ArticleBMC bioinformatics2011
PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Networks Models of Actin Dynamics during Spermatozoa Postejaculatory Life: A Comparison among Human-Made and Text Mining-Based Models.BioMed research international · 2016Pooled it
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- LAITOR4HPC: A text mining pipeline based on HPC for building interaction networks.BMC bioinformatics · 2020Article
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- On the Conformational Dynamics of β-Amyloid Forming Peptides: A Computational Perspective.Frontiers in bioengineering and biotechnology · 2020Review
- Translating cancer genomics into precision medicine with artificial intelligence: applications, challenges and future perspectives.Human genetics · 2019Review
- Biological networks in Parkinson's disease: an insight into the epigenetic mechanisms associated with this disease.BMC genomics · 2017Article
- Text Mining in Biomedical Domain with Emphasis on Document Clustering.Healthcare informatics research · 2017Review
- SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets.Nucleic acids research · 2016Article
- Text Mining for Protein Docking.PLoS computational biology · 2015Article
- DigSee: Disease gene search engine with evidence sentences (version cancer).Nucleic acids research · 2013Article
- SpermatogenesisOnline 1.0: a resource for spermatogenesis based on manual literature curation and genome-wide data mining.Nucleic acids research · 2013Article
- Mapping molecular association networks of nervous system diseases via large-scale analysis of published research.PloS one · 2013Article
- Systems biology elucidates common pathogenic mechanisms between nonalcoholic and alcoholic-fatty liver disease.PloS one · 2013Article
- Adding protein context to the human protein-protein interaction network to reveal meaningful interactions.PLoS computational biology · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBiological function is greatly dependent on the interactions of proteins with other proteins and genes. Abstracts from the biomedical literature stored in the NCBI's PubMed database can be used for the derivation of interactions between genes and proteins by identifying the co-occurrences of their terms. Often, the amount of interactions obtained through such an approach is large and may mix processes occurring in different contexts. Current tools do not allow studying these data with a focus on concepts of relevance to a user, for example, interactions related to a disease or to a biological mechanism such as protein aggregation.
resultsTo help the concept-oriented exploration of such data we developed PESCADOR, a web tool that extracts a network of interactions from a set of PubMed abstracts given by a user, and allows filtering the interaction network according to user-defined concepts. We illustrate its use in exploring protein aggregation in neurodegenerative disease and in the expansion of pathways associated to colon cancer.
conclusionsPESCADOR is a platform independent web resource available at: http://cbdm.mdc-berlin.de/tools/pescador/
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.