References of "Papanikolaou, Nikolas"
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See detailBioTextQuest+: a knowledge integration platform for literature mining and concept discovery
Papanikolaou, Nikolas; Pavlopoulos, Georgios A.; Pafilis, Evangelos et al

in Bioinformatics (2014)

The iterative process of finding relevant information in biomedical literature and performing bioinformatics analyses might result in an endless loop for an inexperienced user, considering the exponential ... [more ▼]

The iterative process of finding relevant information in biomedical literature and performing bioinformatics analyses might result in an endless loop for an inexperienced user, considering the exponential growth of scientific corpora and the plethora of tools designed to mine PubMed® and related biological databases. Herein, we describe BioTextQuest+, a web-based interactive knowledge exploration platform with significant advances to its predecessor (BioTextQuest), aiming to bridge processes such as bioentity recognition, functional annotation, document clustering and data integration towards literature mining and concept discovery. BioTextQuest+ enables PubMed and OMIM querying, retrieval of abstracts related to a targeted request and optimal detection of genes, proteins, molecular functions, pathways and biological processes within the retrieved documents. The front-end interface facilitates the browsing of document clustering per subject, the analysis of term co-occurrence, the generation of tag clouds containing highly represented terms per cluster and at-a-glance popup windows with information about relevant genes and proteins. Moreover, to support experimental research, BioTextQuest+ addresses integration of its primary functionality with biological repositories and software tools able to deliver further bioinformatics services. The Google-like interface extends beyond simple use by offering a range of advanced parameterization for expert users. We demonstrate the functionality of BioTextQuest+ through several exemplary research scenarios including author disambiguation, functional term enrichment, knowledge acquisition and concept discovery linking major human diseases, such as obesity and ageing. [less ▲]

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See detailOnTheFly 2.0: a tool for automatic annotation of files and biological information extraction.
Pafilis, Evangelos; Pavlopoulos, Georgios; Satagopam, Venkata UL et al

Poster (2013)

Retrieving all of the necessary information from databases about bioentities mentioned in an article is not a trivial or an easy task. Following the daily literature about a specific biological topic and ... [more ▼]

Retrieving all of the necessary information from databases about bioentities mentioned in an article is not a trivial or an easy task. Following the daily literature about a specific biological topic and collecting all the necessary information about the bioentities mentioned in the literature manually is tedious and time consuming. OnTheFly 2.0 is a web application mainly designed for non-computer experts which aims to automate data collection and knowledge extraction from biological literature in a user friendly and efficient way. OnTheFly 2.0 is able to extract bioentities from individual articles such as text, Microsoft Word, Excel and PDF files. With a simple drag-and-drop motion, the text of a document is extensively parsed for bioentities such as protein/gene names and chemical compound names. Utilizing high quality data integration platforms, OnTheFly allows the generation of informative summaries, interaction networks and at-a-glance popup windows containing knowledge related to the bioentities found in documents. OnTheFly 2.0 provides a concise application to automate the extraction of bioentities hidden in various documents and is offered as a web based application. [less ▲]

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