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Article ; Online: Variomes: a high recall search engine to support the curation of genomic variants.

Pasche, Emilie / Mottaz, Anaïs / Caucheteur, Déborah / Gobeill, Julien / Michel, Pierre-André / Ruch, Patrick

2022 Volume 38, Issue 9, Page(s) 2595–2601

Abstract: Motivation: Identification and interpretation of clinically actionable variants is a critical bottleneck. Searching for evidence in the literature is mandatory according to ASCO/AMP/CAP practice guidelines; however, it is both labor-intensive and error- ... ...

Abstract	Motivation: Identification and interpretation of clinically actionable variants is a critical bottleneck. Searching for evidence in the literature is mandatory according to ASCO/AMP/CAP practice guidelines; however, it is both labor-intensive and error-prone. We developed a system to perform triage of publications relevant to support an evidence-based decision. The system is also able to prioritize variants. Our system searches within pre-annotated collections such as MEDLINE and PubMed Central. Results: We assess the search effectiveness of the system using three different experimental settings: literature triage; variant prioritization and comparison of Variomes with LitVar. Almost two-thirds of the publications returned in the top-5 are relevant for clinical decision-support. Our approach enabled identifying 81.8% of clinically actionable variants in the top-3. Variomes retrieves on average +21.3% more articles than LitVar and returns the same number of results or more results than LitVar for 90% of the queries when tested on a set of 803 queries; thus, establishing a new baseline for searching the literature about variants. Availability and implementation: Variomes is publicly available at https://candy.hesge.ch/Variomes. Source code is freely available at https://github.com/variomes/sibtm-variomes. SynVar is publicly available at https://goldorak.hesge.ch/synvar. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Search Engine ; Genomics/methods ; Genome ; PubMed ; Software
Language	English
Publishing date	2022-03-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btac146
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Assessing the use of supplementary materials to improve genomic variant discovery.

Pasche, Emilie / Mottaz, Anaïs / Gobeill, Julien / Michel, Pierre-André / Caucheteur, Déborah / Naderi, Nona / Ruch, Patrick

Database : the journal of biological databases and curation

2023 Volume 2023

Abstract: The curation of genomic variants requires collecting evidence not only in variant knowledge bases but also in the literature. However, some variants result in no match when searched in the scientific literature. Indeed, it has been reported that a ... ...

Abstract	The curation of genomic variants requires collecting evidence not only in variant knowledge bases but also in the literature. However, some variants result in no match when searched in the scientific literature. Indeed, it has been reported that a significant subset of information related to genomic variants are not reported in the full text, but only in the supplementary materials associated with a publication. In the study, we present an evaluation of the use of supplementary data (SD) to improve the retrieval of relevant scientific publications for variant curation. Our experiments show that searching SD enables to significantly increase the volume of documents retrieved for a variant, thus reducing by ∼63% the number of variants for which no match is found in the scientific literature. SD thus represent a paramount source of information for curating variants of unknown significance and should receive more attention by global research infrastructures, which maintain literature search engines. Database URL https://www.expasy.org/resources/variomes.
MeSH term(s)	Search Engine ; Databases, Factual ; Genomics
Language	English
Publishing date	2023-04-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2496706-3
ISSN	1758-0463 ; 1758-0463
ISSN (online)	1758-0463
ISSN	1758-0463
DOI	10.1093/database/baad017
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts.

Gobeill, Julien / Caucheteur, Déborah / Michel, Pierre-André / Mottin, Luc / Pasche, Emilie / Ruch, Patrick

Nucleic acids research

2020 Volume 48, Issue W1, Page(s) W12–W16

Abstract: Thanks to recent efforts by the text mining community, biocurators have now access to plenty of good tools and Web interfaces for identifying and visualizing biomedical entities in literature. Yet, many of these systems start with a PubMed query, which ... ...

Abstract	Thanks to recent efforts by the text mining community, biocurators have now access to plenty of good tools and Web interfaces for identifying and visualizing biomedical entities in literature. Yet, many of these systems start with a PubMed query, which is limited by strong Boolean constraints. Some semantic search engines exploit entities for Information Retrieval, and/or deliver relevance-based ranked results. Yet, they are not designed for supporting a specific curation workflow, and allow very limited control on the search process. The Swiss Institute of Bioinformatics Literature Services (SIBiLS) provide personalized Information Retrieval in the biological literature. Indeed, 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 (https://candy.hesge.ch/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. They cover MEDLINE and PubMed Central Open Access enriched by nearly 2 billion of mapped biomedical entities, and are daily updated.
MeSH term(s)	Data Mining/methods ; MEDLINE ; Precision Medicine ; Search Engine
Language	English
Publishing date	2020-05-04
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkaa328
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Text-Mining Services of the Swiss Variant Interpretation Platform for Oncology.

Caucheteur, Déborah / Gobeill, Julien / Mottaz, Anaïs / Pasche, Emilie / Michel, Pierre-André / Mottin, Luc / Stekhoven, Daniel J / Barbié, Valérie / Ruch, Patrick

Studies in health technology and informatics

2020 Volume 270, Page(s) 884–888

Abstract: The Swiss Variant Interpretation Platform for Oncology is a centralized, joint and curated database for clinical somatic variants piloted by a board of Swiss healthcare institutions and operated by the SIB Swiss Institute of Bioinformatics. To support ... ...

Abstract	The Swiss Variant Interpretation Platform for Oncology is a centralized, joint and curated database for clinical somatic variants piloted by a board of Swiss healthcare institutions and operated by the SIB Swiss Institute of Bioinformatics. To support this effort, SIB Text Mining designed a set of text analytics services. This report focuses on three of those services. First, the automatic annotations of the literature with a set of terminologies have been performed, resulting in a large annotated version of MEDLINE and PMC. Second, a generator of variant synonyms for single nucleotide variants has been developed using publicly available data resources, as well as patterns of non-standard formats, often found in the literature. Third, a literature ranking service enables to retrieve a ranked set of MEDLINE abstracts given a variant and optionally a diagnosis. The annotation of MEDLINE and PMC resulted in a total of respectively 785,181,199 and 1,156,060,212 annotations, which means an average of 26 and 425 annotations per abstract and full-text article. The generator of variant synonyms enables to retrieve up to 42 synonyms for a variant. The literature ranking service reaches a precision (P10) of 63%, which means that almost two-thirds of the top-10 returned abstracts are judged relevant. Further services will be implemented to complete this set of services, such as a service to retrieve relevant clinical trials for a patient and a literature ranking service for full-text articles.
MeSH term(s)	Abstracting and Indexing ; Computational Biology ; Data Mining ; Humans ; MEDLINE ; Switzerland
Language	English
Publishing date	2020-06-22
Publishing country	Netherlands
Document type	Journal Article
ISSN	1879-8365
ISSN (online)	1879-8365
DOI	10.3233/SHTI200288
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The Feature-Viewer: a visualization tool for positional annotations on a sequence.

Paladin, Lisanna / Schaeffer, Mathieu / Gaudet, Pascale / Zahn-Zabal, Monique / Michel, Pierre-André / Piovesan, Damiano / Tosatto, Silvio C E / Bairoch, Amos

Bioinformatics (Oxford, England)

2020 Volume 36, Issue 10, Page(s) 3244–3245

Abstract: Summary: The Feature-Viewer is a lightweight library for the visualization of biological data mapped to a protein or nucleotide sequence. It is designed for ease of use while allowing for a full customization. The library is already used by several ... ...

Abstract	Summary: The Feature-Viewer is a lightweight library for the visualization of biological data mapped to a protein or nucleotide sequence. It is designed for ease of use while allowing for a full customization. The library is already used by several biological data resources and allows intuitive visual mapping of a full spectra of sequence features for different usages. Availability and implementation: The Feature-Viewer is open source, compatible with state-of-the-art development technologies and responsive, also for mobile viewing. Documentation and usage examples are available online.
MeSH term(s)	Computers ; Software
Language	English
Publishing date	2020-01-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btaa055
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: The neXtProt peptide uniqueness checker: a tool for the proteomics community

Schaeffer, Mathieu / Gateau, Alain / Teixeira, Daniel / Michel, Pierre-André / Zahn-Zabal, Monique / Lane, Lydie

Bioinformatics. 2017 Nov. 01, v. 33, no. 21

2017

Abstract: The neXtProt peptide uniqueness checker allows scientists to define which peptides can be used to validate the existence of human proteins, i.e. map uniquely versus multiply to human protein sequences taking into account isobaric substitutions, ... ...

Abstract	The neXtProt peptide uniqueness checker allows scientists to define which peptides can be used to validate the existence of human proteins, i.e. map uniquely versus multiply to human protein sequences taking into account isobaric substitutions, alternative splicing and single amino acid variants. The pepx program is available at https://github.com/calipho-sib/pepx and can be launched from the command line or through a cgi web interface. Indexing requires a sequence file in FASTA format. The peptide uniqueness checker tool is freely available on the web at https://www.nextprot.org/tools/peptide-uniqueness-checker and from the neXtProt API at https://api.nextprot.org/. lydie.lane@sib.swiss
Keywords	alternative splicing ; amino acid sequences ; amino acids ; bioinformatics ; humans ; peptides ; proteins ; proteomics ; user interface
Language	English
Dates of publication	2017-1101
Size	p. 3471-3472.
Publishing place	Oxford University Press
Document type	Article
ZDB-ID	1468345-3
ISSN	1460-2059 ; 1367-4811 ; 1367-4803
ISSN (online)	1460-2059 ; 1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btx318
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Designing an Optimal Expansion Method to Improve the Recall of a Genomic Variant Curation-Support Service.

Mottaz, Anaïs / Pasche, Emilie / Michel, Pierre-André / Mottin, Luc / Teodoro, Douglas / Ruch, Patrick

Studies in health technology and informatics

2017 Volume 294, Page(s) 839–843

Abstract: The importance of genomic data for health is rapidly growing but accessing and gathering information about variants from different sources is hindered by highly heterogeneous representations of variants, as outlined by clinical associations (AMP/ASCO/CAP) ...

Abstract	The importance of genomic data for health is rapidly growing but accessing and gathering information about variants from different sources is hindered by highly heterogeneous representations of variants, as outlined by clinical associations (AMP/ASCO/CAP) in their recommendations. To enable a smooth and effective retrieval of variant-containing documents from different resources, we developed a tool (https://goldorak.hesge.ch/synvar/) that generates for any given SNP - including variant not present in existing databases - its corresponding description at the genome, transcript and protein levels. It provides variant descriptions in the HGVS format as well as in many non-standard formats found in the literature along with database identifiers. We present the SynVar service and evaluate its impact on the recall of a genomic variant curation-support service. Using SynVar to search variants in the literature enables to increase the recall by +133.8% without a strong impact on precision (i.e. 93%).
MeSH term(s)	Databases, Factual ; Genomics
Language	English
Publishing date	2017-10-05
Publishing country	Netherlands
Document type	Journal Article
ISSN	1879-8365
ISSN (online)	1879-8365
DOI	10.3233/SHTI220603
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The neXtProt peptide uniqueness checker: a tool for the proteomics community.

Schaeffer, Mathieu / Gateau, Alain / Teixeira, Daniel / Michel, Pierre-André / Zahn-Zabal, Monique / Lane, Lydie

Bioinformatics (Oxford, England)

2017 Volume 33, Issue 21, Page(s) 3471–3472

Abstract: Summary: The neXtProt peptide uniqueness checker allows scientists to define which peptides can be used to validate the existence of human proteins, i.e. map uniquely versus multiply to human protein sequences taking into account isobaric substitutions, ...

Abstract	Summary: The neXtProt peptide uniqueness checker allows scientists to define which peptides can be used to validate the existence of human proteins, i.e. map uniquely versus multiply to human protein sequences taking into account isobaric substitutions, alternative splicing and single amino acid variants. Availability and implementation: The pepx program is available at https://github.com/calipho-sib/pepx and can be launched from the command line or through a cgi web interface. Indexing requires a sequence file in FASTA format. The peptide uniqueness checker tool is freely available on the web at https://www.nextprot.org/tools/peptide-uniqueness-checker and from the neXtProt API at https://api.nextprot.org/. Contact: lydie.lane@sib.swiss.
MeSH term(s)	Databases, Protein ; Humans ; Peptides/analysis ; Proteins/analysis ; Proteomics/methods ; Software
Chemical Substances	Peptides ; Proteins
Language	English
Publishing date	2017-06-27
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btx318
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Conference proceedings ; Online: Text-Mining Services of the Swiss Variant Interpretation Platform for Oncology

Caucheteur, Déborah / Gobeill, Julien / Mottaz, Anaïs / Pasche, Emilie / Michel, Pierre-André / Mottin, Luc / Stekhoven, Daniel J. / Barbié, Valérie / Ruch, Patrick

Studies in Health Technology and Informatics, 270 ; Digital Personalized Health and Medicine

2020

Abstract	The Swiss Variant Interpretation Platform for Oncology is a centralized, joint and curated database for clinical somatic variants piloted by a board of Swiss healthcare institutions and operated by the SIB Swiss Institute of Bioinformatics. To support this effort, SIB Text Mining designed a set of text analytics services. This report focuses on three of those services. First, the automatic annotations of the literature with a set of terminologies have been performed, resulting in a large annotated version of MEDLINE and PMC. Second, a generator of variant synonyms for single nucleotide variants has been developed using publicly available data resources, as well as patterns of non-standard formats, often found in the literature. Third, a literature ranking service enables to retrieve a ranked set of MEDLINE abstracts given a variant and optionally a diagnosis. The annotation of MEDLINE and PMC resulted in a total of respectively 785,181,199 and 1,156,060,212 annotations, which means an average of 26 and 425 annotations per abstract and full-text article. The generator of variant synonyms enables to retrieve up to 42 synonyms for a variant. The literature ranking service reaches a precision (P10) of 63%, which means that almost two-thirds of the top-10 returned abstracts are judged relevant. Further services will be implemented to complete this set of services, such as a service to retrieve relevant clinical trials for a patient and a literature ranking service for full-text articles. ISSN:0926-9630 ISSN:1879-8365
Keywords	Precision medicine ; Literature ; Variant ; Terminology ; Text-mining
Subject code	020
Language	English
Publisher	IOS Press
Publishing country	ch
Document type	Conference proceedings ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The neXtProt knowledgebase in 2020: data, tools and usability improvements.

Zahn-Zabal, Monique / Michel, Pierre-André / Gateau, Alain / Nikitin, Frédéric / Schaeffer, Mathieu / Audot, Estelle / Gaudet, Pascale / Duek, Paula D / Teixeira, Daniel / Rech de Laval, Valentine / Samarasinghe, Kasun / Bairoch, Amos / Lane, Lydie

Nucleic acids research

2019 Volume 48, Issue D1, Page(s) D328–D334

Abstract: The neXtProt knowledgebase (https://www.nextprot.org) is an integrative resource providing both data on human protein and the tools to explore these. In order to provide comprehensive and up-to-date data, we evaluate and add new data sets. We describe ... ...

Abstract	The neXtProt knowledgebase (https://www.nextprot.org) is an integrative resource providing both data on human protein and the tools to explore these. In order to provide comprehensive and up-to-date data, we evaluate and add new data sets. We describe the incorporation of three new data sets that provide expression, function, protein-protein binary interaction, post-translational modifications (PTM) and variant information. New SPARQL query examples illustrating uses of the new data were added. neXtProt has continued to develop tools for proteomics. We have improved the peptide uniqueness checker and have implemented a new protein digestion tool. Together, these tools make it possible to determine which proteases can be used to identify trypsin-resistant proteins by mass spectrometry. In terms of usability, we have finished revamping our web interface and completely rewritten our API. Our SPARQL endpoint now supports federated queries. All the neXtProt data are available via our user interface, API, SPARQL endpoint and FTP site, including the new PEFF 1.0 format files. Finally, the data on our FTP site is now CC BY 4.0 to promote its reuse.
MeSH term(s)	Databases, Protein ; Humans ; Internet ; Knowledge Bases ; Mass Spectrometry ; Peptides/chemistry ; Protein Kinases/chemistry ; Protein Kinases/metabolism ; Protein Processing, Post-Translational ; Proteins/chemistry ; Proteins/genetics ; Proteins/metabolism ; Sequence Analysis, RNA ; Software ; Trypsin ; User-Computer Interface
Chemical Substances	Peptides ; Proteins ; Protein Kinases (EC 2.7.-) ; Trypsin (EC 3.4.21.4)
Language	English
Publishing date	2019-12-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkz995
Database	MEDical Literature Analysis and Retrieval System OnLINE

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