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{ "count": 34530, "next": "?page=2", "previous": null, "list": [ { "name": "hgt-site", "description": "Finds candidate sites where foreign DNA, such as bacterial or viral DNA, may have been inserted into a host genome. It takes paired-end reads aligned to the host and the per-read output of a taxonomic classifier run on the reads that did not align, and tests each candidate site against the number of chance chimeras that contamination and library preparation would produce at that position, flagging the likely artefacts rather than discarding them. Reads that cross the junction place the insertion point to the base pair. Kraken2, KrakenUniq, Kaiju, Centrifuge, DIAMOND and BLAST tabular output are all accepted, as is any two-column file of read name and taxid. With a GTF or GFF3 annotation it also reports the gene at each site.", "homepage": "https://github.com/iraajgangavaram/hgt-site", "biotoolsID": "hgt-site", "biotoolsCURIE": "biotools:hgt-site", "version": [ "0.1.0", "0.1.1", "0.2.0", "0.3.0" ], "otherID": [ { "value": "doi:10.5281/zenodo.23842712", "type": "doi", "version": "0.3.0" } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" }, { "uri": "http://edamontology.org/operation_3228", "term": "Structural variation detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" }, { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_3462", "term": "CRAM" } ] }, { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_3003", "term": "BED" }, { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "note": null, "cmd": "hgt-site run --bam sample.bam --kraken-db kraken2-db --host-taxid 9606 -o sample.hgt-site.tsv" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3301", "term": "Microbiology" }, { "uri": "http://edamontology.org/topic_3175", "term": "Structural variation" }, { "uri": "http://edamontology.org/topic_3299", "term": "Evolutionary biology" }, { "uri": "http://edamontology.org/topic_0637", "term": "Taxonomy" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/iraajgangavaram/hgt-site", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/iraajgangavaram/hgt-site/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://iraajgangavaram.github.io/hgt-site/benchmarks/", "type": [ "Other" ], "note": "Benchmarks against LGTSeek, with the scripts and raw results" } ], "download": [ { "url": "https://github.com/iraajgangavaram/hgt-site/archive/refs/tags/0.3.0.tar.gz", "type": "Source code", "note": null, "version": "0.3.0" }, { "url": "https://pypi.org/project/hgt-site/", "type": "Software package", "note": null, "version": "0.3.0" } ], "documentation": [ { "url": "https://iraajgangavaram.github.io/hgt-site/", "type": [ "General" ], "note": null }, { "url": "https://iraajgangavaram.github.io/hgt-site/api/", "type": [ "API documentation" ], "note": null }, { "url": "https://iraajgangavaram.github.io/hgt-site/citation/", "type": [ "Citation instructions" ], "note": null } ], "publication": [], "credit": [ { "name": "Iraaj Gangavaram", "email": null, "url": null, "orcidid": "https://orcid.org/0009-0002-4615-2846", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null } ], "owner": "iraaj", "additionDate": "2026-10-31T22:16:39.204880Z", "lastUpdate": "2026-11-03T21:54:34.935712Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ETAIN 5G Scientist", "description": "How much mobile phone radiation are we exposed to in everyday life? The ETAIN 5G Scientist app shows maps of mobile phone radiation across Europe. It continuously calculates the radiation from cell towers and how strongly your own device transmits during a phone call. The app was developed in the citizen research project ETAIN (Exposure To electromAgnetic fIelds and plaNetary health), which is funded by the EU. ETAIN investigates the effects of mobile phone radiation on human health and on biodiversity. The app is available for Android phones in the Google Play Store. Everyone who uses the app contributes to the research.", "homepage": "https://www.etainproject.eu/etain-5g-scientist", "biotoolsID": "etain_5g_scientist", "biotoolsCURIE": "biotools:etain_5g_scientist", "version": [ "1.9.3" ], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://www.emf-portal.org/uploads/etain_5g_scientist_info_en.pdf", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "Martin Röösli", "email": "martin.roosli@swisstph.ch", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-11-03T16:26:30.987086Z", "lastUpdate": "2026-11-03T16:26:30.989185Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Open Causal Graph Builder", "description": "This tool guides researchers through building a causal graph by clearly defining causes and consequences of each variable in temporal order, then generating a saturated graph containing all plausible relationships between them. The researcher deliberately removes implausible relationships one-by-one, annotating justifications as they go. This ensures that the absence of a relationship (edge) is a deliberate choice rather than a default, and nudges explicit consideration of time throughout the design and visualisation of the causal graph.", "homepage": "https://opencausal.org/build/", "biotoolsID": "open_causal_graph_builder", "biotoolsCURIE": "biotools:open_causal_graph_builder", "version": [], "otherID": [], "relation": [ { "biotoolsID": "opencausal", "type": "includedIn" } ], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1136/jech-2026-SSMabstracts.358", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Hüseyin Küçükali", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-1669-3107", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-11-03T16:18:38.835140Z", "lastUpdate": "2026-11-03T16:18:38.838439Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SpeciesHub", "description": "Platform for managing biodiversity observations, available as a web application and an Android app. Supports data entry with standardised and custom forms, import from spreadsheets, querying, map visualisation, export and team access. Data remains under the control of the owner, who decides what is shared. Public datasets can be published with reduced coordinate precision to protect sensitive locations.", "homepage": "https://specieshub.io", "biotoolsID": "specieshub", "biotoolsCURIE": "biotools:specieshub", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Mobile application", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3050", "term": "Biodiversity" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" }, { "uri": "http://edamontology.org/topic_0610", "term": "Ecology" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.youtube.com/@specieshub-io", "type": [ "Other" ], "note": null } ], "download": [ { "url": "https://play.google.com/store/apps/details?id=io.specieshub", "type": "Downloads page", "note": "Android App", "version": null } ], "documentation": [ { "url": "https://specieshub.io/support", "type": [ "User manual" ], "note": null }, { "url": "https://specieshub.io/terms", "type": [ "Terms of use" ], "note": null } ], "publication": [], "credit": [], "owner": "danas", "additionDate": "2025-12-09T11:58:09.082995Z", "lastUpdate": "2026-11-03T15:30:59.798310Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HESTA: Human Early Embryogenesis Spatiotemporal Transcriptomic Atlas", "description": "The spatial and temporal atlas of gene expression in human embryo at early gestation is critical in understanding embryo development, organogenesis and disease origins. Here, we obtained the spatial-temporal transcriptome from the 77 sagittal sections of 13 human embryos at 12-23 Carnegie stage (CS) by Stereo-seq, established the development trajectory/regulatory profiling of 50 organs, and identified the top organ-specific regulons with the highest score as the potential organ-identity regulators. The atlas refines the key organs/cell types that are vulnerable to virus infection and genetic disorders. We found dynamic changes of imprinting gene expression in specific organs at different stages. Our work, for the first time, revealed the time-lapse and spatial transcriptome dynamics of human embryogenesis after gastrulation.", "homepage": "https://db.cngb.org/hesta/", "biotoolsID": "hesta_databse", "biotoolsCURIE": "biotools:hesta_databse", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3064", "term": "Developmental biology" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "zhicheng", "additionDate": "2026-11-03T14:02:34.318915Z", "lastUpdate": "2026-11-03T14:02:34.321010Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "hesta", "description": "The spatial and temporal atlas of gene expression in human embryo at early gestation is critical in understanding embryo development, organogenesis and disease origins. Here, we obtained the spatial-temporal transcriptome from the 77 sagittal sections of 13 human embryos at 12-23 Carnegie stage (CS) by Stereo-seq, established the development trajectory/regulatory profiling of 50 organs, and identified the top organ-specific regulons with the highest score as the potential organ-identity regulators. The atlas refines the key organs/cell types that are vulnerable to virus infection and genetic disorders. We found dynamic changes of imprinting gene expression in specific organs at different stages. Our work, for the first time, revealed the time-lapse and spatial transcriptome dynamics of human embryogenesis after gastrulation.", "homepage": "https://db.cngb.org/hesta/", "biotoolsID": "hesta", "biotoolsCURIE": "biotools:hesta", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "zhicheng", "additionDate": "2026-11-03T13:53:32.782581Z", "lastUpdate": "2026-11-03T13:53:32.784741Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AgingResearch.News", "description": "AgingResearch.News is a web application for finding and following research on aging and age-related disease. It connects biomedical papers with evidence summaries, clinical trials, research grants and related topics. Readers can search the public site, use topic RSS feeds, or connect an AI assistant through its MCP API. Paper summaries are generated and checked by AI, with links to the underlying research and its limitations. Public reading is free; personalized features and higher API allowances require an account or paid plan.", "homepage": "https://agingresearch.news", "biotoolsID": "agingresearch.news", "biotoolsCURIE": "biotools:agingresearch.news", "version": [], "otherID": [ { "value": "RRID:SCR_029124", "type": "rrid", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" }, { "uri": "http://edamontology.org/operation_0306", "term": "Text mining" }, { "uri": "http://edamontology.org/operation_0305", "term": "Literature search" } ], "input": [], "output": [], "note": "Search new aging research papers, their evidence, clinical trials, grants and drug programs; on the site, through the data API or the MCP server.", "cmd": null } ], "toolType": [ "Web API", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3399", "term": "Geriatric medicine" }, { "uri": "http://edamontology.org/topic_3344", "term": "Biomedical science" }, { "uri": "http://edamontology.org/topic_3379", "term": "Preclinical and clinical studies" }, { "uri": "http://edamontology.org/topic_3336", "term": "Drug discovery" }, { "uri": "http://edamontology.org/topic_0218", "term": "Natural language processing" } ], "operatingSystem": [], "language": [], "license": "Proprietary", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://agingresearch.news/contact", "type": [ "Helpdesk" ], "note": null }, { "url": "https://agingresearch.news/feed.xml", "type": [ "Other" ], "note": null }, { "url": "https://agingresearch.news/status", "type": [ "Technical monitoring" ], "note": null }, { "url": "https://agingresearch.news/api/mcp", "type": [ "Service" ], "note": "Remote MCP server (Streamable HTTP)" }, { "url": "https://github.com/paperfoot/agingresearch-news-mcp", "type": [ "Software catalogue" ], "note": "MCP server listing and client setup" } ], "download": [], "documentation": [ { "url": "https://agingresearch.news/developers", "type": [ "API documentation" ], "note": null }, { "url": "https://agingresearch.news/connect", "type": [ "Quick start guide" ], "note": null }, { "url": "https://agingresearch.news/terms", "type": [ "Terms of use" ], "note": null }, { "url": "https://agingresearch.news/api/v1/openapi.json", "type": [ "API documentation" ], "note": "OpenAPI description of the data API" } ], "publication": [], "credit": [ { "name": "Boris Djordjevic", "email": "boris@agingresearch.news", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "agingresearchnews", "additionDate": "2026-10-12T01:52:33.122770Z", "lastUpdate": "2026-11-03T13:43:14.490943Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SlideScope", "description": "Desktop viewer for scientific and medical images on Windows and macOS, centred on microscopy and whole slide pathology. Opens whole slide scanner formats (Aperio SVS, Hamamatsu NDPI, MIRAX MRXS, Leica SCN, Ventana BIF) alongside acquisition formats (Zeiss CZI, Nikon ND2, Leica LIF, TIFF/OME-TIFF) and DICOM, including CT, MRI and X-ray series, in a single application. Provides pyramid navigation of gigapixel images, metadata inspection, calibrated measurements, annotations, and on-device segmentation and object counting for microscopy images. Medical scans are for viewing and measurement only; not for diagnosis.", "homepage": "https://slidescope.science/", "biotoolsID": "slidescope", "biotoolsCURIE": "biotools:slidescope", "version": [ "1.19.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" }, { "uri": "http://edamontology.org/topic_3383", "term": "Bioimaging" }, { "uri": "http://edamontology.org/topic_3384", "term": "Medical imaging" } ], "operatingSystem": [ "Windows", "Mac" ], "language": [], "license": "Proprietary", "collectionID": [], "maturity": "Mature", "cost": "Commercial", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://slidescope.science/en/downloads/", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "https://slidescope.science/en/learn/", "type": [ "General" ], "note": null }, { "url": "https://slidescope.science/en/how-to-open-czi-files/", "type": [ "User manual" ], "note": "How to open ZEISS CZI files, with the free and paid options" }, { "url": "https://slidescope.science/en/how-to-open-nd2-files/", "type": [ "User manual" ], "note": "How to open Nikon ND2 files, with the free and paid options" }, { "url": "https://slidescope.science/en/how-to-open-svs-files/", "type": [ "User manual" ], "note": "How to open Aperio SVS whole-slide images, with the free and paid options" }, { "url": "https://slidescope.science/en/how-to-open-ndpi-files/", "type": [ "User manual" ], "note": "How to open Hamamatsu NDPI whole-slide images" }, { "url": "https://slidescope.science/en/how-to-open-mrxs-files/", "type": [ "User manual" ], "note": "How to open 3DHISTECH MRXS whole-slide images" }, { "url": "https://www.youtube.com/watch?v=2drQ_Z_1ANE", "type": [ "Training material" ], "note": "SlideScope Science 1.9 product tour video (89 s)" } ], "publication": [], "credit": [], "owner": "ynevet", "additionDate": "2026-08-08T08:00:42.930149Z", "lastUpdate": "2026-11-03T08:19:15.420128Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MEGAM ARG Detection", "description": "Free Windows desktop application that detects antimicrobial resistance genes and resistance mutations in bacterial isolate genomes from FASTA assemblies or FASTQ reads. It combines quality control, assembly, taxonomic classification, annotation, MLST typing and several resistance detectors (AMRFinderPlus, ABRicate, RGI with CARD, PointFinder, KMA) in a single workflow that runs locally, without the command line. Research use; not a clinical diagnostic.", "homepage": "https://megam-arg-detection.com/en/", "biotoolsID": "megam_arg_detection", "biotoolsCURIE": "biotools:megam_arg_detection", "version": [ "2026-11-02" ], "otherID": [], "relation": [ { "biotoolsID": "amrfinderplus", "type": "uses" }, { "biotoolsID": "abricate", "type": "uses" }, { "biotoolsID": "card", "type": "uses" }, { "biotoolsID": "pointfinder", "type": "uses" }, { "biotoolsID": "resfinder", "type": "uses" }, { "biotoolsID": "plasmidfinder", "type": "uses" }, { "biotoolsID": "vfdb", "type": "uses" }, { "biotoolsID": "kma", "type": "uses" }, { "biotoolsID": "kraken2", "type": "uses" }, { "biotoolsID": "prokka", "type": "uses" }, { "biotoolsID": "spades", "type": "uses" }, { "biotoolsID": "mlst", "type": "uses" }, { "biotoolsID": "fastp", "type": "uses" }, { "biotoolsID": "fastqc", "type": "uses" }, { "biotoolsID": "multiqc", "type": "uses" }, { "biotoolsID": "quast", "type": "uses" }, { "biotoolsID": "barrnap", "type": "uses" }, { "biotoolsID": "seqkit", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" }, { "uri": "http://edamontology.org/operation_3218", "term": "Sequencing quality control" }, { "uri": "http://edamontology.org/operation_3482", "term": "Antimicrobial resistance prediction" }, { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" }, { "uri": "http://edamontology.org/operation_3840", "term": "Multilocus sequence typing" }, { "uri": "http://edamontology.org/operation_0310", "term": "Sequence assembly" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [] } ], "note": "FASTQ reads go through quality control and assembly; FASTA assemblies go directly to genome description and resistance detection.", "cmd": null } ], "toolType": [ "Workflow", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3301", "term": "Microbiology" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3324", "term": "Infectious disease" }, { "uri": "http://edamontology.org/topic_3305", "term": "Public health and epidemiology" }, { "uri": "http://edamontology.org/topic_3673", "term": "Whole genome sequencing" } ], "operatingSystem": [ "Windows" ], "language": [], "license": "Freeware", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/rmerah/MEGAM", "type": [ "Repository" ], "note": "Previous version (v3.2, Docker pipeline, MIT licence)." } ], "download": [ { "url": "https://megam-arg-detection.com/telechargements/MEGAM-arg-detection.exe", "type": "Binaries", "note": "Windows 10/11 x64 installer (377 MB). 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Genome Biology, 19:111", "metadata": { "title": "Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data", "abstract": "© 2018 The Author(s).The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. 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An excellent tool for prediction of secondary structure, with access to GenTHREADER for protein fold recognition and MEMSAT-2 transmembrane topology prediction.", "homepage": "http://bioinf.cs.ucl.ac.uk/psipred/", "biotoolsID": "psipred", "biotoolsCURIE": "biotools:psipred", "version": [], "otherID": [ { "value": "RRID:SCR_018546", "type": "rrid", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0469", "term": "Protein secondary structure prediction (turns)" }, { "uri": "http://edamontology.org/operation_0303", "term": "Protein fold recognition" }, { "uri": "http://edamontology.org/operation_0267", "term": "Protein secondary structure prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0082", "term": "Structure prediction" }, { "uri": "http://edamontology.org/topic_0736", "term": "Protein folds and structural domains" }, { "uri": "http://edamontology.org/topic_3542", "term": "Protein secondary structure" }, { "uri": "http://edamontology.org/topic_0130", "term": "Protein folding, stability and design" }, { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://bioinf.cs.ucl.ac.uk/index.php?id=779", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/16.4.404", "pmid": "10869041", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "The PSIPRED protein structure prediction server", "abstract": "The PSIPRED protein structure prediction server allows users to submit a protein sequence, perform a prediction of their choice and receive the results of the prediction both textually via e-mail and graphically via the web. The user may select one of three prediction methods to apply to their sequence: PSIPRED, a highly accurate secondary structure prediction method; MEMSAT 2, a new version of a widely used transmembrane topology prediction method; or GenTHREADER, a sequence profile based fold recognition method. Availability: Freely available to non-commercial users at http://globin.bio.warwick.ac.uk/psipred/.", "date": "2000-01-01T00:00:00Z", "citationCount": 3053, "authors": [ { "name": "McGuffin L.J." }, { "name": "Bryson K." }, { "name": "Jones D.T." } ], "journal": "Bioinformatics" } }, { "doi": "10.1006/jmbi.1999.3091", "pmid": "10493868", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Protein secondary structure prediction based on position-specific scoring matrices", "abstract": "A two-stage neural network has been used to predict protein secondary structure based on the position specific scoring matrices generated by PSI-BLAST. Despite the simplicity and convenience of the approach used, the results are found to be superior to those produced by other methods, including the popular PHD method according to our own benchmarking results and the results from the recent Critical Assessment of Techniques for Protein Structure Prediction experiment (CASP3), where the method was evaluated by stringent blind testing. Using a new testing set based on a set of 187 unique folds, and three-way cross-validation based on structural similarity criteria rather than sequence similarity criteria used previously (no similar folds were present in both the testing and training sets) the method presented here (PSIPRED) achieved an average Q3 score of between 76.5% to 78.3% depending on the precise definition of observed secondary structure used, which is the highest published score for any method to date. Given the success of the method in CASP3, it is reasonable to be confident that the evaluation presented here gives a fair indication of the performance of the method in general.", "date": "1999-09-17T00:00:00Z", "citationCount": 4685, "authors": [ { "name": "Jones D.T." } ], "journal": "Journal of Molecular Biology" } }, { "doi": "10.1093/nar/gkt381", "pmid": "23748958", "pmcid": "PMC3692098", "type": [], "version": null, "note": null, "metadata": { "title": "Scalable web services for the PSIPRED Protein Analysis Workbench.", "abstract": "Here, we present the new UCL Bioinformatics Group's PSIPRED Protein Analysis Workbench. The Workbench unites all of our previously available analysis methods into a single web-based framework. The new web portal provides a greatly streamlined user interface with a number of new features to allow users to better explore their results. We offer a number of additional services to enable computationally scalable execution of our prediction methods; these include SOAP and XML-RPC web server access and new HADOOP packages. All software and services are available via the UCL Bioinformatics Group website at http://bioinf.cs.ucl.ac.uk/.", "date": "2013-01-01T00:00:00Z", "citationCount": 1109, "authors": [ { "name": "Buchan D.W." }, { "name": "Minneci F." }, { "name": "Nugent T.C." }, { "name": "Bryson K." }, { "name": "Jones D.T." } ], "journal": "Nucleic acids research" } } ], "credit": [ { "name": "psipred team", "email": "psipred@cs.ucl.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Bijay", "additionDate": "2017-03-25T16:29:49Z", "lastUpdate": "2026-10-27T09:11:15.415748Z", "editPermission": { "type": "group", "authors": [ "zhouwj", "Bijay", "Yunus", "I3raf", "hou133" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ARYANA-BS", "description": "ARYANA-BS is a software tool for context-aware alignment of bisulfite sequencing reads. 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It enables search of genetic variation information by gene, variant or region.", "homepage": "http://gnomad.broadinstitute.org/", "biotoolsID": "gnomad", "biotoolsCURIE": "biotools:gnomad", "version": [], "otherID": [ { "value": "RRID:SCR_014964", "type": "rrid", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" }, { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3077", "term": "Data acquisition" }, { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "ODbL-1.0", "collectionID": [ "RD-connect", "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/macarthur-lab/gnomadjs/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [ { "url": "http://gnomad.broadinstitute.org/faq", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1038/nature19057", "pmid": "27535533", "pmcid": "PMC5018207", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Analysis of protein-coding genetic variation in 60,706 humans", "abstract": "© 2016 Macmillan Publishers Limited. All rights reserved.Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. Here we describe the aggregation and analysis of high-quality exome (protein-coding region) DNA sequence data for 60,706 individuals of diverse ancestries generated as part of the Exome Aggregation Consortium (ExAC). This catalogue of human genetic diversity contains an average of one variant every eight bases of the exome, and provides direct evidence for the presence of widespread mutational recurrence. We have used this catalogue to calculate objective metrics of pathogenicity for sequence variants, and to identify genes subject to strong selection against various classes of mutation; identifying 3,230 genes with near-complete depletion of predicted protein-truncating variants, with 72% of these genes having no currently established human disease phenotype. Finally, we demonstrate that these data can be used for the efficient filtering of candidate disease-causing variants, and for the discovery of human 'knockout' variants in protein-coding genes.", "date": "2016-08-17T00:00:00Z", "citationCount": 5437, "authors": [ { "name": "Lek M." }, { "name": "Karczewski K.J." }, { "name": "Minikel E.V." }, { "name": "Samocha K.E." }, { "name": "Banks E." }, { "name": "Fennell T." }, { "name": "O'Donnell-Luria A.H." }, { "name": "Ware J.S." }, { "name": "Hill A.J." }, { "name": "Cummings B.B." }, { "name": "Tukiainen T." }, { "name": "Birnbaum D.P." }, { "name": "Kosmicki J.A." }, { "name": "Duncan L.E." }, { "name": "Estrada K." }, { "name": "Zhao F." }, { "name": "Zou J." }, { "name": "Pierce-Hoffman E." }, { "name": "Berghout J." }, { "name": "Cooper D.N." }, { "name": "Deflaux N." }, { "name": "DePristo M." }, { "name": "Do R." }, { "name": "Flannick J." }, { "name": "Fromer M." }, { "name": "Gauthier L." }, { "name": "Goldstein J." }, { "name": "Gupta N." }, { "name": "Howrigan D." }, { "name": "Kiezun A." }, { "name": "Kurki M.I." }, { "name": "Moonshine A.L." }, { "name": "Natarajan P." }, { "name": "Orozco L." }, { "name": "Peloso G.M." }, { "name": "Poplin R." }, { "name": "Rivas M.A." }, { "name": "Ruano-Rubio V." }, { "name": "Rose S.A." }, { "name": "Ruderfer D.M." }, { "name": "Shakir K." }, { "name": "Stenson P.D." }, { "name": "Stevens C." }, { "name": "Thomas B.P." }, { "name": "Tiao G." }, { "name": "Tusie-Luna M.T." }, { "name": "Weisburd B." }, { "name": "Won H.-H." }, { "name": "Yu D." }, { "name": "Altshuler D.M." }, { "name": "Ardissino D." }, { "name": "Boehnke M." }, { "name": "Danesh J." }, { "name": "Donnelly S." }, { "name": "Elosua R." }, { "name": "Florez J.C." }, { "name": "Gabriel S.B." }, { "name": "Getz G." }, { "name": "Glatt S.J." }, { "name": "Hultman C.M." }, { "name": "Kathiresan S." }, { "name": "Laakso M." }, { "name": "McCarroll S." }, { "name": "McCarthy M.I." }, { "name": "McGovern D." }, { "name": "McPherson R." }, { "name": "Neale B.M." }, { "name": "Palotie A." }, { "name": "Purcell S.M." }, { "name": "Saleheen D." }, { "name": "Scharf J.M." }, { "name": "Sklar P." }, { "name": "Sullivan P.F." }, { "name": "Tuomilehto J." }, { "name": "Tsuang M.T." }, { "name": "Watkins H.C." }, { "name": "Wilson J.G." }, { "name": "Daly M.J." }, { "name": "MacArthur D.G." }, { "name": "Abboud H.E." }, { "name": "Abecasis G." }, { "name": "Aguilar-Salinas C.A." }, { "name": "Arellano-Campos O." }, { "name": "Atzmon G." }, { "name": "Aukrust I." }, { "name": "Barr C.L." }, { "name": "Bell G.I." }, { "name": "Bergen S." }, { "name": "Bjorkhaug L." }, { "name": "Blangero J." }, { "name": "Bowden D.W." }, { "name": "Budman C.L." }, { "name": "Burtt N.P." }, { "name": "Centeno-Cruz F." }, { "name": "Chambers J.C." }, { "name": "Chambert K." }, { "name": "Clarke R." }, { "name": "Collins R." }, { "name": "Coppola G." }, { "name": "Cordova E.J." }, { "name": "Cortes M.L." }, { "name": "Cox N.J." }, { "name": "Duggirala R." }, { "name": "Farrall M." }, { "name": "Fernandez-Lopez J.C." }, { "name": "Fontanillas P." }, { "name": "Frayling T.M." }, { "name": "Freimer N.B." }, { "name": "Fuchsberger C." }, { "name": "Garcia-Ortiz H." }, { "name": "Goel A." }, { "name": "Gomez-Vazquez M.J." }, { "name": "Gonzalez-Villalpando M.E." }, { "name": "Gonzalez-Villalpando C." }, { "name": "Grados M.A." }, { "name": "Groop L." }, { "name": "Haiman C.A." }, { "name": "Hanis C.L." }, { "name": "Hattersley A.T." }, { "name": "Henderson B.E." }, { "name": "Hopewell J.C." }, { "name": "Huerta-Chagoya A." }, { "name": "Islas-Andrade S." }, { "name": "Jacobs S.B." }, { "name": "Jalilzadeh S." }, { "name": "Jenkinson C.P." }, { "name": "Moran J." }, { "name": "Jimenez-Morale S." }, { "name": "Kahler A." }, { "name": "King R.A." }, { "name": "Kirov G." }, { "name": "Kooner J.S." }, { "name": "Kyriakou T." }, { "name": "Lee J.Y." }, { "name": "Lehman D.M." }, { "name": "Lyon G." }, { "name": "MacMahon W." }, { "name": "Magnusson P.K." }, { "name": "Mahajan A." }, { "name": "Marrugat J." }, { "name": "Martinez-Hernandez A." }, { "name": "Mathews C.A." }, { "name": "McVean G." }, { "name": "Meigs J.B." }, { "name": "Meitinger T." }, { "name": "Mendoza-Caamal E." }, { "name": "Mercader J.M." }, { "name": "Mohlke K.L." }, { "name": "Moreno-Macias H." }, { "name": "Morris A.P." }, { "name": "Najmi L.A." }, { "name": "Njolstad P.R." }, { "name": "O'Donovan M.C." }, { "name": "Ordonez-Sanchez M.L." }, { "name": "Owen M.J." }, { "name": "Park T." }, { "name": "Pauls D.L." }, { "name": "Posthuma D." }, { "name": "Revilla-Monsalve C." }, { "name": "Riba L." }, { "name": "Ripke S." }, { "name": "Rodriguez-Guillen R." }, { "name": "Rodriguez-Torres M." }, { "name": "Sandor P." }, { "name": "Seielstad M." }, { "name": "Sladek R." }, { "name": "Soberon X." }, { "name": "Spector T.D." }, { "name": "Tai S.E." }, { "name": "Teslovich T.M." }, { "name": "Walford G." }, { "name": "Wilkens L.R." }, { "name": "Williams A.L." } ], "journal": "Nature" } } ], "credit": [ { "name": null, "email": "exomeconsortium@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "harry_morgan", "additionDate": "2017-09-26T07:57:36Z", "lastUpdate": "2026-10-27T09:04:33.736809Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SuperPred", "description": "The SuperPred web server compares the structural fingerprint of an input molecule to a database of drugs connected to their drug targets and affected pathways. As the biological effect is well predictable, if the structural similarity is sufficient, the web-server allows prognoses about the medical indication area of novel compounds and to find new leads for known targets. Such information can be useful in drug classification and target prediction.", "homepage": "http://bioinformatics.charite.de/superpred", "biotoolsID": "superpred", "biotoolsCURIE": "biotools:superpred", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2489", "term": "Protein subcellular localisation prediction" }, { "uri": "http://edamontology.org/operation_0360", "term": "Structural similarity search" }, { "uri": "http://edamontology.org/operation_2436", "term": "Gene-set enrichment analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0209", "term": "Medicinal chemistry" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3336", "term": "Drug discovery" }, { "uri": "http://edamontology.org/topic_3375", "term": "Drug metabolism" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://prediction.charite.de/index.php?site=faq", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkn307", "pmid": "18499712", "pmcid": "PMC2447784", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Janette Nickel", "email": "janette.nickel@charite.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Bjoern-Oliver Gohlke", "email": "Bjoern-Oliver.Gohlke@charite.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Priyanka Banerjee", "email": "Priyanka.Banerjee@charite.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Jevgeni Ehreman", "email": "Jevgeni.Ehreman@charite.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Mathias Dunke", "email": "mathias.dunkel@charite.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "c6", "additionDate": "2017-03-24T14:34:07Z", "lastUpdate": "2026-10-27T09:04:32.857961Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Rhea", "description": "Rhea is a comprehensive and non-redundant resource of expert-curated chemical and transport reactions of biological interest developed by the Swiss-Prot group at SIB Swiss Institute of Bioinformatics.\nRhea can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analysis. Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature list as well as additional reactions, including spontaneously occurring reactions. \nRhea is built on ChEBI (Chemical Entities of Biological Interest) ontology of small molecules to describe its reaction participants. \nSince December 2018, Rhea is the standard for enzyme annotation in UniProt.", "homepage": "https://www.rhea-db.org/", "biotoolsID": "rhea", "biotoolsCURIE": "biotools:rhea", "version": [], "otherID": [], "relation": [ { "biotoolsID": "chebi", "type": "uses" }, { "biotoolsID": "uniprotkb", "type": "usedBy" }, { "biotoolsID": "metabolights", "type": "usedBy" }, { "biotoolsID": "reactome", "type": "usedBy" } ], "function": [], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0821", "term": "Enzymes" }, { "uri": "http://edamontology.org/topic_3314", "term": "Chemistry" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC-BY-NC-4.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [ "Data" ], "elixirNode": [ "Switzerland" ], "elixirCommunity": [], "link": [], "download": [ { "url": "https://www.rhea-db.org/download", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "https://www.rhea-db.org/documentation", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gky876", "pmid": "30272209", "pmcid": "PMC6324061", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Updates in Rhea: SPARQLing biochemical reaction data", "abstract": "Rhea (http://www.rhea-db.org) is a comprehensive and non-redundant resource of over 11 000 expert-curated biochemical reactions that uses chemical entities from the ChEBI ontology to represent reaction participants. Originally designed as an annotation vocabulary for the UniProt Knowledgebase (UniProtKB), Rhea also provides reaction data for a range of other core knowledgebases and data repositories including ChEBI and MetaboLights. Here we describe recent developments in Rhea, focusing on a new resource description framework representation of Rhea reaction data and an SPARQL endpoint (https://sparql.rhea-db.org/sparql) that provides access to it. We demonstrate how federated queries that combine the Rhea SPARQL endpoint and other SPARQL endpoints such as that of UniProt can provide improved metabolite annotation and support integrative analyses that link the metabolome through the proteome to the transcriptome and genome. These developments will significantly boost the utility of Rhea as a means to link chemistry and biology for a more holistic understanding of biological systems and their function in health and disease.", "date": "2019-01-08T00:00:00Z", "citationCount": 51, "authors": [ { "name": "Lombardot T." }, { "name": "Morgat A." }, { "name": "Axelsen K.B." }, { "name": "Aimo L." }, { "name": "Hyka-Nouspikel N." }, { "name": "Niknejad A." }, { "name": "Ignatchenko A." }, { "name": "Xenarios I." }, { "name": "Coudert E." }, { "name": "Redaschi N." }, { "name": "Bridge A." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "SIB Swiss Institute of Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null }, { "name": "Contact Form", "email": null, "url": "http://www.rhea-db.org/feedback", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "SIB", "additionDate": "2017-03-30T23:00:36Z", "lastUpdate": "2026-10-27T09:04:31.678072Z", "editPermission": { "type": "group", "authors": [ "alanbridge", "amorgat", "n.m.palmblad@lumc.nl" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "OMA", "description": "Project that aims to identify orthologs among publicly available, complete genomes. With many hundreds of genomes analyzed to date, it is one of the largest projects of its kind.", "homepage": "http://omabrowser.org/oma/home/", "biotoolsID": "oma", "biotoolsCURIE": "biotools:oma", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2423", "term": "Prediction and recognition" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3021", "term": "UniProt accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3671", "term": "Text" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2974", "term": "Protein sequence (raw)" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0842", "term": "Identifier" }, "format": [] } ], "output": [], "note": "orthology prediction and paralogy OMA group", "cmd": null } ], "toolType": [ "Desktop application", "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3299", 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"Primary" ], "version": null, "note": null, "metadata": { "title": "OMA or tholog y in 2024: impro v ed prokary ot e co v erãg e,ãncestralãnd extant GO enrichment,ã revamped synteny viewerãnd more in the OMA Ecosystem", "abstract": "", "date": "2024-01-05T00:00:00Z", "citationCount": 46, "authors": [], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkaa1007", "pmid": "33174605", "pmcid": "PMC7779010", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "OMA orthology in 2021: Website overhaul, conserved isoforms, ancestral gene order and more", "abstract": "", "date": "2021-01-08T00:00:00Z", "citationCount": 144, "authors": [], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkx1019", "pmid": "29106550", "pmcid": "PMC5753216", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The OMA orthology database in 2018: Retrieving evolutionary relationships among all domains of life through richer web and 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