Moving beyond free text. Authors Scientist does research Scientist publishes research results in journal article Old Paradigm:

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Presentation transcript:

Moving beyond free text

Authors

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

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

Read 3,404 articles???

Read 592,000 articles???

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

Example – Journal article about gene function

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

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

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

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

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

Science Direct: Scientific Publishers are interested in this problem…

Databases are interested in this problem…

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

Example: Morphological description of species

Example: Morphological description of species

PO: (leaf), PATO: (decreased width) PO: (ovule), PATO: (abnormal) PO: (seed), PATO: (reduced) Example: Mutant phenotype description

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 New Paradigm: