An Analysis of the Abstracts Presented at the Annual Meetings of the Society for Neuroscience from 2001 to 2006

Annual meeting abstracts published by scientific societies often contain rich arrays of information that can be computationally mined and distilled to elucidate the state and dynamics of the subject field. We extracted and processed abstract data from the Society for Neuroscience (SFN) annual meeting abstracts during the period 2001–2006 in order to gain an objective view of contemporary neuroscience. An important first step in the process was the application of data cleaning and disambiguation methods to construct a unified database, since the data were too noisy to be of full utility in the raw form initially available. Using natural language processing, text mining, and other data analysis techniques, we then examined the demographics and structure of the scientific collaboration network, the dynamics of the field over time, major research trends, and the structure of the sources of research funding. Some interesting findings include a high geographical concentration of neuroscience research in the north eastern United States, a surprisingly large transient population (66% of the authors appear in only one out of the six studied years), the central role played by the study of neurodegenerative disorders in the neuroscience community, and an apparent growth of behavioral/systems neuroscience with a corresponding shrinkage of cellular/molecular neuroscience over the six year period. The results from this work will prove useful for scientists, policy makers, and funding agencies seeking to gain a complete and unbiased picture of the community structure and body of knowledge encapsulated by a specific scientific domain

An analysis of the abstracts presented at the annual meetings of the Society for Neuroscience from 2001 to 2006

Annual meeting abstracts published by scientific societies often contain rich arrays of information that can be computationally mined and distilled to elucidate the state and dynamics of the subject field. We extracted and processed abstract data from the Society for Neuroscience (SFN) annual meeting abstracts during the period 2001-2006 in order to gain an objective view of contemporary neuroscience. An important first step in the process was the application of data cleaning and disambiguation methods to construct a unified database, since the data were too noisy to be of full utility in the raw form initially available. Using natural language processing, text mining, and other data analysis techniques, we then examined the demographics and structure of the scientific collaboration network, the dynamics of the field over time, major research trends, and the structure of the sources of research funding. Some interesting findings include a high geographical concentration of neuroscience research in the north eastern United States, a surprisingly large transient population (66% of the authors appear in only one out of the six studied years), the central role played by the study of neurodegenerative disorders in the neuroscience community, and an apparent growth of behavioral/systems neuroscience with a corresponding shrinkage of cellular/molecular neuroscience over the six year period. The results from this work will prove useful for scientists, policy makers, and funding agencies seeking to gain a complete and unbiased picture of the community structure and body of knowledge encapsulated by a specific scientific domain

A review on machine learning approaches and trends in drug discovery

Abstract: Drug discovery aims at finding new compounds with specific chemical properties for the treatment of diseases. In the last years, the approach used in this search presents an important component in computer science with the skyrocketing of machine learning techniques due to its democratization. With the objectives set by the Precision Medicine initiative and the new challenges generated, it is necessary to establish robust, standard and reproducible computational methodologies to achieve the objectives set. Currently, predictive models based on Machine Learning have gained great importance in the step prior to preclinical studies. This stage manages to drastically reduce costs and research times in the discovery of new drugs. This review article focuses on how these new methodologies are being used in recent years of research. Analyzing the state of the art in this field will give us an idea of where cheminformatics will be developed in the short term, the limitations it presents and the positive results it has achieved. This review will focus mainly on the methods used to model the molecular data, as well as the biological problems addressed and the Machine Learning algorithms used for drug discovery in recent years.Instituto de Salud Carlos III; PI17/01826Instituto de Salud Carlos III; PI17/01561Xunta de Galicia; Ref. ED431D 2017/16Xunta de Galicia; Ref. ED431D 2017/23Xunta de Galicia; Ref. ED431C 2018/4

Seeking social capital and expertise in a newly-formed research community: a co-author analysis

This exploratory study applies social network analysis techniques to existing, publicly available data to understand collaboration patterns within the co-author network of a federally-funded, interdisciplinary research program. The central questions asked: What underlying social capital structures can be determined about a group of researchers from bibliometric data and other publicly available existing data? What are ways social network tools characterize the interdisciplinarity or cross-disciplinarity of co-author teams? The names of 411 grantees were searched in the Web of Science indexing database; author information from the WoS search results resulted in a 191-member co-author network. Research domains were included as attribute data for the co-author network. UCINet social network analysis software calculated a large 60 node component and two larger components with 12 and 8 nodes respectively, the remainder of the network consisted of smaller 2-5 node components. Within the 191-node co-author network the following analyses were performed to learn more about the structural social capital of this group: Degree and Eigenvector centrality measures, brokerage measures, and constraint measures. Additionally, ten randomly selected dyads and the five 4-node cliques within the 191-node network were examined to find patterns of cross-disciplinary collaboration among researcher and within award teams. Award numbers were added as attribute data to five 4-node cliques and 10 random dyads; these showed instances of collaboration among interdisciplinary award teams. Collaboration patterns across disciplines are discussed. Data from this research could serve as a baseline measure for growth in future analyses of the case studied. This method is recommended as a tool to gain insights to a research community and to track publication collaboration growth over time. This research method shows potential as a way to identify aspects of a research community’s social structural capital, particularly within an interdisciplinary network to highlight where researchers are working well together or to learn where there is little collaboration

Opportunities at the interface of network science and metabolic modeling

Metabolism plays a central role in cell physiology because it provides the molecular machinery for growth. At the genome-scale, metabolism is made up of thousands of reactions interacting with one another. Untangling this complexity is key to understand how cells respond to genetic, environmental, or therapeutic perturbations. Here we discuss the roles of two complementary strategies for the analysis of genome-scale metabolic models: Flux Balance Analysis (FBA) and network science. While FBA estimates metabolic flux on the basis of an optimization principle, network approaches reveal emergent properties of the global metabolic connectivity. We highlight how the integration of both approaches promises to deliver insights on the structure and function of metabolic systems with wide-ranging implications in discovery science, precision medicine and industrial biotechnology

ResearchFlow: Understanding the Knowledge Flow between Academia and Industry

Understanding, monitoring, and predicting the flow of knowledge between academia and industry is of critical importance for a variety of stakeholders, including governments, funding bodies, researchers, investors, and companies. To this purpose, we introduce ResearchFlow, an approach that integrates semantic technologies and machine learning to quantifying the diachronic behaviour of research topics across academia and industry. ResearchFlow exploits the novel Academia/Industry DynAmics (AIDA) Knowledge Graph in order to characterize each topic according to the frequency in time of the related i) publications from academia, ii) publications from industry, iii) patents from academia, and iv) patents from industry. This representation is then used to produce several analytics regarding the academia/industry knowledge flow and to forecast the impact of research topics on industry. We applied ResearchFlow to a dataset of 3.5M papers and 2M patents in Computer Science and highlighted several interesting patterns. We found that 89.8% of the topics first emerge in academic publications, which typically precede industrial publications by about 5.6 years and industrial patents by about 6.6 years. However this does not mean that academia always dictates the research agenda. In fact, our analysis also shows that industrial trends tend to influence academia more than academic trends affect industry. We evaluated ResearchFlow on the task of forecasting the impact of research topics on the industrial sector and found that its granular characterization of topics improves significantly the performance with respect to alternative solutions

Crowdsourcing Linked Data on listening experiences through reuse and enhancement of library data

Research has approached the practice of musical reception in a multitude of ways, such as the analysis of professional critique, sales figures and psychological processes activated by the act of listening. Studies in the Humanities, on the other hand, have been hindered by the lack of structured evidence of actual experiences of listening as reported by the listeners themselves, a concern that was voiced since the early Web era. It was however assumed that such evidence existed, albeit in pure textual form, but could not be leveraged until it was digitised and aggregated. The Listening Experience Database (LED) responds to this research need by providing a centralised hub for evidence of listening in the literature. Not only does LED support search and reuse across nearly 10,000 records, but it also provides machine-readable structured data of the knowledge around the contexts of listening. To take advantage of the mass of formal knowledge that already exists on the Web concerning these contexts, the entire framework adopts Linked Data principles and technologies. This also allows LED to directly reuse open data from the British Library for the source documentation that is already published. Reused data are re-published as open data with enhancements obtained by expanding over the model of the original data, such as the partitioning of published books and collections into individual stand-alone documents. The database was populated through crowdsourcing and seamlessly incorporates data reuse from the very early data entry phases. As the sources of the evidence often contain vague, fragmentary of uncertain information, facilities were put in place to generate structured data out of such fuzziness. Alongside elaborating on these functionalities, this article provides insights into the most recent features of the latest instalment of the dataset and portal, such as the interlinking with the MusicBrainz database, the relaxation of geographical input constraints through text mining, and the plotting of key locations in an interactive geographical browser