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CoLIS Doctoral Forum

CoLIS Doctoral Forum. Objectivity and the Gene Ontology: how do biologists working within the e-science paradigm classify theoretical entities?. Background. Long history of classification in biology Classification feeds the e-science paradigm

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CoLIS Doctoral Forum

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  1. CoLIS Doctoral Forum Objectivity and the Gene Ontology: how do biologists working within the e-science paradigm classify theoretical entities?

  2. Background • Long history of classification in biology • Classification feeds the e-science paradigm • Gene Ontology is a tool for ‘the unification of biology’ • Parallels with LIS research

  3. Research question 1 • What can we learn about the success of the Gene Ontology? • Purpose of question = exploratory / descriptive • Strategy = archival analysis + history • “GO developed quickly because a Consortium controlled the design and creation of the ontology” • “GO was adopted by biologists because it was avowedly realist in its objectives”

  4. Research question 2 • Why do GO annotators index inconsistently? • Purpose of question = explanatory • Strategy = Case study • “Annotation inconsistency is created by the rigid structure and rules of the Gene Ontology” • “Annotators index inconsistently because their subjective appraisals of relevance are different”

  5. Question 1 : What can we learn about the success of the Gene Ontology? Model : Realism, reductionism, sociology Concept : Ontology, universals, particulars, indexing, information Theory : Unity of science, monism, formal ontology, organizational theory Hypothesis : It is easy to classify one reality Methodology : Domain analysis Methods : Archival analysis, bibliometrics, information history, philosophy

  6. Question 2 : Why do GO annotators index inconsistently? Model : Cognitive models of information Concept : Relevance, subjectivity, concept Theory : Ontology, concept theory, relevance theory, STS theory Hypothesis : Biological reality depends on subjective understanding of concepts Methodology : Concept analysis Method : Case study, content analysis, participant observation

  7. Methodology • Epistemological model to balance the objective and subjective qualities of biological knowledge • Bibliometric study of Gene Ontology papers • Archival analysis of Gene Ontology development materials • Concept analysis of specific terms in ontology, and their historical derivation • Case study of Gene Ontology annotators

  8. Problems • What methods are available for analysing semi-structured Sourceforge development threads? • What historical methods are appropriate for studying the recent history of an organisation? • What different methods exist for analysing concepts? • How can I integrate interviews into my research?

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