary of environment descriptors. A prototype dictionary
has been created according to the naming information available in the <a href="http://environmentontology.org/" target="_blank">Environment Ontology (EnvO)</a>.
<o:p></o:p></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;"><br /></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;">EnvO is a
community resource offering a controlled, structured vocabulary for ecosystems
types (“biomes”), environmental materials, and environmental features (e.g.
habitats). <o:p></o:p></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;"><br /></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;">The different
types and sources of EnvO term names and synonyms have been explored and the more precise
ones have been selected. <o:p></o:p></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;"><br /></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;">Further steps
include actions that will improve the match between the way terms are written
in the text and the way they exist in EnvO e.g. by automatically adding the plural
form of the terms in the dictionary. <o:p></o:p></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;"><br /></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;">Another important
aspect of the ENVIRONMENTS-EOL project is the <b>evaluation of the accuracy</b> of the
environment descriptive term identification. To this end, the creation of a
manually annotated corpus (gold standard) is necessary. <o:p></o:p></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;"><br /></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;">Such a corpus
comprises a set of documents in which environment descriptors have been
manually identified and mapped to unique identifiers in community resources
(e.g. the </span><span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-font-family: Calibri; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-hansi-font-family: Calibri;">Environment Ontology terms</span><span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;">). <o:p></o:p></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;"><br /></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;">Once such a gold
standard corpus is in place, its manually annotated tags can be compared with
those predicted by named entity recognition software. In this way the accuracy
of the latter can be calculated.<o:p></o:p></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;"><br /></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;">Reflecting on the
experience gained from the creation of an manually annotated corpus of
taxonomic mentions (<a href="http://species.jensenlab.org/" target="_blank">S800 corpus</a>) and on
the pilot annotation of environment descriptive terms in <a href="http://pubmed.org/" target="_blank">PubMed</a> abstracts (Thanks to <a href="http://www.marbigen.org/users/christina-pavloudi" target="_blank">Christina</a> for her support) a guideline document is now in place.<o:p></o:p></span></span></div>
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<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;"><span style="font-family: inherit;"><br /></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-bidi-font-family: Arial;">Such a document
will provide the cutator team (<a href="http://www.marbigen.org/users/katerina-vasileiadou" target="_blank">Aikaterini</a>, <a href="http://www.marbigen.org/users/christina-pavloudi" target="_blank">Christina</a>, <a href="http://epafilis.info/" target="_blank">Evangelos</a>, <a href="http://www.mpi-bremen.de/en/Page6679.html" target="_blank">Julia</a>,
<a href="http://www.marbigen.org/users/lucia-fanini" target="_blank">Lucia</a>, <a href="http://www.marbigen.org/users/sarah-faulwetter" target="_blank">Sarah</a>) a </span><span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-font-family: Calibri; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-hansi-font-family: Calibri;">guide with examples of documents in which environment
descriptors have been manually identified and mapped to the corresponding EnvO terms. <o:p></o:p></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="background: white; color: #222222; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-font-family: Calibri; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-hansi-font-family: Calibri;"><span style="font-family: inherit;"><br /></span></span></div>
<span style="background-color: white; background-position: initial initial; background-repeat: initial initial; color: #222222; font-size: 12pt; line-height: 115%;"><div style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: 12pt; line-height: 115%;">Additionally, this guide elaborates on the main categories employed by
EnvO, presents </span><span style="font-size: 12pt; line-height: 115%;">web-search tools
dedicated to EnvO and text editors to facilitate the annotation task, discusses
issues already spotted e.g. how to handle environmental descriptors currently
missing from EnvO, and enlists <i>hints and tips</i> that could assist the tedious
task of the manual annotation.</span></span></div>
</span>evangeloshttp://www.blogger.com/profile/03781515992542140689noreply@blogger.com0tag:blogger.com,1999:blog-6792233955350026448.post-29207518574819857512013-03-30T17:16:00.001+02:002013-03-30T17:23:31.243+02:00Welcome to ENVIRONMENTS-EOL, a few words on the project<!--[if gte mso 9]><xml>
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Large-scale biological questions such as retrieving all species belonging to a specific group (e.g. Invertebrates), associated with a particular environment (e.g. coral reefs) and occurring in a specific region (e.g. Indo-Pacific Ocean) require the combinatorial analysis of information available in a diverse range of resources.<br />
<br />
Taxonomy information along with species occurrence data (stored in centralized biodiversity resources) can be combined to this end. To fill-in, however, the missing pieces of the puzzle, input based on knowledge existing in the scientific literature is required.<br />
<br />
The Encyclopedia of Life (http://eol.org) by collecting the available information about a given taxon is a <i>one-stop-shop</i> that greatly facilitates answering such questions.<br />
<div>
<br />
The identification of environment descriptive terms, such as terrestrial, aquatic, lagoon, coral reef, in EOL text can drive the mining of species environmental context information.<br />
<br />
ENVIRONMENTS is an open source tool supporting such identification. It does so by looking up words in the text against a dictionary of environment descriptors.<br />
<br />
The Environment Ontology (http://environmentontology.org/), a community resource offering a controlled, structured vocabulary for ecosystems types (“biomes”), environmental materials, and environmental features (e.g. habitats), serves as the source of names and synonyms for the creation of such a dictionary.<br />
<br />
While the environment descriptive term identification is the core of the project, tasks such as:</div>
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<li><span style="background-color: white; color: #222222; line-height: 115%; text-indent: -18pt;">the evaluation of the accuracy of the method (via the creation of a
manually annotated, gold standard, corpus)</span></li>
<li><span style="background-color: white; color: #222222; line-height: 115%; text-indent: -18pt;">the assessment of the contribution of the different EOL page sections to
the environmental context mining</span></li>
<li><span style="background-color: white; color: #222222; line-height: 115%; text-indent: -18pt;">the consideration of taxonomy and species occurrence information</span></li>
<li><span style="background-color: white; color: #222222; line-height: 115%; text-indent: -18pt;">the generation of summarizing visualizations supporting comparisons and
biological inferences</span></li>
</ul>
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<br />
are equally important in answering large-scale biological questions like the one in the beginning of this post.<br />
<br />
What lies ahead is a challenging project comprising a diverse range of tasks. As response, a team of researchers with diverse backgrounds (molecular biology, microbial ecology, data analysis, text/literature mining, bioinformatics, statistics and more) has been put together to this end.<br />
<br />
Through the posts in this blog, it will, hopefully, be possible to keep you up-to-date with the project developments, provide you with more information on the tasks involved, present to you and bring you in contact with the people contributing to the different tasks.<br />
<br />
Stay tuned!</div>
<!--EndFragment-->evangeloshttp://www.blogger.com/profile/03781515992542140689noreply@blogger.com0tag:blogger.com,1999:blog-6792233955350026448.post-41036350773147798712013-01-30T16:02:00.000+02:002013-01-30T16:02:08.098+02:00The ENVIRONMENTS - EOL project is about to take off<span style="background-color: white; font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif; line-height: 20px;">Please find below an excerpt from the Encyclopedia of Life press release for the 2013 EOL Rubenstein Fellows. It announces ENVIRONMENTS as well as other six projects, all aiming at employing EOL contents to answer large scale biological questions. The complete press release can be found here: </span><a href="http://eol.org/info/485" style="background-color: white; font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif; line-height: 20px;">http://eol.org/info/485</a><span style="background-color: white; font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif; line-height: 20px;">.</span><br />
<div>
<span style="background-color: white;"><span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;"><br /></span></span></div>
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<span style="background-color: white;"><span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif; font-size: large;">The Encyclopedia of Life Announces 2013 Rubenstein Fellows</span></span></h1>
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<em><span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">Seven teams of biologists, information scientists and software developers to collaborate on Big Data research through EOL</span></em></h4>
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<span style="background-color: white;"><span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;"><em>Washington, D.C. - January 28, 2013</em> - The Encyclopedia of Life (EOL) is pleased to announce the winners of the 2013 EOL Rubenstein Research Fellowship awards. The seven awardees will lead research teams seeking to answer novel research questions not readily addressable without the extensive data resources served by EOL. EOL Rubenstein Research Fellow awards are made possible by a generous gift to EOL by David M. Rubenstein through the Smithsonian Institution’s National Museum of Natural History. .......... </span></span><span style="background-color: white; font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif;">(</span><b style="background-color: white; font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif;">Read more</b><span style="background-color: white; font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif;">: </span><span style="background-color: white; font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif; font-size: small;"> <a href="http://eol.org/info/485">http://eol.org/info/485</a> </span><span style="background-color: white; font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif;">)</span></div>
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