ArticlePloS one2012
Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Pre-trained models, data augmentation, and ensemble learning for biomedical information extraction and document classification.Database : the journal of biological databases and curation · 2022Article
- DES-Tcell is a knowledgebase for exploring immunology-related literature.Scientific reports · 2021Article
- Triage of documents containing protein interactions affected by mutations using an NLP based machine learning approach.BMC genomics · 2020Article
- Redox control of vascular biology.BioFactors (Oxford, England) · 2020Review
- DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases.Oxidative medicine and cellular longevity · 2020Article
- Extracting chemical-protein interactions from literature using sentence structure analysis and feature engineering.Database : the journal of biological databases and curation · 2019Article
- Literature-Based Enrichment Insights into Redox Control of Vascular Biology.Oxidative medicine and cellular longevity · 2019Review
- DES-Mutation: System for Exploring Links of Mutations and Diseases.Scientific reports · 2018Article
- DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species.Scientific reports · 2017Article
- Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery.Briefings in bioinformatics · 2016Review
- Fundamentals of protein interaction network mapping.Molecular systems biology · 2015Review
- Article
- Adding protein context to the human protein-protein interaction network to reveal meaningful interactions.PLoS computational biology · 2013Article
- CoCiter: an efficient tool to infer gene function by assessing the significance of literature co-citation.PloS one · 2013Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundProtein interaction networks (PINs) specific within a particular context contain crucial information regarding many cellular biological processes. For example, PINs may include information on the type and directionality of interaction (e.g. phosphorylation), location of interaction (i.e. tissues, cells), and related diseases. Currently, very few tools are capable of deriving context-specific PINs for conducting exploratory analysis.
resultsWe developed a literature-based online system, Context-specific Protein Network Miner (CPNM), which derives context-specific PINs in real-time from the PubMed database based on a set of user-input keywords and enhanced PubMed query system. CPNM reports enriched information on protein interactions (with type and directionality), their network topology with summary statistics (e.g. most densely connected proteins in the network; most densely connected protein-pairs; and proteins connected by most inbound/outbound links) that can be explored via a user-friendly interface. Some of the novel features of the CPNM system include PIN generation, ontology-based PubMed query enhancement, real-time, user-queried, up-to-date PubMed document processing, and prediction of PIN directionality.
conclusionsCPNM provides a tool for biologists to explore PINs. It is freely accessible at http://www.biotextminer.com/CPNM/.
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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.