IB2011
International Botanical Congress 2011 & BHL-Australia meetings
Melbourne
Freeland arrives: AA7356, 22 July, 8:20am
Freeland departs: AA7349, 30 July, 9:35am
July 25
IBC2011
XVIII International Botanical Congress
T06: Systematics, Evolution, Biogeography & Biodiversity Info
SYM136: Informatics Tools For The Semantic Enhancement Of Taxonomic Literature
Organiser: Mr Christopher Freeland - Missouri Botanical Garden
1600 - 1800, Room 204
In recent years there has been a radical change regarding the availability of digital taxonomic literature, including both contemporary publications as well as legacy texts. Projects like the Biodiversity Heritage Library and Plazi, among others, have digitized and made available a wealth of scientific texts that support the online review of protologues and species descriptions, as well as other traditional uses of taxonomic literature. While this advent has been exceptionally useful for systematists and has undoubtedly expedited the taxonomic process, making this literature available in digital form opens the possibility for new secondary analyses that are impossible to accomplish with traditional printed texts. Scholars working in natural language processing, semantic markup, and other efforts within biodiversity informatics are developing new tools for the use of these digitized materials beyond the traditional human-paper interaction. These new human-machine and machine-machine interactions are facilitated by emerging software tools that enhance the traditional scientific publication, turning these texts into rich, interactive datasets that can be incorporated into other analyses. This seminar will explore the motivation behind the digitization of historic taxonomic literature as well as the contemporary publication of new treatments and texts, and how those texts can be enhanced by these new informatics tools. Panelists will review the progress made through both legacy digitization as well as contemporary publication, and special focus will be given to scholars who are currently building the informatics tools that help provide fine-grained, semantic description of traditional taxonomic texts. Using these novel algorithms and applications, presenters will detail how taxonomic publications can be enhanced through semantic description and how these enriched texts can expedite the taxonomic process and facilitate the open sharing of organismal data to a global audience of scholars and students.
July 27
BHL-Australia meeting
Museum Victoria
Agenda:
US agenda items:
- Code sharing & Codevelopment
- How to revise US app with AUS UI/UX code
- Availability of UI/UX designers for ongoing enhancements
- How to implement new features
- Evaluation / comparison of BHL-US/BHL-AUS from users
- Use same questions from BHL-EU eval?
- Linked data
- How do we approach something like http://data.bnf.fr or BL's new data portal? BHL is data-rich & mostly structured.
- Scanning
- - Jul 19, 2011 What institutions are planning to scan content for BHL-AU? Is it just the Museum Victoria?
- Is there a plan for the content that will be scanned?
- Will the content be scanned using an Internet Archive Scribe or will the content be scanned via other means and uploaded to IA/loaded to the BHL-AU collection in some other way? If so, how can BHL-US get the BHL-AU content into its collection?
- What are Australia's copyright restrictions?
- Will the institutions doing the scanning check the BHL portal before they send content for scanning?
- Would the scanning institutions be willing to participate in our scanning workflow tools?
- Has the BHL-AU been in discussions with Boris Jacob of BHL-E regarding the GRIB?
- BHL-US/AU Portal Synchronization
- - Jul 20, 2011 How often is the BHL-AU collection updated? (looks like it might be daily?)
- If we perform any edits to the BHLUS portal metadata and etc., such as merging two titles together into a single record, how/when will this get reflected if at all in the BHL-AU?
July 28
IBC2011
Botanical Names Services: New ways to compare and link “apples to apples.”
Well before Linnaeus arrived on the scene, humans used names for organisms to compare “apples to apples.” In modern times, paper has been the medium for botanical name information storage and retrieval, typically using index cards. More recently, databases have become the digital replacement for index cards with public access through web applications. Today, these databases can have service layers built on them which present an exciting phase shift for connectivity amongst disparate data resources fostering communication and discovery. Although botanists were quick to realize the potential of the digital era and build tools to manage the vast factual knowledge associated with botanical names and their applications, we still face a considerable task in sorting out a legacy of name use (and abuse). However, there is now ever mounting demand for digital botanical name information for incorporation in tools and resources both within and outside our domain. Botanical names allow discovery and comparison between data resources from taxonomic and ecological to genetic and phylogenetic. Newer semantic web technologies enable richer means for linking amongst taxon names, taxon concepts, and information about those taxa. Further, name data available as controlled vocabularies substantially improves data quality in collection databases and other applications. The traditional nomenclatural databases, including the International Plant Names Index (IPNI), Index Fungorum, and Algaebase, all have web-accessible information on names available and are heavily referenced. Additionally, some of these databases have services built on them allowing linking between “Malus domestica Borkh. to Malus domestica Borkh.” data resources. This linking requires globally unique identifiers and a resolution service to insure consistency and versioning. Recently, biodiversity informaticians working with the natural science community have focused efforts on a generic layer cake of services with the three key layers including a global list of names, a nomenclatural interpretation of these names, and taxonomic concepts based on these names. With the basal Global Names Index (globalnames.org) accomplished, current focus is on the middle nomenclatural layer, as the next component of an open Global Names Architecture (for more detail see: gnapartnership.org) which supports the linking of name usages. The connections made possible through name services lower the barrier to extending the current nomenclators toward implementation of a names registration system. When new names or revisions are entered in the registration database they become immediately linked and discoverable to compare with other concepts. This registration system coupled with electronic publishing have the potential to fundamentally shift the way taxonomists work and are currently being implemented in the zoological and mycological domains. To complement this shift, several workbench tools are under development to speed the taxonomic process of discovery, revision and publication. These tools rely on names to discover and accumulate knowledge from various botanical resources including connection to names in marked-up literature accomplished using new parsing tools. This symposium will update participants on the botanical name resources, infrastructure, and tools in various stages of development leading us into a brave new world of interconnected data.
lipscombb Jul 19, 2011 What institutions are planning to scan content for BHL-AU? Is it just the Museum Victoria?