1. Integration of the UC Davis Biological Collections Data via a Web Portal [A Pilot Project]
Project Goals
To develop a Web Portal allowing better & more use of the information stored in our biological datasets.
Use current & developing computer technologies allowing for this access & data integration.
Develop methods and Web tools to simplify dataset integration among our biological datasets.
Fulfill & meet the needs of our user community needing access to our datasets.

2. WEB UC Davis Biological Collections webservice: DiGIR
How will this work?
-Darwin Core (provider)
-Complete datasets
Registry returns matching web service
Query UDDI Registry
Query Web services
UDDI registry for Web Services
DiGIR
Go Get species: Lycopersicon esculentum
Data/WEB Stream…
WEB
Darwin Core (providers)

3. Concepts for integrating the museum datasets
Use the Dublin Core Metadata & Darwin Core Profile as the integrating elements for all the museum datasets.
Develop dynamic methods to “mine” these above “core” data from the individual museum datasets.
Use an enterprise database system as a repository for the integrated museum datasets and to “serve out” the data.
Develop a Web service for distributing the dataset queries in response to Web requests.
Develop a Web Portal interface using the Web service.
Develop methods to “Serve out” the data attributes that are not part of Dublin/Darwin core elements.

4. Biological Collection summaries
 Approx. holdings
  Database system 
  Approx. records
Herbarium 
250,000+ (200+ Types)
  ACCESS 
  15,000
TGRC (Tomato Genetics Resource Center) 
1,200+ Wild species (4,500 genetic accessions)
  4,500
Phaff (Yeast collection) 
6,000+ yeast strains
  FileMaker 
  6,500
Wildlife and Fisheries 
12,000+
  12,000
Anthropology 
500+(bones/fossils mainly)
  300
Conservatory (Botanical) 
3,000+
  ACCESS/FileMaker 
  5,600
* Other database systems yet to work with:
Bohart (Entomology)
6,000,000+
  FileMaker -
Arboretum 
4,000+
 FileMaker
Nematology
11,000+ Types (53,000 general)
...others (Vet/Med)

5. Darwin profile of Datasets
Objective: To export the elements from the UC Davis biological collection datasets into the DiGIR part of the UC Davis Biological Collections "Web service".
The next slides show the beginnings of the Web Service prototype…

6. Museum datasets matched to the Darwin Profile
The Darwin Profile is composed of 48 elements, in groups:

7. An ACCESS prototype of the integrated databases
Links to independent database tables listed here are prefixed by their names, e.g. "Herbarium_Labels". Imported data (Darwin core) created from these table links, are prefixed by "Darwin", e.g."Darwin_Herbarium":

8. An ACCESS prototype of the integrated databases
Queries were created to parse out only the Darwin Core elements from the tables. e.g. qryDarwin_Herbarium

9. Museum test database (Example)
The above shows the Phaff Yeast dataset fields matched to the Darwin Profile elements. … Similarly the other datasets have been matched to the Darwin Profile.

10. Next Step: To continue our Prototype development:
Museum test database
Next Step: To continue our Prototype development:
To develop queries into all these Darwin Profile datasets; All contain the same data element sets which will allow for a “UC Davis Museums” combined dataset query.
Essentially complete the implementation of DiGIR, as a priority and secondarily develop methods to serve out the additional data attributes residing in the individual museum/biological collections datasets.

11. Integration of the UC Davis Biological Collections Data via a Web Portal [What Next?]
Next on the agenda:
Discuss & demonstrate how the Wildlife & Fisheries database system will serve as the “prototype” database system for our combined biological datasets.
Discuss collaborative efforts with other groups on the UC Davis campus and other institutions.
Discuss software researched to develop our Web Service; e.g. XML, Open source development tools, Microsoft .NET development tools, SRB (Storage Resource Broker).

12. How to integrate? Decisions to make.
Integrated database prototype, our approach:
Queries made against the linked tables can generate the output for the Darwin core elements. However, we are not certain how to present DiGIR with queries rather then tables; Thus we created intermediate tables from the linked tables.
Is our approach of combining all our biological collection datasets into 1 repository to “serve out” the Darwin core elements as done in this prototype a good idea?
What is DiGIR’s preferred method?

13. Integrating Dataset Issues
Directors, Curators, faculty & staff have concerns/issues about the Web Portal:
Security (If their respective databases are made directly available via the Web Portal system).
-Corruption possibilities Data validation/quality control (once their datasets are served out via the Web Portal).
-They cannot assure that their datasets are up-to-date & complete. How will the Web Portal address this?

14. Addressing these Issues
Security: - Databases will be uploaded to the Web Portal server entirely (for small datasets). All requirements to prepare & make available the datasets will entirely take place on the Web Portal server.
Larger datasets (or if incompatible with Web Portal Server) will require programming tools to be developed o the data server that stores these before being exported to the Web Portal server.
Quality Assurance: - The individual dataset holders will have control over their upload and/or running of procedures to export their datasets to the Web Portal server. Meta data will accompany the data defining the dataset limitations, etc. [e.g. DiGIR provides this sort of meta data information through the resource descriptive files]