Information retrieval ≈ Information retrieval
View article: Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update Open
Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of …
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The 2021 WHO Classification of Tumors of the Central Nervous System: a summary Open
The fifth edition of the WHO Classification of Tumors of the Central Nervous System (CNS), published in 2021, is the sixth version of the international standard for the classification of brain and spinal cord tumors. Building on the 2016 u…
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Complex heatmaps reveal patterns and correlations in multidimensional genomic data Open
Summary: Parallel heatmaps with carefully designed annotation graphics are powerful for efficient visualization of patterns and relationships among high dimensional genomic data. Here we present the ComplexHeatmap package that provides ric…
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The Cambridge Structural Database Open
The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal–organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of …
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MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization Open
This article describes several features in the MAFFT online service for multiple sequence alignment (MSA). As a result of recent advances in sequencing technologies, huge numbers of biological sequences are available and the need for MSAs …
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UniProt: the Universal Protein Knowledgebase in 2023 Open
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication we describe enhancements made to our data…
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SQuAD: 100,000+ Questions for Machine Comprehension of Text Open
We present the Stanford Question Answering Dataset (SQuAD), a new reading comprehension dataset consisting of 100,000+ questions posed by crowdworkers on a set of Wikipedia articles, where the answer to each question is a segment of text f…
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DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update) Open
DAVID is a popular bioinformatics resource system including a web server and web service for functional annotation and enrichment analyses of gene lists. It consists of a comprehensive knowledgebase and a set of functional analysis tools. …
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User's guide to correlation coefficients Open
When writing a manuscript, we often use words such as perfect, strong, good or weak to name the strength of the relationship between variables. However, it is unclear where a good relationship turns into a strong one. The same strength of …
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PRESS Peer Review of Electronic Search Strategies: 2015 Guideline Statement Open
The PRESS 2015 Guideline Statement should help to guide and improve the peer review of electronic literature search strategies.
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UniProt: the universal protein knowledgebase Open
The UniProt knowledgebase is a large resource of protein sequences and associated detailed annotation. The database contains over 60 million sequences, of which over half a million sequences have been curated by experts who critically revi…
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The EMBL-EBI search and sequence analysis tools APIs in 2019 Open
The EMBL-EBI provides free access to popular bioinformatics sequence analysis applications as well as to a full-featured text search engine with powerful cross-referencing and data retrieval capabilities. Access to these services is provid…
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The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019 Open
This FAIRsharing record describes: The Genome-Wide Association Studies (GWAS) Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with ot…
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ClinVar: improving access to variant interpretations and supporting evidence Open
ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) is a freely available, public archive of human genetic variants and interpretations of their significance to disease, maintained at the National Institutes of Health. Interpretations of the c…
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MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights Open
Since its first release over a decade ago, the MetaboAnalyst web-based platform has become widely used for comprehensive metabolomics data analysis and interpretation. Here we introduce MetaboAnalyst version 5.0, aiming to narrow the gap f…
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The Gene Ontology resource: enriching a GOld mine Open
The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two y…
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The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications Open
UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode-the nuclear ribosomal internal transcribed spacer (ITS) region-and off…
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Deep Neural Networks for YouTube Recommendations Open
YouTube represents one of the largest scale and most sophisticated industrial recommendation systems in existence. In this paper, we describe the system at a high level and focus on the dramatic performance improvements brought by deep lea…
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The Reactome Pathway Knowledgebase Open
The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism, and other cellular processes as an ordered network of molecular transformations-an extended versio…
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Scene Parsing through ADE20K Dataset Open
Scene parsing, or recognizing and segmenting objects and stuff in an image, is one of the key problems in computer vision. Despite the community's efforts in data collection, there are still few image datasets covering a wide range of scen…
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Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks Open
Large pre-trained language models have been shown to store factual knowledge in their parameters, and achieve state-of-the-art results when fine-tuned on downstream NLP tasks. However, their ability to access and precisely manipulate knowl…
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ANALISIS DATA KUALITATIF Open
Data collection is interactive with data analysis, data collection is an integral part of data analysis activities. Data reduction is an attempt to deduce data, then sorting through data in certain conceptual units, certain categories, and…
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Journal of Education and Practice Open
The purpose of this study was to examine the interaction effects of gender and programs of study on attitudes of postgraduate diploma in teaching (PGDT) students towards the teaching profession. The main aim of the study was to find out wh…
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DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants Open
The information about the genetic basis of human diseases lies at the heart of precision medicine and drug discovery. However, to realize its full potential to support these goals, several problems, such as fragmentation, heterogeneity, av…
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Semantics derived automatically from language corpora contain human-like biases Open
Machines learn what people know implicitly AlphaGo has demonstrated that a machine can learn how to do things that people spend many years of concentrated study learning, and it can rapidly learn how to do them better than any human can. C…
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CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database Open
The Comprehensive Antibiotic Resistance Database (CARD; http://arpcard.mcmaster.ca) is a manually curated resource containing high quality reference data on the molecular basis of antimicrobial resistance (AMR), with an emphasis on the gen…
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Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool Open
The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the management, display, annotation and manipulation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 6 introduces a modern…
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Citation-based clustering of publications using CitNetExplorer and VOSviewer Open
Clustering scientific publications in an important problem in bibliometric research. We demonstrate how two software tools, CitNetExplorer and VOSviewer, can be used to cluster publications and to analyze the resulting clustering solutions…
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Heatmapper: web-enabled heat mapping for all Open
Heatmapper is a freely available web server that allows users to interactively visualize their data in the form of heat maps through an easy-to-use graphical interface. Unlike existing non-commercial heat map packages, which either lack gr…
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The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog) Open
The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. The new infrastructure includes a new graphical user interface (www.ebi…