Linking data to publications: Towards the execution of papers

Linking data to publica0ons:Towards the execu0on of papers

Anita de Waard Elsevier Labs/UUtrecht

h5p://elsatglabs.com/labs/anita

http://elsatglabs.com/labs/anita

http://elsatglabs.com/labs/anita

Cycle of Scien,fic Inves,ga,on

2CoSI model by Gully Burns, ISI/USC

Domain-speci!cReasoning Model

Observations Interpretations

Experimental Design Model

formulate hypotheses

make predictions

design experiments

gather data

make observational assertions make interpretational assertions

aggregate assertions

perform experiments







make predictions

design experiments

gather data



perform experiments

Conclusions

Background

HypothesesExperimental Design

Experimental Objects

Observed Results

Processed Data/Sta0s0cs







make predictions

design experiments

gather data



perform experiments

Publica0on

Results

Methods

Figures Conclusions

Background

HypothesesExperimental Design


Observed Results








make predictions

design experiments

gather data



perform experiments

Publica0on

Results

Methods

Figures

Conclusions

Background

Hypotheses

Experimental Design


Observed Results


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1. Current prac?ce: store data in repository, link from document, and vice versa

Observed Results

Data Repository


Sta,s,cs storage system

Experimental Design

Workflow Repository

Publica0on

Figures

Conclusions

Background

Hypotheses

Results

Methods

Current Prac,ce: linking to documents Least favorite: raw research data delivered as supplementary data

Much beGer: linking into/from data centres, e.g. Pangea:

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Linking data and papers: ‘the publisher’s’ posi,on: STM’s “Brussels Declara,on”, 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 ...”

• Publishers are (in general) not interested in owning or charging for research data repositories

• Publishers are very interested in linking to and from data, and want to work with data repositories to do this effec,vely

• Publishers believe in (and know) the concept of Digital Object Iden,fiers:

–Where possible: one repository for iden,fiers

–Persistent and unique (don’t keep same ID if content changes)

–Where possible, link back to the publica,on

Linking data and papers: ‘the publisher’s’ posi,on: STM’s “Brussels Declara,on”, 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 ...”

• Publishers are (in general) not interested in owning or charging for research data repositories

• Publishers are very interested in linking to and from data, and want to work with data repositories to do this effec,vely

• Publishers believe in (and know) the concept of Digital Object Iden,fiers:

–Where possible: one repository for iden,fiers

–Persistent and unique (don’t keep same ID if content changes)

–Where possible, link back to the publica,on

Complete agreement with MacKenzie Smith’s “Requirements for Data Cita,on!”

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2. Store data in repository, link within document.

Workflow Repository

Experimental Design

Data Repository

Observed Results

So]ware Repository

Code/Sta0s0cs

Publica0on

Figures

Conclusions

Background

Hypotheses

Results

Methods

Enabler at Elsevier -‐ Linked Data: access any level of granularity of content

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Dublin Core and SKOS


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SWAN’s PAV (Provenance, Authoring and Versioning) ontology

Dublin Core and SKOS


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SWAN’s PAV (Provenance, Authoring and Versioning) ontology

Dublin Core and SKOS1. Where the document region is completely described by an existing ID, use that ID to define the region.Example: http://api.elsevier.com/content/article/DOI:10.1016/S0030-3992(02)00069-5#p0100 specifies a document region as the element with ID "p0100".2. Where the document region can be completely described by an element within an ID'd element, navigate outwards to an ID that encloses the region, and use a relative Xpath.Example: #xpath-e(id('s0050')/ce:para[4]) specifies a document region as the fourth ce:para element within an element with ID "s0050".3. Where the document region cannot be completely described by an element within the content, use the above locators combined with substrings.Example: #xpath-e(substring(id('p0100'),10,20)) specifies a document region as beingcharacters 10–20 in the element with ID "p0100".4. Where the source content does not contain IDs, use absolute Xpaths to navigate to the appropriate element, and use substrings as required.Example: #xpath-e(article/body/ce:sections/ce:section[4]/ce:para[4]) points to a particularce:para as defined by the given Xpath. An example of an absolute Xpath with substrings is left as an exercise for the reader.

http://api.elsevier.com/content/article/DOI:10.1016/S0030-3992(02)00069-

http://api.elsevier.com/content/article/DOI:10.1016/S0030-3992(02)00069-

Authors manually iden,fy (and tag) en,,es for which associated data is in databases, like GenBank, Uniprot, PDB, etc

Or: automa,c en,ty iden,fica,on and linking to relevant databases.

Few (modest) examples of linking within document

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Workflow Repository

Experimental Design

Data Repository

Observed Results

So]ware Repository

Code/Sta0s0cs

Publica0on

Figures

Conclusions

Background

Hypotheses

Results

Methods

3. The future being made today: let’s execute the paper!

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Workflow Repository

Experimental Design

Data Repository

Observed Results

So]ware Repository

Code/Sta0s0cs


Research Process

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Workflow Repository

Data Repository

So]ware Repository


Research Report

Background

Hypotheses

Research Process

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Workflow Repository

Data Repository

So]ware Repository


Research Report

Background

Hypotheses

Research Process

Experimental Design

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Workflow Repository

Data Repository

So]ware Repository


Experimental Design

Research Report

Background

Hypotheses

Research Process

Experimental Design

Observed Results

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Workflow Repository

Data Repository

So]ware Repository


Experimental DesignObserved Results

Research Report

Background

Hypotheses

Research Process

Experimental Design

Observed Results

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Workflow Repository

Data Repository

So]ware Repository


Experimental Design

Observed Results

Research Report

Background

Hypotheses

Research Process

Experimental Design

Observed Results

Code/Sta0s0cs

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Workflow Repository

Data Repository

So]ware Repository


Experimental Design

Observed Results

Code/Sta0s0cs

Research Report

Conclusions

Background

Hypotheses

Research Process

Experimental Design

Observed Results

Code/Sta0s0cs

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Workflow Repository

Data Repository

So]ware Repository


Experimental Design

Observed Results

Code/Sta0s0cs

Research Report

Conclusions

Background

Hypotheses

Research Process

Experimental Design

Observed Results

Code/Sta0s0cs

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Workflow Repository

Data Repository

So]ware Repository


Experimental Design

Observed Results

Code/Sta0s0cs

Maintain context: -‐ Experimental-‐ Narra0ve-‐ Domain

Research Process

Experimental Design

Observed Results

Code/Sta0s0cs

Research Report

Conclusions

Background

Hypotheses

Experimental Design

Observed Results

Code/Sta0s0cs

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Workflow Repository

Data Repository

So]ware Repository

3. Even be5er: why move anything anywhere??

Research Process

Experimental Design

Observed Results

Code/Sta0s0cs

Research Report

Conclusions

Background

Hypotheses

Experimental Design

Observed Results

Code/Sta0s0cs

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Workflow Repository

Data Repository

So]ware Repository

3. Even be5er: why move anything anywhere??

Experimental Design

Observed Results

Code/Sta0s0cs

3.Science in the cloud

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3.Science in the cloud

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Proposal Advantages to the scien4st

Store research plan, results, thoughts, observa0ons, etc. locally/in the cloud in a system that adds metadata.

Always keep track of your own data! Maintain copyright and access privileges.

Allow access to the data, workflow etc. to the data repository, who1. validates quality (content and form) 2. assigns a UID 3. adver0ses its existence

Data is veXed, iden0fied, and adver0sed.If scien0st/funding body wants: data repository controls access rightsdata repository maintains archive

Allow access to the collected thoughts, (with links to data) to the publisher, who1. validates quality (content and form) 2. assigns a UID 3. adver0ses its existence

Content veXed, iden0fied, and adver0sed.. If scien0st/funding body wants: publisher/library controls access rightspublisher/library maintains archive

Others -‐ perhaps publishers, perhaps data repositories, perhaps (egad!) so[ware developers -‐ build tools, to place thoughts and data into context.

BeXer so[ware! BeXer links to everything else we do.

Technology 1: Workflow tools

http://wings.isi.edu/

http://VisTrails.org

http://MyExperiment.org

http://wings.isi.edu

http://wings.isi.edu





Technology 2: Executable Papers

Technology 3: Applica,on Plahorms

In summary:

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In summary:• Publishers are in general not interes0ng in owning or charging for research data repositories (Brussels declara0on)

• Publishers are very interested in linking to and from data, and want to work with data repositories to do this effec0vely

• Publishers believe in Digital Object Iden0fiers• Publishers embrace open standards and interoperability, and are adap0ng their infrastructure to be future-‐compliant:

– In par0cular, we think scien0sts should keep (track of) their work

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– In par0cular, we think scien0sts should keep (track of) their work–We also think novel informa0on architectures work for science, including Linked Data, the concept of app servers, and the cloud

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– In par0cular, we think scien0sts should keep (track of) their work–We also think novel informa0on architectures work for science, including Linked Data, the concept of app servers, and the cloud

• Publishers believe in a future that stores and shares science in a beXer and more produc0ve way, and inven0ng it together: FoRCE11: The Future of Research Communica0ons and eScience

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http://force11.org

http://force11.org

Linking data to publications: Towards the execution of papers

Technology

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