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What is Organic Data Publishing

We are investigating a novel approach to data publishing that is organic in its organization, requires minimal effort from the contributor, has parsimonious design, and is accessible to all scientists as well as other potential contributors. We offer a minimal pre-defined structure, and allow contributors to describe their data by easily defining their own metadata properties to suit their particular datasets, and to reuse common available vocabularies when it is convenient. The normalization of metadata will be organic, as other scientists aggregate datasets in the repository and find the need to aggregate them.

See also this article: “Organic Data Publishing: A New Approach to Scientific Data Sharing”. Workshop on Linked Science (LISC) at the International Semantic Web Conference (ISWC), November 2012.

To create an account, email: Contact.gif

Structured Content in a Semantic Wiki

This site uses a semantic wiki framework, RDF as the semantic representation standard. We have developed it as an extension of Semantic MediaWiki that enables contributors to use structured semantic properties to describe the contents of the wiki.

Another way in which this wiki structures content is though pre-defined categories. Pages can have special categories, which gives the wiki pages a pre-defined semantic structure. Special categories include Task, Answer, Data, Workflow, and ExecutedWorkflow.

In addition, each page has a section called "Structured Properties", where contributors can specify properties and values of the topic of the page. Any contributor can define new properties on the fly. Any contributor can change an existing property by one that is used elsewhere, effectively normalizing the use of the property across pages and therefore across objects.

Contributions are also structured. At the bottom of each page, the contributors to that page are shown together with the details of their contributions to that page. Contributors also have their own pages, which include any background information they wish to share, and where the edits that they have made are automatically summarized and shown.

Accessing Structured Content Externally

Build your own apps with the content of this wiki ! You can find extensive documentation about its API here.

Using Structured Content to Dynamically Create Sections of Wiki Pages

Those properties can then be used to answer queries that aggregate automatically those properties and pages. Below are some examples of how a query can be stated using those structured properties, and the automatically generated table that answers the query. These queries can be used to create dynamically generated content.

Example: Collection

 OwnerNumber of samples
Sample Collection ESIPESIP3,000
Sample Collection ISIISI5,000

Example: Get a List of Lakes

 Area of CatchmentLatitudeLongitude
Lake Monona
Lake Wingra43.053-89.422

Example: Datasets

AvgHourly SMN 2010 03 02Z37.347-120.976
AvgHourly SMN 2010 03 03Z37.347-120.976
AvgHourly SMN 2010 03 04Z37.347-120.976
AvgHourly SMN 2010 03 05Z37.347-120.976
AvgHourly SMN 2010 03 06Z37.347-120.976
AvgHourly SMN 2010 03 07Z37.347-120.976
AvgHourly SMN 2010 03 08Z37.347-120.976
AvgHourly SMN 2010 03 09Z37.347-120.976
AvgHourly SMN 2010 03 10Z37.347-120.976
AvgHourly SMN 2010 03 11Z37.347-120.976
AvgHourly SMN 2010 03 12Z37.347-120.976
AvgHourly SMN 2010 03 13Z37.347-120.976
AvgHourly SMN 2010 03 14Z37.347-120.976
AvgHourly SMN 2010 03 15Z37.347-120.976
AvgHourly SMN 2010 03 16Z37.347-120.976
AvgHourly SMN 2010 03 17Z37.347-120.976
AvgHourly SMN 2010 03 18Z37.347-120.976
AvgHourly SMN 2010 03 19Z37.347-120.976
AvgHourly SMN 2010 03 20Z37.347-120.976
AvgHourly SMN 2010 03 21Z37.347-120.976
AvgHourly SMN 2010 03 22Z37.347-120.976
AvgHourly SMN 2010 03 23Z37.347-120.976
AvgHourly SMN 2010 03 24Z37.347-120.976
AvgHourly SMN 2010 03 25Z37.347-120.976
AvgHourly SMN 2010 03 26Z37.347-120.976
AvgHourly SMN 2010 03 27Z37.347-120.976
AvgHourly SMN 2010 03 28Z37.347-120.976
AvgHourly SMN 2010 03 29Z37.347-120.976
AvgHourly SMN 2010 03 30Z37.347-120.976
… further results

Example: Get a List of Workflow Templates (limit to 5)

{{ #ask: [[Category:Workflow]]
 | mainlabel=Workflows
 | format=broadtable
 | limit=5

Example: Get a List of Workflow Executions (limit to 10)

{{ #ask: [[Category:ExecutedWorkflow]]
 | mainlabel=Executed Workflows
 | format=broadtable
 | limit=10
Executed Workflows
AF EDM Execution 2 March 2012 to 31 March 2012
AF EDM Execution 2 March 2012 to 8 March 2012
AF EM Execution 2 March 2012 to 31 March 2012
AF EM Execution 2 March 2012 to 8 March 2012
AF NTM Execution 2 March 2012 to 31 March 2012
AF NTM Execution 2 March 2012 to 8 March 2012

Example: Get a List of Tasks and their Answers (limited to 5)

{{ #ask: [[Category:Task]]
 | ?Answer
 | mainlabel=Task
 | format=broadtable
 | default=No Tasks in Knowledge Base
 | limit=5
Another SubTask
Calculate CO2 levels for the air around the lake
ESIP curation procedures
Global distribution of carbon in lakes and how they process carbonCarbon Budget for Lake Mendota
Lake Casitas

Example: Get Tasks whose answers have some property set

{{ #ask: [[Category:Task]] [[Answer.Has Dataset::2012-Dataset]]
 | mainlabel=Task
 | format=broadtable
 | ?Answer
Global distribution of carbon in lakes and how they process carbonCarbon Budget for Lake Mendota

Example: Get a particular Task's SubTasks

{{ #ask: [[Global_distribution_of_carbon_in_lakes_and_how_they_process_carbon]]
 | ?SubTask
 | mainlabel=Task
 | format=broadtable
Global distribution of carbon in lakes and how they process carbonCalculate the carbon Budget for a lake
Calculate CO2 levels for the air around the lake