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We live in an age of information overload . . .

We live in an age of information overload . . . Attwood TK et al . (2009) Calling International Rescue: knowledge lost in literature and data landslide! Biochemical Journal 424:317–333. . . . and we need help badly. About a million new biomedical journal articles are published annually

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We live in an age of information overload . . .

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  1. We live in an age of information overload . . . Attwood TK et al. (2009) Calling International Rescue: knowledge lost in literature and data landslide! Biochemical Journal 424:317–333.

  2. . . . and we need help badly • About a million new biomedical journal articles are published annually • Without computation assistance to filter and integrate information, we are lost • To permit computers to help us, we need two technologies: • A mechanism for describing things using common machine-readable vocabularies that permit unambiguous definition of entities and their relationships – semantic integration • A mechanism for merging such descriptive information by the use of a common machine-processable format – syntactic integration • Tim Berners-Lee developed the World Wide Web Consortium as an organization to develop technology standards for this: • OWL, the Web Ontology Language, for creating ontologies (structured vocabularies) for describing things • RDF, the Resource Description Framework, for structuring resource descriptions in a common format

  3. A bluffer’s guide to RDF, ontologies and linked data • The principles are very simple • All entities (ontology classes) and their relationships (ontology properties) are identified by unique URIs, thus being semantically defined on the Web • The URIs reference publicly available and commonly accepted ontologies (structured vocabularies), so that the meaning of terms is unambiguous • Each relationship is expressed as a subject– predicate – object‘triple’ • The syntax is defined by W3C’s Resource Description Framework (RDF) • Examples: :my-article rdf:typefabio:JournalArticle . :my-article dc:creator "Shotton, David" . :my-article dc:title “CiTO, the Citation Typing Ontology” . • Such statements can be combined into interconnected information networks (RDF graphs), forming ‘linked data’ • thereby creating a web of knowledge, the Semantic Web • in which the truth content of each original statement is maintained

  4. 20 Questions for Data Management Planning http://www.miidi.org/dmp

  5. First add metadata for the DMP itself

  6. Next, on the second tab, describe your data

  7. Then, on the third tab, describe data sharing and publication

  8. Finally, on the fourth tab, storage, backup and archiving

  9. Using the Save tab, save your DMP as an XML file

  10. Choose to save the file, rather than open it, and specify where

  11. You can view and save your DMP20 Report as HTML . . .

  12. . . . or as RDF, just by clicking the appropriate button

  13. Save your DMP for inclusion in your data package • Save the XML version on your desktop as YourFamilyName.xml • Save the RDF version on your desktop as YourFamilyName.ttl • This saves it in Turtle format, a human-readable version of RDF • N.B. File names should not contain spaces! Use underscores or hypens, e.g. • Stanton-Jones.xml • van_der_Sompel.ttl • Later, you will use DataStage to include these files in your data package and submit them to a data repository

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