Linking Data from

ScienceDirect Articles

Presented by: IJsbrand Jan AalbersbergHannover, DataCite MeetingDate: June 8, 2010

Linking to & from Data

from & to ScienceDirect Articles

Presented by: IJsbrand Jan AalbersbergHannover, DataCite Meeting Date: June 8, 2010

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

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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

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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

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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

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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

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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

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The Present (PANGAEA linking)1. Author submits article to publisher2. Author submits data set to repository3. At article publication, repository links article DOI to

associated data set DOI, creating actual connection4. User sees link to ScienceDirect from PANGAEA5. User sees link to PANGAEA from ScienceDirect:

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SD Server

USERSD Article

PANGAEA Server

link

articles

data + associations

PANGAEA links to ScienceDirect

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ScienceDirect links to PANGAEA

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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

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SD Server

USER

SD Article

Supplementary Data Server

articles

data sets

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:

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Data Set Server

USER

Data Set

Article Server

data sets

articles

A Future (inline supplementary data)

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A Future (inline supplementary data)

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Structures submitted as supplementary data files (MOL files)

Displayed inline through Reaxys application / service

Linking to & from Data

from & to ScienceDirect Articles

Presented by: IJsbrand Jan AalbersbergHannover, DataCite Meeting Date: June 8, 2010

Presented by: IJsbrand Jan AalbersbergHannover, DataCite Meeting Date: June 8, 2010

Creating the best User Experience

by integrating Data with Articles

Presented by: IJsbrand Jan AalbersbergHannover, DataCite Meeting Date: June 8, 2010

Creating the best User Experienceby integrating Data with Articles

requires close collaboration between data set repositories and publishers