Linking data from sciencedirect articles
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Linking Data from ScienceDirect Articles. Presented by: IJsbrand Jan Aalbersberg Hannover, DataCite Meeting Date: June 8, 2010. Linking to & from Data from & to ScienceDirect Articles. Presented by: IJsbrand Jan Aalbersberg Hannover, DataCite Meeting Date: June 8, 2010.

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Linking Data from ScienceDirect Articles

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Linking data from sciencedirect articles

Linking Data fromScienceDirect Articles

Presented by: IJsbrand Jan Aalbersberg

Hannover, DataCite Meeting

Date: June 8, 2010


Linking to from data from to sciencedirect articles

Linking to & from Data from & to ScienceDirect Articles

Presented by: IJsbrand Jan Aalbersberg

Hannover, DataCite Meeting

Date: June 8, 2010


Linking data in sciencedirect

Linking Data in ScienceDirect

  • The Past

    • Supplementary data

    • Entity links to databases

  • The Present

    • Some considerations

    • PANGAEA-type linking

  • A Future

    • Getting even closer connected


The past supplementary data

The Past (supplementary data)

  • Raw research data delivered as supplementary data

    • Available for limited number of data set types / formats

    • Data distributed over multiple articles and publishers

    • Format frozen in time – not maintained for preservation

    • Only available for smaller data sets (at most few 10 MBs)

    • Limited access due to use of existing publishing platforms

    • Data and article remain nicely coupled / packaged

    • Supplementary data always being peer-reviewed


The past entity linking manual

The Past (entity linking - manual)

  • Authors manually identify (and tag) entities that are mentioned in articles and of which associated data is present (or registered) in databases, like GenBank, MINT, Uniprot, PDB, CCDC, ...

    • Very accurate and unambiguous

    • However, requiring author effort

    • Publisher takes care of actual linking

    • Reciprocal linking usually taken care of


The past present entity linking automatic

The Past/Present (entity linking – automatic)

  • Sometimes automatically (e.g., NextBio and Reflect)

    • Easily extendable to new / other entities

    • Works retrospectively on older content

    • Does create recall / precision errors


The present some considerations

The Present (some considerations)

  • STM, “Brussels Declaration”, June 2006:

    • “... believe that, as a general principle, data sets, raw data outputs of research, and sets or subsets of that data should wherever possible be made freely accessible ...”

  • Data sets should be freely accessible – at publisher?

    • Scientists prefer independent data repositories

    • Need for single domain-specific coordination

    • Huge costs for maintenance and preservation

  • Proper deposit mechanism needed

    • Through publisher? Extra overhead vs. ease of use

  • Enforcing deposit prior to publication

    • If community-supported, surely a possibility

  • Data set standardization is needed for optimal use


The present more considerations

The Present (more considerations)

  • Scientist needs the combination of formal publication record and the raw data sets

  • To get optimal interoperability, close collaboration between publisher and data set repositories needed

  • Publisher should “enable and support” raw data sets

    • Submission: enforce if supported by community

    • Discoverability: interconnect article with data sets

  • Reciprocal linking at deepest level possible

    • PANGAEA-type linking

  • Data feeds from publisher to repositories?

  • Managing large amount of data set repositories?

    • DataCite as single discussion partner


The present pangaea linking

The Present (PANGAEA linking)

  • Author submits article to publisher

  • Author submits data set to repository

  • At article publication, repository links article DOI to associated data set DOI, creating actual connection

  • User sees link to ScienceDirect from PANGAEA

  • User sees link to PANGAEA from ScienceDirect:

SD Article

SD Server

articles

USER

PANGAEA Server

data + associations

link


Pangaea links to sciencedirect

PANGAEA links to ScienceDirect


Sciencedirect links to pangaea

ScienceDirect links to PANGAEA


A future tighter interoperability

A Future (tighter interoperability)

  • Not just a link to / from data and journal article

  • But provide integrated experience for scientist

  • Single page (environment) with data and article

SD Article

SD Server

articles

USER

Supplementary Data Server

data sets


A future tighter interoperability1

A Future (tighter interoperability)

  • Not just a link to / from data and journal article

  • But provide integrated experience for scientist

  • Single page (environment) with data and article

    • Some users prefer it other way around; so also offer:

Data Set

Data Set Server

data sets

USER

Article Server

articles


A future inline supplementary data

A Future (inline supplementary data)


A future inline supplementary data1

A Future (inline supplementary data)

  • Structures submitted as supplementary data files (MOL files)

  • Displayed inline through Reaxys application / service


Linking to from data from to sciencedirect articles1

Linking to & from Data from & to ScienceDirect Articles

Presented by: IJsbrand Jan Aalbersberg

Hannover, DataCite Meeting

Date: June 8, 2010


Linking data from sciencedirect articles

Creating the best User Experienceby integrating Data with Articles

Presented by: IJsbrand Jan Aalbersberg

Hannover, DataCite Meeting

Date: June 8, 2010


Linking data from sciencedirect articles

Creating the best User Experienceby integrating Data with Articlesrequires close collaboration between

data set repositories and publishers

Presented by: IJsbrand Jan Aalbersberg

Hannover, DataCite Meeting

Date: June 8, 2010


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