Connecting datasets and publications automatically
Wouldn’t it be great for a scientific data archive to know what publications made use of their data sets? Pingback mechanisms, used in blog systems, can send citation notifications automatically. Can the same be applicable for online journal systems, notifying each other and data archives about citations? It all comes down to agree on using a really simple standard.

MESUR.org: Related journals, based on citation clickstreams. From: Bollen J, Van de Sompel H, Hagberg A, Bettencourt L, Chute R, et al. (2009) Clickstream Data Yields High-Resolution Maps of Science. PLoS ONE 4(3): e4803. doi:10.1371/journal.pone.0004803

This idea is just giving an impression about how to tackle one of the problems in the scholarly community where it is common practice to create bi-directional citation links in retrospect, which is very labor intensive. A given is that in journals like Plos a link is provided, citing the dataset. Yet at the datacenter there is no information back to the article, because they are unaware of this citation. This comes with the reality that there is no notification mandate at the journal side, and it is labor intensive if not automated.

If a notification partnership between journal and data center will become reality, why not automate it?
The technology is already there developed in the web-log community, using a Ping-back mechanism. Blogs that cite one another automatically send notification messages where they can refer back to the originating blog.

The steps how it works, and how it can work for journals and data centers, is explained below.

For the example we use the following ingredients

• The article A in journal system X has a DOI 10.x/a
• The dataset B in data archive Y has a DOI 10.y/b
• The journal system is posting information about the article on the website, including citation information referring to the dataset.
• Both journal system and data archive are using Pingback mechanisms according to the specifications.

The illustration on the right is following the steps described below.

An editor it finishing a publication in an online journal system, he is minting the DOI for the article A, and fills-in the metadata, also the citation information where the DOI of the dataset B is typed in.

At the moment when the article A is published on the web the Ping-back mechanism kicks in. It essentially sends a RPC Pingback notification to the Dataset B’s web address http://dx.doi.org/10.y/b.

Because the data archive, where dataset B resides, understands Pingback RPC requests, it automatically makes a check in the HTML at the web address where the Article A resides on the Journal System at http://dx.doi.org/10.x/a . The data archive is expecting to find in the HTML of the article something that looks like:

This way the dataset automatically is becoming aware of the  Articles it is cited, used or aggregated in.
A fully installed mechanism works bi-directional, so also where a dataset is making an assertion to an article, the article becomes aware it is being asserted.

Advanced Pingback in RDF

Perhaps we would like to add more information about the nature of the link between the two locations. This can ideally be done in RDF. Where in the Linked Data mindset RDF documents are linking to each other, not HTML documents.
This will lead to the following advanced Pingback check. This falls outside the Pingback specification, and therefor is not a standard.

The 3TU data center is already expressing their data sets descriptions in RDF. example: http://data.3tu.nl/repository/resource:location-49760597/object/ORE
The folowing could easily be done for them.

The example continues:
Metadata is given to the article A, also the dataset it has used, using rdf-statement ore:aggregates, in a ResourceMap for the article. This will result in a RDF/n-tripples expression (object, predicate, subject) :  10.x/a aggregates 10.y/b

<http://dx.doi.org/10.x/a>
<http://www.openarchives.org/ore/terms/aggregates>
<http://dx.doi.org/10.y/b>

Now, at the moment when the article A is published on the web the Ping-back mechanism kicks in. It essentially sends a RPC Pingback notification to the Dataset B’s web address http://dx.doi.org/10.y/b.

Because the data archive, where dataset B resides, understands Pingback RPC requests, it automatically makes a check in the rdf at the web address where the Article A resides on the Journal System at http://dx.doi.org/10.x/a . The data archive is expecting to find in the rdf of the article something that looks like the tripple:

http://dx.doi.org/10.x/a

http://www.openarchives.org/ore/terms/aggregates

http://dx.doi.org/10.y/b

If the data archive finds this tripple with the data set id as the object, and the ore:aggregates term as the predicate, it will grab the id of the subject in this tripple, and add it to it’s own ResourceMap. That looks like:

http://dx.doi.org/10.y/b

http://www.openarchives.org/ore/terms/isAggregatedBy

http://dx.doi.org/10.x/a

more specific towards citation

The examples above use the Object Reuse and Exchange (ORE) ontology, which makes the relations between the two very generic. We use this standard because it is widely used. However when we want to be more specific about the fact that this article cites the dataset, additional assertions can be made by using the Semantic Publishing and Referencing (SPAR) ontology. This lead to the following tripple:

http://dx.doi.org/10.x/a

http://purl.org/spar/cito/cites

http://dx.doi.org/10.y/b

The RPC of the Ping-back mechanism can automatically create an inverse relation at the data center side.

http://dx.doi.org/10.y/b

http://purl.org/spar/cito/isCitedBy

http://dx.doi.org/10.x/a

even more specific citation of a dataset

Even neater is to make an assertion specific to that fact that a DataSource is cited, where the predicate is a sub-class of “cites” in the ontology.

http://dx.doi.org/10.x/a

http://purl.org/spar/cito/citesAsDataSource

http://dx.doi.org/10.y/b

And the inverse

http://dx.doi.org/10.y/b

http://purl.org/spar/cito/isCitedAsDataSourceBy

http://dx.doi.org/10.x/a

Standard for Pingback in RDF embedded in HTML

Now it all comes to create a simple standard.

So for the sake of simplicity I would presume that MicroData would be the standard to use for RDF integration in HTML5 publishing and authoring tools. I base this on that fact that Google, Bing and Yahoo have come up with Schema.org to set a standard vocabulary for enriching HTML. (I am not going into the discussion whether this is a good thing ruling a whole hard working community out, etc.)
So when a publishing tool is going to post a page where citation is involved, this is what the Ping-back mechanism of the data center side should pick-up an be able to process.

Below an example I have reused and changed a bit from http://www.schema.org/Article
The HTML text

How to Tie a Reef Knot
by John Doe
This article is based on data set http://dx.doi.org/10.y/b

The enriched version

  How to Tie a Reef Knot
  by John Doe
  This article is based on data set http://dx.doi.org/10.y/b
  

The Pingback-RDF mechanism at the data center side would be able to, first parse RDF that is embedded in this HTML file. Next to check if the global identifier of the data set appears as being cited. If so, it then can extract the metadata of the article and publish a ‘citedBy’ link on it’s own page.

I am curious what you think of it, so lease leave some comments.

References

ResourceMaps http://www.openarchives.org/ore/1.0/primer.html

Enhanced Publications http://www.surffoundation.nl/enhancedpublications

Ping-back http://www.hixie.ch/specs/pingback/pingback

DataCite http://datacite.org/whycitedata

Journal System http://pkp.sfu.ca/?q=ojs

Data Archive http://datacentrum.3tu.nl/

Semantic Publishing and Referencing http://purl.org/spar/

Piwowar HA, Day RS, Fridsma DB (2007) Sharing Detailed Research Data Is Associated with Increased Citation Rate. PLoS ONE 2(3): e308. doi:10.1371/journal.pone.0000308

Introducing the Semantic Publishing and Referencing (SPAR) Ontologies | by David Shotton

How to use Citation Typing Ontology (CiTO) in your blog posts | by Martin Fenner

Last weekend  Google, Microsoft’s BING and Yahoo! agreed to use the MicroData format as a common standard and schema.org as a common vocabulary to make search even more efficient.  Will this also be the answer for describing inter-related scholarly work, aka Enhanced Publications?

The standard the Big3 have announced can be found on http://www.schema.org/ . With this HTML pages can be enriched, by simply making semantic annotations to your current HTML markup. For Institutional repostitories, who are already being crawled by search engines, this means they can finaly rely on a standard that makes sense to annotate their HTML pages, and use it as a machine readable metadata record!

According to schema.org repositories can use the semantic class http://www.schema.org/ScholarlyArticle to express more details. For example a Dspace  jump-off page from  Utrecht University can easily be  enriched. http://igitur-archive.library.uu.nl/law/2011-0328-200533/UUindex.html

Before

<body>...

<table border=0 id="abstract">

 <tr><td>De logeerbuik: draagmoederschap in Nederland</td></tr>

</table>

<table border=0 id="abstract">

  <tr><td>authors </td><td>Vonk, Machteld</td></tr>

  <tr><td>source </td><td>Actuele ontwikkelingen in het familierecht - vijfde Ucerf symposium,

                          (2011), pp. 63-72</td></tr>

  <tr><td>full text </td><td><a href="http://igitur-archive.library.uu.nl/law/2011-0328-200533/

                              De%20logeerbuik%20UCERF%20Draagmoederschap.pdf"

                              onMousedown="stats('&jop=1')">[Full text]</a><br> </td></tr>

   <tr><td>publisher </td><td>Ars Aequi</td></tr>

   <tr><td>URL publisher </td><td><a href="http://uitgeverij.arsaequi.nl/">

                                   [Website publisher]</a> </td></tr>

   <tr><td>document type </td><td>Article</td></tr>

   <tr><td>version </td><td>Final Author version</td></tr>

   <tr><td>disciplines </td><td>Rechtsgeleerdheid</td></tr>

   <tr><td>abstract </td><td>Draagmoederschap is in Nederland niet specifiek geregeld.

                             In dit artikel wordt de Nederlandse situatie beschreven. Bepaalde vormen

                             van draagmoederschap zijn toegestaan en worden door de medische stand

                             gefaciliteerd, maar zijn niet door de wetgever specifiek geregeld.

                             Vervolgens wordt naar de Engelse Parental Order gekeken, die overdracht

                             van ouderschap na draagmoederschap mogelijk maakt. Op grond van de

                             beschrijving van beide systemen komen voorstellen en relevante elementen

                             voor een mogelijke regeling aan de orde.</td></tr>

   <tr><td>keywords </td><td>draagmoederschap, kunstmatige voortplanting</td></tr>

</table>

...

</body>

After

<body itemscope itemtype="http://schema.org/ScholarlyArticle">

...

<table border=0 id="abstract">

 <tr><td itemprop="name">De logeerbuik: draagmoederschap in Nederland</td></tr>

</table>

<table border=0 id="abstract">

  <tr><td>authors </td><td itemprop="author" itemscope itemtype="http://schema.org/Person" 

                           itemprop="name">Vonk, Machteld</td></tr>

  <tr><td>source </td><td>Actuele ontwikkelingen in het familierecht - vijfde Ucerf symposium, (2011),

                          pp. 63-72</td></tr>

  <tr><td>full text </td><td itemprop="encodings"><a itemscope itemtype="http://schema.org/MediaObject"

                             itemprop="contentURL" href="http://igitur-archive.library.uu.nl/law/2011-

                             0328-200533/De%20logeerbuik%20UCERF%20Draagmoederschap.pdf"

                             onMousedown="stats('&jop=1')">[Full text]</a><br> </td></tr>

   <tr><td >publisher </td><td itemprop="publisher" itemscope itemtype="http://schema.org/Organization"

                               itemprop="name">Ars Aequi</td></tr>

   <tr><td>URL publisher </td><td><a href="http://uitgeverij.arsaequi.nl/">[Website publisher]</a>

                                  </td></tr>

   <tr><td>document type </td><td>Article</td></tr>

   <tr><td>version </td><td>Final Author version</td></tr>

   <tr><td>disciplines </td><td itemprop="keywords">Rechtsgeleerdheid</td></tr>

   <tr><td>abstract </td><td itemprop="description">Draagmoederschap is in Nederland niet specifiek

                                                    geregeld. In dit artikel wordt de Nederlandse

                                                    situatie beschreven. Bepaalde vormen van

                                                    draagmoederschap zijn toegestaan en worden door

                                                    de medische stand gefaciliteerd, maar zijn niet

                                                    door de wetgever specifiek geregeld. Vervolgens

                                                    wordt naar de Engelse Parental Order gekeken, die

                                                    overdracht van ouderschap na draagmoederschap

                                                    mogelijk maakt. Op grond van de beschrijving van

                                                    beide systemen komen voorstellen en relevante

                                                    elementen voor een mogelijke regeling aan de orde.

                                                    </td></tr>

   <tr><td>keywords </td><td itemprop="keywords">draagmoederschap, kunstmatige voortplanting</td></tr>

</table>

...

</body>

Enhanced Publications

To make the relation between the Scholarly article and Datasets or other related material, there is a need for anaddition vocabulary. The Big3 set the standard to be the MicroData format, yet the schema.org does not seem to fit for inter-relating scholarly work. Or does it? Can we mis-use some vocabulary elements to so stuff still get’s validly indexed by the Big3?

Please send your comments below.

“Page not found” nowadays in the dynamic information society a common phrase when you use your old bookmarks. To find your beloved document you have to “Google” it. A web-crawling search engine is by far the most reliable resolver of the documents, but there is no guarantee. This is fine, you get some, you loose some. However when considering working in a academic arena, this really gets annoying. New Knowledge is build  on older knowledge to reject or refine this knowledge, to answer new questions. when you cannot read back that older knowledge, then there is a Knowledge Gap. The Knowledge Gap might be a risk for shifting  the paradigm for all the continued research stacked on top of this gap.

Having a domain name and making coolURI’s, and pretending to say “this will be always the same” is not enough any more. Universities merge, change names, and server architecture changes due to internal policy decisions.

In order to provide for a reliable information infrastructure we need a few things: a digital object, an identifier, a trusted digital archive and a trusted resolver. For the end-user, man or machine, it must be really simple to use; type in the identifier and you get the digital object.

Under the hood there is much more going on. The internet as we know it might change (considering net neutrality issues and ipv6 transitions), so the identifier must be technology independent and the resolver must be follow the changes of the net to keep the user access to the digital object.  The file formats changes over time due to popularity of software to use to access the information of the bits and bytes inside a digital object, therefore specialised Long Term Preservation Archives are build to store and make available digital object in future formats. All organisations involved in this trusted information infrastructure keep the resolver updated, whether a digital object has moved, has duplicate locations or has different file formats.

In the current repository landscape a scientist who want to make their digital object future proof, they have to deposit it in an officially approved repository, and get back a persistent identifier. The trusted repositories have the mandate to create their own identifiers. Resolvers can hand out sub-namespaces in the identifier to these repositories. The repository must update the resolver to provide a new identifier and the new location of the digital object. The Long term archive must fetch the new digital object, store it for future access and update the resolver with the backup location of the digital object. This triangle of systems provide the core of trust.

Every academic community has its own demands for what data to deliver, how it is resolved, what additional services should be provided etc. So the infrastructure must provide flexibility and yet be very reliable. All these triangles form an information network. The resolvers provide the access of this information, these access points can be united in a meta resolver. The meta resolver is the single point of access where the end-user (man or machine) can query all the underlying triangles of trust at once. The meta resolver does not have to be visible, in practice it is just the browser address bar, where the persistent identifier is fetched and sent to the meta resolver to provide the end-user with the digital object.

Read more:

• Persistent Identifiers; PersID reports
• Riding the wave – How Europe can gain from the rising tide of scientific data – Final report of the High Level Expert Group on Scientific Data – October 2010 (1,4 Mb)
• Interoperability Solutions for European Public Administrations (interesting comments @TalkStandards)

The speed of alt-metrics presents the opportunity to create real-time recommendation and collaborative filtering systems: instead of subscribing to dozens of tables-of-contents, a researcher could get a feed of this week’s most significant work in her field. This becomes especially powerful when combined with quick “alt-publications” like blogs or preprint servers, shrinking the communication cycle from years to weeks or days. Faster, broader impact metrics could also play a role in funding and promotion decisions.

read more on http://altmetrics.org

Alt-metrics expand our view of what impact looks like, but also of what’s making the impact. This matters because expressions of scholarship are becoming more diverse. Articles are increasingly joined by:

• The sharing of “raw science” like datasets, code, and experimental designs
• Semantic publishing or “nanopublication,” where the citeable unit is an argument or passage rather than entire article.
• Widespread self-publishing via blogging, microblogging, and comments or annotations on existing work.

Because alt-metrics are themselves diverse, they’re great for measuring impact in this diverse scholarly ecosystem. In fact, alt-metrics will be essential to sift these new forms, since they’re outside the scope of traditional filters. This diversity can also help in measuring the aggregate impact of the research enterprise itself.

http://www.ideo.com/

The Future of the Book. from IDEO on Vimeo.

Scientometrics 2.0: Toward new metrics on scholarly impact on the social web
by: Jason Priem and Bradley M. Hemminger
Source: First Monday, Volume 15, Number 7 – 5 July 2010
Source: http://www.uic.edu/htbin/cgiwrap/bin/ojs/index.php/fm/article/view/2874/2570

Abstract
The growing flood of scholarly literature is exposing the weaknesses of current, citation–based methods of evaluating and filtering articles. A novel and promising approach is to examine the use and citation of articles in a new forum: Web 2.0 services like social bookmarking and microblogging. Metrics based on this data could build a “Scientometics 2.0,” supporting richer and more timely pictures of articles’ impact. This paper develops the most comprehensive list of these services to date, assessing the potential value and availability of data from each. We also suggest the next steps toward building and validating metrics drawn from the social Web.

This Library could be useful for creating visualisations of the relationships in Enhanced Publications

http://thejit.org/demos/

http://wiki.surffoundation.nl/display/vpinfra/1.3+ORE+visualiser

Source: www.nytimes.com/2010/08/24/arts/24peer.html?pagewanted=2&_r=3

“What we’re experiencing now is the most important transformation in our reading and writing tools since the invention of movable type,” said Katherine Rowe, a Renaissance specialist and media historian at Bryn Mawr College. “The way scholarly exchange is moving is radical, and we need to think about what it means for our fields.”

For professors, publishing in elite journals is an unavoidable part of university life. The grueling process of subjecting work to the up-or-down judgment of credentialed scholarly peers has been a cornerstone of academic culture since at least the mid-20th century.

Onderstaand artikel gaat over de trends in Science 2.0

Link: http://firstmonday.org/htbin/cgiwrap/bin/ojs/index.php/fm/article/view/2961/2573

Met dank aan: Wilfred Mijnhardt

Samenvatting:

• Iedereen is auteur en schrijft blogs en tweets (microblog): artikelen met workflow “werk, schrijf, publiceer” daalt. (publish-then-filter approach)

• Meer gefragmenteerde wetenschappelijke output met ‘draft’ status

• Open peer review/discussies van deze wetenschappelijke fragmenten (“Liquid science”)

• Hiervoor moeten alle wetenschappelijke fragmenten publiekelijk toegankelijk zijn

• Alle wetenschappelijke fragmenten worden relationeel met elkaar verbonden, ook de discussies en commentaren zijn waardevol in het wetenschappelijke kenniscreatie proces.

• Wetenschap wordt vergeleken met de “cultural goods market”; wetenschappelijke output met muziek in de entertainment industrie. Wetenschap gaat dezelfde trend door als de entertainement industrie die zich kenmerkt door i) uncertain demand; (ii) short period of profitability; (iii) infinite variety of supply; and, (iv) vertical differentiation of markets.

• • Zoals in de creatieve industrie regelen wetenschappelijke communities de distributie en peer review van de wetenschappelijke fragmenten zelf.
  • De rol van uitgevers als “quality control gatekeeper” wordt op de proefgesteld. Zij moeten het gaan hebben van peer-review services.

• Information overload en reputation management: “trusted filter services” zorgen ervoor dat de juiste persoon de juiste schifting in informatie krijgt aangereikt.  Referenties en links naar deze wetenschappelijke fragmenten vormen het nieuwe reputatie model.

• Reputatie managment wordt het allerbelangrijkste in thet wetenschappelijke communicatie proces. Hiervoor is het van belang dat er zeer betrouwbare reputatie management systemen komen, die open en transparant te werk gaan. (MV: Google is niet open genoeg?) (MV: een betrouwbare Digital Author Identifier is van belang) (MV: horen usage statistics ook bij deze reputatie?)

• Nieuw wetenschappelijk beleid is noodzakelijk om het nieuwe reputatie model niet de overhand te laten krijgen, waar in die lijn, met resources/budgeten gestuurd wordt richting instellingen en individuen met de meeste reputatie. Het niewue beleid moet ervoor zorgen dat “second-tier science” (MV: HBO?) een kans krijgen de wetenschappelijke kennis door te laten vloeien in de rest van de maatschappij.

[presentation by Ben Bosman, @mire]

@mire has build a GUI for statistics on Dspace at the administrator side.

User requirments: a survey has been held. Repository managers would like to see the popularity of items, collectiions or communities.

Technology: They use Apache Solr (fork of Lucene) for indexing and fast search and faceted browsing.

Advantages: statistics are context aware. This means the items are aware of the D-space hierarchy, group items, bitstream and pageviews

Visualize: using the SOLR faceted search, the popular items, collections and communities can be easily shown in matter of milliseconds. This can be represented in charts, and data tables.

Reporting: Also an reporting function is available where the administrator can create reports with the facets they like by the press of a button. This can be exported in different wordprocessing formats and dataformats.

thoughts and possibilities

Within Knowledge Exchange “Usage Statistics” strand the country initiatives PIRUS (UK), OAstatistik (DE) and SURE (NL) are working together to create Guidelines to facilitate the exchange of Usage Statistics. These statistics come from distributed repositories and will be stored in a central database. This database will provide an API where the statistics data can be used in GUI services.

OpenAIRE is creating a GUI with the datavisualisation API’s from Google. (Like we have seen in the presentation about Usage statistics and Google Analytics) However, according to Ben Bosman it is very risky to rely on third party visualisations you cannot control. API specifications can change and the visual design can change.

I was thinking about using the GUI from @mire. In theory it could work, becouse their internal format for storing usage events look very similar to the OpenURL Context Objects. However Ben was very reserved when this idea was postulated. He told me that their GUI is tightly integrated with the Dspace  framework. The eye-candy of their module is great, but it is not OpenSource. This might not be a deadend. We could discover some posibilities.

What is needed to create a GUI with either OpenAIRE or @mire

1. User requirements study: what type of person/role needs what type of information.
2. @mire GUI: A repository tab in the administrator GUI
3. @mire GUI: the xml format they are using for usage events needs to be mapped to the KE format for OpenURL Context Objects. It is quite similar so an XSL might do the trick.

Tip for the people who are implementing OAI-PMH statistics services on repositories. (Dspace, Fedora, eprint)

If you want transmit the Geo location of countries or Cities with the OpenURL Context Objects before scrambling the ip-address, you can use GeoLite. A free version of the mapping of ip-addresses to countries and cities. An API implementation can be used.