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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, November 2012.

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: Get a List of Lakes

 Area of CatchmentLatitudeLongitude
Lake Monona
Lake Wingra43.053-89.422

Example: Get a List of Geochemistry datasets

No Datasets so far


Get a List of Workflow Templates (limit to 5)

{{ #ask: [[Category:Workflow]]
 | mainlabel=Workflows
 | format=broadtable
 | limit=5
}}
Workflows
AQUAFLOW EDM
AQUAFLOW EM
AQUAFLOW NTM

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


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
}}
TaskAnswer
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

Get a particular Task's SubTasks

{{ #ask: [[Global_distribution_of_carbon_in_lakes_and_how_they_process_carbon]]
 | ?SubTask
 | mainlabel=Task
 | format=broadtable
}}
TaskSubTask
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

Get Tasks whose answers have some property set

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