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TDWG - SDD Oct 20, 2002 Search & Browsing Beyond Keys over Standards TDWG General Presentation Sessions P. Bryan Heidorn October 20, 2002
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TDWG - SDD Oct 20, 2002 Search & Browsing Why Structured Data Description? Interactive Keys Search Authoring –Structure –Vocabulary
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TDWG - SDD Oct 20, 2002 Search & Browsing Interactive Keys Interchange of information between programs. –E.g. DeltaAccess and LucID
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TDWG - SDD Oct 20, 2002 Search & Browsing Interchange LucID Delta Access SDD
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TDWG - SDD Oct 20, 2002 Search & Browsing Federation (very difficult) Key
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TDWG - SDD Oct 20, 2002 Search & Browsing SDD Supports text Hybid text and defined Characteristics Leaf characters may be defined while the flower characteristics are no. Reuse of Flora for Search Automatic Markup and Classification Still can help people with ID
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TDWG - SDD Oct 20, 2002 Search & Browsing Search Warning that this is not a SDD standard but an SDD inspired implementation from the Australia discussion. SDD supports hybrid text and character encoded documents How do you search a hybrid or partly encoded document? Some fields based on full text, some based on DB search
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TDWG - SDD Oct 20, 2002 Search & Browsing Search Biological Information Browsing Environment – (http://www.biobrowser.org)http://www.biobrowser.org Search subparts of descriptions –Find the blue flowers not blue mountains –Flowers: …. Blue –Location: Blue Mountains Search Part Hierarchy
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TDWG - SDD Oct 20, 2002 Search & Browsing Marking Structure Taxon files ML FNA Structured files Fragment Unlabeled fragments Unlabeled fragments Unlabeled fragments Unlabeled fragments Manual Labeling Training Set Training Set Training Set Training Set Labeled Fragments Reassembly Labeled Fragments Labeled Fragments Labeled Fragments
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TDWG - SDD Oct 20, 2002 Search & Browsing Classification = Markup Support Vector Machine (Hong Cui) Any distance measure Clustering / Classification
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TDWG - SDD Oct 20, 2002 Search & Browsing Converting Documents to XML FNA Composite files Perl FNA Genus files FNA Genus files FNA Genus files FNA Genus files FNA HTML files FNA HTML files FNA HTML files FNA Species files FNA Family files FNA Family files FNA Family files FNA Family files
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TDWG - SDD Oct 20, 2002 Search & Browsing Simple FNA.dtd
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TDWG - SDD Oct 20, 2002 Search & Browsing - http://www.canis.uiuc.edu/~webvibe/fna_images/plates/I24900139.html 3. Abies grandis (Douglas ex D. Don in Lambert) Lindley, Penny Cycl. 1: 30. 1833 - Grand fir, lowland white fir, sapin grandissime Pinus grandis Douglas ex D. Don in Lambert, Descr. Pinus [ed. 3] 2: unnumbered page between 144 and 145. 1832 Trees to 75m; trunk to 1.55m diam.; crown conic, in age round, with age …. brown, often with reddish periderm visible in furrows bounded by hard flat opposite, light gray, sessile, apex rounded; scales ca. 2--2.5 ´ 2--2.5cm, densely … bracts included. Seeds 6--8 ´ 3--4mm, body tan; wing. Moist, coastal coniferous forests and mountain slopes; 0-- 1500m; B.C.; Calif., Idaho, Mont., Oreg., Wash.
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TDWG - SDD Oct 20, 2002 Search & Browsing Structured Index Swish-ex Structured Index FNA Structured files
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TDWG - SDD Oct 20, 2002 Search & Browsing Swish-ex Based on Berkeley swish-e XML support added Hierarchical Key Structure Related to DTD
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TDWG - SDD Oct 20, 2002 Search & Browsing FNA Nomenclature 00 Morphology 01 Distribution 10 References 11 Plant 01|000 Bark 01|001 Leaf 0|010 Others.. 0|011… Size 0|010|000 Margin 0|010|001 Apex 0|010|010 Petiole 0|010|011
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TDWG - SDD Oct 20, 2002 Search & Browsing XML Query Interface Add the query string to a tree node, for example COMMAN NAME = dog-face
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TDWG - SDD Oct 20, 2002 Search & Browsing The query propagates to the text field, and it is ready to be sent to Server/database
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TDWG - SDD Oct 20, 2002 Search & Browsing The results are fetched back from the database, and show up on screen
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TDWG - SDD Oct 20, 2002 Search & Browsing Query results are displayed in BIBE as documents, the relationships between key terms are currently mapped as shown below.
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TDWG - SDD Oct 20, 2002 Search & Browsing Processing Thesaurus and Definition Taxon files Thesaurus Processor Taxon Files With Definitions Structured Thesaurus Glossary files
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TDWG - SDD Oct 20, 2002 Search & Browsing Thesaurus Automatic Query Expansion Vocabulary switching Novice to expert (acorn) becomes (acorn or glans) (roundish) becomes (obovate or roundish) (Illinois) becomes (ill or illinois)
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TDWG - SDD Oct 20, 2002 Search & Browsing Inline Definitions
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TDWG - SDD Oct 20, 2002 Search & Browsing Clicking on a set of documents reveals a list of files. By choosing a file, users investigate text and images from The Flora of North America.
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TDWG - SDD Oct 20, 2002 Search & Browsing Clicking on a set of documents reveals a list of files. By choosing a file, users investigate text and images from The Flora of North America.
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TDWG - SDD Oct 20, 2002 Search & Browsing Extracting Adjectives from unstructured document sections
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TDWG - SDD Oct 20, 2002 Search & Browsing Outline Run FNA files through Brill tagger (p- o-s) to: tokenize tag the files, i.e. mark parts of speech: nouns, verbs, adjectives, adverbs Modify Brill lexicon (Wall Street Journal-based) to fit FNA files Run an extraction program through the tagged files Marija Markovic, Adjective Extraction
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TDWG - SDD Oct 20, 2002 Search & Browsing Why Adjectives Useful (with Nouns) for retrieval Complex plant morphology sections around 30 fields in FNA XML files Essential for other compounds art, definitions, links
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TDWG - SDD Oct 20, 2002 Search & Browsing Examples conspicuous foliaceous #-keeled #-locular #-ribbed #-ridged #-veined #-flowered #-loculed #-lobed #-dentate #-merous #-lobed V-shaped abaxial apical aromatic axillary basal bell-shaped bisexual blue-violet canary central chasmogamous cleistogamous club-shaped cream-brown cuneate-obovoid cylindric distal ellipsoid elliptic equal fetid
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TDWG - SDD Oct 20, 2002 Search & Browsing Authoring OpenKey Project
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TDWG - SDD Oct 20, 2002 Search & Browsing Participants University of Illinois –Grad. School of Library and Information Science –Herbarium Illinois Natural History Survey and Herbarium University of North Carolina –School of Information and Library Science North Carolina Botanical Garden
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TDWG - SDD Oct 20, 2002 Search & Browsing Participants University of Illinois –Grad. School of Library and Information Science Lesley Deem, Xiao Hu, Jing Wu, –Herbarium, Dave Siegler Illinois Natural History Survey and Herbarium, Ken Robertson, Michael Jeffords University of North Carolina –School of Information and Library Science Jane Greenberg, Evaline Daniels –North Carolina Botanical Garden Bob White
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TDWG - SDD Oct 20, 2002 Search & Browsing Project Objectives Develop a Distributed Search and Identification Support –Character Lists, Taxonomic descriptions Develop Distributed Taxonomic Descriptions –Text, in situ images, ID images, herbarium sheets Highlight Museum Holdings Audience: Citizen Scientists, Schools, Scientists
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TDWG - SDD Oct 20, 2002 Search & Browsing Addressed Issues Encountered with Collaboration Inability to produce a final character matrix –Introduction of new characteristics Differing definitions of “like” terms. –Need to be defined in context –Can not proliferate (reuse)
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TDWG - SDD Oct 20, 2002 Search & Browsing Distributed Properties Image and / or Character States need not be harvested until access time No “change” or “new” log in http unlike Open Archive Property definitions but not references may change without notification New instances may be added without notification
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TDWG - SDD Oct 20, 2002 Search & Browsing Schemata Taxon Description Characteristic Character Value Character Image Contributor
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TDWG - SDD Oct 20, 2002 Search & Browsing Component of Description Taxon Characteristic CharacterImages CharacterState *Contributor Contributor ID ImageID RefKey:CharacteristicID: Value RefKey:CharacteristicID ValueID *Contributor may be used for all objects
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TDWG - SDD Oct 20, 2002 Search & Browsing Decomposition and Distribution The selection of characteristics and their values can be distributed No need to have definitive set Potential for reuse in new taxonomic descriptions Potential for differing definitions but in well defined space
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TDWG - SDD Oct 20, 2002 Search & Browsing Taxonomic Description Project Definition (ala Autralia 2002) Identification – Taxon Species Echinacea pallida (Nutt.) Nutt Pale purple coneflower
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TDWG - SDD Oct 20, 2002 Search & Browsing Taxon (Australia, 2002) (type should be in Characteristic definitions)
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TDWG - SDD Oct 20, 2002 Search & Browsing (Not SDD but SDD inspired) Preamble….. (State)
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TDWG - SDD Oct 20, 2002 Search & Browsing Character State Leaf Shape lanceolate http://www.isrl.uiuc.edu/~openkey/demo/lanceolate.xml http://www.isrl.uiuc.edu/~openkey/demo/lanceolate 2.xml Lance-shaped; much longer than wide, with the widest point below the middle. oval elliptic-lanceolate
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TDWG - SDD Oct 20, 2002 Search & Browsing Federation of Characters and States Key States Shared Character Lists Key Characters
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TDWG - SDD Oct 20, 2002 Search & Browsing Character Sharing UI Database UNC Database Federated Database OA Server OA Harvester Polyclave Server The world PV.XML DELTA Access LuCID
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TDWG - SDD Oct 20, 2002 Search & Browsing This is the values of a "character" or "characteristic" of an item, the value of a property. For example the legal values for /leaves/leaf_arrangement are alternate, opposite, basal,whorled and cauline Character Schema Element
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TDWG - SDD Oct 20, 2002 Search & Browsing Image Schema
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TDWG - SDD Oct 20, 2002 Search & Browsing PlantCharacteristic Leaf-Stem Alternate Leaf Arrangements - Alternate http://soldev.isrl.uiuc.edu/~webvibe/PlantChara cters/images/AlternateLeaf.jpg Illinois Natural History Survey
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TDWG - SDD Oct 20, 2002 Search & Browsing PlantCharacteristic Observing, Photographing, and Collecting Plants. Illinois Natural History Survey Circular 55, 1980 January 29, 2002 Another Image pbheidorn P. Bryan Heidorn University of Illinois, GSLIS
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TDWG - SDD Oct 20, 2002 Search & Browsing Conclusion Many aspects of traditional printed flora can be used to enhance the functionality of electronic flora. Full-text Search and ID are related tasks.
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