Special Libraries Associatin

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Information about Special Libraries Associatin

Published on July 28, 2008

Author: drielinger

Source: slideshare.net

Biodiversity Informatics Evolving in the Biological Sciences National Geographic News, 05/21/08 Tuatara Libraries ?????

Evolving in the Biological Sciences

encyclopedists Nomencaltor Animalia “ Seahorse” Conrad Gesner 1570

Nomencaltor Animalia

“ Seahorse”

Conrad Gesner 1570

encyclopedists Denis Diderot – 1751 Encyclopedie Precursor to Sematic Web Thinking “ So great is the power of linkage and order that even the mundane becomes important” DD Encyclopedia… the word signifies unity of knowledge

Denis Diderot – 1751

Encyclopedie

Precursor to Sematic Web Thinking

“ So great is the power of linkage and order that even the mundane becomes important” DD

Encyclopedia… the word signifies unity of knowledge

Serine Molecule Biodiversity Heritage Library Synthesis Center Field Museum Informatics Marine Biological Laboratory & MOBOT Education & Outreach Smithsonian/Harvard Secretariat Smithsonian

“ The launch of the Encyclopedia of Life will have a profound and creative effect in science… this effort will lay out new directions for research in Every branch of biology: E.O. Wilson

“ The launch of the Encyclopedia of Life will have a profound and creative effect in science… this effort will lay out new directions for research in Every branch of biology:

E.O. Wilson

HOW to build this enterprise Recognition of the importance of all types of material in all formats Recognition that a single set of rules, a single mechanism, a single type of discovery tool cannot accomplish everything Recognition that entities other than libraries can, want to, and will contribute to the information-finding construct Recognition that all of us are part of the whole, and that it is an interdependent relationship, not the relationship of an all-powerful mother ship (LC) to a fleet of shuttle craft Recognition that the way we have made decisions in the past may no longer serve us well

Recognition of the importance of all types of material in all formats

Recognition that a single set of rules, a single mechanism, a single type of discovery tool cannot accomplish everything

Recognition that entities other than libraries can, want to, and will contribute to the information-finding construct

Recognition that all of us are part of the whole, and that it is an interdependent relationship, not the relationship of an all-powerful mother ship (LC) to a fleet of shuttle craft

Recognition that the way we have made decisions in the past may no longer serve us well

Collaborative Tree of Life distributed semantic Biodiversity Heritage Library ever evolving TED all information Synthesis Center Oh wow! SpeciesBase ClassificationBank Education and Outreach ANTS index MacArthur Foundation taxonomic intelligence modular software communal ownership user defined AvenueA | Razorfish OBIS MBL free visualization images WorkBench sounds phylogeny web 2.0 names-based infrastructure Atlas of Living Australia February 2008 Google Marine Biological Laboratory all species Smithsonian FISHBASE Harvard Field Museum Tree of Life E. O. Wilson aggregation / mashup EDIT ScratchPad widgets MOBOT NHM AMNH NYBotancial Sloan Foundation GBIF llison l NameBank videos National Geographic any classification TDWG/BIS

Collaborative Tree of Life distributed semantic Biodiversity Heritage Library ever evolving TED all information Synthesis Center Oh wow! SpeciesBase ClassificationBank Education and Outreach ANTS index MacArthur Foundation taxonomic intelligence modular software communal ownership user defined AvenueA | Razorfish OBIS MBL free visualization images WorkBench sounds phylogeny web 2.0 names-based infrastructure Atlas of Living Australia February 2008 Google Marine Biological Laboratory all species Smithsonian FISHBASE Harvard Field Museum Tree of Life E. O. Wilson aggregation / mashup EDIT ScratchPad widgets MOBOT NHM AMNH NYBotancial Sloan Foundation GBIF llison l NameBank videos National Geographic any classification TDWG/BIS

Biodiversity Heritage Library Mission: Provide Open Access to Biodiversity Literature Goals: Digitize the core published literature on biodiversity and put on the Web Agree on approaches with the global taxonomic community, rights holders and others

Digitize the core published literature on biodiversity and put on the Web

Agree on approaches with the global taxonomic community, rights holders and others

 

 

BHL

Internet Archive Scribe: Boston

How big is the Biodiversity domain? Over 5.4 million books dating back to 1469 800,000 monographs 40,000 journal titles (12,5000 current) 50% pre-1923

Over 5.4 million books dating back to 1469

800,000 monographs

40,000 journal titles (12,5000 current)

50% pre-1923

Classes of Texts Public Domain – pre 1923 Non-profit society journals Post 1923 monographs/journals Monographs without © renewals Commercial journals with permission

Public Domain – pre 1923

Non-profit society journals

Post 1923 monographs/journals

Monographs without © renewals

Commercial journals with permission

Where are we? 5,000,000 scanned pages 13,000 volumes BHL Portal Sloan, MacArthur, Moore Foundation- funding 49 full run journals

5,000,000 scanned pages

13,000 volumes

BHL Portal

Sloan, MacArthur, Moore Foundation- funding

49 full run journals

Carolus Linnaeus, “father of modern taxonomy” “ Who Knowth not the name Knowth not the subject” Linnaeus, 1737, Critica Botanica n 210. Royal Science Academy of Sweden, portrait

“ Who Knowth not the name

Knowth not the subject”

Linnaeus, 1737,

Critica Botanica n 210.

“ All accumulated information of a species is tied to a scientific name, a name that serves as a link between what has been learned in the past and what we today add to the body of knowledge.” ~ Grimaldi& Engel, 2005, Evolution of the Insects

Information about named groups (taxa) of organisms (taxon-related information) Extends back at least 1000 years In books, journals, surveys, museum specimens, herbaria…. In many languages and is distributed From T.E. Glover, The Fishes of Southwestern Japan, c.1870

Information about named groups (taxa) of organisms (taxon-related information)

Extends back at least 1000 years

In books, journals, surveys, museum specimens, herbaria….

In many languages and is distributed

The challenge for contemporary DIGITAL libraries Goal: Use one name to find the content for all names

Names – the only universal metadata for Biology Names offer a logical way to search for and index content Names annotate data objects All names annotate all data objects A compilation of all names ever used is the foundation of a universal index for biology or for a semantic web for biology

Names annotate data objects

All names annotate all data objects

A compilation of all names ever used is the foundation of a universal index for biology or for a semantic web for biology

Who is affected by these problems? Libraries Publishers Museums Federal Agencies

Serious challenges in federated environments One organism 4 scientific names 4 maps We want one map

Reconciliation – linking alternative names for the same organism A query initiated with any name, can be expanded to all names and will unify data associated with each

 

All names & all Classifications ClassificationBank Alternative names reconciled Similar names disambiguated Exploit hierarchies to browse and search, build a comprehensive classification Improve performance with federated systems Read documents, web sites, databases and taxonomically indexing the content Create a unified portal to information about organisms on the internet Taxonomic intelligence is the inclusion of taxonomic practices, skills and knowledge within informatics services to manage information about organisms

All names & all Classifications ClassificationBank

Alternative names reconciled

Similar names disambiguated

Exploit hierarchies to browse and search, build a comprehensive classification

Improve performance with federated systems

Read documents, web sites, databases and taxonomically indexing the content

Create a unified portal to information about organisms on the internet

data from various sources may be merged red dots on the map link back to the website that provided the geographical co-ordinates Specimen distribution data from remote sources

data from various sources may be merged

red dots on the map link back to the website that provided the geographical

co-ordinates

Taxonomic Intelligence Lexicon of Scientific Names Reconciliation and Disambiguation Hierarchical Inclusion Integration into Information Retrieval Linkage to Other Data Types (e.g., Molecular, Morphological, Phenotype)

Lexicon of Scientific Names

Reconciliation and Disambiguation

Hierarchical Inclusion

Integration into Information Retrieval

Linkage to Other Data Types (e.g., Molecular, Morphological, Phenotype)

uBio 10.7 Million+ Name Strings Reconciliation Groups http:// www.ubio.org FIND IT – scientific name recognition algorithm Training and improving algorithm

10.7 Million+ Name Strings

Reconciliation Groups

http:// www.ubio.org

FIND IT – scientific name recognition algorithm

Training and improving algorithm

uBioRSS Taxonomically Intelligent RSS Feed Aggregator

MBL WHOI Library – Woods Hole authors’ publications

MBL WHOI Library – Woods Hole species publications

Taxonomically intelligent scientific text parsing

 

 

Search Browse

Search

Browse

Taxonomic intelligence works miracles It will benefit any initiative that uses distributed and heterogeneous information about biology Distributed content on the same species can be drawn together because different names will be standardized through reconciliation We can read documents, find names, catalog and taxonomically index documents Produce a framework around which we can organize and assemble remote and local content

It will benefit any initiative that uses distributed and heterogeneous information about biology

Distributed content on the same species can be drawn together because different names will be standardized through reconciliation

We can read documents, find names, catalog and taxonomically index documents

Produce a framework around which we can organize and assemble remote and local content

Acknowledgments Catherine Norton Patrick Leary David Remsen Diane Rielinger David Patterson Neil Sarkar Gerald Weissmann A.W. Mellon Foundation Alfred P. Sloan Foundation John D. & Catherine T. MacArthur Foundation Internet Archive Christopher Freeland Tom Garnett Martin Kalfatovic Graham Higley BHL & EOL Teams

 

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