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

BiSciCol: Tracking Biodiversity Objects to Brokering Standards“Or, Gustav’s Big Problem”

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 at Gaineseville, University of Colorado at Boulder, Bishop Museum, University of California at Berkeley, Smithsonian Institution, University of Arizona at Tucson

Relies on globally unique identifiers (GUIDs) to track objects

Implements a Linked Data approachProvides support for the Global Names

Architecture

From “Facebook Visualizer”

Tracking FaceBook relationships …

Can we track relationships for Biological Objects as well?

Why? Here is Gustav’s Problem….

(Prefers to collect stuff)

Lots of Data ….

Generates …

Due to project requirements and integration needs, Gustav is left navigating a plethora of redundant and disconnected distributed Databases. Lots of effort to track objectsAnd their derivatives.

Can we borrow from Facebook and social networking to help solve Gustav’s Problem?

Taxonomic Type Filter

Class Filter

X

X

Specimens

Tissues

Sequences

FunctionsX Infer Relationships Across providers

A Biological Relationship Graph …

Moorea Biocode Example: Tracking biological material from field collection through analysis, across multiple systems

(Biocode Event)

(Essig Museum Specimen)

(Smithsonian Tissue)

(CAMERA Gut Sample Event)

(Genbank Sequence)

(metagenomic Sequencing)

Key Blast*n

Taxon*nTaxon

Blast

Taxon

(Key)

(Taxon)

How do we Track Biological Objects

and their Relations Across Distributed,

Heterogeneous systems?

Tracking Biological Object Relationships

Group like terms into classes. In Darwin Core, for example we have the following “groups of terms”: Events, Locations, Occurrences, GeologicalContext, Identification, Taxon.

Assign Identifiers. Use globally unique, resolvable, persistent identifiers for each class or term.Link Identifiers using Relationship Terms. For example, “This object is related to that object.”

Put this data on the Web.

Related Projects that are Grouping Like terms into Classes

Darwin-SW (http://code.google.com/p/darwin-sw/) Building an ontology of Darwin Core Terms to make it possible to describe biodiversity resources on the web.

Gene Ontology (http://www.geneontology.org/) Standardizing the representation of gene and gene product attributes across species and databases.

ENVO (http://environmentontology.org/) Annotating the environment for any biological sample.

OBO Foundry (http://www.obofoundry.org/)A suite of orthogonal interoperable reference ontologies in the biomedical domain

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/

Linking Identifiers Using Relationship Terms

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

Getting the most out of your data:Inferring Object Relationships

Facebook Inferencing:“Let us sell you, to others (or vice-versa)”BiSciCol Inferencing:“What relationships exist that haven’t been explicitly expressed”

Location1(Essig Museum)

Organism2(Smithsonian)

sameAs

inferred

Organism1(Essig Museum)

relatedTo

Tissue1(Essig Museum)

relatedTo

Tissue2 (Smithsonian)

relatedToGeoreference1(BioGeomancer)

relatedTo

48.198,16.371;crs=wgs84;u=40

hasSpatialThingGeoreference

Even though Tissue #2 is not directly related to Location1, we can Still infer its relationship through Organism1 and Organism2 being the same as each other.

Tissue1(Essig Museum)

infe

rred

Tissue2(Smithsonian)

inferred

Inferred Relationship Chains

Tools in Development

“Bio-Plugins”

Update Mechanisms

Gustav’s Watchlist:GP12345-3939-33939 (Occurrence)BE99999-3939-3dd39 (Event)GP12346-3939-33II3 (Occurrence)GP12dd6-3939-3xxxI (Tissue)GP9999-xkx9d-dkdkd (Occurrence)…

BiSciCol API(Search on Date And return graphOf object)

Search Descendents(By Recent Modification)

Updates

Genomic Rosetta Stone

Uses GUIDs, classed data, and links to tie Organismal data to Genomic Data.

“Triplifier” linking biological objects

Mysql

KEMU

“Triplifier”Create links fromNative data formats

Mysql

BiSciCol

Darwin Core Archive

Example Taxonomic Query

Aedes increpitusSearch Scientific Name: Run

Client Interface:

BISCICOL SERVICE LOOKUP:dwc:IdentificationID1 :relatedTo http://lsid.itis.gov/urn:lsid:itis.gov:itis_tsn:126314dwc:IdentificationID1 :relatedTo dwc:OccurrenceID1dwc:IdentificationID2 :relatedTo http://lsid.itis.gov/urn:lsid:itis.gov:itis_tsn:126317dwc:IdentificationID2 :relatedTo dwc:OccurrenceID3

Results:OccurrenceID1 (Aedes increpitus  Dyar, 1916 ) OccurrenceID3 (Aedes vittata  Theobald, 1903)

Taxon SERVICE (ITIS / GNUB)http://lsid.itis.gov/urn:lsid:itis.gov:itis_tsn:126314http://lsid.itis.gov/urn:lsid:itis.gov:itis_tsn:126317http://gnub.org/8E19F1DC-74BA-47D4-A505-6498414B4CCE

Working with LocationsE.g. Tracking location in space of a moving individual (whales)

EventID1

EventID2

EventID3

IndividualID1 GeoreferenceID1

GeoreferenceID2

GeoreferenceID3

Data Impact Factor – Graph Metrics

Occurrence:MBIO1234 (“2011-10-18 09:10:00”)DNA Extraction:Extrac9999 (“2011-10-18 09:00:00”)Sequence:s1113939999 (“2011-10-18 08:00:00”)Occurrence:MBIO1235 (“2011-10-17 00:00:00”)Photo:P123456 (“2011-10-17 00:00:00”)

Whats New?

Occurrences

MBIO99999(1024 total descendents)

IMBL8888888(723 total descendents)

Events

Biocode10234(4234 direct children)

Expedition21234(1023 direct children)

Collectors

Gustav Paulay(102,000 direct children)

Christopher Meyer(83,000 direct children)

Craig Moritz(523 direct children)

[ ] GBIF Relations Graph[X] Moorea Biocode[X] SI MSNGR System[+] Add New Graph

Graphs

Web Interface (Demonstration Wed. 2pm at BiSciCol

Meeting)

Summary

All objects are re-usable in the semantic web. We only need to express an identifier once and then it can be linked by anything else (either directly or indirectly)

By using sameAs relations it is possible to infer relations for data that was not previously expressed.

Queries are easily federated – possibility to create global graphs and ask questions against heterogeneous databases.Graph based databases can help us understand the relevance of individual objects. For example, indicate the number of relations a particular object has for 1st, 2nd, 3rd, or nth order relations.

“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/