Mining+Biodiversity

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The Mining Biodiversity project is an international collaboration between the University of Manchester's National Centre for Text Mining (UK), Missouri Botanical Garden's Center for Biodiversity informatics (USA), Dalhousie University’s Big Data Analytics Institute and Ryerson University's Social Medial Lab (Canada).

Goal:
Its overarching goal is to transform the Biodiversity Heritage Library (BHL), a digital library of over 40 million pages of taxonomic literature, into a next-generation social digital resource to facilitate the collaborative study and discussion of legacy biodiversity documents by a worldwide community. Furthermore, it aims to raise awareness of the changes in biodiversity over time in the general public.

As the BHL holds an immense amount of biodiversity documents, the project will leverage text mining and visualization methods, crowdsourcing and social media to effectively serve its users with semantically enriched content. The resulting digital resource will provide fully interlinked and indexed access to the full content of BHL library documents, via semantically enhanced, interactive browsing and searching capabilities, allowing users to precisely and conveniently locate the information of interest to them.

This project was made possible in part by the [|Institute of Museum and Library Services] [LG-00-14-04-0032-14]

**Project Team (USA)**
Missouri Botanical Garden
 * William Ulate, Senior Project Coordinator, Center for Biodiversity Informatics, P.I.
 * Trish Rose-Sandler, Data Project Coordinator, Center for Biodiversity Informatics
 * Mike Lichtenberg, Programmer, Center for Biodiversity Informatics

Collaborators:
 * Jennifer Hammock, Marine Theme Coordinator, EOL
 * Grace Costantino, BHL Outreach and Communication Manager

Project Narrative
 

Project Management, Dissemination, and Communications Plan
 

Architecture

 * = [[image:MiBIO Architecture.png width="431" height="260" link="file:biodivlib/MiBIO Architecture.png"]] ||= [[image:MiBio Diagram.png width="300" height="244" caption="Figure 2. MiBio Software Modules Diagram" link="file:MiBio Diagram.png"]] ||

**Reports**
> > >
 * Narrative of Activities Performed for the Mining Biodiversity Project b y Grace Costantino, BHL Outreach and Communication Manager and Jen Hammock, EOL Programs Coordinator: [[file:BHLandEOL_Narrative_MiBio_Final.pdf]]
 * BHL Twitter Network Analysis: [[file:BHL Audience Analysis Netlytic.pptx]]
 * Altmetric Report of BHL mentions across the web June 2014-January 2015 [[file:Altmetric Report BHL Mentions Jan 2015.csv]]
 * Survey on Enhancements to BHL Search Functionalities [[file:BHLSurveyResults.pdf]]
 * Mining Biodiversity Project Final Report / White Paper for JISC by NaCTeM
 * Flower names in the vocabulary recognized by the BHLQueryExpansion website available at [[file:flowers.txt]]
 * Final Performance Report for [[file:Final Performance Report LG-00-14-0032-14.pdf]]

Presentations/Papers
> Unlocking biodiversity knowledge through Text Mining and Crowdsourced Tagging of Legacy Literature during the TDWG 2014 Annual Conference. Elmia Congress Centre. Jönköping, Sweden. October 27-31, 2014. See presentation here.
 * As part of the Symposium "Semantics for Biodiversity Science - An Interoperability Frontier", William Ulate presented "Real Use Cases for Semantic Information from the Mining Biodiversity Project" at the [|2016 Biodiversity Informatics Standards (TDWG) Annual Meeting] in Santa Clara de San Carlos, Alajuela, Costa Rica. December 5th, 2016. See the recorded presentation here.
 * As part of the member presentation Expanding Access to Biodiversity Literature, W.Ulate introduced the Mining Biodiversity Project and asked for feedback from the group for the Search User Interface doing Query Expansion using Term Inventory. CBHL 2016 Annual Meeting at the Cleveland Botanical Garden. Ohio, USA. May. 26, 2016. See presentation here.
 * Presented at the [|2016 "Round Three" Digging into Data Challenge Conference] in Glasgow, UK on Jan. 28, 2016 (tweets on #DiDGlasgow). See presentation here.
 * As part of the Symposium, William Ulate presented Unlocking knowledge in biodiversity legacy literature through automatic semantic metadata extraction in the TDWG 2015 Annual Conference. Windsor Hotel. Nairobi, Kenya. September 29, 2015. See presentation here.
 * [|Mining the History of Medicine and Mining Biodiversity], Dr. Sophia Ananiadou, Professor at the University of Manchester, Director of the National Centre for Text Mining (NaCTeM) and the project's P.I. presents on NaCTeM's work (MiBio explanation starts at 4:05).
 * As part of the Symposium Expanding the Usefulness of Literature in Sustaining Biodiversity, William Ulate presented

**Social Media**
>> >>
 * == Full-Text Search enabled  ==
 * Mar.26, 2017 by William Ulate (@WUlate): [|Celebrate #GesnerDay: read detailed 58p. Memoir (1841) http://biodiversitylibrary.org/page/18063871 @BioDivLibrary @rmathematicus @SILibraries @HistSciArt @AMNH]
 * May.25, 2016 by William Ulate (@WUlate): On the etymology of the word "elephant" and the origins of the word "tamarind", the "Indian date"
 * Mar. 24, 2016 by BHL Australia (@bhl_au): Historic Easter Hunt: can you help us find the 1st illustration of a Bilby? The earliest we know of is Kreff (1858)
 * Mar. 22, 2016 by NHM Oology (@NHM_Oology): Making cushion to display Emperor Penguin egg collected by Edward Wilson on Discovery Expedition in 1903 @NHM_Tring
 * Mar. 21, 2016 by William Ulate (@WUlate): Dr. Gates (1971): "when I came 2 @mobotgarden, the word ecology was unknown, today it's 1 of the most popular words" http://www.biodiversitylibrary.org/page/6780068#page/128/mode/2up
 * Mar. 17, 2016 by Dr Meghan Ferriter (‏@MeghaninMotion): @SiobhanLeachman As promised: Rubens Peale via @ArchivesAmerArt! https://transcription.si.edu/project/7060
 * Mar. 17, 2016 by William Ulate ( @WUlate): Shamrock is Wood sorrel (Oxalis Acetosella), white clover (Trifolium repens) or water cress? http://biodiversitylibrary.org/page/20975474
 * Mar. 17, 2016 by William Ulate (@WUlate): Why drinking on St. Patrick's Day (Mar.17th)? Read Proc. of the American Phil. Soc. v.XXVI 1889 N.130 @BioDivLibrary http://www.biodiversitylibrary.org/page/18900181
 * Mar. 17, 2016 by William Ulate (@WUlate): @MoBot_Research @mobotgarden "[Mr.Shaw] a lover of plants 4 themselves and a believer in their influence molding desirable traits in humans"
 * Mar. 11, 2016 by Sandra Knapp (@SandyKnapp): "Collected by who? Zambia 1934..... Stuck again!! @KewDC"
 * Mar. 10, 2016 by NHM Library&Archives (@NHM_Library): "The drawings of Olivia Tonge (blog) http://goo.gl/hcnAnL #InternationalWomensDay #IWD2016"
 * Disqus Comments Feature:
 * Mar. 04, 2016 by BHL (@BioDivLibrary): "How are ppl using comments in BHL? To link #transcriptions & #fieldnotes http://ow.ly/Z1T12"
 * Mar. 04, 2016 by BHL (@BioDivLibrary): "How are ppl using comments in BHL? To highlight type specimens http://ow.ly/Z1Udb "
 * Mar. 04, 2016 by BHL (@BioDivLibrary): "Learn how you can add comments to BHL here: http://ow.ly/Z5qzX See all comments here: http://ow.ly/Z5qNg"
 * Feb. 26, 2016 by BHL (@BioDivLibrary): "Loved reading how BHL comment feature can support #citsci activities too!"
 * Altmetrics & MyTweeps Application:
 * Jan. 28, 2016 by Catherine Grout (@CatherineGrout): "See the widget the Biodiversity Heritage Library made with Altmetrics to understand your Twitter followers @mytweeps.com #DiDGlasgow" https://twitter.com/CatherineGrout/status/692710249845919744
 * Jan. 28, 2016 by Samantha B McGregor (@sammibmcg): " [|My Tweeps app from Mining Biodiversity team lets you find out what your Twitter followers are saying: http://mytweeps.com #DiDGlasgow] " https://twitter.com/sammibmcg/status/692710507082600448

** Initial Grant Award **

 * Round Three (2013) Competition Awards announcement. @http://diggingintodata.org/awards/2013
 * TransAtlantic Digging into Data Challenge 2013 Winners announced. @http://diggingintodata.org/awards/2013/news/transatlantic-digging-data-challenge-2013-winners-announced
 * $5.1 Million Awarded for Delving into Big Humanities and Social Science Data. @https://www.imls.gov/news-events/news-releases/51-million-awarded-delving-big-humanities-and-social-science-data

Related

 * Mining Biodiversity Website.
 * Mining Biodiversity Wiki.
 * Mining Biodiversity: Enriching Biodiversity Heritage with Text Mining and Social Media.
 * Sharing Biodiversity Heritage through Social Media: Mining Biodiversity’s “Big-Data”
 * Digging into Data Challenge Phase 3: Mining Biodiversity

** Contact Us **
include page="include_pagefooter" Unlocking knowledge in biodiversity legacy literature through automatic semantic metadata extraction
 * For more information please contact the project's Principal Investigator (USA), William Ulate-Rodríguez at +1 (314) 577-9473 x6398 or william.ulate@mobot.org