BITEM free Resources and Tools

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

ruch — Thu, 17 Jun 2021 21:25:46 +0000

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

mottin — Fri, 17 Jul 2020 14:58:49 +0000

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/

Link:

DisprotGUI

UniProt Classifier - UPCLASS

teodoro — Wed, 13 Jun 2018 12:16:29 +0000

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.

Link:

UPCLASS

neXtA5: Accelerating Annotation of Articles via Automated Approaches in neXtProt

mottin — Tue, 06 Sep 2016 09:07:51 +0000

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:

Link:

neXtA5

BMJ and Findzebra use cases in a computable format

gaudinat — Wed, 18 Nov 2015 12:22:23 +0000

https://github.com/HESGE/weird_use_cases

EXPAND Comparator

mottin — Thu, 12 Nov 2015 14:01:47 +0000

Comparator source code for expand project: https://github.com/HESGE/ICD-10-GM_BiTeM-adaptation

TwitterHarvest

gaudinat — Mon, 28 Sep 2015 06:57:18 +0000

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

gaudinat — Mon, 24 Aug 2015 07:18:00 +0000

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

vishnyakova — Thu, 27 Feb 2014 11:39:55 +0000

Language Detector detects a language of the provided text in URL

Link:

Language Detector

PTM: Protein Post-Translational Modification services

ruch — Fri, 26 Apr 2013 13:03:22 +0000

http://eagl.unige.ch/PTM/ !