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Mapping the structure and dynamics of genomics-related MeSH terms complex networks.

Siqueiros-García JM, Hernández-Lemus E, García-Herrera R, Robina-Galatas A - PLoS ONE (2014)

Bottom Line: The evolution of such networks in time reflected interesting phenomena in the historical development of genomic research, including what seems to be a phase-transition in a period marked by the completion of the first draft of the Human Genome Project.We also found that different disciplinary areas have different dynamic evolution patterns in their MeSH connectivity networks.In the case of areas related to science, changes in topology were somewhat fast while retaining a certain core-structure, whereas in the humanities, the evolution was pretty slow and the structure resulted highly redundant and in the case of technology related issues, the evolution was very fast and the structure remained tree-like with almost no overlapping terms.

View Article: PubMed Central - PubMed

Affiliation: Ethical, Legal and Social Studies Department, National Institute of Genomic Medicine, Mexico City, D.F., Mexico.

ABSTRACT
It has been proposed that the history and evolution of scientific ideas may reflect certain aspects of the underlying socio-cognitive frameworks in which science itself is developing. Systematic analyses of the development of scientific knowledge may help us to construct models of the collective dynamics of science. Aiming at scientific rigor, these models should be built upon solid empirical evidence, analyzed with formal tools leading to ever-improving results that support the related conclusions. Along these lines we studied the dynamics and structure of the development of research in genomics as represented by the entire collection of genomics-related scientific papers contained in the PubMed database. The analyzed corpus consisted in more than 49,000 articles published in the years 1987 (first appearance of the term Genomics) to 2011, categorized by means of the Medical Subheadings (MeSH) content-descriptors. Complex networks were built where two MeSH terms were connected if they are descriptors of the same article(s). The analysis of such networks revealed a complex structure and dynamics that to certain extent resembled small-world networks. The evolution of such networks in time reflected interesting phenomena in the historical development of genomic research, including what seems to be a phase-transition in a period marked by the completion of the first draft of the Human Genome Project. We also found that different disciplinary areas have different dynamic evolution patterns in their MeSH connectivity networks. In the case of areas related to science, changes in topology were somewhat fast while retaining a certain core-structure, whereas in the humanities, the evolution was pretty slow and the structure resulted highly redundant and in the case of technology related issues, the evolution was very fast and the structure remained tree-like with almost no overlapping terms.

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Related in: MedlinePlus

Global MeSH networks for the period (1987–1990).It is noticeable that there is a progressively growth of the network that induces greater variability in the connection patterns. New terms arise that lead to the generation of a more complex connectivity structure that reduces the relative importance of terms that were initially dominant. Nodes are size and color-coded according with their respective connectivity degree, i.e. big red nodes present a high connectivity, whereas small green nodes have lower values. This is an example of only four years.
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pone-0092639-g001: Global MeSH networks for the period (1987–1990).It is noticeable that there is a progressively growth of the network that induces greater variability in the connection patterns. New terms arise that lead to the generation of a more complex connectivity structure that reduces the relative importance of terms that were initially dominant. Nodes are size and color-coded according with their respective connectivity degree, i.e. big red nodes present a high connectivity, whereas small green nodes have lower values. This is an example of only four years.

Mentions: All global networks displayed are sparse networks [Figures 1 and 2]. According to Watts and Strogatz, small-world topologies might be common to large, sparse or low density networks found in nature [17]. It has been pointed out by others that many real-world complex networks have a small-world effect, but they are different from a real small-world network in that their average path length increases slower than any polynomial function of the system size[16], [18]. If we look up at Figure 3 and Table S1 we may see that there is a strong resemblance of our GNs to small-world networks. Many of the small-world properties networks seem to be modular [16] and this also has implications for our work. If our GNs have a small-world effect topology then it means that genomics, as it has been growing, is becoming a vast sea that is quite navigable with islands of knowledge and lanes between them to be traveled. If GNs have such modular structure is something that remains to be elucidated and is part of our future agenda. Particularly, we would like to see if there are any emergent modules, how are they composed and how do they connect and affect each other. Most of all, emergent modularity might indicate non-trivial ways of organizing collectively produced knowledge, which would be interesting to be studied from a sociological, historical and philosophical point of view.


Mapping the structure and dynamics of genomics-related MeSH terms complex networks.

Siqueiros-García JM, Hernández-Lemus E, García-Herrera R, Robina-Galatas A - PLoS ONE (2014)

Global MeSH networks for the period (1987–1990).It is noticeable that there is a progressively growth of the network that induces greater variability in the connection patterns. New terms arise that lead to the generation of a more complex connectivity structure that reduces the relative importance of terms that were initially dominant. Nodes are size and color-coded according with their respective connectivity degree, i.e. big red nodes present a high connectivity, whereas small green nodes have lower values. This is an example of only four years.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3974714&req=5

pone-0092639-g001: Global MeSH networks for the period (1987–1990).It is noticeable that there is a progressively growth of the network that induces greater variability in the connection patterns. New terms arise that lead to the generation of a more complex connectivity structure that reduces the relative importance of terms that were initially dominant. Nodes are size and color-coded according with their respective connectivity degree, i.e. big red nodes present a high connectivity, whereas small green nodes have lower values. This is an example of only four years.
Mentions: All global networks displayed are sparse networks [Figures 1 and 2]. According to Watts and Strogatz, small-world topologies might be common to large, sparse or low density networks found in nature [17]. It has been pointed out by others that many real-world complex networks have a small-world effect, but they are different from a real small-world network in that their average path length increases slower than any polynomial function of the system size[16], [18]. If we look up at Figure 3 and Table S1 we may see that there is a strong resemblance of our GNs to small-world networks. Many of the small-world properties networks seem to be modular [16] and this also has implications for our work. If our GNs have a small-world effect topology then it means that genomics, as it has been growing, is becoming a vast sea that is quite navigable with islands of knowledge and lanes between them to be traveled. If GNs have such modular structure is something that remains to be elucidated and is part of our future agenda. Particularly, we would like to see if there are any emergent modules, how are they composed and how do they connect and affect each other. Most of all, emergent modularity might indicate non-trivial ways of organizing collectively produced knowledge, which would be interesting to be studied from a sociological, historical and philosophical point of view.

Bottom Line: The evolution of such networks in time reflected interesting phenomena in the historical development of genomic research, including what seems to be a phase-transition in a period marked by the completion of the first draft of the Human Genome Project.We also found that different disciplinary areas have different dynamic evolution patterns in their MeSH connectivity networks.In the case of areas related to science, changes in topology were somewhat fast while retaining a certain core-structure, whereas in the humanities, the evolution was pretty slow and the structure resulted highly redundant and in the case of technology related issues, the evolution was very fast and the structure remained tree-like with almost no overlapping terms.

View Article: PubMed Central - PubMed

Affiliation: Ethical, Legal and Social Studies Department, National Institute of Genomic Medicine, Mexico City, D.F., Mexico.

ABSTRACT
It has been proposed that the history and evolution of scientific ideas may reflect certain aspects of the underlying socio-cognitive frameworks in which science itself is developing. Systematic analyses of the development of scientific knowledge may help us to construct models of the collective dynamics of science. Aiming at scientific rigor, these models should be built upon solid empirical evidence, analyzed with formal tools leading to ever-improving results that support the related conclusions. Along these lines we studied the dynamics and structure of the development of research in genomics as represented by the entire collection of genomics-related scientific papers contained in the PubMed database. The analyzed corpus consisted in more than 49,000 articles published in the years 1987 (first appearance of the term Genomics) to 2011, categorized by means of the Medical Subheadings (MeSH) content-descriptors. Complex networks were built where two MeSH terms were connected if they are descriptors of the same article(s). The analysis of such networks revealed a complex structure and dynamics that to certain extent resembled small-world networks. The evolution of such networks in time reflected interesting phenomena in the historical development of genomic research, including what seems to be a phase-transition in a period marked by the completion of the first draft of the Human Genome Project. We also found that different disciplinary areas have different dynamic evolution patterns in their MeSH connectivity networks. In the case of areas related to science, changes in topology were somewhat fast while retaining a certain core-structure, whereas in the humanities, the evolution was pretty slow and the structure resulted highly redundant and in the case of technology related issues, the evolution was very fast and the structure remained tree-like with almost no overlapping terms.

Show MeSH
Related in: MedlinePlus