1,720,991 research outputs found
Creació d’una interfície gràfica d’usuari entre InterMineR i Cytoscape per fer que les bases de dades siguin FAIR
Full text linkTreballs Finals de Grau d'Enginyeria Biomèdica. Facultat de Medicina i Ciències de la Salut. Universitat de Barcelona. Curs: 2020-2021. Directors: Rachel Lyne and Gos Micklem i Tutor: Santiago Marco[spa] InterMine és un sistema del tipus magatzem de dades que permet crear grans bases de dades biològiques fàcilment des de fonts heterogènies en serveis web RESTful.
El sistema proporciona eines estadístiques i d’anàlisis de dades potents. InterMine
com a plataforma té una interfície web des d’on l’usuari pot fer cerques i incorpora
recursos especialitzats com mètodes d’anàlisis d’enriquiment de conjunts de gens.
InterMineR és una de les biblioteques informàtiques que dóna suport a la plataforma
des de l’entorn de programació de R Studio. En aquest projecte, s’han implementat
noves funcionalitats per permetre que l’usuari treballi amb col·leccions i conjunts de
dades creats des de el servei web, anomenats llistes. Les noves funcions han estat
incorporades i publicades en la nova versió del paquet a Bioconductor.
L’objectiu principal d’aquest projecte ha estat la creació d’una interfície gràfica d’usuari
(GUI) per fer cerques a les bases de dades d’InterMine i generar visualitzacions
de xarxes Cytoscape. S’ha desenvolupat un programari executable en entorns d’escriptori.
Aquest permet als usuaris reduir la complexitat de les dades i extreure’n
significat amb fins de recerca. S’espera que permeti analitzar amb més profunditat
les fonts d’InterMine i augmentar-ne la FAIR (dades trobables, accessibles,
interoperables i reutilitzables en anglès).[eng] InterMine is a biological data warehousing system for creating large biological databases of heterogenous data sources easily in RESTful web services. It provides powerful statistical and analysis tools. InterMine as a platform has a web interface in which user can run searches and incorporates specialized resources such as enrichment statistics. InterMineR is one of the software ’client’ libraries that interfaces the biological
databases built using the InterMine platform with a programming environment, in
this case R. In this project, new functionalities have been implemented to enable the
user to work with stored collections of data and saved results sets created from a
web-service, called lists. The new functions have been merged and published in the
new Bioconductor version of the package.
The main aim of this project is to create a graphical user interface (GUI) to query
the InterMine databases and generating Cytoscape network visualizations. We
developed a software that runs on desktop environment. It allows users to reduce the
complexity of the data and extract meaning from it. It will allow data in InterMines
to be further analysed - increasing its FAIRness
The genome sequence of the dinoflagellate Symbiodinium sp., a symbiont from
No full textDinoflagellates are ubiquitous marine and freshwater protists. As free-living
photosynthetic plankton, they account for ~50% of the primary productivity of oceans
and lakes
im-tables-biojs
No full text<p>BioJS InterMine Table component. Supplementary materials for F1000 paper.</p>
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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