biscicol ievobio
DESCRIPTION
A general presentation of the BiSciCol project showing use cases, describing technical background, and describing application possibilities.TRANSCRIPT
John Deck, University of California, BerkeleyBrian Stucky, Colorado University, Boulder
Nico Cellinese, University of Florida, GainesvilleNeil Davies, University of California, BerkeleyRob Guralnick, Colorado University, Boulder
Chris Meyer, Smithsonian InstitutionTom Orrell, Smithsonian Institution
Richard Pyle, Bishop MuseumKate Rachwal, University of Florida, Gainesville
Russell Watkins, University of Florida, Gainesville
BiSciCol: a Tagging and TrackingInfrastructure for Biological Science
Collections
Biological Science Collections Tracker working towards building an infrastructure
designed to tag and track scientific collections and all of their derivatives.
National Science Foundation funded 2010 – 2014
Partners are University of Florida, Colorado University, Bishop Museum, UC Berkeley, Smithsonian Institution, University of Arizona
Relies on globally unique identifiers (GUIDs) to track objects
Implements a Linked Data approachProvides support for the Global Names
Architecture
OutlineUse Cases – Why this is importantTechnical Background
Globally Unique Identifiers (GUIDs)RDF/ BiSciCol ImplementationCombining GraphsBiSciCol Taxonomy / GNUB Integration
Tools and Potential Tools in DevelopmentHow the BiSciCol Application WorksOnline search interfaceAlert systemAnnotation Network Service
How to get Involved
Use Case: Notify people interested in a collecting event that identifications have been made
(Biocode Event)
(Essig Museum Specimen)
(Smithsonian Tissue)
(Bishop Museum Tissue)
(Genbank Sequence)
(BOLD Barcode)
(Key/Person) (Blast)
(Taxon)(Taxon)
(Blast)
(Taxon)
Use Case: For Taxon X, find specimens with recent modification dates for image or tissue samples.
(Identification)
(Taxon)
DateLastModified“2011-06-01”
DateLastModified“2011-06-20”
(Bishop Museum Tissue)
(CalPhotos Image)
(Essig Museum Specimen)
Use Case: Map all place names/localities associated with Taxon X
(Specimen) (Identification)(Location)
(Specimen)(Location)
(Taxon)
(Identification)
Use Case: Provide collection permit information and use restrictions on tissue samples from SpecimenX
(Bishop Museum Tissue)
(Smithsonian Tissue)
(Collecting Permit)
(Essig Specimen) (Biocode Event)
Technical Background
Globally Unique Identifiers (GUIDs)RDF/ BiSciCol ImplementationCombining GraphsBiSciCol Taxonomy / GNUB Integration
Creating Globally Unique Identifiers (GUIDs)
Globally unique (mandatory) Persistent (not mandatory, but very helpful) Resolvable (not mandatory, but very helpful)
Resolution/Domain + Identifier
JDeckSpecimen1 (A named identifier)http://mycollection.org/specimen/
http://mycollection.org/specimen/JDeckSpecimen1http://mycollection.org/specimen/uuid=7217D220-836A-11DF-8395-0800200C9A66
Examples:
http://example.org/urn:lsid:example.org:specimen/7217D220-836A-11DF-8395-0800200C9A66
+1-541-914-4739 (Unique, at least for phones)7217D220-836A-11DF-8395-0800200C9A66 (opaque)
http://example.org/urn:lsid:example.org:specimen/
BiSciCol Implementation of the Resource Description Framework (RDF)
PredicateAn RDF
Statement:Subject Object
relatedTo (Transitive):
relatedToGUID1 GUID2 GUID3
relatedTo GUID1 <-> GUID2GUID2 <-> GUID3GUID1 <-> GUID3
ORPredicate
GUID1 GUID2
A Simple BiSciCol Graph
(graph=set of RDF Statements):
relatedTo
a aDate Date
GUID1 GUID2 GUID3
relatedTo
Event
“2011-06-20”“2011-05-01”
Tissue
“2011-06-01”
Specimen
a Date
Combining Graphs
SPARQLQuery language for RDFqueries multiple graphs
A set of institutions we are interested in
XML(Graph)
(Graph)N3/Turtle
(Graph)
Web Page Tags (RDFa/Microformats)
BiSciCol / Global Names Architecture Integration
Building a framework for linking taxon concepts to GUIDsLinking Occurrences to Taxons
GUID3(Taxon)
GUID2(IdentificationKey/Person/Blast)
GUID1(Occurrence) relatedTorelatedTo
The Global Names Architecture is a BiSciCol partner that is creating resolvable Identifiers for all taxons through its global names usage bank service (GNUB).
Linking Taxons to GNUB grants us search capabilities for taxon names across all systems.
Taxon = defined by Darwin Core Taxon Class
GUID3(Taxon)
Linking Taxons to Taxons (e.g. GNUB to myAuthority)
rela
tedTo
GUID1(Identification)
GUID2(Taxon)
relatedTo
GUID4(Identification)
relatedTo
Tools & Potential Tools in Development
What the BiSciCol Application DoesOnline search interfaceAlert systemAnnotation Network Service
What the BiSciCol Application Doeshttp://code.google.com/p/biscicol/
Search
Service
MapServic
e
XML(Graph)
(Graph)
N3/Turtle(Graph)
BiSciCol Application (Java)
Internet
SPARQL
Model ClassCombine graph
query results into asingle graph
(model)
Object ClassWork with graph
results in memory(Ancestors, Siblings,
Descendants)
Render ClassProvides image/textrepresentation of
results
RDFa web tags (indexer -> graph)
Online Search Interface Demonstration
Alert System (Proposed)
BiSciCol Applicatio
nDiscovers
/Traverses Relations
hips
XML(Graph)
(Graph)
N3/Turtle(Graph)
RSS Feed, Emails, etc..
Application to store identifiers1) User X stores objects: JDeckSpecmen1 JDeckEvent1,etc..2) Schedules Jobs 3) Runs Queries Recent Changes New identifications
Ser
vice
s
Annotation Network Service (Proposed)
Facilitating Feedback from Third Parties
Generate annotation &Store in a service
Relate AnnotationGUIDTo Specimen GUID
Now discoverable and Linked into BiSciCol
“Create stable identifiers, link them to other stable identifiers,
and put them on the web.”
How to Get Involved
http://biscicol.blogspot.com/http://code.google.com/p/biscicol/