A<scp>li</scp>B<scp>aba</scp>: PubMed as a graph

Plake, Conrad; Schiemann, Torsten; Pankalla, Marcus; Hakenberg, Jörg; Leser, Ulf

doi:10.1093/bioinformatics/btl408

Cited by 113 publications

(85 citation statements)

References 5 publications

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“…To identify and classify relevant facts for a pilot study of the TWIST1 gene, we provide graphically summarized information on preliminary association by confidence values of textual evidence (Fig. 1d) [43]. Nodes represent biological entities with different colors for different classes.…”

Section: Discussionmentioning

confidence: 99%

Association of TWIST1 gene polymorphisms with bone mineral density in postmenopausal women

et al. 2009

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Section: Discussionmentioning

confidence: 99%

Association of TWIST1 gene polymorphisms with bone mineral density in postmenopausal women

et al. 2009

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“…extends the pairwise co-occurrence model with event extraction and discovery of indirect associations between the biomedical concepts [222]. Based on PubMed abstracts, AliBaba builds networks of interacting proteins, genes-disease associations and subcellular location of proteins [234]. Networks extracted from text can be complemented with experimental data using IntAct [235] and CoPub [236].…”

Section: Building Network and Pathways From Literaturementioning

confidence: 99%

Functional Genomics, Proteomics, Metabolomics and Bioinformatics for Systems Biology

et al. 2013

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This chapter introduces Systems Biology, its context, aims, concepts and strategies, then describes approaches used in genomics, epigenomics, transcriptomics, proteomics, metabolomics and lipidomics, and how recent technological advances in these fields have moved the bottleneck from data production to data analysis. Methods for clustering, feature selection, prediction analysis, text mining and pathway analysis used to analyse and integrate the data produced are then presented.

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“…XplorMed performs statistical analysis of the words in the abstracts of the citations in the query result and proposes query refinements/extensions to the user in a multistep process. Ali Baba [9], [17] displays the results on a graph where edges denote associations between the result nodes, which are typically genes and proteins. iHOP [10] shows to the user the genes associated to a query gene, where the association is measured through co-occurrence in a sentence.…”

Section: B Evaluation Of Execution Times For Heuristic-reducedoptmentioning

confidence: 99%

BioNav: Effective Navigation on Query Results of Biomedical Databases

Kashyap

Hristidis

Petropoulos

et al. 2009

2009 IEEE 25th International Conference on Data Engineering

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Abstract-Search queries on biomedical databases like PubMed often return a large number of results, only a small subset of which is relevant to the user. Ranking and categorization, which can also be combined, have been proposed to alleviate this information overload problem. Results categorization for biomedical databases is the focus of this work. A natural way to organize biomedical citations is according to their MeSH annotations. MeSH is a comprehensive concept hierarchy used by PubMed. In this paper, we present the BioNav system, a novel search interface that enables the user to navigate large number of query results by organizing them using the MeSH concept hierarchy. First, the query results are organized into a navigation tree. At each node expansion step, BioNav reveals only a small subset of the concept nodes, selected such that the expected user navigation cost is minimized. In contrast, previous works expand the hierarchy in a predefined static manner, without navigation cost modelling. We show that the problem of selecting the best concepts to reveal at each node expansion is NP-complete and propose an efficient heuristic as well as a feasible optimal algorithm for relatively small trees. We show experimentally that BioNav outperforms state-of-the-art categorization systems with respect to the user navigation cost. We have implemented BioNav for the MEDLINE database at http://db.cse.buffalo.edu/bionav.

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AliBaba: PubMed as a graph

Abstract: http://alibaba.informatik.hu-berlin.de/

Cited by 113 publications

References 5 publications

Association of TWIST1 gene polymorphisms with bone mineral density in postmenopausal women

Association of TWIST1 gene polymorphisms with bone mineral density in postmenopausal women

Functional Genomics, Proteomics, Metabolomics and Bioinformatics for Systems Biology

BioNav: Effective Navigation on Query Results of Biomedical Databases

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