ReviewBMC bioinformatics2007
LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics.
Review in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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
11 citing papers in PubMed.
- An ontology-guided semantic data integration framework to support integrative data analysis of cancer survival.BMC medical informatics and decision making · 2018Article
- PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasets.Journal of biomedical semantics · 2017Article
- Interfaces to PeptideAtlas: a case study of standard data access systems.Briefings in bioinformatics · 2012Article
- Semantically enabled and statistically supported biological hypothesis testing with tissue microarray databases.BMC bioinformatics · 2011Article
- When one and one gives more than two: challenges and opportunities of integrative omics.Frontiers in genetics · 2011Article
- Data integration for dynamic and sustainable systems biology resources: challenges and lessons learned.Chemistry & biodiversity · 2010Review
- Biomedical informatics and translational medicine.Journal of translational medicine · 2010Review
- Francisella tularensis novicida proteomic and transcriptomic data integration and annotation based on semantic web technologies.BMC bioinformatics · 2009Article
- BioGateway: a semantic systems biology tool for the life sciences.BMC bioinformatics · 2009Article
- Using semantic web technologies to annotate and align microarray designs.Cancer informatics · 2009Article
- Life Sciences and the web: a new era for collaboration.Molecular systems biology · 2008Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
backgroundA key abstraction in representing proteomics knowledge is the notion of unique identifiers for individual entities (e.g. proteins) and the massive graph of relationships among them. These relationships are sometimes simple (e.g. synonyms) but are often more complex (e.g. one-to-many relationships in protein family membership).
resultsWe have built a software system called LinkHub using Semantic Web RDF that manages the graph of identifier relationships and allows exploration with a variety of interfaces. For efficiency, we also provide relational-database access and translation between the relational and RDF versions. LinkHub is practically useful in creating small, local hubs on common topics and then connecting these to major portals in a federated architecture; we have used LinkHub to establish such a relationship between UniProt and the North East Structural Genomics Consortium. LinkHub also facilitates queries and access to information and documents related to identifiers spread across multiple databases, acting as "connecting glue" between different identifier spaces. We demonstrate this with example queries discovering "interologs" of yeast protein interactions in the worm and exploring the relationship between gene essentiality and pseudogene content. We also show how "protein family based" retrieval of documents can be achieved. LinkHub is available at hub.gersteinlab.org and hub.nesg.org with supplement, database models and full-source code.
conclusionLinkHub leverages Semantic Web standards-based integrated data to provide novel information retrieval to identifier-related documents through relational graph queries, simplifies and manages connections to major hubs such as UniProt, and provides useful interactive and query interfaces for exploring the integrated data.
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.