BITEM free Resources and Tools

Variomes: A High Recall Search Engine to Support the Curation of Genomic Variants

Precision oncology relies on the use of treatments targeting specific genetic variants. However, identifying clinically actionable variants as well as relevant information likely to be used to treat a patient with a given cancer is a labor-intensive task, which includes searching the literature for a large set of variants. The lack of universally adopted standard nomenclature for variants requires the development of variant-specific literature search engines. We develop a system to perform triage of publications relevant to support an evidence-based decision.

DisprotGUI

DisprotGUI is a service platform developed to help DisProt curators dealing with literature (MEDLINE/PMC).
The documents were fully annotated using the Disprot ontology and indexed into SIBiLS. On the top of that, the search engine is set up to rank the articles according to their potential interest for the curation.
 
Related webservices are described here: http://candy.hesge.ch/disprotGUI/documentation/

UniProt Classifier - UPCLASS

To provide a systematic way of categorizing computationally mapped bibliography in UniProt, we developed a pipeline to automatically classify publications for accession annotations. This service is useful for enriching automatically mapped bibliography in Uniprot but it could be also helpful to help curators to decide whether a publication is relevant for further curation for a protein accession.

 

neXtA5: Accelerating Annotation of Articles via Automated Approaches in neXtProt

An annotation tool developped to help neXtProt curators dealing with litterature.
The tool has been setup on the axis: Diseases, (GO) {Biological Process, Molecular Function, Cellular Components}, and Protein Interactions (focussing on binding). Additional entities (Species, ECO, and drugs) are now annotated for curation purposes.
 
Related webservices are also available via APIs:

TwitterHarvest

This tool allows to harvest twitter continuously from keywords or locations. The harvested results are written on the file system.
https://www.npmjs.com/package/twitter-harvest (and github https://github.com/hesge/twitter-harvest)

Webcheck: An open source monitoring service for web services

This is a really simple monitoring service to check continuoustly health of the Web sites or web services from JSON object or regular expression.
It'is wriitten with Node.js
More information here: 
https://github.com/HESGE/checkweb

Language Detector

Language Detector detects a language of the provided text in URL

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