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BITEM free Resources and Tools

SIBiLS - Swiss Institute of Bioinformatics Literature Services

SIBiLS allow fully customizable search in semantically enriched contents, based on keywords and/or mapped biomedical entities from a growing set of standardized and legacy vocabularies. The services have been used and favourably evaluated to assist the curation of genes and gene products, by delivering customized literature triage engines to different curation teams. SIBiLS are freely accessible via REST APIs and are ready to empower any curation workflow, built on modern technologies scalable with big data: MongoDB and Elasticsearch.

BMJ and Findzebra use cases in a computable format

We formatted these resources to generate a set of relevance judgements for the evaluation of Clinical Decision Support Systems in the field of Rare Diseases. We merged two originally published BMJ and IJMI data sets in a convenient and interoperable format following TREC standards (QREL). Such a benchmark is appropriate to assess the effectiveness of the WeIRD diagnosis support system.

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.

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.

eBioDiv - Literature services for BioDiversity

The proposed e-BiodDiv can be defined like open biodiversity FAIR-ification services for biospecimens stored in Swiss natural history museums. It will on the one hand provide a service for Swiss biodiversity scientists to access and disseminate their research data about species in legacy and prospective publications, provide access to data about their collections, scientists and specimens. It will complement the recently funded SwissBioCollection program and genomic data. On the other hand, importing treatments into SIBiLS opens them for text and data mining through SIBiLS dedicated tools, and by the life science community.

UPCLASS - UniProt Classifier

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.

EXPAND Comparator

Comparator source code for expand project

  • MVC-MTC: functions delta_MVC_MTC() + translation()
  • MVC-HUG: function transcoding_Map_HUG()