Semantic MediaWiki BCHB697

Outline Wikipedia & MediaWiki Semantic MediaWiki Collecting and sharing community-based knowledge about "stuff" Not good for lists, collections, aggregations Semantic MediaWiki ...for semantic tagging of content …using templates and categories to structure pages …as triple-store …for generation of aggregate/tabulated content …as triple-store presentation layer …for form-based user-input BCHB697 - Edwards

Wikipedia & MediaWiki Wikipedia MediaWiki is the software "stack" Individuals create, edit, discuss human readable text articles - knowledge Simple markup language (WikiText) Headings, links, images, tables, … MediaWiki is the software "stack" Linux, Apache, MySQL, PHP (LAMP) BCHB697 - Edwards

Wikipedia Page BCHB697 - Edwards

Wikipedia List Page BCHB697 - Edwards

Wikipedia List Page BCHB697 - Edwards

Wikipedia List Pages Who maintains the list? How to keep the list content consistent with each page? How can the information on each page be extracted to form/format the list? What about other aggregate information? Oldest, youngest president? Longest serving? Number of republican presidents? BCHB697 - Edwards

Wikipedia lacks Semantics BCHB697 - Edwards

Wikipedia lacks Semantics BCHB697 - Edwards

Semantic MediaWiki Augment the MediaWiki software to permit semantic annotation of wiki pages inline with WikiText markup. Name: Thomas Jefferson; Category: US President, US Vice President, Founding Father; Elected: 1801; Ordinal: 3; Terms: 2 ... [[Name::Thomas Jefferson]] served [[Terms::2]] terms as [[Category::US President]]. ... BCHB697 - Edwards

Semantic MediaWiki Categories Properties Templates (…from MediaWiki) Define the type of page: US President Properties Define the semantic values a page can hold – property name and datatype Example: Name, Elected, Ordinal, Terms Datatypes: Number, Date, Page, Text, … Templates (…from MediaWiki) Automatic, parameterized generation of WikiText incl. semantic annotations BCHB697 - Edwards

Semantic MediaWiki …becomes… {{USPresident |name=Thomas Jefferson |terms=2 }} …becomes… [[Name::Thomas Jefferson]] served [[Terms::2]] terms as [[Category::US President]]. BCHB697 - Edwards

Thomas Jefferson (US President) Semantic MediaWiki {{USPresident |name=Thomas Jefferson |terms=2 }} …becomes… Thomas Jefferson (US President) Elected 1801 Terms 2 BCHB697 - Edwards

Semantic MediaWiki as Triple-Store Conceptually, SMW is a triple-store: TS: Subject, predicate, object SMW: Page, property, value The page URL in SMW becomes the URI When the value of a SMW property is of datatype Page, we are linking URIs SMW provides a triple-store "view" of each page's properties and their values BCHB697 - Edwards

Semantic MediaWiki as Triple-Store BCHB697 - Edwards

Semantic MediaWiki as Triple-Store BCHB697 - Edwards

Semantic MediaWiki as Triple-Store BCHB697 - Edwards

Semantic MediaWiki for generation of aggregations Inline "queries" generate lists, tables, etc. based on semantic annotation …becomes… {{#ask: [[Category:US President]] }} George Washington, John Adams, Thomas Jefferson, ... BCHB697 - Edwards

Semantic MediaWiki for generation of aggregations BCHB697 - Edwards

Semantic MediaWiki for generation of aggregations BCHB697 - Edwards

Semantic MediaWiki for generation of aggregations BCHB697 - Edwards

Semantic MediaWiki for generation of aggregations BCHB697 - Edwards

Semantic MediaWiki for generation of aggregations BCHB697 - Edwards

Semantic MediaWiki as presentation layer Notice that SMW provides Instance pages, Tables, lists of related content, WikiText presentation (incl. images) SMW can also integrate with triple-store "back-end" to support sharing triples by SPARQL SMW is a sharable triple-store with a presentation layer BCHB697 - Edwards

SMW triples via SPARQL BCHB697 - Edwards

Semantic MediaWiki for User-Contributions The core use-case for MediaWiki is community (user) contributions Can we expect users to edit this? {{Motif |accession=G59126YU |aglycon=Ser/Thr |collection=GM |displayhgv=true |glytoucan=G59126YU |name=O-Linked mannose O-Mannosyl Glycan / Mammalian O-Mannosyl Glycan-Mammalian |redend=true |topology=GM.G59126YU }} BCHB697 - Edwards

Semantic MediaWiki for User-Contributions: Page Forms BCHB697 - Edwards

Semantic MediaWiki: Pros Easy presentation of triple-store data-model Inline queries provide access to data-model in arbitrary pages User data-model provides for community contributions, and Page Forms makes it easy to develop controlled entry forms Triple-store data can be exposed via SPARQL for others to re-use. BCHB697 - Edwards

Semantic MediaWiki: Cons Not really designed for automated creating and editing of pages Python modules for bots exist, but… …slow. Don't get full presentation flexibility of HTML + JavaScript We have been exploring the use of JS widgets Triples generated by SMW don't look quite like hand-crafted ontology driven triples… BCHB697 - Edwards

Exercise Check out the SMW sites: GlycoMotif, and SNPedia Look at the source of an entry, look for templates and semantic content Look at the property values in "Browse properties" BCHB697 - Edwards