Triplifier talk
18
John Deck, University of California, Berkeley Brian Stucky, University of Colorado, Boulder Lukasz Ziemba, University of Florida, Gaineseville Nico Cellinese, University of Florida, Gainesville Rob Guralnick, University of Colorado, Boulder BiSciCol Team Reed Beaman, Nico Cellinese, Jonathan Coddington, Neil Davies, John Deck, Rob Guralnick, Bryan P. Heidorn, Chris Meyer, Tom Orrell, Rich Pyle, Kate Rachwal, Brian Stucky, Rob Whitton, Lukasz Ziemba Data Curation and Biodiversity Research -- Lessons from BiSciCol and a look at the “Triplifier Simplifier”
description
Connecting content with a tool to convert database and spreadsheet data to be useable on the semantic web.
Transcript of Triplifier talk
John Deck, University of California, BerkeleyBrian Stucky, University of Colorado, BoulderLukasz Ziemba, University of Florida, GainesevilleNico Cellinese, University of Florida, GainesvilleRob Guralnick, University of Colorado, Boulder
BiSciCol TeamReed Beaman, Nico Cellinese, Jonathan Coddington, Neil Davies, John
Deck, RobGuralnick, Bryan P. Heidorn, Chris Meyer, Tom Orrell, Rich Pyle, Kate
Rachwal, BrianStucky, Rob Whitton, Lukasz Ziemba
Data Curation and
Biodiversity Research --
Lessons from BiSciCol and
a look at the “Triplifier
Simplifier”
• BiSciCol is National Science Foundation funded 2010 – 2014
• Infrastructure to tag & track specimens & derivates in cyberspace
• Relies on globally unique identifiers (GUIDs) to track objects
• Implements a Linked Data approach
• Provides support for the Global Names Architecture
Taxonomic Type Filter
Class Filter
X
X
Specimens
Tissues
Sequences
A Biological Relationship Graph …
Why Linked Data? Why BiSciCol?
(Prefers to collect stuff)
Generates Lots of Data…
Here is Gustav’s Problem
Biodiversity Data Challenges
Data is Distributed
Rapidly Changing
Technologies
Covers Multiple
Domains
Group data into classes.
Publish.[ ] Ocean Sampling Day
[X] Moorea Biocode
[X] SI MSNGR System
[+] Add My Data
Link identifiers.
Is a dwc:Event
Solving Biodiversity Data Challenges with
BiSciCol and Linked Data
Assign identifiers. Is a dwc:Event
The Triplifier(Advanced Interface)
Powered by:
Naming and Identifying Objects
Linking Objects
Publishing
Loading Data
Advanced Interface: Loading Data
MySQL
Darwin Core
Archive
Mysql
DarwinCoreArchive
KEMU
Spreadsheets
Advanced Interface: Entities
Ceusters W, Smith B. Strategies for Referent Tracking in Electronic Health R Biomed Inform. 2006 Jun;39(3):362-78.
78
From Gary Larsen and adapted by Barry Smith in Referent Tracking presentation at the Semantics of Biodiversity Workshop, 2012.
Result is identifiers assigned to Entities:78 a door .
427 a cat .
<http://biocode.berkeley.edu/collectorspecimens/BMOO_2665> a <dwc:Occurrence> .
<http://biocode.berkeley.edu/collectorevents/MIB_25> a <dwc:Event> .
Tissue
Advanced Interface: Entity Relations
Relations as Triples:<http://biocode.berkeley.edu/collectorevents/MIB_25> <ma:isSourceOf> <http://biocode.berkeley.edu/collectorspecimens/BMOO_2665> .
<http://biocode.berkeley.edu/collectorevents/MIB_37> <ma:isSourceOf> <http://biocode.berkeley.edu/collectorspecimens/BMOO_2667> .
<http://biocode.berkeley.edu/collectorspecimens/BMOO_2665> <ma:isSourceOf> <http://biocode.berkeley.edu/plate_well/Plate_M037F10> .
<http://biocode.berkeley.edu/collectorspecimens/BMOO_2667> <ma:isSourceOf> <http://biocode.berkeley.edu/plate_well/Plate_M028G5> .
Qu
ery
Response
Triplify!: View graph based data
The Triplifier (Simple Interface)
Publish
What challenges are we facing now?
(for BiSciCol, Linked Data, and data integration
In general)
Identifier IssuesPersistence
Assignment at the source is difficult
The digestible RFID tag
Solutions: • DOIs (http://doi.org/)• EZIDs (http://ezid.net/)
Solutions: • Calculated namespaces (e.g. geo:lat,lng) via PDAs• UUIDs (randomly unique)
Solution: • Promote use of URIs for identifiers in all Standards.
Semantic web requires URIs but many standards (including Darwin Core) do not require URIs for identifiersscheme : string
URI
Classification Issues
Solutions: • Continue working on clarity in term
definitions• Work from upper level ontologies (e.g.
Basic Formal Ontology) to derive definitions.
Confusion between representational units
“Sample, Specimen, Individual, Aggregation”
Inadequate representational units
“Occurrence”
Relation Issues
Solution: • apply directional links only where
appropriate.
Non-sensical conclusions are possible!
Adoption IssuesCritical mass required for effective utilization
Reality is complicated
Solutions: • Work collaboratively (e.g.
BioPortal, hackathons, interdisciplinary workshops)
Solutions: • Work with aggregators (GBIF, VertNet, NCBI).• View Triples as a publishable unit
• BiSciCol tackles biodiversity data challenges:
• Tracking and integration of objects across disciplines
• Linking derivatives back to their source
• BiSciCol is about community, collaborative practice
• Commitment to standards, ontologies
• Agreement on permanent, resolvable identifiers
• Triplification of data sources to enhance linked data
The BiSciCol Mission
http://biscicol.blogspot.com/ http://biscicol.org
