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Biodiversity Informatics: Mining Untapped Resources

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  • Figure 1. Bar graphs depicting phylogenetically corrected mean differences between species groups for two climate change response traits: the correlation coefficient between first flowering day and annual spring temperature for the time period of 1888–1902 (A; i.e., flowering time tracking ), and the shift in mean first flowering day during the period exhibiting the most dramatic increase in mean annual temperature, from 1900–2006 (B; i.e., flowering time shift ).
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  • Mblwhoil2010 Heidorn

    1. 1. Biodiversity Informatics: Mining Untapped Resources February 8, 2010 Marine Biology Laboratory and Woods Hole Oceanographic Institute Library P. Bryan Heidorn Director University of Arizona School of Information Resources and Library Science
    2. 2. <ul><li>Biodiversity Information Diversity </li></ul><ul><li>Wrongly perceived as bioinformatics and two sets of base-pairs </li></ul><ul><li>Biodiversity = Data Complexity </li></ul><ul><ul><ul><li>Requires new information theory and cyberinfrastructure </li></ul></ul></ul><ul><ul><ul><li>Largely unrecognized as an interesting problem are in computer science </li></ul></ul></ul>
    3. 3. The problem <ul><li>Information is not in accessible </li></ul><ul><li>Computer Science, Information Science and Technology has not addressed the problem </li></ul>
    4. 4. <ul><li>Dark data is the data that we know is/was there but we can’t see it. </li></ul>Hubble Space Telescope composite image &quot;ring&quot; of dark matter in the galaxy cluster Cl 0024+17
    5. 5. Naive View of Science Data GenBank PDB f ( x )= ax k + o ( x k ) Power Law of Science Data f ( x )= ax k + o ( x k )| X<.20 Data Volume Science Projects and Initiatives
    6. 6. Does NSF’s Data Follow the Power Law? I do not know but if $1 = X bytes…..
    7. 7. 20-80 Rule The small are big! Total Grants 9347 $2,137,636,716 20% 80% Number Grants 1869 7478 Total Dollars $1,199,088,125 $938,548,595 Range $6,892,810-$350,000 $350,000- $831
    8. 8. Related Ideas <ul><li>John Porter: </li></ul><ul><ul><li>Deep verses Wide databases </li></ul></ul><ul><li>Swanson: </li></ul><ul><ul><li>Undiscovered Public Knowledge </li></ul></ul><ul><li>Science Commons: </li></ul><ul><ul><li>Big Verses Small science </li></ul></ul>
    9. 9. Where to find dark data <ul><li>Literature/Biodiversity Heritage Library </li></ul><ul><li>Museum Specimens </li></ul><ul><li>Field notes </li></ul><ul><li>(Un)Experimental data sets </li></ul><ul><li>Citizen Observations </li></ul>
    10. 10. What is dark data good for? <ul><li>Ecological Niche Modeling </li></ul><ul><li>Climate Change niche change prediction </li></ul><ul><li>Taxonomic Name Resolution </li></ul><ul><li>Literature Search Support </li></ul><ul><ul><li>Taxonomic intelligence </li></ul></ul><ul><ul><li>Key-like – character searching </li></ul></ul><ul><li>Phenology and Phenology change </li></ul><ul><li>Food-web / trophic level </li></ul>
    11. 11. <ul><li>Global Biodiversity Information Facility has 100s of millions of specimen records </li></ul>Animalia
    12. 12. <ul><li>Global Earth Observation System of Systems (GEOSS) and Historical Data </li></ul><ul><li>Unpublished observations of flowing time in Concord by Alfred Hosmer from 1888 to 1902 </li></ul><ul><li>Photographs of Flowers </li></ul><ul><li>Blue Hill Observatory meteorological data </li></ul><ul><li>Richard B. Primack, Abraham J. Miller-Rushing, Daniel Primack, and Sharda Mukunda (2007). Using Photographs to Show the Effects of Climate Change on Flowering Time. Arnoldia 65(1), p2-9. </li></ul>Historical and Current Data need to be in a form that allow for use and reuse.
    13. 13. <ul><li>Willis CG, Ruhfel BR, Primack RB, Miller-Rushing AJ, Losos JB, et al. 2010 Favorable Climate Change Response Explains Non-Native Species' Success in Thoreau's Woods. PLoS ONE 5(1): e8878. doi:10.1371/journal.pone.0008878 </li></ul>Favorable Climate Change Response Explains Non-Native Species’ Success in Thoreau’s Woods
    14. 14. The problem with Museum Specimens <ul><ul><li>>1 Billion Natural History Specimens </li></ul></ul><ul><ul><li>Collected over 250 years / many languages </li></ul></ul><ul><ul><li>No publishing standards </li></ul></ul><ul><ul><li>Near infinite classes </li></ul></ul><ul><ul><ul><li>Your high school teacher lied </li></ul></ul></ul><ul><ul><li>6 min / label * 1B labels = 100M hours </li></ul></ul><ul><ul><li>Saving 1 min = 16.7 Million hours </li></ul></ul><ul><ul><li>$10/hr = $167,000,000 </li></ul></ul><ul><ul><li>1/4790 of U.S. deregulation financial bailout </li></ul></ul>
    15. 15. Natural History Specimens
    16. 16. Automatic Metadata Extraction (Darwin Core) From Museum Specimen Labels … <co> Curtis, </co><hdlc> North American Pl </hdlc><cnl> No.</cnl><cn> 503*</cn> <gn> Polygala</gn><sp> ambigua,</sp><sa> Nutt.,</sa><val> var.</val> <hb> Coral soil,</hb><lc> Cudjoe Key, South Florida. </lc><col> Legit</col><co> A. H. Curtiss.</co><dt>February</dt>… With Qin Wei, Univ of Illinois
    17. 17. S ample records
    18. 18. Sample OCR Output <ul><li>Yale University Herbarium </li></ul><ul><li>~r-^&quot;&quot;&quot; r-n------- </li></ul><ul><li>YU.001300 </li></ul><ul><li>Curtisb, North American Pl </li></ul><ul><li>C^o.nr r^-n </li></ul><ul><li>ANTS, </li></ul><ul><li>No. 503* &quot;^ </li></ul><ul><li>Polygala ambigna, Nntt., var. </li></ul><ul><li>Coral soil, Cudjoe Key, South Florida. </li></ul><ul><li>Legit A. H. Curtiss. </li></ul>
    19. 19. Label Labels <ul><li>bc - barcode </li></ul><ul><li>bt - barcode text </li></ul><ul><li>cm - common/colloquial name </li></ul><ul><li>cn - collection number </li></ul><ul><li>co - collector </li></ul><ul><li>cd - collection date </li></ul><ul><li>fm - family name </li></ul><ul><li>ft - footer info </li></ul>
    20. 20. Label Labels <ul><li>gn - genus name </li></ul><ul><li>hd - header info </li></ul><ul><li>in - infra name </li></ul><ul><li>ina - infra name author </li></ul><ul><li>lc - location </li></ul><ul><li>pd - plant description </li></ul><ul><li>sa - scientific name author </li></ul><ul><li>sp - species name </li></ul>
    21. 21. Example Training Record <ul><li><?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;?> </li></ul><ul><li><?oxygen RNGSchema=&quot;http://www3.isrl.uiuc.edu/~TeleNature/Herbis/semanticrelax.rng&quot; type=&quot;xml&quot;?> </li></ul><ul><li><labeldata> </li></ul><ul><li><bt>Yale University Herbarium </li></ul><ul><li></bt><ns> ~r-^&quot;&quot;&quot; r-n------</ns><bc> YU.001300 </li></ul><ul><li></bc><co cc=&quot;Curtiss&quot; > Curtisb, </co><hdlc cc=&quot;North American Plants&quot; > North American Pl </li></ul><ul><li></hdlc><ns>C^o.nr r^-n </li></ul><ul><li>ANTS,</ns> </li></ul><ul><li><cnl> No.</cnl><cn> 503*</cn><ns> &quot;^</ns> </li></ul><ul><li><gn> Polygala</gn><sp> ambigna,</sp><sa> Nntt.,</sa><val> var.</val> </li></ul><ul><li><hb> Coral soil,</hb><lc> Cudjoe Key, South Florida. </li></ul><ul><li></lc><col> Legit</col><co> A. H. Curtiss.</co> </li></ul><ul><li></labeldata> </li></ul>
    22. 22. Supervised Learning Framework Gold Classified Labels Training Phase Application Phase Machine Learner Unclassified Labels Segmented Text Silver Classified Labels Segmentation Machine Classifier Unclassified Labels Human Editing Trained Model
    23. 23. Herbis Experimental Data <ul><li>295 marked up records </li></ul><ul><li>74 label states </li></ul><ul><li>5-fold cross-validation </li></ul>
    24. 24. Performances of NB and HMM
    25. 25. Element Identifiers
    26. 26. Improved Performance With Field Element Identifiers
    27. 28. Learning w/ pre categorization Gold Labels Machine Learner Model n Classified Labels Class 1 Labels Categor- ization Class 2 Labels Class n Labels Machine Learner Machine Learner Model 2 Model 1 Class 1 Labels Categor- ization Class 2 Labels Class n Labels Machine Classification Machine Classification Machine Classification Classified Labels Classified Labels Unclassified Labels
    28. 29. FIG. 5. Improved Performance of Specialist Model Specialist100 Curtiss VS 100 General Iterations 0 200 0 100 Specialist Random
    29. 30. P. Bryan Heidorn 1 , Hong Zhang 1 , Eugene Chung 2 and BGWG 1 Graduate School of Library and Information Science, 2 Linguistics, University of Illinois Machine Learning in BioGeomancer’s Locality Specification SPNHC & NSCA 2006
    30. 31. BioGeomancer Working Group (BGWG) http://203.202.1.217/bgwebsite/index.html <ul><li>Worldwide collaboration of natural history and geospatial data experts </li></ul><ul><li>Maximize the quality and quantity of biodiversity data that can be mapped </li></ul><ul><li>Support of scientific research, planning, conservation, and management </li></ul><ul><li>Promotes discussion, manages geospatial data and data standards, and develops software tools in support of this mission </li></ul>
    31. 32. Participants
    32. 33. Example Locality Types Record # Specification of Location Locality Type 43 dario 7 mi wnw of; RIO VIEJO FOH; F 86 near Aleutian Islands; S of Amukta Pass NF; FH 100 INDIAN CREEK, 11 MI. W HWY 160 P; POH 109 TIESMA RD, 1.5 MI NW EDGEWATER; OFF LAKE MICHIGAN R P; FOH; NP 160 WALTMAN, 9 MI N, 2.5 MI W OF FOO 181 0.4 mi N Collinston on LA 138 FPOH 204 Seward Peninsula; vic. Bluff, S coast F; NF; FS
    33. 35. <ul><ul><li>JOH : offset from a junction at heading </li></ul></ul><ul><ul><li>e.g. 0.5 mi. W Sandhill and Hagadorn Roads </li></ul></ul><ul><ul><li>[ FEATURE [ CITY = Sandhill ]] </li></ul></ul><ul><ul><li>[ FEATURE [ ROAD= Hagadorn Roads ]] </li></ul></ul><ul><ul><li>OFFSET VALUE = 0.5 </li></ul></ul><ul><ul><li> DIRECTION= W </li></ul></ul><ul><ul><li> UNIT = mile </li></ul></ul><ul><ul><li> JUNCITON [ FEATURE [ CITY = Sandhill ]] </li></ul></ul><ul><ul><li> [ FEATURE [ ROAD= Hagadorn Roads ]] </li></ul></ul>FRAME
    34. 36. Xiaoya Tang and P. Bryan Heidorn <ul><li>Different vocabularies in queries and documents </li></ul>Long leaves … ... Leaves 20–75, many-ranked, spreading and recurved, not twisted, gray-green (rarely variegated with linear cream stripes), to 1 m  1.5–3.5 cm, ……... Inflorescences: ……. spikes very laxly 6–11-flowered, erect to spreading, 2–3-pinnate, ……. User query Description of leaf Length in texts
    35. 37. Information Extraction From FNA Templates for useful information Extraction Rules Structured information Leaf_Shape obovate Leaf_Shape orbiculate Blade_Dimension 3—9 x 3—8 cm ………… .. ………… .. Original documents ……… .. Leaf blade obovate to nearly orbiculate, 3--9 × 3--8 cm, leathery, base obtuse to broadly cuneate, margins flat, coarsely and often irregularly doubly serrate to nearly dentate, . ……………… Knowledge bases … .. PartBlade: Leaf blade Blades blade …… Pattern:: * <PartBlade> ' ' <leafShape> * ( <leafShape> ) ',' * Output:: leaf {leafShape $1} Pattern:: * <PartBlade> * ', ' ( <Range> ' ' * <LengUnit> ) * <PartBase> Output:: leaf {bladeDimension $1} User log analysis Leaf_Shape Leaf_Margin Leaf_Apex    Leaf_Base Blade_Dimension … .. … .. 
    36. 38. Results – System Performance NT: number of tasks accomplished in total NTH: number of tasks accomplished per hour TSR: task success rate SSR: search success rate NSST: number of searches to accomplish a task TST: time spent to accomplish a task NDVST: number of documents viewed to accomplish a task Group NT NTH TSR SSR NSST TST NDVST SEARFA 6.75 8.078 0.860 0.210 4.779 338.8 11.16 SEARF 4.50 3.598 0.568 0.053 9.584 435.2 14.75 Sig.(ANOVA) 0.005 0.005 0.000 0.011 0.000 0.72 0.162
    37. 39. Education Programs <ul><li>Biological Information Specialist </li></ul><ul><li>Concentration in Data Curation (MSLIS) </li></ul><ul><li>Certificate of Advanced Study in Data Curation </li></ul><ul><li>Information and professional education in biodiversity informatics </li></ul>
    38. 40. Biological Information Specialists <ul><li>At present: </li></ul><ul><li>Biologists at all degree levels self-trained in information technology </li></ul><ul><li>Information technologists at all degree levels self-trained in biology </li></ul><ul><ul><ul><li>(both with gaps in knowledge for many months, years) </li></ul></ul></ul><ul><li>Differing roles of BIS in large and small </li></ul>
    39. 41. Master of Science in Biological Informatics <ul><li>Degree Program began September 2007 </li></ul><ul><li>Part of campus-wide bioinformatics masters program </li></ul><ul><li>NSF/CISE/IIS, Education Research and Curriculum Development, 0534567 (Palmer, PI) </li></ul><ul><li>Combines Biology, Bioinformatics, Computer Science core with LIS courses </li></ul>
    40. 42. What does a BIS need to know? <ul><li>Biological training and interest in solving biological research problems </li></ul><ul><li>Information skills </li></ul><ul><li>Evaluation and implementation of information systems: user based assessment and continual quality improvement for the development of tools that work and are used. </li></ul><ul><li>Information acquisition, management, and dissemination: development of digital libraries, data archives, institutional repositories, and related tools. </li></ul><ul><li>Information organization and integration: ontology development, structuring information for optimal use and sharing, and standards development. </li></ul>
    41. 43. UIUC bioinformatics core coursework <ul><li>Cross-disciplinary course distribution requirement </li></ul><ul><ul><ul><li>Bioinformatics: Computing in Molecular Biology Algorithms in Bioinformatics Principles of Systematics </li></ul></ul></ul><ul><ul><ul><li>Computer Science: Algorithms Database Systems </li></ul></ul></ul><ul><ul><ul><li>Biology: Human Genetics Introductory Biochemistry Macromolecular Modeling </li></ul></ul></ul>
    42. 44. Sample of existing LIS courses <ul><li>Information Organization and Knowledge Representation </li></ul><ul><li>LIS 551 Interfaces to Information Systems </li></ul><ul><li>LIS 590DM Document Modeling </li></ul><ul><li>LIS 590RO Representing and Organizing Information Resources </li></ul><ul><li>LIS590ON Ontologies in Natural Science </li></ul><ul><li>Information Resources, Uses and users </li></ul><ul><li>LIS 503 Use and Users of Information </li></ul><ul><li>LIS 522 Information Sources in the Sciences </li></ul><ul><li>LIS 590TR Information Transfer and Collaboration in Science </li></ul><ul><li>Information Systems </li></ul><ul><li>LIS 456 Information Storage and Retrieval </li></ul><ul><li>LIS 509 Building Digital Libraries </li></ul><ul><li>LIS 566 Architecture of Network Information Systems </li></ul><ul><li>LIS 590EP Electronic Publishing </li></ul><ul><li>Disciplinary Focus </li></ul><ul><li>LIS 530B Health Sciences Information Services and Resources </li></ul><ul><li>LIS 590HI Healthcare Informatics (Healthcare Infrastructure) </li></ul><ul><li>LIS 590EI/BDI Ecological Informatics (Biodiversity Informatics) </li></ul>
    43. 45. MSLIS Data Curation Concentration <ul><li>Data Curation Educational Program (DCEP) </li></ul><ul><ul><li>IMLS – Laura Bush 21 st Century Librarian Program, </li></ul></ul><ul><ul><ul><li>RE-05-06-0036-06 (Heidorn, PI) </li></ul></ul></ul><ul><li>Students with the DC concentration will be trained to add value to data and promote sharing across labs and disciplinary specializations </li></ul>
    44. 46. New research directions <ul><li>IGERT </li></ul><ul><li>Interactive Keys? </li></ul><ul><li>Focus on integration and scale </li></ul><ul><li>Informatics infrastructure as competitive edge </li></ul><ul><ul><li>Sample areas of development </li></ul></ul><ul><ul><li>Landinformatics Group </li></ul></ul><ul><ul><ul><li>Atmospheric science, hydrology, nutrient balance, carbon cycle, ecology, agronomy </li></ul></ul></ul><ul><li>BREC </li></ul><ul><li>Focus on data integration problems across larger range of sciences </li></ul>
    45. 47. Example Service <ul><li>JRS Biodiversity Foundation </li></ul><ul><li>National Science Foundation </li></ul><ul><li>Taxonomic Database Working Group </li></ul>
    46. 48. JRS Biodiversity Foundation <ul><li>History: The J.R.S. Biodiversity Foundation was created in January 2004 when the nonprofit publishing company, BIOSIS was sold to Thomson Scientific. The proceeds from that sale were applied to fund an endowment and create a new grant-making foundation. </li></ul><ul><li>Mission: The Foundation defined a mission within the field of biodiversity: To enhance knowledge and promote the understanding of biological diversity for the benefit and sustainability of life on earth. </li></ul><ul><li>JRS Biodiversity Foundation </li></ul>
    47. 49. JRS Biodiversity Foundation <ul><li>Scope: To further advance the Foundation’s mission a scope was developed as: Interdisciplinary activities primarily carried out via collaborations in developing countries and economies in transition. The Foundation Board of Trustees has expressed a particular interest in focusing its grant-making in Africa. </li></ul><ul><li>Strategic Interest: Within those bounds a considered course has been chosen to: Advance projects, or parts of biodiversity projects that focus on: (1) collecting data, (2) aggregating, synthesizing, publishing data, and making it more widely available to potential end users, and (3) interpreting and gaining insight from data to inform policy-makers </li></ul>
    48. 50. <ul><li>Grant Making: about $2M/yr </li></ul><ul><ul><li>Animal Tracking in South Africa </li></ul></ul><ul><ul><li>Specimen Digitization in Ghana </li></ul></ul><ul><ul><li>Social Value of Conservation in Peru </li></ul></ul><ul><ul><li>Species Pages and BD Education in Costa Rica </li></ul></ul><ul><ul><li>Niche Modeling in Brazil </li></ul></ul><ul><ul><li>Travel Grants </li></ul></ul><ul><ul><li>Lake Victoria Data Library Project in Tanzania, Uganda and Kenya </li></ul></ul><ul><li>e-Biosphere ‘09 </li></ul>JRS Biodiversity Foundation
    49. 51. National Science Foundation <ul><li>Advances in Biological Informatics </li></ul><ul><li>Data Working Group </li></ul><ul><li>Plant Science Cyberinfrastructure Center (iPlant) </li></ul><ul><li>Cyber-enabled Discovery and Innovation </li></ul><ul><li>Hiring Committees </li></ul><ul><li>Division of Biological Infrastructure Planning </li></ul>
    50. 54. ALISE and AMISE <ul><li>Historical Analysis of 100 Years back </li></ul><ul><li>Use Library and Museum Resources </li></ul><ul><li>Prepare for Blitz </li></ul><ul><ul><li>K-12 / Graduate / Hobbyist </li></ul></ul><ul><li>BioDiversity Blitz </li></ul><ul><li>Build time capsule for Bicentenial in Cultural Heritage Institutions **Libraries and Museums** </li></ul>

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