Doi> Norman Paskin, International DOI Foundation Digital Object Identifiers for Science Data.

doi>

Norman Paskin, International DOI Foundation

Digital Object Identifiers for Science Data

doi>Digital Object Identifier = DOI

• A name (not a location) for an entity on digital networks • A system for persistent and actionable identification and interoperable exchange

of managed information on digital networks – Standards-based components (detail in a moment)– Now to become an International Standard (in ISO TC46)

• Developed as cross-industry, cross-sector, not-for-profit effort managed by an open membership collaborative development body– International DOI Foundation (IDF)

• In widespread use now:– Over 15 million assigned, over 1000 naming authorities (users)– Key feature of scientific primary publishing as part of CrossRef system– Adopted for government documents (EC, OECD, UK, etc)

• In use, is a mechanism “behind the scenes”, – e.g. looks like a URL in a web context

• Offers interoperable common system for identification of science data: two projects considered as examples:– TIB project (citation of primary data sets)– Names for Life (biological taxonomy)

doi>• The word “identifier” can mean several different things, e.g.:

– Labels : Output of numbering schemes e.g. “ISBN 3-540-40465-1”– Specifications for using labels: e.g. on internet URL, URN, URI (URI =

Uniform Resource Identifier) – Implemented systems: Labels, following a specification, in a system e.g.

DOI system. Packaged system offering label + tools + implementation mechanisms

• Requirements: reliability, automated global access, and interoperability – Interoperability = the possibility of use in services outside the direct

control of the issuing assigner.

• Persistence implies interoperability (with the future)• Interoperability implies extensibility (do not know future uses)• Hence DOI is a generic framework applicable to any digital object

– Digital object can be a representation of any entity

Identifiers

Data ModelInternet

Resolution

Numbering scheme

Policies

DOI is the combination of these four components

doi>

DOI syntax can include any

existing identifier “label”formal or informal,

of any entity

• An identifier “container” e.g.– 10.1234/NP5678– 10.5678/ISBN-0-7645-4889-4– 10.2224/2004-10-ISO-DOI

• NISO Z39.84, DOI Syntax

Data ModelResolutionby Handle

Numbering scheme

Policies

doi>

Internet resolution allows a DOI to link to

any & multiple piecesof current data

• Resolve from DOI to data– initially to location (URL) – persistence

• May be to multiple data:– Multiple locations– Metadata– Services– Extensible user-defined

• Uses the Handle system- Implementing URI/URN concept- Running on TCP/IP (common co-inventor)- IETF RFCs 3650, 3651, 3652- See Release 1.0, September 2003 "Online Registries: The DNS

and Beyond...“ [doi:10.1340/309registries ]


Numbering scheme

Policies

doi>

<indecs> Data Dictionary

+DOI AP framework

• DOI Data Model = Metadata tools: – a data dictionary to define +– a grouping mechanism to relate

• Necessary for interoperability – “Enabling information that originates in one

context to be used in another in ways that are as highly automated as possible”.

• Able to use existing metadata – Mapped using a standard dictionary– Can describe any entity at any level of granularity– indecsDD which incorporates ISO MPEG 21 RDD

• IDF is the MPEG21 RDD registration authority


Numbering scheme

Policies

doi>

DOI policies allow any model

for practical implementations

• Implementation through IDF– Governance and agreed scope, policy, “rules of the road” – Technical infrastructure: resolution mechanism, proxy servers,

mirrors, back-up, central dictionary, – Social infrastructure: persistence commitments, fall-back procedures,

cost-recovery (self-sustaining), shared use of system– Not a standard but a Registration Authority/maintenance agency

• IDF delegates through Registration Agencies – Each can develop own applications– Use in “own brand” ways appropriate for their community


Numbering scheme

Policies

doi>

DOI to become ISO TC46/SC9 standard

Home of “identification numbering”: identifiers for semantically meaningful entities:

ISO 2108 International Standard Book Numbering (ISBN)

ISO 3297 International Standard Serial Number (ISSN)

ISO 3901 International Standard Recording Code (ISRC)

ISO 10444 International Standard Technical Report Number (ISRN)

ISO 10957 International Standard Music Number (ISMN)

ISO 15706 International Standard Audiovisual Number (ISAN)

ISO 15707 International Standard Musical Work Code (ISWC)

ISO Project 20925 Version identifier for Audiovisual Works (V-ISAN)

ISO Project 21047 International Standard Text Code (ISTC)

http://www.collectionscanada.ca/iso/tc46sc9/index.htmInformation and Documentation - Identification and Description

doi>

Resolve

The Handle resolution technology allows you to access any kind of Service associated with your DOI.eg

Services can include metadata services

Identify

DOI syntax can include any existing identifier, formal or informal, of any entityeg

10.2341/0-7645-4889-110.5678/978-0-7645-4889-410.1000/ISBN 076454889110.1234/Norman_presentation10.2224/2004-10-28-ISO-DOI

Describe

DOI metadata can be of any type, standard or proprietaryeg OnixForBooksOnixForSerialsIEEE/LOMMARCDublin CoreProprietary scheme

(to interoperate with anyone else in the DOI network, map to the <indecs> Data Dictionary (iDD).

DOI combination of components

A package of services is an Application Profile

doi>DOI and scientific data

• DOI is already the core technology for maintaining cross-reference – persistent links between a citation and internet access to article

• CrossRef system used by 350+ publishers representing bulk of STM articles (as pre-publication link builder) www.crossref.org

• 9,000 DOIs per day added to CrossRef. – Over 12 million DOIs now registered with CrossRef, – Over 850,000 assigned to books and conference proceedings.

• Several projects suggested to IDF using DOIs for data (not connected with CrossRef)– physico-chemical property data; biological microscopy images. – See Paskin, ICSTI 2002 paper

• Some projects have developed their own identifiers, very useful for their own area– E.g. Life Science Identifier (I3C/IBM): simple URN mechanism, non-generic, non-global– These can be incorporated into a DOI if needed to make globally interoperable and

extensible

• Two projects in particular have developed DOI applications:

doi>(1) TIB: Citation of Primary Data

• Problem: re-use of existing data sets– Attribution of data source: make data publications citable in a standard

way (cf. articles Citation Index) – Archiving of data in context so as to be discoverable and interoperable

(usable by others)

• Background – CODATA National Committee WG, grant-aided by DFG (Sept 2001 to May

2002): Report "Concept of Citing Scientific Primary Data“– Continuation as project for pilot implementation funded by DFG Oct 2003

to Oct 2005 at TIB (German National Library of Science & Technology)– Development of DOI registration agency for Data

• Solution:- DOIs for data sets, with associated metadata - Core management metadata applicable to all datasets - Structured metadata extensible to specific science disciplines

doi>(1) Citation of Primary Data: illustration of solution

• During her research for the World Data Center Climate (WDCC) Dr. Weather gains primary data about the weather in Hannover in the year 2003.– Primary data is tested, evaluated, stored and administrated at the WDCC.– Primary data is registered and allocated DOI at the TIB– With quality control of metadata, no change once allocated, etc

• Dr Weather can now cite this with a resolvable DOI e.g DOI:10.1594 /WDCC/W_Han_2003_MMB_210.1594 (Prefix) = TIB as the registration agency.

WDCC = research institute. W_Han_2003_MMB_2 = internal name of the Data

• DOI is resolvable directly, or via http as http://dx.doi.org/10.1594/WDCC/W_Han_2003_MMB_2

doi>(1) Citation of Primary Data: illustration of solution

Usage scenario 1:• Dr. Storm is reading publications from Dr. Weather in a journal and would like to analyse her

data under different aspects.• Can resolve the DOI to obtain the data set for use• In his publication ”Comparison of the weather from Hannover and Miami” Dr. Storm cites Dr.

Weather’s data using its DOI, referring to the uniqueness and own identity of the original data.• Citation example:

Weather, 2003: “Weather in Hannover for 2003”doi: 10.1594/WDCC/W_Han_2003_MMB_2

Usage scenario 2: • Mr. Nice is writing a paper about the sales figures of ice cream in Hannover in 2003, but he has

no information about the weather.• Searches via TIB central registration agency metadata search• Result is doi:10.1594/WDCC/W_Han_2003_MMB_2• He resolves the DOI to find the data.• The metadata refers him to the WDCC as publisher and data archive.• In his paper he cites the data using the DOI.

doi>(2) Names for life: Biological taxonomy

• Problem: “Future-proofing biological nomenclature”– See Garrity and Lyons, OMICS, 2003

• For a given nomenclature in a biological taxonomy, change occurs– e.g. new species recognised, species reassigned as the founding

species of new genera; synonyms; species split into subspecies which later became separate species;

– resulting in changes of names, genera, families, classes, relationships over time

– How does researcher keep track?

• Solution: DOI proposed as tool– a data model of nomenclature and taxonomy– enabling disambiguation of synonyms and competing taxonomies– a metadata resolution service– enabling dissemination of archived and updated information objects

through persistent links

macleodii(T)

communis

Alteromonas

vaga

nomenclature

(2) Names for Life: illustration of problem doi>

macleodii(T)

communis

Alteromonas

1972

vaga

nomenclature

communisvagahaloplanktis

Alteromonasmacleodii(T)

1972 1973

nomenclature

communisvagahaloplanktisrubra

Alteromonas

1972 1973 1976

macleodii(T)

nomenclature

communisvagahaloplanktisrubracitrea

Alteromonas

1972 1973 1976 1977

macleodii(T)

nomenclature

communisvagahaloplanktisrubracitreaesperjianaundina

Alteromonas

1972 1973 1976 1977 1978

macleodii(T)

nomenclature

communisvagahaloplanktisrubracitreaesperjianaundinaaurantia

Alteromonas

1972 1973 1976 1977 1978 1979

macleodii(T)

nomenclature

communisvagahaloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedai

Alteromonas

1972 1973 1976 1977 1978 1979 1981

macleodii(T)

nomenclature

communisvagahaloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedailuteoviolaceae

Alteromonas

1972 1973 1976 1977 1978 1979 1981 1982

macleodii(T)

nomenclature

communisvagahaloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedailuteoviolaceae

vagacommunis(T)

Marinomonas Alteromonas

commune

vagum

1972 1973 1976 1977 1978 1979 1981 1982 1984

multiglobiferum

japonicumminutiumbiejerinckiimaris

maris

hiroshimense

pelagicumpusillum

jannaschiikreigii

Oceanosprillum

mariswilliamsae

linum(T) macleodii(T)

nomenclature

communisvagahaloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedai

vaga benthicahanedai

Marinomonas Alteromonasputrifaciens(T)

Shewanella


maris

hiroshimensemultiglobiferumpelagicumpusillumcommunejannaschiikreigiivagum

Oceanosprillum

mariswilliamsae

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986

luteoviolaceae

communis(T)linum(T) macleodii(T)

nomenclature

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987

communisvagahaloplanktisrubracitreaesperjianaundinaaurantia

hanedailuteoviolaceaedenitrificans


Marinomonas Alteromonas Shewanella


maris


Oceanosprillum

mariswilliamsae

putrifaciens

putrifaciens(T)communis(T)linum(T) macleodii(T)

nomenclature

communisvagahaloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedailuteoviolaceaedenitrificans


Marinomonas Alteromonas Shewanella


maris


Oceanosprillum

mariswilliamsae

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988

colwelliana


nomenclature


Marinomonas Shewanella


maris

hiroshimensemultiglobiferumpelagicumpusillumcommunejannaschiikreigiivagumbiejerinckii

pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae


tetradonis

Alteromonas

colwelliana

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990

colwelliana


nomenclature

vaga benthicahanedaicolwellianaalgae



tetradonisatlanticacarageenovora

Alteromonas

colwelliana

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992


maris


pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae


nomenclature



communisvagahaloplanktis

putrifacienshanedai

denitrificans

rubracitreaesperjianaundinaaurantia

luteoviolaceae


Alteromonas

colwelliana

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995


maris


pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae

distinctafulginea

atlanticaaurantiacarrageenovoracitreaesperjianaluteoviolaceanigrifacienspisicidarubra

haloplanktis haloplanktis(T)

Pseudoalteromonas

undina

haloplanktis tetradonis


nomenclature





Alteromonas

colwelliana

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997


maris


pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae

distinctafulginea


Pseudoalteromonas

undinaantartica

elyakoviii

haloplanktistetradonis

haloplanktishaloplanktis(T)


nomenclature





Alteromonas

colwelliana

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000


maris


pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae

distinctafulginea


Pseudoalteromonas

undinaantartica

elyakoviii

fridgidimarinageldimarinawoodyiiamazonensisbalticaoneidensispealeanaviolacea

bacteriolyticaprydzensistunicatadistinctaelyakoviipeptidolytica


mediterannea



nomenclature





Alteromonas

colwelliana

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001


maris


pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae

distinctafulginea


Pseudoalteromonas

undinaantartica

elyakoviii

fridgidimarinageldimarinawoodyiiamazonensisbalticaoneidensispealeanaviolacea

bacteriolyticaprydzensistunicatadistinctaelyakoviipeptidolyticatetrodonis

japonica


mediterannea



nomenclature





Alteromonas

colwelliana

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002


maris


pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae

distinctafulginea

Pseudoalteromonas

elyakoviii

fridgidimarinageldimarinawoodyiiamazonensisbalticaoneidensispealeanaviolaceajaponicadenitrificanslivingstonensisalleyanna

atlanticaaurantiacarrageenovoracitreaesperjianaluteoviolaceanigrifacienspisicidarubraundinaantarticabacteriolyticaprydzensistunicatadistinctaelyakoviipeptidolyticatetrodonis


mediterannea



nomenclature





Alteromonas

colwelliana

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 2004


maris


pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae

distinctafulginea

Pseudoalteromonas

elyakoviii

fridgidimarinageldimarinawoodyiiamazonensisbalticaoneidensispealeanaviolaceajaponicadenitrificanslivingstonensisalleyanna

atlanticaaurantiacarrageenovoracitreaesperjianaluteoviolaceanigrifacienspisicidarubraundinaantarticabacteriolyticaprydzensistunicatadistinctaelyakoviipeptidolyticatetrodonis


11 others

mariniintestinasaireschlegelianagaetbuli

mediteranneaprimoryensis



nomenclature

name

taxon

combinedname

exemplar

nomos

journalarticle

geneannotation

anyonline

information

strainrecord

links from the web

journalarticle

strainrecord

geneannotation

journalarticle

journalarticle

links to the web

DOI

DOIDOI

DOI

DOI

(2) Names for Life: illustration of solution

dissemination

name

taxon

combinedname

exemplar

nomos

By reasoning over information objects, construct services that can be offered through multiple resolution.

Look up this name Look up this name and all its synonyms and all its synonyms in PubMedin PubMed

Determine whether thisDetermine whether thisexemplar is part of a taxon exemplar is part of a taxon in another nomosin another nomos

Compare this name to Compare this name to the current state the current state (contents) (contents) of the taxonof the taxon

(2) Names for Life: illustration of solution

doi>

doi>Summary: DOI

• A system for persistent and actionable identification and interoperable exchange of managed information on digital networks – Standards-based components (detail in a moment)– Now to become an International Standard (in ISO TC46)

• Developed as cross-industry, cross-sector, not-for-profit effort managed by an open membership collaborative development body– International DOI Foundation (IDF)

• In widespread use now:– Over 15 million assigned, over 1000 naming authorities (users)– Key feature of scientific primary publishing as part of CrossRef system– Adopted for government documents (EC, OECD, UK, etc)

• In use, is a mechanism “behind the scenes”, – e.g. looks like a URL in a web context

• Offers interoperable common system for identification of science data: two projects considered as examples:– TIB project (citation of primary data sets)– Names for Life (biological taxonomy)

doi>[email protected]

Doi> Norman Paskin, International DOI Foundation Digital Object Identifiers for Science Data.

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