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

Cycle of Scien,ﬁc Inves,ga,on make observational assertions make interpretational assertions gather data aggregate assertions Observations Interpretations Experimental Domain-speci c Design Model Reasoning Modelperform experiments make predictions design experiments formulate hypotheses CoSI model by Gully Burns, ISI/USC 2

Cycle of Scien,ﬁc Inves,ga,on make observational assertions make interpretational assertions Processed Data/Sta0s0cs Conclusions gather data aggregate assertions Observations Interpretations Observed Results Experimental Domain-speci c Design Model Reasoning Model Background perform experiments make predictionsExperimental Objects design experiments formulate hypotheses Experimental Design Hypotheses CoSI model by Gully Burns, ISI/USC 2

Cycle of Scien,ﬁc Inves,ga,on Publica0on make observational assertions make interpretational assertions Processed Data/Sta0s0cs Figures Conclusions gather data aggregate assertions Observations Interpretations Observed Results Results Experimental Domain-speci c Design Model Reasoning Model Background perform experiments make predictionsExperimental Objects design experiments formulate hypotheses Methods Experimental Design Hypotheses CoSI model by Gully Burns, ISI/USC 2

Cycle of Scien,ﬁc Inves,ga,on Publica0on make observational assertions make interpretational assertions Processed Data/Sta0s0cs Background gather data aggregate assertions Observations Interpretations Observed Results Hypotheses Experimental Domain-speci c Design Model Methods Reasoning Model Results perform experiments make predictionsExperimental Objects design experiments Figures formulate hypotheses Experimental Design Conclusions CoSI model by Gully Burns, ISI/USC 2

1. Current prac?ce: store data in repository, link from document, and vice versa Publica0onBackground Workﬂow RepositoryHypotheses Experimental DesignMethods Data RepositoryResults Observed ResultsFigures Sta,s,cs storage systemConclusions Processed Data/Sta0s0cs 3

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: 3

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

2. Store data in repository, link within document. Publica0on Background Workﬂow Repository Hypotheses Experimental Design Methods Data Repository Results Observed Results Figures So]ware Repository Conclusions Code/Sta0s0cs 6

Enabler at Elsevier -‐ Linked Data: access any level of granularity of content 7

Enabler at Elsevier -‐ Linked Data: access any level of granularity of content Dublin Core and SKOS 7

Enabler at Elsevier -‐ Linked Data: access any level of granularity of content Dublin Core and SKOS SWAN’s PAV (Provenance, Authoring and Versioning) ontology 7

Enabler at Elsevier -‐ Linked Data: access any level of granularity of content1. Where the document region is completely described by an existing ID, use that ID to Dublin Core and SKOSdefine 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 IDdelement, 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 SWAN’s PAV (Provenance, Authoring and Versioning) ontologyce:para element within an element with ID "s0050".3. Where the document region cannot be completely described by an element within thecontent, 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 tothe 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 isleft as an exercise for the reader. 7

Few (modest) examples of linking within document 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. 4

3. The future being made today: let’s execute the paper! Publica0on Background Workﬂow Repository Hypotheses Experimental Design Methods Data Repository Results Observed Results Figures So]ware Repository Conclusions Code/Sta0s0cs 9

3. The future being made today: let’s execute the paper! Workﬂow Repository Experimental Design Data Repository Observed Results So]ware Repository Code/Sta0s0cs 9

3. The future being made today: let’s execute the paper! Workﬂow Repository Research Process Data Repository So]ware Repository 10

3. The future being made today: let’s execute the paper! Research Report Background Workﬂow Repository Hypotheses Research Process Data Repository So]ware Repository 10

3. The future being made today: let’s execute the paper! Research Report Background Experimental Design Workﬂow Repository Hypotheses Research Process Data Repository So]ware Repository 10

3. The future being made today: let’s execute the paper! Research Report Background Workﬂow Repository Hypotheses Experimental Design Experimental Design Research Process Data Repository So]ware Repository 10

3. The future being made today: let’s execute the paper! Research Report Background Workﬂow Repository Hypotheses Observed Results Experimental Design Experimental Design Research Process Data Repository So]ware Repository 10

3. The future being made today: let’s execute the paper! Research Report Background Workﬂow Repository Hypotheses Experimental Design Experimental Design Observed Results Research Process Data Repository Observed Results So]ware Repository 10

3. The future being made today: let’s execute the paper! Research Report Background Workﬂow Repository Hypotheses Experimental Design Experimental Design Code/Sta0s0cs Observed Results Research Process Data Repository Observed Results So]ware Repository 10

3. The future being made today: let’s execute the paper! Research Report Background Workﬂow Repository Hypotheses Experimental Design Experimental Design Observed Results Research Process Data Repository Code/Sta0s0cs Observed Results So]ware Repository Code/Sta0s0cs 10

3. The future being made today: let’s execute the paper! Research Report Background Workﬂow Repository Hypotheses Experimental Design Experimental Design Observed Results Research Process Data Repository Code/Sta0s0cs Observed Results Conclusions So]ware Repository Code/Sta0s0cs 10

3. The future being made today: let’s execute the paper! Research Report Background Workﬂow Repository Hypotheses Experimental Design Experimental Design Observed Results Research Process Data Repository Code/Sta0s0cs Observed Results Maintain context: Conclusions -‐ Experimental So]ware Repository -‐ Narra0ve Code/Sta0s0cs -‐ Domain 10

3. Even be5er: why move anything anywhere?? Research Report Background Experimental Design Workﬂow Repository Hypotheses Observed Results Code/Sta0s0cs Research Process Data Repository Conclusions So]ware Repository 11

3. Even be5er: why move anything anywhere?? Research Report Background Experimental Design Workﬂow Repository Hypotheses Observed Results Experimental Design Experimental Design Code/Sta0s0cs Observed Results Research Process Data Repository Code/Sta0s0cs Observed Results Conclusions So]ware Repository Code/Sta0s0cs 11

3.Science in the cloud 12

3.Science in the cloudProposal Advantages to the scien4stStore research plan, results, thoughts, Always keep track of your own data! observa0ons, etc. locally/in the cloud in a Maintain copyright and access system that adds metadata. privileges. Allow access to the data, workflow etc. to Data is veXed, iden0fied, and the data repository, who adver0sed.1. validates quality (content and form) If scien0st/funding body wants: 2. assigns a UID data repository controls access rights3. adver0ses its existence data repository maintains archiveAllow access to the collected thoughts, Content veXed, iden0fied, and (with links to data) to the publisher, who adver0sed.. 1. validates quality (content and form) If scien0st/funding body wants: 2. assigns a UID publisher/library controls access rights3. adver0ses its existence publisher/library maintains archiveOthers -‐ perhaps publishers, perhaps data BeXer so[ware! repositories, perhaps (egad!) so[ware BeXer links to everything else we do.developers -‐ build tools, to place thoughts and data into context. 12

Technology 1: Workﬂow tools http://VisTrails.org http://MyExperiment.orghttp://wings.isi.edu/

Technology 2: Executable Papers

Technology 3: Applica,on Plahorms

In summary: 16

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 16

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 – We also think novel informa0on architectures work for science, including Linked Data, the concept of app servers, and the cloud 16

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 – 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 16

Linking data to publications: Towards the execution of papers

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