Formalising Laboratory Reporting Guidelines with Semantic Web Technologies – Motivation – Main Research Question

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Formalising Laboratory Reporting Guidelines with Semantic Web Technologies – Motivation – Main Research Question

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Annotating the Context of Laboratory Experiments

a Case in Column Chromatography

Created by Dena Tahvildari

PhD Candidate VU Amsterdam and Wageningen UR

Collaborators: Anne Vissers, Guus Schreiber, Jan Top

email: d.tahvildari@vu.nl

Problem 1

The reproducibility of the method/protocol is limited

  • insufficient granularity
  • inadequate

Problem 2

the use of reporting guidelines is limited

  • they can be imprecise or ambiguous
  • no computational support

Solution

explicit representation of guidelines and protocols ontologies + NLP

Main Research Question

Can a formal representation of reporting guidelines contribute to the quality of laboratory method descriptions?

Can MIAPE reporting guidelines be used as a knowledge acquisition source to create an ontology?

Method

select a use case -- MIAPE-CC, create vocabulary from MIAPE-CC reporting guidelines, create a corpus: collect "material and method sections" from publications, measure the occurrence of extracted terms in the material and method sections,
7 classes were defined. 83 terms were collected. class hierarchy were defined. properties were identified. encoded into RDF format.
62 published papers were collected from PubMed. create a corpus prepare the corpus match the labels from the vocabulary to the tokens

Result

  • 40 terms never occurred in any of the method description sections (48%).
  • 43 remaining terms occurred at least in one method section (51%).
classes never occurred occurred general descriptors 4 1 sample 9 8 equipment 22 2 mobile Phase 0 2 column run 0 5 pre and post run processes 2 6 column output 13 9

Explanation

authors do not report on the general information in the method sections authors do not use high level classes -- for example the concept "manufacturer" Branched sugar arabinon was obtained from British Sugar – Mcleary. authors use synonyms - eluent is a synonym for "solutions" is synonym for "mobile phase"

Conclusion

MIAPE could be used for creating the required ontology, but it needs to be further elaborated.

The next step

complete the vocabulary -- class hierarchy, properties and instances textual corpus ---> sentence segmentation, measure the concept frequency, outlook: use the vocabulary in an editorial software

Documentation

- Doctoral consortium paper - ESWC2015 - code and data

Back up slides

Definitions

  • Reproducibility
  • Minimum Information About Proteomic Experiment
  • Ontology

Related Work

Annotating the Context of Laboratory Experiments a Case in Column Chromatography Created by Dena Tahvildari PhD Candidate VU Amsterdam and Wageningen UR Collaborators: Anne Vissers, Guus Schreiber, Jan Top email: d.tahvildari@vu.nl