diff --git a/data/aniseed/aniseed.biotools.json b/data/aniseed/aniseed.biotools.json index bb17c0f9b6342..166aba3759ac6 100644 --- a/data/aniseed/aniseed.biotools.json +++ b/data/aniseed/aniseed.biotools.json @@ -12,6 +12,7 @@ "email": "christelle.dantec@crbm.cnrs.fr", "name": "Christelle Dantec", "orcidid": "https://orcid.org/0000-0001-7247-6460", + "rorid": "01xpc6869", "typeEntity": "Person", "typeRole": [ "Primary contact" @@ -22,6 +23,7 @@ "email": "patrick.lemaire@crbm.cnrs.fr", "name": "Patrick Lemaire", "orcidid": "https://orcid.org/0000-0003-4925-2009", + "rorid": "01xpc6869", "typeEntity": "Person", "typeRole": [ "Primary contact" @@ -29,7 +31,7 @@ "url": "http://www.crbm.cnrs.fr/en/team/lemaire/" }, { - "email": "contact@aniseed.cnrs.fr", + "email": "contact@aniseed.fr", "typeRole": [ "Support" ] @@ -41,25 +43,25 @@ "type": [ "API documentation" ], - "url": "https://www.aniseed.cnrs.fr/api" + "url": "https://www.aniseed.fr/api" }, { "type": [ "Contributions policy" ], - "url": "https://www.aniseed.cnrs.fr/aniseed/default/privacyPolicy" + "url": "https://www.aniseed.fr/aniseed/default/privacyPolicy" }, { "type": [ "Terms of use" ], - "url": "https://www.aniseed.cnrs.fr/aniseed/default/termOfUse" + "url": "https://www.aniseed.fr/aniseed/default/termOfUse" } ], "download": [ { "type": "Biological data", - "url": "https://www.aniseed.cnrs.fr/aniseed/download/download_data", + "url": "https://www.aniseed.fr/aniseed/download/download_data", "version": "2019" } ], @@ -161,7 +163,7 @@ "PHP", "Python" ], - "lastUpdate": "2023-09-17T17:31:01.864728Z", + "lastUpdate": "2023-09-25T14:25:18.910230Z", "license": "GPL-3.0", "link": [ { @@ -182,7 +184,13 @@ "type": [ "Service" ], - "url": "https://www.aniseed.cnrs.fr" + "url": "https://morphonet.org/" + }, + { + "type": [ + "Service" + ], + "url": "https://www.aniseed.fr" } ], "maturity": "Mature", @@ -468,7 +476,7 @@ "name": "Yokomori R." } ], - "citationCount": 61, + "citationCount": 62, "date": "2018-01-01T00:00:00Z", "journal": "Nucleic Acids Research", "title": "ANISEED 2017: Extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets" @@ -583,9 +591,94 @@ }, { "doi": "10.1093/nar/gkz955", - "type": [ - "Primary" - ], + "metadata": { + "abstract": "ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions, using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different view-point. A developmental browser summarizes the information in a gene- or territory-centric manner. Advanced genomic browsers integrate the genetic features surrounding genes or gene sets within a species. A Genomicus synteny browser explores the conservation of local gene order across deuterostome. This new release covers an extended taxonomic range of 14 species, including for the first time a non-ascidian species, the appendicularian Oikopleura dioica. Functional annotations, provided for each species, were enhanced through a combination of manual curation of gene models and the development of an improved orthology detection pipeline. Finally, gene expression profiles and anatomical territories can be explored in 4D online through the newly developed Morphonet morphogenetic browser.", + "authors": [ + { + "name": "Besnardeau L." + }, + { + "name": "Dantec C." + }, + { + "name": "Dardaillon J." + }, + { + "name": "Dauga D." + }, + { + "name": "Davidson B." + }, + { + "name": "Debiasse M.B." + }, + { + "name": "Douzery E." + }, + { + "name": "Dumollard R." + }, + { + "name": "Fagotto M." + }, + { + "name": "Faure E." + }, + { + "name": "Fujiwara S." + }, + { + "name": "Gueroult-Bellone M." + }, + { + "name": "Lemaire P." + }, + { + "name": "Louis A." + }, + { + "name": "Naville M." + }, + { + "name": "Nishida H." + }, + { + "name": "Nitta K.R." + }, + { + "name": "Onuma T.A." + }, + { + "name": "Reeves W." + }, + { + "name": "Roest Crollius H." + }, + { + "name": "Ryan J.F." + }, + { + "name": "Simion P." + }, + { + "name": "Veeman M." + }, + { + "name": "Volff J.-N." + }, + { + "name": "Wang K." + } + ], + "citationCount": 31, + "date": "2020-01-01T00:00:00Z", + "journal": "Nucleic Acids Research", + "title": "ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates" + }, + "version": "2019" + }, + { + "doi": "10.1093/nar/gkz955", "version": "2019" } ], @@ -613,6 +706,14 @@ { "biotoolsID": "interpro", "type": "uses" + }, + { + "biotoolsID": "morphonet", + "type": "usedBy" + }, + { + "biotoolsID": "morphonet", + "type": "uses" } ], "toolType": [ diff --git a/data/celltrackvis/celltrackvis.biotools.json b/data/celltrackvis/celltrackvis.biotools.json new file mode 100644 index 0000000000000..845ab039eb8ba --- /dev/null +++ b/data/celltrackvis/celltrackvis.biotools.json @@ -0,0 +1,108 @@ +{ + "accessibility": "Open access", + "additionDate": "2023-09-25T12:40:15.653732Z", + "biotoolsCURIE": "biotools:celltrackvis", + "biotoolsID": "celltrackvis", + "confidence_flag": "tool", + "cost": "Free of charge", + "credit": [ + { + "email": "ydchung@korea.ac.kr", + "name": "Yon Dohn Chung", + "typeEntity": "Person" + } + ], + "description": "interactive browser-based visualization for analyzing cell trajectories and lineages.", + "documentation": [ + { + "type": [ + "Training material" + ], + "url": "http://scbeom.github.io/ctv_tutorial" + } + ], + "editPermission": { + "type": "private" + }, + "function": [ + { + "operation": [ + { + "term": "Cell migration analysis", + "uri": "http://edamontology.org/operation_3446" + }, + { + "term": "Simulation analysis", + "uri": "http://edamontology.org/operation_0244" + }, + { + "term": "Trajectory visualization", + "uri": "http://edamontology.org/operation_3890" + } + ] + } + ], + "homepage": "http://github.com/scbeom/celltrackvis", + "language": [ + "Python" + ], + "lastUpdate": "2023-09-25T12:40:15.656573Z", + "license": "GPL-3.0", + "name": "CellTrackVis", + "operatingSystem": [ + "Linux", + "Mac", + "Windows" + ], + "owner": "Pub2Tools", + "publication": [ + { + "doi": "10.1186/S12859-023-05218-Y", + "metadata": { + "abstract": "Background: Automatic cell tracking methods enable practitioners to analyze cell behaviors efficiently. Notwithstanding the continuous development of relevant software, user-friendly visualization tools have room for further improvements. Typical visualization mostly comes with main cell tracking tools as a simple plug-in, or relies on specific software/platforms. Although some tools are standalone, limited visual interactivity is provided, or otherwise cell tracking outputs are partially visualized. Results: This paper proposes a self-reliant visualization system, CellTrackVis, to support quick and easy analysis of cell behaviors. Interconnected views help users discover meaningful patterns of cell motions and divisions in common web browsers. Specifically, cell trajectory, lineage, and quantified information are respectively visualized in a coordinated interface. In particular, immediate interactions among modules enable the study of cell tracking outputs to be more effective, and also each component is highly customizable for various biological tasks. Conclusions: CellTrackVis is a standalone browser-based visualization tool. Source codes and data sets are freely available at http://github.com/scbeom/celltrackvis with the tutorial at http://scbeom.github.io/ctv_tutorial.", + "authors": [ + { + "name": "Choi Y.S." + }, + { + "name": "Chung Y.D." + }, + { + "name": "Kim D.Y." + }, + { + "name": "Kim W." + }, + { + "name": "Nguyen T.T.D." + }, + { + "name": "Shim C." + } + ], + "date": "2023-12-01T00:00:00Z", + "journal": "BMC Bioinformatics", + "title": "CellTrackVis: interactive browser-based visualization for analyzing cell trajectories and lineages" + }, + "pmcid": "PMC10053428", + "pmid": "36991341" + } + ], + "toolType": [ + "Desktop application" + ], + "topic": [ + { + "term": "Cell biology", + "uri": "http://edamontology.org/topic_2229" + }, + { + "term": "Imaging", + "uri": "http://edamontology.org/topic_3382" + }, + { + "term": "Literature and language", + "uri": "http://edamontology.org/topic_3068" + } + ] +} diff --git a/data/ciona_robusta_anatomy_and_development_ontology/ciona_robusta_anatomy_and_development_ontology.biotools.json b/data/ciona_robusta_anatomy_and_development_ontology/ciona_robusta_anatomy_and_development_ontology.biotools.json index e411f31aa12cf..e41b4bb7993bd 100644 --- a/data/ciona_robusta_anatomy_and_development_ontology/ciona_robusta_anatomy_and_development_ontology.biotools.json +++ b/data/ciona_robusta_anatomy_and_development_ontology/ciona_robusta_anatomy_and_development_ontology.biotools.json @@ -11,7 +11,7 @@ "download": [ { "type": "Downloads page", - "url": "https://www.aniseed.cnrs.fr/aniseed/download/download_data" + "url": "https://www.aniseed.fr/aniseed/download/download_data" } ], "editPermission": { @@ -69,11 +69,11 @@ ] } ], - "homepage": "https://www.aniseed.cnrs.fr/aniseed/anatomy/find_devstage", + "homepage": "https://www.aniseed.fr/aniseed/anatomy/find_devstage", "language": [ "Other" ], - "lastUpdate": "2020-06-16T10:55:27Z", + "lastUpdate": "2023-09-25T13:07:23.980491Z", "license": "Freeware", "maturity": "Legacy", "name": "Ciona robusta Anatomy and Development Ontology", @@ -82,7 +82,7 @@ { "doi": "10.1093/nar/gkv966", "metadata": { - "abstract": "© The Author(s) 2015.Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organisms in the field of embryonic development, regeneration and stem cells. ANISEED is the main information system in the field of ascidian developmental biology. This article reports the development of the system since its initial publication in 2010. Over the past five years, we refactored the system from an initial custom schema to an extended version of the Chado schema and redesigned all user and back end interfaces. This new architecture was used to improve and enrich the description of Ciona intestinalisembryonic development, based on an improved genome assembly and gene model set, refined functional gene annotation, and anatomical ontologies, and a new collection of full ORF cDNAs. The genomes of nine ascidian species have been sequenced since the release of the C. intestinalisgenome. In ANISEED 2015, all nine new ascidian species can be explored via dedicated genome browsers, and searched by Blast. In addition, ANISEED provides full functional gene annotation, anatomical ontologies and some gene expression data for the six species with highest quality genomes. ANISEED is publicly available at: http://www.aniseed.cnrs.fr.", + "abstract": "Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organisms in the field of embryonic development, regeneration and stem cells. ANISEED is the main information system in the field of ascidian developmental biology. This article reports the development of the system since its initial publication in 2010. Over the past five years, we refactored the system from an initial custom schema to an extended version of the Chado schema and redesigned all user and back end interfaces. This new architecture was used to improve and enrich the description of Ciona intestinalisembryonic development, based on an improved genome assembly and gene model set, refined functional gene annotation, and anatomical ontologies, and a new collection of full ORF cDNAs. The genomes of nine ascidian species have been sequenced since the release of the C. intestinalisgenome. In ANISEED 2015, all nine new ascidian species can be explored via dedicated genome browsers, and searched by Blast. In addition, ANISEED provides full functional gene annotation, anatomical ontologies and some gene expression data for the six species with highest quality genomes. ANISEED is publicly available at: http://www.aniseed.cnrs.fr.", "authors": [ { "name": "Brown T.C." @@ -169,7 +169,7 @@ "name": "Yasuo H." } ], - "citationCount": 43, + "citationCount": 53, "date": "2016-01-01T00:00:00Z", "journal": "Nucleic Acids Research", "title": "ANISEED 2015: A digital framework for the comparative developmental biology of ascidians" @@ -271,7 +271,7 @@ "name": "Tassy O." } ], - "citationCount": 84, + "citationCount": 90, "date": "2010-01-01T00:00:00Z", "journal": "Genome Research", "title": "The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program" diff --git a/data/deepstabp/deepstabp.biotools.json b/data/deepstabp/deepstabp.biotools.json new file mode 100644 index 0000000000000..9bb9a1af258b2 --- /dev/null +++ b/data/deepstabp/deepstabp.biotools.json @@ -0,0 +1,148 @@ +{ + "accessibility": "Open access", + "additionDate": "2023-09-25T17:54:30.731190Z", + "biotoolsCURIE": "biotools:deepstabp", + "biotoolsID": "deepstabp", + "confidence_flag": "tool", + "cost": "Free of charge", + "credit": [ + { + "email": "timo.muehlhaus@rptu.de", + "name": "Timo Mühlhaus", + "orcidid": "https://orcid.org/0000-0003-3925-6778", + "typeEntity": "Person" + } + ], + "description": "An AI based web tool to predict the melting temperature (Tm) of proteins based on their amino acid sequence and various growth conditions.", + "editPermission": { + "type": "public" + }, + "function": [ + { + "input": [ + { + "data": { + "term": "Protein sequence", + "uri": "http://edamontology.org/data_2976" + }, + "format": [ + { + "term": "FASTA", + "uri": "http://edamontology.org/format_1929" + }, + { + "term": "plain text format (unformatted)", + "uri": "http://edamontology.org/format_1964" + } + ] + } + ], + "operation": [ + { + "term": "Editing", + "uri": "http://edamontology.org/operation_3096" + }, + { + "term": "Protein feature detection", + "uri": "http://edamontology.org/operation_3092" + }, + { + "term": "Variant effect prediction", + "uri": "http://edamontology.org/operation_0331" + } + ], + "output": [ + { + "data": { + "term": "Protein property", + "uri": "http://edamontology.org/data_0897" + } + } + ] + } + ], + "homepage": "https://csb-deepstabp.bio.rptu.de", + "language": [ + "JavaScript", + "Python" + ], + "lastUpdate": "2023-09-25T17:54:30.733846Z", + "license": "MIT", + "link": [ + { + "type": [ + "Other" + ], + "url": "https://git.nfdi4plants.org/f_jung/deepstabp" + }, + { + "type": [ + "Repository" + ], + "url": "https://github.com/CSBiology/deepStabP" + } + ], + "name": "DeepSTABp", + "operatingSystem": [ + "Linux", + "Mac", + "Windows" + ], + "owner": "Pub2Tools", + "publication": [ + { + "doi": "10.3390/IJMS24087444", + "metadata": { + "abstract": "Proteins are essential macromolecules that carry out a plethora of biological functions. The thermal stability of proteins is an important property that affects their function and determines their suitability for various applications. However, current experimental approaches, primarily thermal proteome profiling, are expensive, labor-intensive, and have limited proteome and species coverage. To close the gap between available experimental data and sequence information, a novel protein thermal stability predictor called DeepSTABp has been developed. DeepSTABp uses a transformer-based protein language model for sequence embedding and state-of-the-art feature extraction in combination with other deep learning techniques for end-to-end protein melting temperature prediction. DeepSTABp can predict the thermal stability of a wide range of proteins, making it a powerful and efficient tool for large-scale prediction. The model captures the structural and biological properties that impact protein stability, and it allows for the identification of the structural features that contribute to protein stability. DeepSTABp is available to the public via a user-friendly web interface, making it accessible to researchers in various fields.", + "authors": [ + { + "name": "Frey K." + }, + { + "name": "Jung F." + }, + { + "name": "Muhlhaus T." + }, + { + "name": "Zimmer D." + } + ], + "date": "2023-04-01T00:00:00Z", + "journal": "International Journal of Molecular Sciences", + "title": "DeepSTABp: A Deep Learning Approach for the Prediction of Thermal Protein Stability" + }, + "pmcid": "PMC10138888", + "pmid": "37108605", + "type": [ + "Primary" + ] + } + ], + "toolType": [ + "Desktop application", + "Web application" + ], + "topic": [ + { + "term": "Protein folding, stability and design", + "uri": "http://edamontology.org/topic_0130" + }, + { + "term": "Protein modifications", + "uri": "http://edamontology.org/topic_0601" + }, + { + "term": "Proteomics", + "uri": "http://edamontology.org/topic_0121" + }, + { + "term": "Sequence analysis", + "uri": "http://edamontology.org/topic_0080" + }, + { + "term": "Small molecules", + "uri": "http://edamontology.org/topic_0154" + } + ] +} diff --git a/data/dipwmsearch/dipwmsearch.biotools.json b/data/dipwmsearch/dipwmsearch.biotools.json new file mode 100644 index 0000000000000..97396e6fd1749 --- /dev/null +++ b/data/dipwmsearch/dipwmsearch.biotools.json @@ -0,0 +1,110 @@ +{ + "accessibility": "Open access", + "additionDate": "2023-09-25T18:20:46.182047Z", + "biotoolsCURIE": "biotools:dipwmsearch", + "biotoolsID": "dipwmsearch", + "confidence_flag": "tool", + "cost": "Free of charge", + "credit": [ + { + "email": "rivals@lirmm.fr", + "name": "Eric Rivals", + "orcidid": "https://orcid.org/0000-0003-3791-3973", + "typeEntity": "Person" + } + ], + "description": "Python package for searching di-PWM motifs.", + "editPermission": { + "type": "public" + }, + "function": [ + { + "operation": [ + { + "term": "Database search", + "uri": "http://edamontology.org/operation_2421" + }, + { + "term": "Sequence motif recognition", + "uri": "http://edamontology.org/operation_0239" + }, + { + "term": "Transcription factor binding site prediction", + "uri": "http://edamontology.org/operation_0445" + } + ] + } + ], + "homepage": "https://gite.lirmm.fr/rivals/dipwmsearch/", + "language": [ + "Python" + ], + "lastUpdate": "2023-09-25T18:20:46.184376Z", + "license": "CECILL-B", + "link": [ + { + "type": [ + "Repository" + ], + "url": "https://pypi.org/project/dipwmsearch/" + } + ], + "name": "dipwmsearch", + "operatingSystem": [ + "Linux", + "Mac" + ], + "owner": "Pub2Tools", + "publication": [ + { + "doi": "10.1093/BIOINFORMATICS/BTAD141", + "metadata": { + "abstract": "Motivation: Seeking probabilistic motifs in a sequence is a common task to annotate putative transcription factor binding sites or other RNA/DNA binding sites. Useful motif representations include position weight matrices (PWMs), dinucleotide PWMs (di-PWMs), and hidden Markov models (HMMs). Dinucleotide PWMs not only combine the simplicity of PWMs—a matrix form and a cumulative scoring function—but also incorporate dependency between adjacent positions in the motif (unlike PWMs which disregard any dependency). For instance to represent binding sites, the HOCOMOCO database provides di-PWM motifs derived from experimental data. Currently, two programs, SPRy-SARUS and MOODS, can search for occurrences of di-PWMs in sequences. Results: We propose a Python package called dipwmsearch, which provides an original and efficient algorithm for this task (it first enumerates matching words for the di-PWM, and then searches these all at once in the sequence, even if the latter contains IUPAC codes). The user benefits from an easy installation via Pypi or conda, a comprehensive documentation, and executable scripts that facilitate the use of di-PWMs.", + "authors": [ + { + "name": "Cazaux B." + }, + { + "name": "Mille M." + }, + { + "name": "Ripoll J." + }, + { + "name": "Rivals E." + } + ], + "date": "2023-04-01T00:00:00Z", + "journal": "Bioinformatics", + "title": "dipwmsearch: a Python package for searching di-PWM motifs" + }, + "pmcid": "PMC10081870", + "pmid": "37010504" + } + ], + "toolType": [ + "Library" + ], + "topic": [ + { + "term": "ChIP-seq", + "uri": "http://edamontology.org/topic_3169" + }, + { + "term": "Epigenetics", + "uri": "http://edamontology.org/topic_3295" + }, + { + "term": "Genomics", + "uri": "http://edamontology.org/topic_0622" + }, + { + "term": "Sequence sites, features and motifs", + "uri": "http://edamontology.org/topic_0160" + }, + { + "term": "Whole genome sequencing", + "uri": "http://edamontology.org/topic_3673" + } + ] +} diff --git a/data/granie/granie.biotools.json b/data/granie/granie.biotools.json new file mode 100644 index 0000000000000..1bce2f91693de --- /dev/null +++ b/data/granie/granie.biotools.json @@ -0,0 +1,170 @@ +{ + "accessibility": "Open access", + "additionDate": "2023-09-25T16:56:32.452403Z", + "biotoolsCURIE": "biotools:granie", + "biotoolsID": "granie", + "confidence_flag": "high", + "cost": "Free of charge", + "credit": [ + { + "email": "judith.zaugg@embl.de", + "name": "Judith B Zaugg", + "orcidid": "https://orcid.org/0000-0001-8324-4040", + "typeEntity": "Person" + } + ], + "description": "R package for reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data.", + "documentation": [ + { + "type": [ + "User manual" + ], + "url": "https://grp-zaugg.embl-community.io/GRaNIE/" + } + ], + "editPermission": { + "type": "private" + }, + "function": [ + { + "operation": [ + { + "term": "Essential dynamics", + "uri": "http://edamontology.org/operation_3891" + }, + { + "term": "Filtering", + "uri": "http://edamontology.org/operation_3695" + }, + { + "term": "Gene regulatory network analysis", + "uri": "http://edamontology.org/operation_1781" + }, + { + "term": "Gene regulatory network prediction", + "uri": "http://edamontology.org/operation_2437" + }, + { + "term": "Transcriptional regulatory element prediction", + "uri": "http://edamontology.org/operation_0438" + } + ] + } + ], + "homepage": "https://git.embl.de/grp-zaugg/GRaNIE", + "language": [ + "R" + ], + "lastUpdate": "2023-09-25T16:56:32.454867Z", + "license": "Artistic-2.0", + "link": [ + { + "type": [ + "Other" + ], + "url": "https://apps.embl.de/grn/" + }, + { + "type": [ + "Repository" + ], + "url": "https://bioconductor.org/packages/GRaNIE" + } + ], + "name": "GRaNIE", + "operatingSystem": [ + "Linux", + "Mac", + "Windows" + ], + "owner": "Pub2Tools", + "publication": [ + { + "doi": "10.15252/MSB.202311627", + "metadata": { + "abstract": "Enhancers play a vital role in gene regulation and are critical in mediating the impact of noncoding genetic variants associated with complex traits. Enhancer activity is a cell-type-specific process regulated by transcription factors (TFs), epigenetic mechanisms and genetic variants. Despite the strong mechanistic link between TFs and enhancers, we currently lack a framework for jointly analysing them in cell-type-specific gene regulatory networks (GRN). Equally important, we lack an unbiased way of assessing the biological significance of inferred GRNs since no complete ground truth exists. To address these gaps, we present GRaNIE (Gene Regulatory Network Inference including Enhancers) and GRaNPA (Gene Regulatory Network Performance Analysis). GRaNIE (https://git.embl.de/grp-zaugg/GR aNIE) builds enhancer-mediated GRNs based on covariation of chromatin accessibility and RNA-seq across samples (e.g. individuals), while GRaNPA (https://git.embl.de/grp-zaugg/GRaNPA) assesses the performance of GRNs for predicting cell-type-specific differential expression. We demonstrate their power by investigating gene regulatory mechanisms underlying the response of macrophages to infection, cancer and common genetic traits including autoimmune diseases. Finally, our methods identify the TF PURA as a putative regulator of pro-inflammatory macrophage polarisation.", + "authors": [ + { + "name": "Arnold C." + }, + { + "name": "Bunina D." + }, + { + "name": "Claringbould A." + }, + { + "name": "Daga N." + }, + { + "name": "Kamal A." + }, + { + "name": "Kholmatov M." + }, + { + "name": "Moussa R." + }, + { + "name": "Mueller-Dott S." + }, + { + "name": "Nogina D." + }, + { + "name": "Pabst C." + }, + { + "name": "Palla G." + }, + { + "name": "Reyes-Palomares A." + }, + { + "name": "Servaas N.H." + }, + { + "name": "Sigalova O." + }, + { + "name": "Zaugg J.B." + } + ], + "citationCount": 3, + "date": "2023-06-12T00:00:00Z", + "journal": "Molecular Systems Biology", + "title": "GRaNIE and GRaNPA: inference and evaluation of enhancer-mediated gene regulatory networks" + }, + "pmcid": "PMC10258561", + "pmid": "37073532", + "type": [ + "Primary" + ] + } + ], + "toolType": [ + "Library" + ], + "topic": [ + { + "term": "Epigenetics", + "uri": "http://edamontology.org/topic_3295" + }, + { + "term": "Gene regulation", + "uri": "http://edamontology.org/topic_0204" + }, + { + "term": "Molecular interactions, pathways and networks", + "uri": "http://edamontology.org/topic_0602" + }, + { + "term": "RNA-Seq", + "uri": "http://edamontology.org/topic_3170" + }, + { + "term": "Transcription factors and regulatory sites", + "uri": "http://edamontology.org/topic_0749" + } + ] +} diff --git a/data/granpa/granpa.biotools.json b/data/granpa/granpa.biotools.json new file mode 100644 index 0000000000000..0fb21a8c5966c --- /dev/null +++ b/data/granpa/granpa.biotools.json @@ -0,0 +1,152 @@ +{ + "accessibility": "Open access", + "additionDate": "2023-09-25T17:04:35.235693Z", + "biotoolsCURIE": "biotools:granpa", + "biotoolsID": "granpa", + "confidence_flag": "high", + "cost": "Free of charge", + "credit": [ + { + "email": "judith.zaugg@embl.de", + "name": "Judith B Zaugg", + "orcidid": "https://orcid.org/0000-0001-8324-4040", + "typeEntity": "Person" + } + ], + "description": "R package for assessing the biological relevance of any TF-Gene GRNs using a machine learning framework to predict cell-type specific differential expression.", + "documentation": [ + { + "type": [ + "User manual" + ], + "url": "https://grp-zaugg.embl-community.io/GRaNPA" + } + ], + "editPermission": { + "type": "private" + }, + "function": [ + { + "operation": [ + { + "term": "Essential dynamics", + "uri": "http://edamontology.org/operation_3891" + }, + { + "term": "Gene regulatory network analysis", + "uri": "http://edamontology.org/operation_1781" + }, + { + "term": "Gene regulatory network prediction", + "uri": "http://edamontology.org/operation_2437" + }, + { + "term": "Pathway analysis", + "uri": "http://edamontology.org/operation_3928" + } + ] + } + ], + "homepage": "https://git.embl.de/grp-zaugg/GRaNPA", + "language": [ + "R" + ], + "lastUpdate": "2023-09-25T17:04:35.238281Z", + "license": "Artistic-2.0", + "name": "GRaNPA", + "operatingSystem": [ + "Linux", + "Mac", + "Windows" + ], + "owner": "Pub2Tools", + "publication": [ + { + "doi": "10.15252/MSB.202311627", + "metadata": { + "abstract": "Enhancers play a vital role in gene regulation and are critical in mediating the impact of noncoding genetic variants associated with complex traits. Enhancer activity is a cell-type-specific process regulated by transcription factors (TFs), epigenetic mechanisms and genetic variants. Despite the strong mechanistic link between TFs and enhancers, we currently lack a framework for jointly analysing them in cell-type-specific gene regulatory networks (GRN). Equally important, we lack an unbiased way of assessing the biological significance of inferred GRNs since no complete ground truth exists. To address these gaps, we present GRaNIE (Gene Regulatory Network Inference including Enhancers) and GRaNPA (Gene Regulatory Network Performance Analysis). GRaNIE (https://git.embl.de/grp-zaugg/GR aNIE) builds enhancer-mediated GRNs based on covariation of chromatin accessibility and RNA-seq across samples (e.g. individuals), while GRaNPA (https://git.embl.de/grp-zaugg/GRaNPA) assesses the performance of GRNs for predicting cell-type-specific differential expression. We demonstrate their power by investigating gene regulatory mechanisms underlying the response of macrophages to infection, cancer and common genetic traits including autoimmune diseases. Finally, our methods identify the TF PURA as a putative regulator of pro-inflammatory macrophage polarisation.", + "authors": [ + { + "name": "Arnold C." + }, + { + "name": "Bunina D." + }, + { + "name": "Claringbould A." + }, + { + "name": "Daga N." + }, + { + "name": "Kamal A." + }, + { + "name": "Kholmatov M." + }, + { + "name": "Moussa R." + }, + { + "name": "Mueller-Dott S." + }, + { + "name": "Nogina D." + }, + { + "name": "Pabst C." + }, + { + "name": "Palla G." + }, + { + "name": "Reyes-Palomares A." + }, + { + "name": "Servaas N.H." + }, + { + "name": "Sigalova O." + }, + { + "name": "Zaugg J.B." + } + ], + "citationCount": 3, + "date": "2023-06-12T00:00:00Z", + "journal": "Molecular Systems Biology", + "title": "GRaNIE and GRaNPA: inference and evaluation of enhancer-mediated gene regulatory networks" + }, + "pmcid": "PMC10258561", + "pmid": "37073532", + "type": [ + "Primary" + ] + } + ], + "toolType": [ + "Library" + ], + "topic": [ + { + "term": "Epigenetics", + "uri": "http://edamontology.org/topic_3295" + }, + { + "term": "Gene regulation", + "uri": "http://edamontology.org/topic_0204" + }, + { + "term": "Molecular interactions, pathways and networks", + "uri": "http://edamontology.org/topic_0602" + }, + { + "term": "RNA-Seq", + "uri": "http://edamontology.org/topic_3170" + }, + { + "term": "Transcription factors and regulatory sites", + "uri": "http://edamontology.org/topic_0749" + } + ] +} diff --git a/data/idia/idia.biotools.json b/data/idia/idia.biotools.json new file mode 100644 index 0000000000000..9e71b547cb477 --- /dev/null +++ b/data/idia/idia.biotools.json @@ -0,0 +1,130 @@ +{ + "accessibility": "Open access", + "additionDate": "2023-09-25T20:53:22.903009Z", + "biotoolsCURIE": "biotools:idia", + "biotoolsID": "idia", + "confidence_flag": "tool", + "cost": "Free of charge", + "credit": [ + { + "email": "xuan.guo@unt.edu", + "name": "Xuan Guo", + "typeEntity": "Person" + } + ], + "description": "An integrative signal extractor for data-independent acquisition proteomics.", + "editPermission": { + "type": "private" + }, + "function": [ + { + "input": [ + { + "data": { + "term": "Mass spectrum", + "uri": "http://edamontology.org/data_0943" + }, + "format": [ + { + "term": "mzXML", + "uri": "http://edamontology.org/format_3654" + } + ] + } + ], + "operation": [ + { + "term": "Filtering", + "uri": "http://edamontology.org/operation_3695" + }, + { + "term": "Peptide database search", + "uri": "http://edamontology.org/operation_3646" + }, + { + "term": "Protein identification", + "uri": "http://edamontology.org/operation_3767" + } + ], + "output": [ + { + "data": { + "term": "Mass spectrum", + "uri": "http://edamontology.org/data_0943" + }, + "format": [ + { + "term": "MGF", + "uri": "http://edamontology.org/format_3651" + }, + { + "term": "mzML", + "uri": "http://edamontology.org/format_3244" + } + ] + } + ] + } + ], + "homepage": "https://github.com/Biocomputing-Research-Group/IDIA", + "language": [ + "Java" + ], + "lastUpdate": "2023-09-25T20:53:22.905395Z", + "license": "GPL-3.0", + "name": "IDIA", + "operatingSystem": [ + "Linux", + "Mac", + "Windows" + ], + "owner": "Pub2Tools", + "publication": [ + { + "doi": "10.1109/BIBM55620.2022.9994873", + "metadata": { + "abstract": "In proteomics, data-independent acquisition (DIA)has been shown to provide less biased and more reproducible results than data-dependent acquisition. Recently, many researchers have developed a series of methods to identify peptides and proteins by using spectrum libraries for DIA data. However, spectrum libraries are not always available for novel organisms or microbial communities. To detect peptides and proteins without a spectrum library, we developed IDIA, a library-free method using DIA data to generate pseudo-spectra that can be searched using conventional sequence database searching software. IDIA integrates two isotopic trace detection strategies and employs B-spline and Gaussian filters to help extract high-quality pseudo-spectra from the complex DIA data. The experimental results on human and yeast data demonstrated that our approach remarkably produced more peptide and protein identifications than the two state-of-the-art library-free methods, i.e., DIA-Umpire and Group-DIA. IDIA is freely available under the GNU GPL license at https://github.com/Biocomputing-Research-Group/IDIA.", + "authors": [ + { + "name": "Guo X." + }, + { + "name": "Li J." + }, + { + "name": "Pan C." + } + ], + "date": "2022-01-01T00:00:00Z", + "journal": "Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022", + "title": "IDIA: An Integrative Signal Extractor for Data-Independent Acquisition Proteomics" + }, + "pmcid": "PMC10077956", + "pmid": "37034305", + "type": [ + "Primary" + ] + } + ], + "toolType": [ + "Command-line tool" + ], + "topic": [ + { + "term": "Proteomics", + "uri": "http://edamontology.org/topic_0121" + }, + { + "term": "Proteomics experiment", + "uri": "http://edamontology.org/topic_3520" + }, + { + "term": "Sequence analysis", + "uri": "http://edamontology.org/topic_0080" + }, + { + "term": "Small molecules", + "uri": "http://edamontology.org/topic_0154" + } + ] +} diff --git a/data/isnodi_mdrf/isnodi_mdrf.biotools.json b/data/isnodi_mdrf/isnodi_mdrf.biotools.json new file mode 100644 index 0000000000000..32d9a7e8743ed --- /dev/null +++ b/data/isnodi_mdrf/isnodi_mdrf.biotools.json @@ -0,0 +1,100 @@ +{ + "accessibility": "Open access", + "additionDate": "2023-09-25T17:45:48.313559Z", + "biotoolsCURIE": "biotools:isnodi_mdrf", + "biotoolsID": "isnodi_mdrf", + "confidence_flag": "tool", + "cost": "Free of charge", + "credit": [ + { + "name": "Bin Liu", + "orcidid": "https://orcid.org/0000-0003-3685-9469" + } + ], + "description": "Identifying snoRNA-disease associations based on multiple biological data by ranking framework.", + "editPermission": { + "type": "public" + }, + "function": [ + { + "input": [ + { + "data": { + "term": "RNA sequence", + "uri": "http://edamontology.org/data_3495" + }, + "format": [ + { + "term": "FASTA", + "uri": "http://edamontology.org/format_1929" + } + ] + } + ], + "operation": [ + { + "term": "Aggregation", + "uri": "http://edamontology.org/operation_3436" + }, + { + "term": "Nucleic acid sequence analysis", + "uri": "http://edamontology.org/operation_2478" + } + ], + "output": [ + { + "data": { + "term": "Score", + "uri": "http://edamontology.org/data_1772" + } + } + ] + } + ], + "homepage": "http://bliulab.net/iSnoDi-MDRF/", + "lastUpdate": "2023-09-25T17:45:48.316096Z", + "name": "iSnoDi-MDRF", + "operatingSystem": [ + "Linux", + "Mac", + "Windows" + ], + "owner": "Pub2Tools", + "publication": [ + { + "doi": "10.1109/TCBB.2023.3258448", + "metadata": { + "abstract": "Accumulating evidence indicates that the dysregulation of small nucleolar RNAs (snoRNAs) is relevant with diseases. Identifying snoRNA-disease associations by computational methods is desired for biologists, which can save considerable costs and time compared biological experiments. However, it still faces some challenges as followings: (i) Many snoRNAs are detected in recent years, but only a few snoRNAs have been proved to be associated with diseases; (ii) Computational predictors trained with only a few known snoRNA-disease associations fail to accurately identify the snoRNA-disease associations. In this study, we propose a ranking framework, called iSnoDi-MDRF, to identify potential snoRNA-disease associations based on multiple biological data, which has the following highlights: (i) iSnoDi-MDRF integrates ranking framework, which is not only able to identify potential associations between known snoRNAs and diseases, but also can identify diseases associated with new snoRNAs. (ii) Known gene-disease associations are employed to help train a mature model for predicting snoRNA-disease association. Experimental results illustrate that iSnoDi-MDRF is very suitable for identifying potential snoRNA-disease associations. The web server of iSnoDi-MDRF predictor is freely available at http://bliulab.net/iSnoDi-MDRF/.", + "authors": [ + { + "name": "Liu B." + }, + { + "name": "Zhang W." + } + ], + "date": "2023-01-01T00:00:00Z", + "journal": "IEEE/ACM Transactions on Computational Biology and Bioinformatics", + "title": "iSnoDi-MDRF: identifying snoRNA-disease associations based on multiple biological data by ranking framework" + }, + "pmid": "37030816" + } + ], + "toolType": [ + "Web application" + ], + "topic": [ + { + "term": "Functional, regulatory and non-coding RNA", + "uri": "http://edamontology.org/topic_0659" + }, + { + "term": "Laboratory techniques", + "uri": "http://edamontology.org/topic_3361" + }, + { + "term": "Pathology", + "uri": "http://edamontology.org/topic_0634" + } + ] +} diff --git a/data/mbonita/mbonita.biotools.json b/data/mbonita/mbonita.biotools.json new file mode 100644 index 0000000000000..0fae1c5a64d76 --- /dev/null +++ b/data/mbonita/mbonita.biotools.json @@ -0,0 +1,121 @@ +{ + "accessibility": "Open access", + "additionDate": "2023-09-25T18:35:03.752451Z", + "biotoolsCURIE": "biotools:mbonita", + "biotoolsID": "mbonita", + "confidence_flag": "tool", + "cost": "Free of charge", + "credit": [ + { + "email": "Juilee_Thakar@URMC.rochester.edu", + "name": "Juilee Thakar", + "orcidid": "https://orcid.org/0000-0003-4479-4183", + "typeEntity": "Person" + } + ], + "description": "Multi-omics boolean omics network invariant-time analysis.", + "editPermission": { + "type": "private" + }, + "function": [ + { + "operation": [ + { + "term": "Aggregation", + "uri": "http://edamontology.org/operation_3436" + }, + { + "term": "Enrichment analysis", + "uri": "http://edamontology.org/operation_3501" + }, + { + "term": "Network analysis", + "uri": "http://edamontology.org/operation_3927" + }, + { + "term": "Pathway analysis", + "uri": "http://edamontology.org/operation_3928" + } + ] + } + ], + "homepage": "https://github.com/Thakar-Lab/mBONITA", + "language": [ + "C", + "Python" + ], + "lastUpdate": "2023-09-25T18:35:03.755242Z", + "license": "MIT", + "name": "mBONITA", + "operatingSystem": [ + "Linux", + "Mac", + "Windows" + ], + "owner": "Pub2Tools", + "publication": [ + { + "doi": "10.1021/ACS.JPROTEOME.2C00730", + "metadata": { + "abstract": "Multiomics profiling provides a holistic picture of a condition being examined and captures the complexity of signaling events, beginning from the original cause (environmental or genetic), to downstream functional changes at multiple molecular layers. Pathway enrichment analysis has been used with multiomics data sets to characterize signaling mechanisms. However, technical and biological variability between these layered data limit an integrative computational analyses. We present a Boolean network-based method, multiomics Boolean Omics Network Invariant-Time Analysis (mBONITA), to integrate omics data sets that quantify multiple molecular layers. mBONITA utilizes prior knowledge networks to perform topology-based pathway analysis. In addition, mBONITA identifies genes that are consistently modulated across molecular measurements by combining observed fold-changes and variance, with a measure of node (i.e., gene or protein) influence over signaling, and a measure of the strength of evidence for that gene across data sets. We used mBONITA to integrate multiomics data sets from RAMOS B cells treated with the immunosuppressant drug cyclosporine A under varying O2 tensions to identify pathways involved in hypoxia-mediated chemotaxis. We compare mBONITA’s performance with 6 other pathway analysis methods designed for multiomics data and show that mBONITA identifies a set of pathways with evidence of modulation across all omics layers. mBONITA is freely available at https://github.com/Thakar-Lab/mBONITA.", + "authors": [ + { + "name": "Crystal A." + }, + { + "name": "Hilchey S.P." + }, + { + "name": "Meng J." + }, + { + "name": "Min X." + }, + { + "name": "Palshikar M.G." + }, + { + "name": "Thakar J." + }, + { + "name": "Zand M.S." + } + ], + "citationCount": 1, + "date": "2023-05-05T00:00:00Z", + "journal": "Journal of Proteome Research", + "title": "Executable Network Models of Integrated Multiomics Data" + }, + "pmcid": "PMC10167691", + "pmid": "37000949", + "type": [ + "Primary" + ] + } + ], + "toolType": [ + "Workflow" + ], + "topic": [ + { + "term": "Molecular interactions, pathways and networks", + "uri": "http://edamontology.org/topic_0602" + }, + { + "term": "Proteomics", + "uri": "http://edamontology.org/topic_0121" + }, + { + "term": "Proteomics experiment", + "uri": "http://edamontology.org/topic_3520" + }, + { + "term": "Sequence analysis", + "uri": "http://edamontology.org/topic_0080" + }, + { + "term": "Transcriptomics", + "uri": "http://edamontology.org/topic_3308" + } + ] +} diff --git a/data/mineprot/mineprot.biotools.json b/data/mineprot/mineprot.biotools.json index f2c4d7779cefe..d309a9e79571b 100644 --- a/data/mineprot/mineprot.biotools.json +++ b/data/mineprot/mineprot.biotools.json @@ -50,9 +50,16 @@ "PHP", "Python" ], - "lastUpdate": "2023-08-11T07:50:56.014918Z", + "lastUpdate": "2023-09-24T07:55:22.045888Z", "license": "MIT", "link": [ + { + "note": "MineProt is included in the ELIXIR Research Data Management Kit as the recommended solution for building a dedicated web service for large-scale modelling efforts.", + "type": [ + "Software catalogue" + ], + "url": "https://rdmkit.elixir-europe.org/structural_bioinformatics#solutions" + }, { "type": [ "Repository" @@ -70,6 +77,26 @@ "publication": [ { "doi": "10.1093/database/baad059", + "metadata": { + "abstract": "AlphaFold-like systems are rapidly expanding the scale of proteome structuring, and MineProt provides an effective solution for custom curation of these novel high-throughput data. It enables researchers to build their own server in simple steps, run almost out-of-the-box scripts to annotate and curate their proteins, analyze their data via a user-friendly online interface, and utilize plugins to extend the functionality of server. It is expected to support researcher productivity and facilitate data sharing in the new era of structural proteomics. Database URL MineProt is open-source software available at https://github.com/huiwenke/MineProt.", + "authors": [ + { + "name": "Lu Z." + }, + { + "name": "Tong C." + }, + { + "name": "Zhao Z." + }, + { + "name": "Zhu Y." + } + ], + "date": "2023-08-10T00:00:00Z", + "journal": "Database : the journal of biological databases and curation", + "title": "MineProt: a stand-alone server for structural proteome curation" + }, "pmid": "37562062" } ], diff --git a/data/morphonet/morphonet.biotools.json b/data/morphonet/morphonet.biotools.json new file mode 100644 index 0000000000000..b342c9067efdf --- /dev/null +++ b/data/morphonet/morphonet.biotools.json @@ -0,0 +1,261 @@ +{ + "accessibility": "Open access", + "additionDate": "2023-09-25T13:33:15.447513Z", + "biotoolsCURIE": "biotools:morphonet", + "biotoolsID": "morphonet", + "cost": "Free of charge", + "credit": [ + { + "email": "emmanuel.faure@lirmm.fr", + "name": "Emmanuel FAURE", + "orcidid": "https://orcid.org/0000-0003-2787-0885", + "rorid": "013yean28", + "typeEntity": "Person" + } + ], + "description": "MorphoNet is an interactive morphodynamic web browser designed to help scientists, teachers and students share, analyze and visualize the large 3D morphological datasets that can be generated by modern imaging technology, ranging from live light sheet microscopy of cells and embryos to X Ray tomography of fossils.", + "documentation": [ + { + "type": [ + "FAQ" + ], + "url": "https://forum.image.sc/" + }, + { + "type": [ + "General" + ], + "url": "https://morphonet.org/help" + } + ], + "download": [ + { + "type": "API specification", + "url": "https://morphonet.org/helpfiles/API/index.html" + }, + { + "type": "Downloads page", + "url": "https://morphonet.org/downloads" + } + ], + "editPermission": { + "type": "public" + }, + "elixirNode": [ + "France" + ], + "elixirPlatform": [ + "Tools" + ], + "function": [ + { + "operation": [ + { + "term": "Visualisation", + "uri": "http://edamontology.org/operation_0337" + } + ] + } + ], + "homepage": "https://morphonet.org", + "language": [ + "Python" + ], + "lastUpdate": "2023-09-25T14:12:08.944886Z", + "link": [ + { + "type": [ + "Helpdesk", + "Helpdesk" + ], + "url": "https://morphonet.org/help" + }, + { + "type": [ + "Service" + ], + "url": "https://www.aniseed.fr" + }, + { + "type": [ + "Social media" + ], + "url": "https://twitter.com/MorphoTweet" + } + ], + "maturity": "Mature", + "name": "MorphoNet", + "operatingSystem": [ + "Linux", + "Mac", + "Windows" + ], + "owner": "cdantec", + "publication": [ + { + "doi": "10.1038/s41467-019-10668-1", + "metadata": { + "abstract": "Powerful novel imaging and image-processing methods are revolutionizing many fields of biology, at scales ranging from the molecule to the functional organ. To support this big-data revolution, we develop a concept of generic web-based morphodynamic browser to interactively visualize complex image datasets, with applications in research and education. MorphoNet handles a broad range of natural or simulated morphological data, onto which quantitative geometric or genetic data can be projected.", + "authors": [ + { + "name": "Carlier A." + }, + { + "name": "Faure E." + }, + { + "name": "Godin C." + }, + { + "name": "Laussu J." + }, + { + "name": "Leggio B." + }, + { + "name": "Lemaire P." + } + ], + "citationCount": 26, + "date": "2019-12-01T00:00:00Z", + "journal": "Nature Communications", + "title": "MorphoNet: an interactive online morphological browser to explore complex multi-scale data" + }, + "pmcid": "PMC6597584", + "type": [ + "Primary" + ] + }, + { + "doi": "10.1093/nar/gkz955", + "metadata": { + "abstract": "ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions, using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different view-point. A developmental browser summarizes the information in a gene- or territory-centric manner. Advanced genomic browsers integrate the genetic features surrounding genes or gene sets within a species. A Genomicus synteny browser explores the conservation of local gene order across deuterostome. This new release covers an extended taxonomic range of 14 species, including for the first time a non-ascidian species, the appendicularian Oikopleura dioica. Functional annotations, provided for each species, were enhanced through a combination of manual curation of gene models and the development of an improved orthology detection pipeline. Finally, gene expression profiles and anatomical territories can be explored in 4D online through the newly developed Morphonet morphogenetic browser.", + "authors": [ + { + "name": "Besnardeau L." + }, + { + "name": "Dantec C." + }, + { + "name": "Dardaillon J." + }, + { + "name": "Dauga D." + }, + { + "name": "Davidson B." + }, + { + "name": "Debiasse M.B." + }, + { + "name": "Douzery E." + }, + { + "name": "Dumollard R." + }, + { + "name": "Fagotto M." + }, + { + "name": "Faure E." + }, + { + "name": "Fujiwara S." + }, + { + "name": "Gueroult-Bellone M." + }, + { + "name": "Lemaire P." + }, + { + "name": "Louis A." + }, + { + "name": "Naville M." + }, + { + "name": "Nishida H." + }, + { + "name": "Nitta K.R." + }, + { + "name": "Onuma T.A." + }, + { + "name": "Reeves W." + }, + { + "name": "Roest Crollius H." + }, + { + "name": "Ryan J.F." + }, + { + "name": "Simion P." + }, + { + "name": "Veeman M." + }, + { + "name": "Volff J.-N." + }, + { + "name": "Wang K." + } + ], + "citationCount": 31, + "date": "2020-01-01T00:00:00Z", + "journal": "Nucleic Acids Research", + "title": "ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates" + }, + "type": [ + "Other" + ] + } + ], + "relation": [ + { + "biotoolsID": "aniseed", + "type": "usedBy" + }, + { + "biotoolsID": "aniseed", + "type": "uses" + }, + { + "biotoolsID": "ciona_robusta_anatomy_and_development_ontology", + "type": "uses" + } + ], + "toolType": [ + "Database portal", + "Desktop application", + "Web API", + "Web application" + ], + "topic": [ + { + "term": "Biological databases", + "uri": "http://edamontology.org/topic_3071" + }, + { + "term": "Biological databases", + "uri": "http://edamontology.org/topic_3071" + }, + { + "term": "Computational biology", + "uri": "http://edamontology.org/topic_3307" + }, + { + "term": "Developmental biology", + "uri": "http://edamontology.org/topic_3064" + } + ], + "version": [ + "2.1.3-35b3182" + ] +} diff --git a/data/nerel_bio/nerel_bio.biotools.json b/data/nerel_bio/nerel_bio.biotools.json new file mode 100644 index 0000000000000..96605cba2fc92 --- /dev/null +++ b/data/nerel_bio/nerel_bio.biotools.json @@ -0,0 +1,107 @@ +{ + "additionDate": "2023-09-25T18:51:15.713904Z", + "biotoolsCURIE": "biotools:nerel_bio", + "biotoolsID": "nerel_bio", + "confidence_flag": "tool", + "credit": [ + { + "email": "tutubalinaev@gmail.com", + "name": "Elena Tutubalina", + "orcidid": "https://orcid.org/0000-0001-7936-0284", + "typeEntity": "Person" + } + ], + "description": "Biomedical corpus for nested named entity recognition.", + "editPermission": { + "type": "private" + }, + "function": [ + { + "operation": [ + { + "term": "Named-entity and concept recognition", + "uri": "http://edamontology.org/operation_3280" + }, + { + "term": "Relation extraction", + "uri": "http://edamontology.org/operation_3625" + }, + { + "term": "Text annotation", + "uri": "http://edamontology.org/operation_3778" + } + ] + } + ], + "homepage": "https://github.com/nerel-ds/NEREL-BIO", + "lastUpdate": "2023-09-25T18:51:15.716490Z", + "name": "NEREL-BIO", + "owner": "Pub2Tools", + "publication": [ + { + "doi": "10.1093/BIOINFORMATICS/BTAD161", + "metadata": { + "abstract": "Motivation: This article describes NEREL-BIO-an annotation scheme and corpus of PubMed abstracts in Russian and smaller number of abstracts in English. NEREL-BIO extends the general domain dataset NEREL by introducing domain-specific entity types. NEREL-BIO annotation scheme covers both general and biomedical domains making it suitable for domain transfer experiments. NEREL-BIO provides annotation for nested named entities as an extension of the scheme employed for NEREL. Nested named entities may cross entity boundaries to connect to shorter entities nested within longer entities, making them harder to detect. Results: NEREL-BIO contains annotations for 700+ Russian and 100+ English abstracts. All English PubMed annotations have corresponding Russian counterparts. Thus, NEREL-BIO comprises the following specific features: Annotation of nested named entities, it can be used as a benchmark for cross-domain (NEREL → NEREL-BIO) and cross-language (English → Russian) transfer. We experiment with both transformer-based sequence models and machine reading comprehension models and report their results.", + "authors": [ + { + "name": "Baral E." + }, + { + "name": "Batura T." + }, + { + "name": "Braslavski P." + }, + { + "name": "Ivanov V." + }, + { + "name": "Loukachevitch N." + }, + { + "name": "Manandhar S." + }, + { + "name": "Rozhkov I." + }, + { + "name": "Tutubalina E." + } + ], + "date": "2023-04-01T00:00:00Z", + "journal": "Bioinformatics", + "title": "NEREL-BIO: A dataset of biomedical abstracts annotated with nested named entities" + }, + "pmcid": "PMC10129873", + "pmid": "37004189", + "type": [ + "Primary" + ] + } + ], + "toolType": [ + "Ontology" + ], + "topic": [ + { + "term": "Anatomy", + "uri": "http://edamontology.org/topic_3067" + }, + { + "term": "Genetics", + "uri": "http://edamontology.org/topic_3053" + }, + { + "term": "Natural language processing", + "uri": "http://edamontology.org/topic_0218" + }, + { + "term": "Ontology and terminology", + "uri": "http://edamontology.org/topic_0089" + }, + { + "term": "Tomography", + "uri": "http://edamontology.org/topic_3452" + } + ] +} diff --git a/data/predinid/predinid.biotools.json b/data/predinid/predinid.biotools.json new file mode 100644 index 0000000000000..678656b4c96bc --- /dev/null +++ b/data/predinid/predinid.biotools.json @@ -0,0 +1,125 @@ +{ + "accessibility": "Open access", + "additionDate": "2023-09-25T17:27:23.425935Z", + "biotoolsCURIE": "biotools:predinid", + "biotoolsID": "predinid", + "confidence_flag": "tool", + "cost": "Free of charge", + "credit": [ + { + "email": "zhenyuyue@ahau.edu.cn", + "name": "Zhenyu Yue", + "orcidid": "https://orcid.org/0000-0002-9370-2540" + }, + { + "name": "Ke Li", + "orcidid": "https://orcid.org/0000-0001-7279-5015" + } + ], + "description": "Predicting pathogenic inframe indels in humans through graph convolution neural network with graph sampling technique.", + "download": [ + { + "type": "Software package", + "url": "http://predinid.bio.aielab.cc/static/userDownload/PredinID.rar" + } + ], + "editPermission": { + "type": "private" + }, + "function": [ + { + "input": [ + { + "data": { + "term": "Sequence variations", + "uri": "http://edamontology.org/data_3498" + } + } + ], + "operation": [ + { + "term": "Aggregation", + "uri": "http://edamontology.org/operation_3436" + }, + { + "term": "Network analysis", + "uri": "http://edamontology.org/operation_3927" + }, + { + "term": "Virulence prediction", + "uri": "http://edamontology.org/operation_3461" + } + ], + "output": [ + { + "data": { + "term": "Score", + "uri": "http://edamontology.org/data_1772" + } + } + ] + } + ], + "homepage": "http://predinid.bio.aielab.cc/", + "lastUpdate": "2023-09-25T17:27:23.428576Z", + "name": "PredinID", + "operatingSystem": [ + "Linux", + "Mac", + "Windows" + ], + "owner": "Pub2Tools", + "publication": [ + { + "doi": "10.1109/TCBB.2023.3266232", + "metadata": { + "abstract": "Inframe insertion/deletion (indel) variants may alter protein sequence and function, which are closely related to an extensive variety of diseases. Although recent researches have paid attention to the associations between inframe indels and diseases, modeling indels in silico and interpreting their pathogenicity remain challenging, mainly due to the lack of experimental information and computational methodologies. In this paper, we propose a novel computational method named PredinID (Predictor for inframe InDels) via graph convolutional network (GCN). PredinID leverages k-nearest neighbor algorithm to construct the feature graph for aggregating more informative representation, regarding the pathogenic inframe indel prediction as a node classification task. An edge-based sampling strategy is designed for extracting information from both the potential connections of feature space and the topological structure of subgraphs. Evaluated by 5-fold cross-validations, the PredinID method achieves satisfactory performance and is superior to four classic machine learning algorithms and two GCN methods. Comprehensive experiments show that PredinID has superior performances when compared with the state-of-the-art methods on the independent test set. Moreover, we also implement a web server at http://predinid.bio.aielab.cc/, to facilitate the use of the model.", + "authors": [ + { + "name": "Chen G." + }, + { + "name": "Li K." + }, + { + "name": "Wang X." + }, + { + "name": "Xiang Y." + }, + { + "name": "Yue Z." + }, + { + "name": "Zhang Y." + } + ], + "date": "2023-01-01T00:00:00Z", + "journal": "IEEE/ACM Transactions on Computational Biology and Bioinformatics", + "title": "PredinID: predicting pathogenic inframe indels in human through graph convolution neural network with graph sampling technique" + }, + "pmid": "37040252" + } + ], + "toolType": [ + "Web application" + ], + "topic": [ + { + "term": "Agricultural science", + "uri": "http://edamontology.org/topic_3810" + }, + { + "term": "Genetic variation", + "uri": "http://edamontology.org/topic_0199" + }, + { + "term": "Machine learning", + "uri": "http://edamontology.org/topic_3474" + }, + { + "term": "Pathology", + "uri": "http://edamontology.org/topic_0634" + } + ] +} diff --git a/data/prothon/prothon.biotools.json b/data/prothon/prothon.biotools.json new file mode 100644 index 0000000000000..11b24294a0bf5 --- /dev/null +++ b/data/prothon/prothon.biotools.json @@ -0,0 +1,126 @@ +{ + "accessibility": "Open access", + "additionDate": "2023-09-25T19:18:38.412908Z", + "biotoolsCURIE": "biotools:prothon", + "biotoolsID": "prothon", + "confidence_flag": "high", + "cost": "Free of charge", + "credit": [ + { + "email": "steve@phas.ubc.ca", + "name": "Steven S. Plotkin", + "orcidid": "https://orcid.org/0000-0001-8998-877X", + "typeEntity": "Person" + } + ], + "description": "A local order parameter-based method for efficient comparison of protein ensembles.", + "editPermission": { + "type": "public" + }, + "function": [ + { + "input": [ + { + "data": { + "term": "Trajectory data", + "uri": "http://edamontology.org/data_3870" + } + }, + { + "data": { + "term": "Topology data", + "uri": "http://edamontology.org/data_3872" + }, + "format": [ + { + "term": "PDB", + "uri": "http://edamontology.org/format_1476" + } + ] + } + ], + "operation": [ + { + "term": "Essential dynamics", + "uri": "http://edamontology.org/operation_3891" + }, + { + "term": "Molecular dynamics", + "uri": "http://edamontology.org/operation_2476" + }, + { + "term": "Protein comparison", + "uri": "http://edamontology.org/operation_2997" + } + ], + "output": [ + { + "data": { + "term": "Structure similarity score", + "uri": "http://edamontology.org/data_0888" + } + } + ] + } + ], + "homepage": "https://github.com/PlotkinLab/Prothon", + "language": [ + "Python" + ], + "lastUpdate": "2023-09-25T19:18:38.415458Z", + "license": "GPL-3.0", + "name": "PROTHON", + "operatingSystem": [ + "Linux", + "Mac", + "Windows" + ], + "owner": "Pub2Tools", + "publication": [ + { + "doi": "10.1021/acs.jcim.3c00145", + "metadata": { + "abstract": "The comparison of protein conformational ensembles is of central importance in structural biology. However, there are few computational methods for ensemble comparison, and those that are readily available, such as ENCORE, utilize methods that are sufficiently computationally expensive to be prohibitive for large ensembles. Here, a new method is presented for efficient representation and comparison of protein conformational ensembles. The method is based on the representation of a protein ensemble as a vector of probability distribution functions (pdfs), with each pdf representing the distribution of a local structural property such as the number of contacts between Cβ atoms. Dissimilarity between two conformational ensembles is quantified by the Jensen-Shannon distance between the corresponding set of probability distribution functions. The method is validated for conformational ensembles generated by molecular dynamics simulations of ubiquitin, as well as experimentally derived conformational ensembles of a 130 amino acid truncated form of human tau protein. In the ubiquitin ensemble data set, the method was up to 88 times faster than the existing ENCORE software, while simultaneously utilizing 48 times fewer computing cores. We make the method available as a Python package, called PROTHON, and provide a GitHub page with the Python source code at https://github.com/PlotkinLab/Prothon.", + "authors": [ + { + "name": "Aina A." + }, + { + "name": "Hsueh S.C.C." + }, + { + "name": "Plotkin S.S." + } + ], + "date": "2023-06-12T00:00:00Z", + "journal": "Journal of Chemical Information and Modeling", + "title": "PROTHON: A Local Order Parameter-Based Method for Efficient Comparison of Protein Ensembles" + }, + "pmid": "37178169", + "type": [ + "Primary" + ] + } + ], + "toolType": [ + "Library" + ], + "topic": [ + { + "term": "Molecular dynamics", + "uri": "http://edamontology.org/topic_0176" + }, + { + "term": "NMR", + "uri": "http://edamontology.org/topic_0593" + }, + { + "term": "Proteins", + "uri": "http://edamontology.org/topic_0078" + }, + { + "term": "Small molecules", + "uri": "http://edamontology.org/topic_0154" + } + ] +} diff --git a/data/protvar/protvar.biotools.json b/data/protvar/protvar.biotools.json index ecb865baf1b36..b7c19bdb56d30 100644 --- a/data/protvar/protvar.biotools.json +++ b/data/protvar/protvar.biotools.json @@ -12,7 +12,36 @@ "email": "jstephenson@ebi.ac.uk", "name": "James Stephenson", "orcidid": "https://orcid.org/0000-0002-6427-5703", - "typeEntity": "Person" + "typeEntity": "Person", + "typeRole": [ + "Documentor", + "Maintainer", + "Primary contact" + ], + "url": "https://www.ebi.ac.uk/people/person/james-stephenson/" + }, + { + "name": "Prabhat Totoo", + "orcidid": "https://orcid.org/0000-0001-5923-4467", + "typeEntity": "Person", + "typeRole": [ + "Developer", + "Maintainer" + ], + "url": "https://www.ebi.ac.uk/people/person/prabhat-totoo/" + }, + { + "name": "EMBL-EBI", + "typeEntity": "Institute", + "typeRole": [ + "Provider" + ], + "url": "https://www.ebi.ac.uk/" + }, + { + "name": "Open Targets", + "typeEntity": "Consortium", + "url": "https://www.opentargets.org/" } ], "description": "ProtVar helps users to contextualise and evaluate human missense variation at a per-residue level. It can be accessed via genomic coordinates, IDs or protein positions in over 92% of human proteins. Functional and structural annotations, predictions and co-located variants can be explored via an interactive UI or accessed programatically via an API.", @@ -108,7 +137,21 @@ "language": [ "Java" ], - "lastUpdate": "2023-09-21T09:15:55.111166Z", + "lastUpdate": "2023-09-25T09:31:39.599149Z", + "link": [ + { + "type": [ + "Mailing list" + ], + "url": "https://docs.google.com/forms/d/e/1FAIpQLSd7P85zRHVspesU3kgF3qWpzSDSYFsyeGFmnkuyzB00HNDmDw/viewform?usp=sf_link" + }, + { + "type": [ + "Social media" + ], + "url": "https://twitter.com/EBIProtVar" + } + ], "maturity": "Mature", "name": "ProtVar", "operatingSystem": [ @@ -118,10 +161,42 @@ ], "owner": "JStephenson", "relation": [ + { + "biotoolsID": "alphafold_2", + "type": "uses" + }, + { + "biotoolsID": "cadd_phred", + "type": "uses" + }, + { + "biotoolsID": "clinvar", + "type": "uses" + }, + { + "biotoolsID": "crossmap", + "type": "uses" + }, + { + "biotoolsID": "dbsnp", + "type": "uses" + }, + { + "biotoolsID": "ensembl", + "type": "uses" + }, + { + "biotoolsID": "eve", + "type": "uses" + }, { "biotoolsID": "open_targets_platform", "type": "usedBy" }, + { + "biotoolsID": "pdbe", + "type": "uses" + }, { "biotoolsID": "uniprot", "type": "usedBy" diff --git a/data/pxstools/pxstools.biotools.json b/data/pxstools/pxstools.biotools.json new file mode 100644 index 0000000000000..ff19ed059b484 --- /dev/null +++ b/data/pxstools/pxstools.biotools.json @@ -0,0 +1,87 @@ +{ + "accessibility": "Open access", + "additionDate": "2023-09-25T17:15:56.465153Z", + "biotoolsCURIE": "biotools:pxstools", + "biotoolsID": "pxstools", + "confidence_flag": "tool", + "cost": "Free of charge", + "credit": [ + { + "email": "chirag_patel@hms.harvard.edu", + "name": "Chirag J Patel", + "orcidid": "https://orcid.org/0000-0002-8756-8525", + "typeEntity": "Person" + } + ], + "description": "R package of tools for conducting exposure-wide analysis and deriving polyexposure risk scores.", + "editPermission": { + "type": "public" + }, + "function": [ + { + "operation": [ + { + "term": "Aggregation", + "uri": "http://edamontology.org/operation_3436" + }, + { + "term": "Regression analysis", + "uri": "http://edamontology.org/operation_3659" + }, + { + "term": "Standardisation and normalisation", + "uri": "http://edamontology.org/operation_3435" + } + ] + } + ], + "homepage": "https://github.com/yixuanh/PXStools", + "language": [ + "R" + ], + "lastUpdate": "2023-09-25T17:15:56.467728Z", + "name": "PXStools", + "operatingSystem": [ + "Linux", + "Mac", + "Windows" + ], + "owner": "Pub2Tools", + "publication": [ + { + "doi": "10.1093/IJE/DYAC216", + "metadata": { + "abstract": "Motivation: Investigating the aggregate burden of environmental factors on human traits and diseases requires consideration of the entire ‘exposome’. However, current studies primarily focus on a single exposure or a handful of exposures at a time, without considering how multiple exposures may be simultaneously associated with each other or with the phenotype. Polyexposure risk scores (PXS) have been shown to predict and stratify risk for disease beyond or complementary to genetic and clinical risk. PXStools provides an analytical package to standardize exposome-wide studies as well as derive and validate polyexposure risk scores. Implementation: PXStools is a package for the statistical R. General features: The package allows users to (i) conduct exposure-wide association studies; (ii) derive and validate polyexposure risk scores with and without accounting for exposure interactions, using new approaches in regression modelling (hierarchical lasso);(iii) compare goodness of fit between models with and without multiple exposures; and (iv) visualize results. A data frame with a unique identifier, phenotype and exposures is needed as the only input. Various customizations are allowed including data preprocessing (removing missing or unwanted responses), covariates adjustment, multiple hypothesis correction and model specification (linear, logistic, survival).", + "authors": [ + { + "name": "He Y." + }, + { + "name": "Patel C.J." + } + ], + "date": "2023-04-01T00:00:00Z", + "journal": "International Journal of Epidemiology", + "title": "Software Application Profile: PXStools—an R package of tools for conducting exposure-wide analysis and deriving polyexposure risk scores" + }, + "pmcid": "PMC10114106", + "type": [ + "Primary" + ] + } + ], + "topic": [ + { + "term": "GWAS study", + "uri": "http://edamontology.org/topic_3517" + }, + { + "term": "Genotype and phenotype", + "uri": "http://edamontology.org/topic_0625" + }, + { + "term": "Machine learning", + "uri": "http://edamontology.org/topic_3474" + } + ] +} diff --git a/data/pyeulercurves/pyeulercurves.biotools.json b/data/pyeulercurves/pyeulercurves.biotools.json new file mode 100644 index 0000000000000..2418bf3e95743 --- /dev/null +++ b/data/pyeulercurves/pyeulercurves.biotools.json @@ -0,0 +1,18 @@ +{ + "additionDate": "2023-09-25T10:44:21.242823Z", + "biotoolsCURIE": "biotools:pyeulercurves", + "biotoolsID": "pyeulercurves", + "description": "A python package to compute Euler Characteristic Curves of point-cloud or image data.", + "editPermission": { + "type": "private" + }, + "homepage": "https://github.com/dioscuri-tda/pyEulerCurves", + "language": [ + "C++", + "Python" + ], + "lastUpdate": "2023-09-25T10:44:21.245639Z", + "license": "MIT", + "name": "pyEulerCurves", + "owner": "dgurnari" +} diff --git a/data/vt3d/vt3d.biotools.json b/data/vt3d/vt3d.biotools.json new file mode 100644 index 0000000000000..d90245bcfc15f --- /dev/null +++ b/data/vt3d/vt3d.biotools.json @@ -0,0 +1,120 @@ +{ + "accessibility": "Open access", + "additionDate": "2023-09-25T18:46:03.722676Z", + "biotoolsCURIE": "biotools:vt3d", + "biotoolsID": "vt3d", + "confidence_flag": "high", + "cost": "Free of charge", + "credit": [ + { + "email": "fanguangyi@genomics.cn", + "name": "Guangyi Fan" + }, + { + "email": "xumengyang@genomics.cn", + "name": "Mengyang Xu", + "orcidid": "https://orcid.org/0000-0002-4487-7088" + } + ], + "description": "Visualization toolbox for 3D transcriptomic data.", + "documentation": [ + { + "type": [ + "Training material" + ], + "url": "http://www.bgiocean.com/vt3d_example" + } + ], + "editPermission": { + "type": "public" + }, + "function": [ + { + "operation": [ + { + "term": "Visualisation", + "uri": "http://edamontology.org/operation_0337" + } + ] + } + ], + "homepage": "https://github.com/BGI-Qingdao/VT3D", + "language": [ + "Python" + ], + "lastUpdate": "2023-09-25T18:46:03.725417Z", + "license": "GPL-3.0", + "link": [ + { + "type": [ + "Repository" + ], + "url": "https://github.com/BGI-Qingdao/VT3D_Browser" + } + ], + "name": "VT3D", + "operatingSystem": [ + "Linux", + "Mac", + "Windows" + ], + "owner": "Pub2Tools", + "publication": [ + { + "doi": "10.1016/J.JGG.2023.04.001", + "metadata": { + "abstract": "Data visualization empowers researchers to communicate their results that support scientific reasoning in an intuitive way. 3D spatially resolved transcriptomic atlases constructed from multi-view and high-dimensional data have rapidly emerged as a powerful tool to unravel spatial gene expression patterns and cell type distribution in biological samples, revolutionizing the understanding of gene regulatory interactions and cell niches. However, limited accessible tools for data visualization impede the potential impact and application of this technology. Here we introduce VT3D, a visualization toolbox that allows users to explore 3D transcriptomic data, enabling gene expression projection to any 2D plane of interest, 2D virtual slice creation and visualization, and interactive 3D data browsing with surface model plots. In addition, it can either work on personal devices in standalone mode or be hosted as a web-based server. We apply VT3D to multiple datasets produced by the most popular techniques, including both sequencing-based approaches including Stereo-seq, spatial transcriptomics (ST), and Slide-seq, and imaging-based approaches including MERFISH and STARMap, and successfully build a 3D atlas database that allows interactive data browsing. We demonstrate that VT3D bridges the gap between researchers and spatially resolved transcriptomics, thus accelerating related studies such as embryogenesis and organogenesis processes. The source code of VT3D is available at https://github.com/BGI-Qingdao/VT3D, and the modeled atlas database is available at http://www.bgiocean.com/vt3d_example.", + "authors": [ + { + "name": "Fan G." + }, + { + "name": "Guo L." + }, + { + "name": "Han K." + }, + { + "name": "Huang Z." + }, + { + "name": "Li Y." + }, + { + "name": "Liu X." + }, + { + "name": "Liu X." + }, + { + "name": "Qi Y." + }, + { + "name": "Xu M." + } + ], + "date": "2023-01-01T00:00:00Z", + "journal": "Journal of Genetics and Genomics", + "title": "VT3D: a visualization toolbox for 3D transcriptomic data" + }, + "pmid": "37054878" + } + ], + "toolType": [ + "Command-line tool" + ], + "topic": [ + { + "term": "Data visualisation", + "uri": "http://edamontology.org/topic_0092" + }, + { + "term": "Imaging", + "uri": "http://edamontology.org/topic_3382" + }, + { + "term": "Transcriptomics", + "uri": "http://edamontology.org/topic_3308" + } + ] +}