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Life Sciences Identifiers. Ricardo Pereira TDWG Infrastructure Team (TIP). Data is Available. Many projects exchanging data over the Net. From Botanicus.org. Existing identifiers. Taxon names Catalog numbers Others Institution Code, Collection Codes. Problems to solve.

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Life sciences identifiers l.jpg

Life Sciences Identifiers

Ricardo Pereira

TDWG Infrastructure Team (TIP)


Data is available l.jpg
Data is Available

  • Many projects exchanging data over the Net


Existing identifiers l.jpg

From Botanicus.org

Existing identifiers

  • Taxon names

  • Catalog numbers

  • Others

    • Institution Code, Collection Codes


Problems to solve l.jpg
Problems to solve

  • Integrating data

Specimens

Taxon Name

Taxon

Observations

A computer can’t,

because it is all

loosely linked by

the taxon name.

With some effort

a scientist who comes

along can put all that

information together.

Publications


Problems to solve5 l.jpg

Data

+

Terms &

Coditions

Problems to solve

  • Giving proper attribution

It’s difficult

to keep

attribution

Information

with the data

Museum A

Museum B

Reports


Problems to solve6 l.jpg
Problems to solve

  • Tracking provenance

A scientist can tell

where a record came

from by looking at

the collection code

It may be awkward

for a computer to

do it based just

on collection codes


Solution l.jpg
Solution

  • Globally Unique Identifiers (GUID)

    • A scheme to identify and access data objects on the Web.

    • Identifiers are persistent

      • They are permanently associated with a data object.

    • Identifiers are globally unique

    • Identifiers are actionable or locatable

    • Provides mechanisms to describe objects: metadata

TDWG Architecture

Globally Unique Identifiers

TDWG

Ontology

ExchangeProtocols


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Existing GUID Systems

  • Life Science Identifiers (LSID)

    urn:lsid:herbimi.info:specimens:100069

  • Handle System

    10.1045/january99-bearman

  • Digital Object Identifiers (DOI)

    doi:10.1000/182

  • Persistent URLs (PURLs)

    http://purl.oclc.org/OCLC/PURL/FAQ


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TDWG picked LSIDs

  • Existing standard for retrieving data and metadata

  • Decentralised

  • Easy to assign large numbers of LSIDs

  • Conceptually distinct from URLs

  • LSIDs are names not addresses like URLs

  • Integrates with TDWG architecture

    • Returns RDF

    • LSIDs gets you to the data (resolvable)


Life science identifiers lsid l.jpg
Life Science Identifiers (LSID)

urn:lsid:zoobank.org:act:20889795-7EC7-42F3-A4C3-D1D97704A609

A taxon name from ZooBank

urn:lsid:herbimi.info:specimens:100069

A fungi specimen from Herb. IMI

urn:lsid:ubio.org:classificationbank:1164063

The description of a genus from UBio

urn:lsid:gdb.org:GenomicSegment:GDB132938

A segment of the human genome from GDB


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LSID Resolution Protocol

  • Well defined way to get data and metadata from an LSID

    urn:lsid:gdb.org:GenomicSegment:GDB132938

Data

Metadata


Lsids at work l.jpg
LSIDs at work

  • Integrating data

Specimens

Taxon Concept

Taxon

LSIDs make

links unanbiguous.

A computer can

Integrate all the

Information.

Observations

Publications


Lsids at work13 l.jpg
LSIDs at work

  • Giving proper attribution

Every record has an

LSID that can take

the user back to

attribution information

Museum A

Museum B

Metadata


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LSIDs at Work

  • Tracking provenance

2

1

By inspecting the

metadata associated

with an LSID,

a computer can find

the original source

of a record that

has been aggregated


What gets an lsid l.jpg

Specimens

Observations

Images

Taxon Concepts

Taxon Names

What gets an LSID

  • Data objects that-

    • You serve to your clients

    • You are an authority for

    • You have aggregated

      • Assign new LSIDs

      • Keep a link to the source

  • Examples:

    • Taxon Names

    • Taxon Concepts

    • Observations

    • Specimens

    • Images


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What we have done

  • Support: LSID Website, Proxy & Software

  • Spec: LSID Applicability Statement

    • Specifies how our community uses LSIDs

  • TIP Funded Projects

  • Deployed LSID Resolvers for Taxon Names

    • Also a few other data types covered

  • Development of LSID clients


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What needs to be done

  • Ratify TDWG LSID Applicability Statement

    • Specifies how our community uses LSIDs

  • Documentation:

    • LSID Setup Guide

  • Continue deployment of LSIDs

    • Increase coverage of other data types:

      • Specimens, Observations, Organizations, People


What can you do l.jpg
What can you do?

  • Respond to the Request for Comments on the LSID Applicability Statement

    • Follow instructions at www.tdwg.org

  • Assign LSIDs to your data objects

    • Lets users refer unambiguously to them

    • Gives you credit for them

    • Lets you express attribution (for derived data)

    • Asserts legal status of data

  • Information: lsids.sf.net


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