List all resources, or create a new resource.

GET /api/t/?topic=%22Proteomics%22
HTTP 200 OK
Allow: GET, POST, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept

{
    "count": 2282,
    "next": "?page=2",
    "previous": null,
    "list": [
        {
            "name": "SperMD",
            "description": "The expression atlas of sperm maturation.\n\nThe Sperm Maturation Database (SperMD) is a freely available database containing multiple omics data determined in human or mouse sperm maturation. We collect and integrate data from multiple studies and present them through a unified framework. This database aims to apply into clinical chemistry and biomarker discovery about male infertility.",
            "homepage": "http://bio-add.org/SperMD",
            "biotoolsID": "spermd",
            "biotoolsCURIE": "biotools:spermd",
            "version": [],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2422",
                            "term": "Data retrieval"
                        },
                        {
                            "uri": "http://edamontology.org/operation_2421",
                            "term": "Database search"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3431",
                            "term": "Deposition"
                        }
                    ],
                    "input": [],
                    "output": [],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Database portal"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_3172",
                    "term": "Metabolomics"
                },
                {
                    "uri": "http://edamontology.org/topic_0121",
                    "term": "Proteomics"
                },
                {
                    "uri": "http://edamontology.org/topic_3308",
                    "term": "Transcriptomics"
                },
                {
                    "uri": "http://edamontology.org/topic_3360",
                    "term": "Biomarkers"
                },
                {
                    "uri": "http://edamontology.org/topic_0625",
                    "term": "Genotype and phenotype"
                }
            ],
            "operatingSystem": [
                "Mac",
                "Linux",
                "Windows"
            ],
            "language": [],
            "license": null,
            "collectionID": [],
            "maturity": null,
            "cost": "Free of charge",
            "accessibility": "Open access",
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [],
            "download": [],
            "documentation": [],
            "publication": [
                {
                    "doi": "10.1186/s12859-024-05631-x",
                    "pmid": "38233783",
                    "pmcid": "PMC10792849",
                    "type": [],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "SperMD: the expression atlas of sperm maturation",
                        "abstract": "The impairment of sperm maturation is one of the major pathogenic factors in male subfertility, a serious medical and social problem affecting millions of global couples. Regrettably, the existing research on sperm maturation is slow, limited, and fragmented, largely attributable to the lack of a global molecular view. To fill the data gap, we newly established a database, namely the Sperm Maturation Database (SperMD, http://bio-add.org/SperMD). SperMD integrates heterogeneous multi-omics data (170 transcriptomes, 91 proteomes, and five human metabolomes) to illustrate the transcriptional, translational, and metabolic manifestations during the entire lifespan of sperm maturation. These data involve almost all crucial scenarios related to sperm maturation, including the tissue components of the epididymal microenvironment, cell constituents of tissues, different pathological states, and so on. To the best of our knowledge, SperMD could be one of the limited repositories that provide focused and comprehensive information on sperm maturation. Easy-to-use web services are also implemented to enhance the experience of data retrieval and molecular comparison between humans and mice. Furthermore, the manuscript illustrates an example application demonstrated to systematically characterize novel gene functions in sperm maturation. Nevertheless, SperMD undertakes the endeavor to integrate the islanding omics data, offering a panoramic molecular view of how the spermatozoa gain full reproductive abilities. It will serve as a valuable resource for the systematic exploration of sperm maturation and for prioritizing the biomarkers and targets for precise diagnosis and therapy of male subfertility.",
                        "date": "2024-12-01T00:00:00Z",
                        "citationCount": 1,
                        "authors": [
                            {
                                "name": "Li Y."
                            },
                            {
                                "name": "Li Q."
                            },
                            {
                                "name": "Wu L."
                            },
                            {
                                "name": "Wang H."
                            },
                            {
                                "name": "Shi H."
                            },
                            {
                                "name": "Yang C."
                            },
                            {
                                "name": "Gu Y."
                            },
                            {
                                "name": "Li J."
                            },
                            {
                                "name": "Ji Z."
                            }
                        ],
                        "journal": "BMC Bioinformatics"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Yiqun Gu",
                    "email": "guyiqun@nrifp.org.cn",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                },
                {
                    "name": "Jianyuan Li",
                    "email": "lijianyuan2021@126.com",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                },
                {
                    "name": "Zhiliang Ji",
                    "email": "appo@xmu.edu.cn",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                }
            ],
            "community": null,
            "owner": "Pub2Tools",
            "additionDate": "2024-06-18T21:14:23.281132Z",
            "lastUpdate": "2024-06-18T21:14:23.284431Z",
            "editPermission": {
                "type": "private",
                "authors": []
            },
            "validated": 0,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": "tool"
        },
        {
            "name": "shinyExprPortal",
            "description": "A configurable 'shiny' portal for sharing analysis of molecular expression data.",
            "homepage": "https://c4tb.github.io/shinyExprPortal/index.html",
            "biotoolsID": "shinyexprportal",
            "biotoolsCURIE": "biotools:shinyexprportal",
            "version": [],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_3766",
                            "term": "Weighted correlation network analysis"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0337",
                            "term": "Visualisation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3223",
                            "term": "Differential gene expression profiling"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3463",
                            "term": "Expression correlation analysis"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3431",
                            "term": "Deposition"
                        }
                    ],
                    "input": [],
                    "output": [],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Library"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0121",
                    "term": "Proteomics"
                },
                {
                    "uri": "http://edamontology.org/topic_0625",
                    "term": "Genotype and phenotype"
                },
                {
                    "uri": "http://edamontology.org/topic_3308",
                    "term": "Transcriptomics"
                },
                {
                    "uri": "http://edamontology.org/topic_0602",
                    "term": "Molecular interactions, pathways and networks"
                },
                {
                    "uri": "http://edamontology.org/topic_0080",
                    "term": "Sequence analysis"
                }
            ],
            "operatingSystem": [
                "Mac",
                "Linux",
                "Windows"
            ],
            "language": [
                "R"
            ],
            "license": "MIT",
            "collectionID": [],
            "maturity": null,
            "cost": "Free of charge",
            "accessibility": null,
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [
                {
                    "url": "https://github.com/C4TB/shinyExprPortal",
                    "type": [
                        "Repository"
                    ],
                    "note": null
                }
            ],
            "download": [],
            "documentation": [],
            "publication": [
                {
                    "doi": "10.1093/bioinformatics/btae172",
                    "pmid": "38552327",
                    "pmcid": "PMC11021805",
                    "type": [],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "shinyExprPortal: a configurable 'shiny' portal for sharing analysis of molecular expression data",
                        "abstract": "Motivation: The scale of omics research presents many obstacles to full sharing and access to analysis results. Current publication models impose limits on the number of pages and figures, requiring careful preparation and selection of content. At the same time, depositing data in open repositories significantly shifts the burden of access and reproduction to readers, who may include people who are not programmers or analysts. Results: We introduce shinyExprPortal, an R package that implements omics web portals with minimal coding effort. The portals allow exploration of transcriptomic or proteomic expression data and phenotypes, showcasing results of various types of analysis including differential expression, co-expression and pathways analysis. The integration with bioinformatics workflows enables researchers to focus on their results and share findings using interactive and publication-quality plots.",
                        "date": "2024-04-01T00:00:00Z",
                        "citationCount": 0,
                        "authors": [
                            {
                                "name": "Henkin R."
                            },
                            {
                                "name": "Goldmann K."
                            },
                            {
                                "name": "Lewis M."
                            },
                            {
                                "name": "Barnes M.R."
                            }
                        ],
                        "journal": "Bioinformatics"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Rafael Henkin",
                    "email": "r.henkin@qmul.ac.uk",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-5511-5230",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                }
            ],
            "community": null,
            "owner": "Pub2Tools",
            "additionDate": "2024-06-18T20:11:16.897199Z",
            "lastUpdate": "2024-06-18T20:11:16.899983Z",
            "editPermission": {
                "type": "public",
                "authors": []
            },
            "validated": 0,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": "tool"
        },
        {
            "name": "DDK-Linker",
            "description": "A network-based strategy identifies disease signals by linking high-throughput omics datasets to disease knowledge.",
            "homepage": "http://ddklinker.ncpsb.org.cn/",
            "biotoolsID": "ddk_linker",
            "biotoolsCURIE": "biotools:ddk_linker",
            "version": [],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_3799",
                            "term": "Quantification"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3431",
                            "term": "Deposition"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3223",
                            "term": "Differential gene expression profiling"
                        }
                    ],
                    "input": [],
                    "output": [],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Web application"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0634",
                    "term": "Pathology"
                },
                {
                    "uri": "http://edamontology.org/topic_0121",
                    "term": "Proteomics"
                },
                {
                    "uri": "http://edamontology.org/topic_0602",
                    "term": "Molecular interactions, pathways and networks"
                },
                {
                    "uri": "http://edamontology.org/topic_0102",
                    "term": "Mapping"
                },
                {
                    "uri": "http://edamontology.org/topic_0749",
                    "term": "Transcription factors and regulatory sites"
                }
            ],
            "operatingSystem": [
                "Mac",
                "Linux",
                "Windows"
            ],
            "language": [
                "R"
            ],
            "license": null,
            "collectionID": [],
            "maturity": null,
            "cost": "Free of charge",
            "accessibility": null,
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [],
            "download": [],
            "documentation": [],
            "publication": [
                {
                    "doi": "10.1093/bib/bbae111",
                    "pmid": "38517698",
                    "pmcid": "PMC10959161",
                    "type": [],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "DDK-Linker: a network-based strategy identifies disease signals by linking high-throughput omics datasets to disease knowledge",
                        "abstract": "The high-throughput genomic and proteomic scanning approaches allow investigators to measure the quantification of genome-wide genes (or gene products) for certain disease conditions, which plays an essential role in promoting the discovery of disease mechanisms. The high-throughput approaches often generate a large gene list of interest (GOIs), such as differentially expressed genes/proteins. However, researchers have to perform manual triage and validation to explore the most promising, biologically plausible linkages between the known disease genes and GOIs (disease signals) for further study. Here, to address this challenge, we proposed a network-based strategy DDK-Linker to facilitate the exploration of disease signals hidden in omics data by linking GOIs to disease knowns genes. Specifically, it reconstructed gene distances in the protein-protein interaction (PPI) network through six network methods (random walk with restart, Deepwalk, Node2Vec, LINE, HOPE, Laplacian) to discover disease signals in omics data that have shorter distances to disease genes. Furthermore, benefiting from the establishment of knowledge base we established, the abundant bioinformatics annotations were provided for each candidate disease signal. To assist in omics data interpretation and facilitate the usage, we have developed this strategy into an application that users can access through a website or download the R package. We believe DDK-Linker will accelerate the exploring of disease genes and drug targets in a variety of omics data, such as genomics, transcriptomics and proteomics data, and provide clues for complex disease mechanism and pharmacological research.",
                        "date": "2024-03-01T00:00:00Z",
                        "citationCount": 1,
                        "authors": [
                            {
                                "name": "Kong X."
                            },
                            {
                                "name": "Diao L."
                            },
                            {
                                "name": "Jiang P."
                            },
                            {
                                "name": "Nie S."
                            },
                            {
                                "name": "Guo S."
                            },
                            {
                                "name": "Li D."
                            }
                        ],
                        "journal": "Briefings in Bioinformatics"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Shuzhen Guo",
                    "email": "guoshz@bucm.edu.cn",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                },
                {
                    "name": "Dong Li",
                    "email": "lidong.bprc@foxmail.com",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-8680-0468",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                }
            ],
            "community": null,
            "owner": "Pub2Tools",
            "additionDate": "2024-06-18T20:03:55.622249Z",
            "lastUpdate": "2024-06-18T20:03:55.624574Z",
            "editPermission": {
                "type": "public",
                "authors": []
            },
            "validated": 0,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": "tool"
        },
        {
            "name": "Bento",
            "description": "Bento is a Python toolkit for performing subcellular analysis of spatial transcriptomics data. The package is part of the Scverse ecosystem. Check out the documentation for installation instructions, tutorials, and API.",
            "homepage": "http://bento-tools.readthedocs.io/",
            "biotoolsID": "bento_py",
            "biotoolsCURIE": "biotools:bento_py",
            "version": [],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2429",
                            "term": "Mapping"
                        },
                        {
                            "uri": "http://edamontology.org/operation_2489",
                            "term": "Subcellular localisation prediction"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3891",
                            "term": "Essential dynamics"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0337",
                            "term": "Visualisation"
                        }
                    ],
                    "input": [],
                    "output": [],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Library"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_3308",
                    "term": "Transcriptomics"
                },
                {
                    "uri": "http://edamontology.org/topic_3512",
                    "term": "Gene transcripts"
                },
                {
                    "uri": "http://edamontology.org/topic_0121",
                    "term": "Proteomics"
                },
                {
                    "uri": "http://edamontology.org/topic_2229",
                    "term": "Cell biology"
                },
                {
                    "uri": "http://edamontology.org/topic_3170",
                    "term": "RNA-Seq"
                }
            ],
            "operatingSystem": [],
            "language": [
                "Python"
            ],
            "license": null,
            "collectionID": [],
            "maturity": null,
            "cost": "Free of charge",
            "accessibility": "Open access",
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [],
            "download": [],
            "documentation": [],
            "publication": [
                {
                    "doi": "10.1186/s13059-024-03217-7",
                    "pmid": "38566187",
                    "pmcid": null,
                    "type": [],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "Bento: a toolkit for subcellular analysis of spatial transcriptomics data",
                        "abstract": "The spatial organization of molecules in a cell is essential for their functions. While current methods focus on discerning tissue architecture, cell–cell interactions, and spatial expression patterns, they are limited to the multicellular scale. We present Bento, a Python toolkit that takes advantage of single-molecule information to enable spatial analysis at the subcellular scale. Bento ingests molecular coordinates and segmentation boundaries to perform three analyses: defining subcellular domains, annotating localization patterns, and quantifying gene–gene colocalization. We demonstrate MERFISH, seqFISH +, Molecular Cartography, and Xenium datasets. Bento is part of the open-source Scverse ecosystem, enabling integration with other single-cell analysis tools.",
                        "date": "2024-12-01T00:00:00Z",
                        "citationCount": 0,
                        "authors": [
                            {
                                "name": "Mah C.K."
                            },
                            {
                                "name": "Ahmed N."
                            },
                            {
                                "name": "Lopez N.A."
                            },
                            {
                                "name": "Lam D.C."
                            },
                            {
                                "name": "Pong A."
                            },
                            {
                                "name": "Monell A."
                            },
                            {
                                "name": "Kern C."
                            },
                            {
                                "name": "Han Y."
                            },
                            {
                                "name": "Prasad G."
                            },
                            {
                                "name": "Cesnik A.J."
                            },
                            {
                                "name": "Lundberg E."
                            },
                            {
                                "name": "Zhu Q."
                            },
                            {
                                "name": "Carter H."
                            },
                            {
                                "name": "Yeo G.W."
                            }
                        ],
                        "journal": "Genome Biology"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Gene W. Yeo",
                    "email": "geneyeo@ucsd.edu",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                },
                {
                    "name": "Clarence K. Mah",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                }
            ],
            "community": null,
            "owner": "Pub2Tools",
            "additionDate": "2024-06-18T16:55:25.160235Z",
            "lastUpdate": "2024-06-18T16:55:25.162283Z",
            "editPermission": {
                "type": "private",
                "authors": []
            },
            "validated": 0,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": "tool"
        },
        {
            "name": "hybrid-DIA",
            "description": "Intelligent Data Acquisition for Simultaneous Targeted and Discovery Phosphoproteomics in Single Spheroids.",
            "homepage": "https://github.com/anamdv/HybridDIA",
            "biotoolsID": "hybrid-dia",
            "biotoolsCURIE": "biotools:hybrid-dia",
            "version": [],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_3638",
                            "term": "SILAC"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3755",
                            "term": "PTM localisation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3435",
                            "term": "Standardisation and normalisation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0417",
                            "term": "PTM site prediction"
                        }
                    ],
                    "input": [],
                    "output": [],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Workflow"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_3520",
                    "term": "Proteomics experiment"
                },
                {
                    "uri": "http://edamontology.org/topic_0121",
                    "term": "Proteomics"
                },
                {
                    "uri": "http://edamontology.org/topic_0602",
                    "term": "Molecular interactions, pathways and networks"
                },
                {
                    "uri": "http://edamontology.org/topic_3077",
                    "term": "Data acquisition"
                }
            ],
            "operatingSystem": [],
            "language": [
                "R",
                "Python"
            ],
            "license": null,
            "collectionID": [],
            "maturity": null,
            "cost": "Free of charge",
            "accessibility": "Open access",
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [],
            "download": [],
            "documentation": [],
            "publication": [
                {
                    "doi": "10.1038/s41467-023-39347-y",
                    "pmid": "37328457",
                    "pmcid": "PMC10276052",
                    "type": [],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids",
                        "abstract": "Achieving sufficient coverage of regulatory phosphorylation sites by mass spectrometry (MS)-based phosphoproteomics for signaling pathway reconstitution is challenging, especially when analyzing tiny sample amounts. To address this, we present a hybrid data-independent acquisition (DIA) strategy (hybrid-DIA) that combines targeted and discovery proteomics through an Application Programming Interface (API) to dynamically intercalate DIA scans with accurate triggering of multiplexed tandem mass spectrometry (MSx) scans of predefined (phospho)peptide targets. By spiking-in heavy stable isotope labeled phosphopeptide standards covering seven major signaling pathways, we benchmark hybrid-DIA against state-of-the-art targeted MS methods (i.e., SureQuant) using EGF-stimulated HeLa cells and find the quantitative accuracy and sensitivity to be comparable while hybrid-DIA also profiles the global phosphoproteome. To demonstrate the robustness, sensitivity, and biomedical potential of hybrid-DIA, we profile chemotherapeutic agents in single colon carcinoma multicellular spheroids and evaluate the phospho-signaling difference of cancer cells in 2D vs 3D culture.",
                        "date": "2023-12-01T00:00:00Z",
                        "citationCount": 12,
                        "authors": [
                            {
                                "name": "Martinez-Val A."
                            },
                            {
                                "name": "Fort K."
                            },
                            {
                                "name": "Koenig C."
                            },
                            {
                                "name": "Van der Hoeven L."
                            },
                            {
                                "name": "Franciosa G."
                            },
                            {
                                "name": "Moehring T."
                            },
                            {
                                "name": "Ishihama Y."
                            },
                            {
                                "name": "Chen Y.-J."
                            },
                            {
                                "name": "Makarov A."
                            },
                            {
                                "name": "Xuan Y."
                            },
                            {
                                "name": "Olsen J.V."
                            }
                        ],
                        "journal": "Nature Communications"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Yue Xuan",
                    "email": "jesper.olsen@cpr.ku.dk",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                },
                {
                    "name": "Jesper V. Olsen",
                    "email": "yue.xuan@thermofisher.com",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                }
            ],
            "community": null,
            "owner": "Pub2Tools",
            "additionDate": "2024-06-18T16:48:32.884877Z",
            "lastUpdate": "2024-06-18T16:48:32.886990Z",
            "editPermission": {
                "type": "private",
                "authors": []
            },
            "validated": 0,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": "tool"
        },
        {
            "name": "DEGRONOPEDIA",
            "description": "Web server for proteome-wide inspection of degrons.\nSearch for degrons, their modifications, conservation, emergence after proteolysis, predict stability of protein N-/C-terminus and many more.",
            "homepage": "http://degronopedia.com",
            "biotoolsID": "degronopedia",
            "biotoolsCURIE": "biotools:degronopedia",
            "version": [],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2421",
                            "term": "Database search"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3904",
                            "term": "Protein disorder prediction"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0417",
                            "term": "PTM site prediction"
                        }
                    ],
                    "input": [],
                    "output": [],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Web application"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0601",
                    "term": "Protein modifications"
                },
                {
                    "uri": "http://edamontology.org/topic_0121",
                    "term": "Proteomics"
                },
                {
                    "uri": "http://edamontology.org/topic_0602",
                    "term": "Molecular interactions, pathways and networks"
                },
                {
                    "uri": "http://edamontology.org/topic_0130",
                    "term": "Protein folding, stability and design"
                }
            ],
            "operatingSystem": [
                "Mac",
                "Linux",
                "Windows"
            ],
            "language": [],
            "license": null,
            "collectionID": [],
            "maturity": null,
            "cost": "Free of charge",
            "accessibility": "Open access",
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [],
            "download": [],
            "documentation": [],
            "publication": [
                {
                    "doi": "10.1093/nar/gkae238",
                    "pmid": "38567734",
                    "pmcid": null,
                    "type": [],
                    "version": null,
                    "note": null,
                    "metadata": null
                }
            ],
            "credit": [
                {
                    "name": "Natalia A. Szulc",
                    "email": "wpokrzywa@iimcb.gov.pl",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                },
                {
                    "name": "Wojciech Pokrzywa",
                    "email": "nszulc@iimcb.gov.pl",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                }
            ],
            "community": null,
            "owner": "Pub2Tools",
            "additionDate": "2024-06-18T16:32:25.967466Z",
            "lastUpdate": "2024-06-18T16:32:25.969525Z",
            "editPermission": {
                "type": "private",
                "authors": []
            },
            "validated": 0,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": "tool"
        },
        {
            "name": "openNAU",
            "description": "An open-source platform for normalizing, analyzing, and visualizing untargeted metabolomics data.",
            "homepage": "https://github.com/zjuRong/openNAU",
            "biotoolsID": "opennau",
            "biotoolsCURIE": "biotools:opennau",
            "version": [],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_3803",
                            "term": "Natural product identification"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3435",
                            "term": "Standardisation and normalisation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0337",
                            "term": "Visualisation"
                        }
                    ],
                    "input": [],
                    "output": [],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Library"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_3172",
                    "term": "Metabolomics"
                },
                {
                    "uri": "http://edamontology.org/topic_0154",
                    "term": "Small molecules"
                },
                {
                    "uri": "http://edamontology.org/topic_3407",
                    "term": "Endocrinology and metabolism"
                },
                {
                    "uri": "http://edamontology.org/topic_3520",
                    "term": "Proteomics experiment"
                },
                {
                    "uri": "http://edamontology.org/topic_0593",
                    "term": "NMR"
                }
            ],
            "operatingSystem": [],
            "language": [
                "R",
                "SQL",
                "PHP"
            ],
            "license": "MIT",
            "collectionID": [],
            "maturity": null,
            "cost": "Free of charge",
            "accessibility": "Open access",
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [],
            "download": [],
            "documentation": [],
            "publication": [
                {
                    "doi": "10.21147/j.issn.1000-9604.2023.05.11",
                    "pmid": "37969962",
                    "pmcid": "PMC10643343",
                    "type": [],
                    "version": null,
                    "note": null,
                    "metadata": null
                }
            ],
            "credit": [
                {
                    "name": "Yongcheng Wang",
                    "email": "yongcheng@zju.edu.cn",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                },
                {
                    "name": "Dandan Zhang",
                    "email": "dandanz@zju.edu.cn",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                },
                {
                    "name": "Maode Lai",
                    "email": "lmd@zju.edu.cn",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                }
            ],
            "community": null,
            "owner": "Pub2Tools",
            "additionDate": "2024-06-18T14:34:13.641984Z",
            "lastUpdate": "2024-06-18T14:34:13.644084Z",
            "editPermission": {
                "type": "public",
                "authors": []
            },
            "validated": 0,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": "tool"
        },
        {
            "name": "MASSef",
            "description": "Bottom-up parameterization of enzyme rate constants.",
            "homepage": "https://github.com/opencobra/MASSef",
            "biotoolsID": "massef",
            "biotoolsCURIE": "biotools:massef",
            "version": [],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0334",
                            "term": "Enzyme kinetics calculation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3660",
                            "term": "Metabolic network modelling"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3435",
                            "term": "Standardisation and normalisation"
                        }
                    ],
                    "input": [],
                    "output": [],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Library"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0821",
                    "term": "Enzymes"
                },
                {
                    "uri": "http://edamontology.org/topic_3407",
                    "term": "Endocrinology and metabolism"
                },
                {
                    "uri": "http://edamontology.org/topic_3474",
                    "term": "Machine learning"
                },
                {
                    "uri": "http://edamontology.org/topic_0121",
                    "term": "Proteomics"
                },
                {
                    "uri": "http://edamontology.org/topic_0154",
                    "term": "Small molecules"
                }
            ],
            "operatingSystem": [
                "Mac",
                "Linux",
                "Windows"
            ],
            "language": [
                "Mathematica"
            ],
            "license": null,
            "collectionID": [],
            "maturity": null,
            "cost": "Free of charge",
            "accessibility": null,
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [],
            "download": [],
            "documentation": [],
            "publication": [
                {
                    "doi": "10.1016/j.mec.2024.e00234",
                    "pmid": "38711578",
                    "pmcid": "PMC11070925",
                    "type": [],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "Bottom-up parameterization of enzyme rate constants: Reconciling inconsistent data",
                        "abstract": "Kinetic models of metabolism are promising platforms for studying complex metabolic systems and designing production strains. Given the availability of enzyme kinetic data from historical experiments and machine learning estimation tools, a straightforward modeling approach is to assemble kinetic data enzyme by enzyme until a desired scale is reached. However, this type of ‘bottom up’ parameterization of kinetic models has been difficult due to a number of issues including gaps in kinetic parameters, the complexity of enzyme mechanisms, inconsistencies between parameters obtained from different sources, and in vitro-in vivo differences. Here, we present a computational workflow for the robust estimation of kinetic parameters for detailed mass action enzyme models while taking into account parameter uncertainty. The resulting software package, termed MASSef (the Mass Action Stoichiometry Simulation Enzyme Fitting package), can handle standard ‘macroscopic’ kinetic parameters, including Km, kcat, Ki, Keq, and nh, as well as diverse reaction mechanisms defined in terms of mass action reactions and ‘microscopic’ rate constants. We provide three enzyme case studies demonstrating that this approach can identify and reconcile inconsistent data either within in vitro experiments or between in vitro and in vivo enzyme function. We further demonstrate how parameterized enzyme modules can be used to assemble pathway-scale kinetic models consistent with in vivo behavior. This work builds on the legacy of knowledge on kinetic behavior of enzymes by enabling robust parameterization of enzyme kinetic models at scale utilizing the abundance of historical literature data and machine learning parameter estimates.",
                        "date": "2024-06-01T00:00:00Z",
                        "citationCount": 0,
                        "authors": [
                            {
                                "name": "Zielinski D.C."
                            },
                            {
                                "name": "Matos M.R.A."
                            },
                            {
                                "name": "de Bree J.E."
                            },
                            {
                                "name": "Glass K."
                            },
                            {
                                "name": "Sonnenschein N."
                            },
                            {
                                "name": "Palsson B.O."
                            }
                        ],
                        "journal": "Metabolic Engineering Communications"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Bernhard O. Palsson",
                    "email": "dczielin@ucsd.edu",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                }
            ],
            "community": null,
            "owner": "Pub2Tools",
            "additionDate": "2024-06-18T13:55:08.494894Z",
            "lastUpdate": "2024-06-18T13:55:08.497648Z",
            "editPermission": {
                "type": "private",
                "authors": []
            },
            "validated": 0,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": "tool"
        },
        {
            "name": "kmerDB",
            "description": "A database encompassing the set of genomic and proteomic sequence information for each species.",
            "homepage": "http://www.kmerdb.com",
            "biotoolsID": "kmerdb",
            "biotoolsCURIE": "biotools:kmerdb",
            "version": [],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_1812",
                            "term": "Parsing"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3472",
                            "term": "k-mer counting"
                        },
                        {
                            "uri": "http://edamontology.org/operation_2421",
                            "term": "Database search"
                        }
                    ],
                    "input": [],
                    "output": [],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Database portal"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0121",
                    "term": "Proteomics"
                },
                {
                    "uri": "http://edamontology.org/topic_0080",
                    "term": "Sequence analysis"
                },
                {
                    "uri": "http://edamontology.org/topic_0154",
                    "term": "Small molecules"
                },
                {
                    "uri": "http://edamontology.org/topic_0621",
                    "term": "Model organisms"
                },
                {
                    "uri": "http://edamontology.org/topic_3520",
                    "term": "Proteomics experiment"
                }
            ],
            "operatingSystem": [
                "Mac",
                "Linux",
                "Windows"
            ],
            "language": [
                "Python"
            ],
            "license": null,
            "collectionID": [],
            "maturity": null,
            "cost": null,
            "accessibility": null,
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [
                {
                    "url": "https://github.com/Georgakopoulos-Soares-lab/kmerdb_stats",
                    "type": [
                        "Repository"
                    ],
                    "note": null
                }
            ],
            "download": [],
            "documentation": [],
            "publication": [
                {
                    "doi": "10.1016/j.csbj.2024.04.050",
                    "pmid": "38711760",
                    "pmcid": "PMC11070822",
                    "type": [],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species",
                        "abstract": "The decrease in sequencing expenses has facilitated the creation of reference genomes and proteomes for an expanding array of organisms. Nevertheless, no established repository that details organism-specific genomic and proteomic sequences of specific lengths, referred to as kmers, exists to our knowledge. In this article, we present kmerDB, a database accessible through an interactive web interface that provides kmer-based information from genomic and proteomic sequences in a systematic way. kmerDB currently contains 202,340,859,107 base pairs and 19,304,903,356 amino acids, spanning 54,039 and 21,865 reference genomes and proteomes, respectively, as well as 6,905,362 and 149,305,183 genomic and proteomic species-specific sequences, termed quasi-primes. Additionally, we provide access to 5,186,757 nucleic and 214,904,089 peptide sequences absent from every genome and proteome, termed primes. kmerDB features a user-friendly interface offering various search options and filters for easy parsing and searching. The service is available at: www.kmerdb.com.",
                        "date": "2024-12-01T00:00:00Z",
                        "citationCount": 0,
                        "authors": [
                            {
                                "name": "Mouratidis I."
                            },
                            {
                                "name": "Baltoumas F.A."
                            },
                            {
                                "name": "Chantzi N."
                            },
                            {
                                "name": "Patsakis M."
                            },
                            {
                                "name": "Chan C.S.Y."
                            },
                            {
                                "name": "Montgomery A."
                            },
                            {
                                "name": "Konnaris M.A."
                            },
                            {
                                "name": "Aplakidou E."
                            },
                            {
                                "name": "Georgakopoulos G.C."
                            },
                            {
                                "name": "Das A."
                            },
                            {
                                "name": "Chartoumpekis D.V."
                            },
                            {
                                "name": "Kovac J."
                            },
                            {
                                "name": "Pavlopoulos G.A."
                            },
                            {
                                "name": "Georgakopoulos-Soares I."
                            }
                        ],
                        "journal": "Computational and Structural Biotechnology Journal"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Georgios A. Pavlopoulos",
                    "email": "pavlopoulos@fleming.gr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                },
                {
                    "name": "Ilias Georgakopoulos-Soares",
                    "email": "izg5139@psu.edu",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                }
            ],
            "community": null,
            "owner": "Pub2Tools",
            "additionDate": "2024-06-18T13:36:21.204627Z",
            "lastUpdate": "2024-06-18T13:36:21.207180Z",
            "editPermission": {
                "type": "public",
                "authors": []
            },
            "validated": 0,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": "tool"
        },
        {
            "name": "prolfqua",
            "description": "Comprehensive R-package for proteomics differential expression analysis.",
            "homepage": "https://github.com/fgcz/prolfqua",
            "biotoolsID": "prolfqua",
            "biotoolsCURIE": "biotools:prolfqua",
            "version": [],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_3630",
                            "term": "Protein quantification"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3223",
                            "term": "Differential gene expression profiling"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3741",
                            "term": "Differential protein expression profiling"
                        },
                        {
                            "uri": "http://edamontology.org/operation_2238",
                            "term": "Statistical calculation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3436",
                            "term": "Aggregation"
                        }
                    ],
                    "input": [],
                    "output": [],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Library"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0121",
                    "term": "Proteomics"
                },
                {
                    "uri": "http://edamontology.org/topic_3520",
                    "term": "Proteomics experiment"
                },
                {
                    "uri": "http://edamontology.org/topic_0080",
                    "term": "Sequence analysis"
                }
            ],
            "operatingSystem": [],
            "language": [
                "R"
            ],
            "license": "MIT",
            "collectionID": [],
            "maturity": null,
            "cost": "Free of charge",
            "accessibility": "Open access",
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [],
            "download": [],
            "documentation": [],
            "publication": [
                {
                    "doi": "10.1021/acs.jproteome.2c00441",
                    "pmid": "36939687",
                    "pmcid": "PMC10088014",
                    "type": [],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "prolfqua: A Comprehensive R-Package for Proteomics Differential Expression Analysis",
                        "abstract": "Mass spectrometry is widely used for quantitative proteomics studies, relative protein quantification, and differential expression analysis of proteins. There is a large variety of quantification software and analysis tools. Nevertheless, there is a need for a modular, easy-to-use application programming interface in R that transparently supports a variety of well principled statistical procedures to make applying them to proteomics data, comparing and understanding their differences easy. The prolfqua package integrates essential steps of the mass spectrometry-based differential expression analysis workflow: quality control, data normalization, protein aggregation, statistical modeling, hypothesis testing, and sample size estimation. The package makes integrating new data formats easy. It can be used to model simple experimental designs with a single explanatory variable and complex experiments with multiple factors and hypothesis testing. The implemented methods allow sensitive and specific differential expression analysis. Furthermore, the package implements benchmark functionality that can help to compare data acquisition, data preprocessing, or data modeling methods using a gold standard data set. The application programmer interface of prolfqua strives to be clear, predictable, discoverable, and consistent to make proteomics data analysis application development easy and exciting. Finally, the prolfqua R-package is available on GitHub https://github.com/fgcz/prolfqua, distributed under the MIT license. It runs on all platforms supported by the R free software environment for statistical computing and graphics.",
                        "date": "2023-04-07T00:00:00Z",
                        "citationCount": 10,
                        "authors": [
                            {
                                "name": "Wolski W.E."
                            },
                            {
                                "name": "Nanni P."
                            },
                            {
                                "name": "Grossmann J."
                            },
                            {
                                "name": "d'Errico M."
                            },
                            {
                                "name": "Schlapbach R."
                            },
                            {
                                "name": "Panse C."
                            }
                        ],
                        "journal": "Journal of Proteome Research"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Witold E. Wolski",
                    "email": "wew@fgcz.ethz.ch",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                }
            ],
            "community": null,
            "owner": "Pub2Tools",
            "additionDate": "2024-06-18T13:20:26.291422Z",
            "lastUpdate": "2024-06-18T13:20:26.293652Z",
            "editPermission": {
                "type": "private",
                "authors": []
            },
            "validated": 0,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": "tool"
        }
    ]
}