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Methodology capture: discriminating between the "best" and the rest of community practice.

Eales JM, Pinney JW, Stevens RD, Robertson DL - BMC Bioinformatics (2008)

Bottom Line: 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.We propose that the practice of expert authors from the field of evolutionary biology is the closest to contemporary best practice in phylogenetic experimental design.Capturing best practice is, however, a complex task and should also acknowledge the differences between fields such as the specific context of the analysis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Faculty of Life Sciences, University of Manchester, Manchester, UK. james.eales@postgrad.manchester.ac.uk

ABSTRACT

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 evolutionary biology is the closest to contemporary best practice in phylogenetic experimental design. Capturing best practice is, however, a complex task and should also acknowledge the differences between fields such as the specific context of the analysis.

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Usage of phylogenetic terms according to field. Venn diagrams showing the usage of phylogenetic terms in articles from all three fields and those from outside the fields. (A) Shows in which field or fields a term was used during the year when it was first mentioned in our corpus; this demonstrates the origin of the term. (B) Shows usage of terms in the three fields (or outside the three fields) but measures usage across all years; this measures communication of the term between fields.
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Figure 4: Usage of phylogenetic terms according to field. Venn diagrams showing the usage of phylogenetic terms in articles from all three fields and those from outside the fields. (A) Shows in which field or fields a term was used during the year when it was first mentioned in our corpus; this demonstrates the origin of the term. (B) Shows usage of terms in the three fields (or outside the three fields) but measures usage across all years; this measures communication of the term between fields.

Mentions: To further investigate the heterogeneous use of different phylogenetic software and methods between fields for each of our phylogenetic terms we analysed: (i) the field or fields in which it was used in its first year (Figure 4A) and (ii) whether it was ever used in each of the fields (Figure 4B). Interestingly, there are a large number of terms that are only used in their first year of reporting (Figure 4A) in evolutionary biology (49/207) and outside of the three fields (101/207). Very few were used in all fields in their first year (2/207), while many more terms (89/207) are used by all fields at some point, and some are only ever used by one (35/207) or two (55/207) of the fields (Figure 4B). Many terms are first published outside the three fields with 80% (81/101) used at least once by one or more of the three fields studied.


Methodology capture: discriminating between the "best" and the rest of community practice.

Eales JM, Pinney JW, Stevens RD, Robertson DL - BMC Bioinformatics (2008)

Usage of phylogenetic terms according to field. Venn diagrams showing the usage of phylogenetic terms in articles from all three fields and those from outside the fields. (A) Shows in which field or fields a term was used during the year when it was first mentioned in our corpus; this demonstrates the origin of the term. (B) Shows usage of terms in the three fields (or outside the three fields) but measures usage across all years; this measures communication of the term between fields.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2553348&req=5

Figure 4: Usage of phylogenetic terms according to field. Venn diagrams showing the usage of phylogenetic terms in articles from all three fields and those from outside the fields. (A) Shows in which field or fields a term was used during the year when it was first mentioned in our corpus; this demonstrates the origin of the term. (B) Shows usage of terms in the three fields (or outside the three fields) but measures usage across all years; this measures communication of the term between fields.
Mentions: To further investigate the heterogeneous use of different phylogenetic software and methods between fields for each of our phylogenetic terms we analysed: (i) the field or fields in which it was used in its first year (Figure 4A) and (ii) whether it was ever used in each of the fields (Figure 4B). Interestingly, there are a large number of terms that are only used in their first year of reporting (Figure 4A) in evolutionary biology (49/207) and outside of the three fields (101/207). Very few were used in all fields in their first year (2/207), while many more terms (89/207) are used by all fields at some point, and some are only ever used by one (35/207) or two (55/207) of the fields (Figure 4B). Many terms are first published outside the three fields with 80% (81/101) used at least once by one or more of the three fields studied.

Bottom Line: 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.We propose that the practice of expert authors from the field of evolutionary biology is the closest to contemporary best practice in phylogenetic experimental design.Capturing best practice is, however, a complex task and should also acknowledge the differences between fields such as the specific context of the analysis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Faculty of Life Sciences, University of Manchester, Manchester, UK. james.eales@postgrad.manchester.ac.uk

ABSTRACT

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 evolutionary biology is the closest to contemporary best practice in phylogenetic experimental design. Capturing best practice is, however, a complex task and should also acknowledge the differences between fields such as the specific context of the analysis.

Show MeSH