Imperial College London
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DrJohnPinney

Central Faculty, Graduate School

Teaching Fellow- Data Science Skills Leader
 
 
 
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Contact

 

+44 (0)20 7594 8629j.pinney

 
 
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Location

 

327Sherfield BuildingSouth Kensington Campus

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Summary

 

Publications

Citation

BibTex format

@article{Eales:2008:10.1186/1471-2105-9-359,
author = {Eales, JM and Pinney, JW and Stevens, RD and Robertson, DL},
doi = {10.1186/1471-2105-9-359},
journal = {BMC Bioinformatics},
title = {Methodology capture: discriminating between the "best" and the rest of community practice.},
url = {http://dx.doi.org/10.1186/1471-2105-9-359},
volume = {9},
year = {2008}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - BACKGROUND: The methodologies we use both enable and help define our research. However, as experimental complexity has increased the choice of appropriate methodologies has become an increasingly difficult task. This makes it difficult to keep track of available bioinformatics software, let alone the most suitable protocols in a specific research area. To remedy this we present an approach for capturing methodology from literature in order to identify and, thus, define best practice within a field. RESULTS: Our approach is to implement data extraction techniques on the full-text of scientific articles to obtain the set of experimental protocols used by an entire scientific discipline, molecular phylogenetics. Our methodology for identifying methodologies could in principle be applied to any scientific discipline, whether or not computer-based. We find a number of issues related to the nature of best practice, as opposed to community practice. We find that there is much heterogeneity in the use of molecular phylogenetic methods and software, some of which is related to poor specification of protocols. We also find that phylogenetic practice exhibits field-specific tendencies that have increased through time, despite the generic nature of the available software. We used the practice of highly published and widely collaborative researchers ("expert" researchers) to analyse the influence of authority on community practice. We find expert authors exhibit patterns of practice common to their field and therefore act as useful field-specific practice indicators. CONCLUSION: We have identified a structured community of phylogenetic researchers performing analyses that are customary in their own local community and significantly different from those in other areas. Best practice information can help to bridge such subtle differences by increasing communication of protocols to a wider audience. We propose that the practice of expert authors from the field of evolutio
AU  - Eales,JM
AU  - Pinney,JW
AU  - Stevens,RD
AU  - Robertson,DL
DO  - 10.1186/1471-2105-9-359
PY  - 2008///
TI  - Methodology capture: discriminating between the "best" and the rest of community practice.
T2  - BMC Bioinformatics
UR  - http://dx.doi.org/10.1186/1471-2105-9-359
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18761740&query_hl=1
VL  - 9
ER  -
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