Biocode Commons Identifiers (BCIDS) A free* for use, persistent identifier solution for biological sample collection from the field, scalable to the billions.

Slides:

Advertisements

Similar presentations

GUIDs in EMu Ian Turnbull KE Software. GUID? UUID? A Globally Unique Identifier (GUID) is a persistent unique reference number used as an identifier.

Advertisements

Copyright Hub Software Engineering Ltd 2010All rights reserved Hub Workflow Product Overview.

Depends entirely on support from the user base Many technical issues still need to be resolved Long term development horizon Proposal for a Simplified.

NYBG + KE EMu The New York Botanical Garden + KE EMu Melissa Tulig Botanical Information Management.

Publish or perish? Linking Scratchpads and the new Biodiversity Data Journal for streamlining publication of botanical data D.N Koureas 1, L. Penev 2 &

John Deck, University of California, Berkeley Brian Stucky, University of Colorado, Boulder Lukasz Ziemba, University of Florida, Gaineseville Nico Cellinese,

BIS TDWG Conference, New Orleans, 2011 GBIF: Issues in providing federated access to digital information related to biological specimens David Remsen Senior.

Collections Management Natural History Museums Common Development A Natural History Example using Darwin Core Much talk of common development Concern over.

Digital Object Identifiers for EOSDIS data HDF Workshop April 17, 2012 John Moses, ESDIS

Metadata Standards for Data Joan Starr California Digital Library June, Second thoughts about.

Advisory Board Meeting  Portland, Oregon  08 November 2000 System Architecture David Maier

Model Eco-systems Decision Systems Lab University of Wollongong.

Personal Data Management Why is this such an issue? Data Provenance Representing links v Representing data Identifying resources: Life Science Identifiers.

 an easy-to-use interface for deposit and update  access via persistent URLs  tools for long-term management  permanent storage Merritt is a new cost-effective.

Linking collections to related resources: Multi-scale, multi-dimensional, multi-disciplinary collaborative research in biodiversity. Is this a “Big.

MDA/KE EMu/ MDA Initiatives and SPECTRUM Nick Poole MDA Director.

EZID (easy-eye-dee) is a service that makes it simple for digital object producers (researchers and others) to obtain and manage long-term identifiers.

Dan Masiga Molecular Biology and Biotechnology Department International Centre of Insect Physiology and Ecology, Nairobi, Kenya BARCODE Data Standard The.

DDI Best Practices Technical Best Practices. High Level Architecture URNs and Entity Resolution Managing Unique Identifiers DDI as Content for Repositories.

SERNEC Image/Metadata Database Goals and Components Steve Baskauf

Studbook Databases Development and Maintenance International Species Information System (ISIS)

IDs in and out of the database Entomological Collections Network (ECN) 2012 November 10 – 11, Knoxville, TN Debbie Paul, Greg Riccardi.

IDigBio is funded by a grant from the National Science Foundation’s Advancing Digitization of Biodiversity Collections Program (Cooperative Agreement EF ).

Managing the Record of Research At the Smithsonian Using SIdora SAA Research Forum August 12, 2014.

EZID long-term identifiers made easy Greg Janée University of California Curation Center California Digital Library July 31, 2012.

EZID Easy Identifiers UC Curation Center California Digital Library.

BARCODE OF LIFE DATA SYSTEMS (BOLD) Riadul Mannan Biodiversity Institute of Ontario.

PiMS 2.2 General Description Anne Pajon EMBO Workshop September 2008.

Integrating Live Plant Images with Other Types of Biodiversity Records Steve Baskauf Vanderbilt Dept. of Biological Sciences

Designing Persistency Delos NoE, Preservation Cluster Workshop: Persistency in Digital Libraries 14. February 2006, Oxford Internet Institute.

Connecting Specimens, Images and Vocabulary Specify, Morphbank, Morphster Beach, Noble, Spears – KU Mast, Riccardi – FSU Miranker, Tirmizi UT.

BIEN Confederated DB (S) Analytical DB(s) Heterogeneous source database(s) of Plots/Specimens/Occurrences Synonymy Names Reference taxonomy *** *** Feedback.

ISTC-CMSA workshop Brief description of collections (~ 37milj objects ~ type specimens)  Recent zoological collections  Section Invertebrates 

What is an Ontology? An ontology is a specification of a conceptualization that is designed for reuse across multiple applications and implementations.

CBoL Taipei, september 2007 BARCODE DATA, MUSEUM CATALOGS AND GBIF Simon Tillier.

Collections Management Proposal for a Simplified Structure for EMu Chicago, Oct 2005.

Field Based Data Validation: a very real experience in wrangling data, taxonomic names, and photos Moorea Biocode Project, supported by the Gordon and.

Biocode Field Information Management System (FIMS) John Deck, UC Berkeley TDWG, 2014.

Alternative Architecture for Information in Digital Libraries Onno W. Purbo

Ontologies Working Group Agenda MGED3 1.Goals for working group. 2.Primer on ontologies 3.Working group progress 4.Example sample descriptions from different.

Don’t make me think Biodiversity Data Publishing Made Easy Laurence Livermore, Vince Smith, Alice Heaton, Simon Rycroft, Ed Baker, Ben Scott & Lyubomir.

June 2006Image LSID resolvers Image LSID Resolution Prototypes Hui Dong, Bob Morris UMass Boston.

Scratchpads and the new Biodiversity Data Journal Biodiversity Data Publishing made… easier Dimitris Koureas Natural History Museum London.

Acronym Soup GBIF, TDWG & GUIDs Jerry Cooper. Global Biodiversity Information Facility (GBIF) Established in 2000 through non-binding MOU (25 countries.

Triple Storage. Copyright  2006 by CEBT Triple(RDF) Storages  A triple store is designed to store and retrieve identities that are constructed from.

Persistent Identifiers (PIDs) & Digital Objects (DOs) Christine Staiger & Robert Verkerk SURFsara.

CAAB and taxon management at CSIRO Marine Research Tony Rees Divisional Data Centre CSIRO Marine Research, Hobart

The library is open Digital Assets Management & Institutional Repository Russian-IUG November 2015 Tomsk, Russia Nabil Saadallah Manager Business.

Riccardi: DIALOGUE Workshop August 1, 2005 Supported by NSF BDI 1 Representing and Using Phylogenetic Characters in Morphbank Greg Riccardi, David Gaitros,

Introduction To Data Standards eRA SBIR Public Briefing March 4, 2002

Converting an Existing Taxonomic Data Resource to Employ an Ontology and LSIDS Jessie Kennedy Rob Gales, Robert Kukla.

Applications in the EDIT Platform for Cybertaxonomy Andreas Müller 1, Andreas Kohlbecker 1, Cherian Mathew 1, Alexander Oppermann 1, Patrick Plitzner 1,

Data Element Classification ISO/IEC 11179, Part 2

John Deck, University of California, Berkeley Brian Stucky, University of Colorado, Boulder Lukasz Ziemba, University of Florida, Gaineseville Nico Cellinese,

GENBANK FILE FORMAT LOCUS –LOCUS NAME Is usually the first letter of the genus and species name, followed by the accession number –SEQUENCE LENGTH Number.

Data Citation Dataverse Mercè Crosas Chief Data Science and Technology Officer, IQSS, Harvard Workshop: Data Citation.

Actionable Identifiers an introduction Joan Starr California Digital Library.

OBIS IODE PO OBIS INCOIS OBIS- SEAMAP Separate files OBIS Nodes Data providers Separate files GBIFLifeWatchGEOSSEOL,…CBDFAOISA Fail-over mirrorGeo-load.

CRISP WP 17 1 / 2 Proposed Metadata Catalogue Architecture Document.

MESA A Simple Microarray Data Management Server. General MESA is a prototype web-based database solution for the massive amounts of initial data generated.

Introduction to Persistent Identifiers

Introduction to Persistent Identifiers

Flexible Extensible Digital Object Repository Architecture

Flexible Extensible Digital Object Repository Architecture

Chapter 2: GUI API Chapter 2.

BrightSign Network Secure, scalable and affordable cloud-based digital sign network service.

Studbook Databases Development and Maintenance.

Fig X. Insert caption here. Fig X. Insert caption here.

CMPE/SE 131 Software Engineering March 7 Class Meeting

GBIF Today and Tomorrow

Presentation transcript:

Biocode Commons Identifiers (BCIDS) A free* for use, persistent identifier solution for biological sample collection from the field, scalable to the billions *updates & element resolution requires EZID account BiSciCol

Linking Samples and Derivatives: An example from the Moorea Biocode Project (Biocode Event) (Essig Museum Specimen) (Smithsonian Tissue) (Gut Sample Event) (Genbank Sequence) (metagenomic Sequencing) KeyBlast*n Taxon*n Taxon Blast Taxon (Key) (Taxon)

Intersection of Standards & Identifiers Location / geo-ref taxonomy Measureme nt environment investigation Nucleic acid sequnece Material Sample Darwin Core MIxS OBI protocols material analysis ID NOTE: Material Sample is a proposed term for both DwC and MIxS

Information Flow ark:/21547/b2_{LocalID} Specimen DBLab DBRepository DB1 a obi:MaterialSample; Repository DB2 Field DB Who, what, whenIdentification, taxonWorkflow Proposed Case SampleID Specimen DBLab DBRepository DB1Repository DB2 Field DB who, what, when (field-data) Identification, taxon + copy of field-data taxon, Workflow, 2 nd copy field-data SpecimenID TissueID RepositoryID1 RepositoryID2 Current Case 3 rd copy field-data

_{LocalID} Anatomy of a BCID ark: ark: = scheme /b2 / = Name assigning authority b2 = Shoulder / Group Identifier (Contains a common concept which all child elements share) LocalID = Local ID, Darwin Core Triple, or UUID BCID / Element Identifier EZID / Group Identifier Defines a grouping of conceptually similar objects or processes: E.g. Sample, Collecting event, Image. This portion registered with EZID for all Data Groups through the BCID EZID Account free of charge. Defines an element contained with a group, available via the BCID resolver or registerable via EZID (requires an individual subscription to EZID)

BCIDs Extends EZIDs (from California Digital Library), based on ARK/DOI technology. Easy to pre-generate identifiers for field sampling and resolve them later BCIDs are API driven, but have a User Interface Open on a limited basis to projects wishing to help test See for more information.