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Moving beyond free text

Moving beyond free text. Authors. Moving beyond free text. Old Paradigm:. Scientist does research. Scientist publishes research results in journal article. Want: All genes involved in seed development (name, species, protein sequence). Read 3,404 articles???. Read 592,000 articles???.

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Moving beyond free text

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  1. Moving beyond free text

  2. Authors Moving beyond free text

  3. Old Paradigm: Scientist does research Scientist publishes research results in journal article

  4. Want: All genes involved in seed development (name, species, protein sequence)

  5. Read 3,404 articles???

  6. Read 592,000 articles???

  7. Old Paradigm - extended: Scientist does research Scientist publishes research results as free text manual curation (+ NLP…?) Results extracted from free text and converted to a structured format (ontology annotations) Database Structured data combined with other data for queries, further analysis

  8. Example – Journal article about gene function

  9. Example – Journal article about gene function The goal: an annotation that captures the result

  10. Example – Journal article about gene function The goal: an annotation that captures the result Manual curation: Time consuming, does not scale well NLP: Very challenging

  11. Example – phylogenetic treatment Relatively high degree of structure compared to journal article May be more amenable to natural language processing but still very challenging, complex information http://www.mobot.org/mobot/research/apweb/welcome.html

  12. Scientist does research Scientist publishes research results as free text manual curation (+ NLP) Can we get authors involved? Results extracted from free text and converted to a structured format (ontology annotations) Database Structured data combined with other data for queries, further analysis

  13. Scientific Publishers are interested in this problem… Link to external resource

  14. Scientific Publishers are interested in this problem… Science Direct: http://www.sciencedirect.com/science/article/pii/S0378111910001502

  15. Scientific Publishers are interested in this problem…

  16. Databases are interested in this problem…

  17. Databases are interested in this problem…

  18. What if we had a good general tool for authors to do this themselves?

  19. Example: Morphological description of species http://herbarium.usu.edu/webmanual/

  20. Example: Morphological description of species http://herbarium.usu.edu/webmanual/

  21. Example: Mutant phenotype description PO:0025034 (leaf), PATO:0000599 (decreased width) PO:0009010 (seed), PATO:0001997 (reduced) PO:0020003 (ovule), PATO:0000460 (abnormal)

  22. New Paradigm: Scientist does research Scientist publishes research results as free text and as annotations using ontology terms Benefit to scientist – wider exposure and reuse of results Benefit to publishers – tagged text allows enhanced presentation for subscribers Benefit to research community – Better access to data

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