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{ "count": 8421, "next": "?page=2", "previous": null, "list": [ { "name": "Lion Localizer", "description": "Software tool for inferring the provenance of lions (Panthera leo) using mitochondrial DNA.", "homepage": "https://lionlocalizer.org", "biotoolsID": "lion_localizer", "biotoolsCURIE": "biotools:lion_localizer", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" }, { "uri": "http://edamontology.org/operation_0487", "term": "Haplotype mapping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_0654", "term": "DNA" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" } ], "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/JHERED/ESAD072", "pmid": "37952226", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Lion Localizer: A software tool for inferring the provenance of lions (Panthera leo) using mitochondrial DNA", "abstract": "The illegal poaching of lions for their body parts poses a severe threat to lion populations across Africa. Poaching accounts for 35% of all human-caused lion deaths, with 51% attributed to retaliatory killings following livestock predation. In nearly half of the retaliatory killings, lion body parts are removed, suggesting that high demand for lion body parts may fuel killings attributed to human-lion conflict. Trafficked items are often confiscated in transit or destination countries far from their country of origin. DNA from lion parts may in some cases be the only available means for examining their geographic origins. In this paper, we present the Lion Localizer, a full-stack software tool that houses a comprehensive database of lion mitochondrial DNA (mtDNA) sequences sourced from previously published studies. The database covers 146 localities from across the African continent and India, providing information on the potential provenance of seized lion body parts. Lion mtDNA sequences of 350 or 1,140 bp corresponding to the cytochrome b region can be generated from lion products and queried against the Lion Localizer database. Using the query sequence, the Lion Localizer generates a listing of exact or partial matches, which are displayed on an interactive map of Africa. This allows for the rapid identification of potential regions and localities where lions have been or are presently being targeted by poachers. By examining the potential provenance of lion samples, the Lion Localizer serves as a valuable resource in the fight against lion poaching. The software is available at https://lionlocalizer.org.", "date": "2024-03-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Au W.C." }, { "name": "Dures S.G." }, { "name": "Ishida Y." }, { "name": "Green C.E." }, { "name": "Zhao K." }, { "name": "Ogden R." }, { "name": "Roca A.L." } ], "journal": "Journal of Heredity" } } ], "credit": [ { "name": "Alfred L Roca", "email": "roca@illinois.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Wesley C Au", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-19T11:31:13.116284Z", "lastUpdate": "2024-04-19T11:31:13.118404Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MetGENE", "description": "Gene-centric metabolomics information retrieval tool.", "homepage": "https://bdcw.org/MetGENE/index.php", "biotoolsID": "metgene", "biotoolsCURIE": "biotools:metgene", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" }, { "uri": "http://edamontology.org/operation_3695", "term": "Filtering" }, { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_3067", "term": "Anatomy" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "PHP", "R" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/metabolomicsworkbench/MetGENE", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/GIGASCIENCE/GIAD089", "pmid": "37983749", "pmcid": "PMC10659118", "type": [], "version": null, "note": null, "metadata": { "title": "MetGENE: gene-centric metabolomics information retrieval tool", "abstract": "Background: Biomedical research often involves contextual integration of multimodal and multiomic data in search of mechanisms for improved diagnosis, treatment, and monitoring. Researchers need to access information from diverse sources, comprising data in various and sometimes incongruent formats. The downstream processing of the data to decipher mechanisms by reconstructing networks and developing quantitative models warrants considerable effort. Results: MetGENE is a knowledge-based, gene-centric data aggregator that hierarchically retrieves information about the gene(s), their related pathway(s), reaction(s), metabolite(s), and metabolomic studies from standard data repositories under one dashboard to enable ease of access through centralization of relevant information. We note that MetGENE focuses only on those genes that encode for proteins directly associated with metabolites. All other gene–metabolite associations are beyond the current scope of MetGENE. Further, the information can be contextualized by filtering by species, anatomy (tissue), and condition (disease or phenotype). Conclusions: MetGENE is an open-source tool that aggregates metabolite information for a given gene(s) and presents them in different computable formats (e.g., JSON) for further integration with other omics studies. MetGENE is available at https://bdcw.org/MetGENE/index.php.", "date": "2023-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Srinivasan S." }, { "name": "Maurya M.R." }, { "name": "Ramachandran S." }, { "name": "Fahy E." }, { "name": "Subramaniam S." } ], "journal": "GigaScience" } } ], "credit": [ { "name": "Shankar Subramaniam", "email": "shsubramaniam@ucsd.edu", "url": null, "orcidid": "https://orcid.org/0000-0002-8059-4659", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Sumana Srinivasan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-19T11:28:09.722051Z", "lastUpdate": "2024-04-19T11:28:09.723894Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MESPEUS", "description": "Database of metal coordination groups in proteins.", "homepage": "http://mespeus.nchu.edu.tw/", "biotoolsID": "mespeus", "biotoolsCURIE": "biotools:mespeus", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3898", "term": "Metal-binding site prediction" }, { "uri": "http://edamontology.org/operation_1834", "term": "Protein-metal contact calculation" }, { "uri": "http://edamontology.org/operation_1831", "term": "Metal-bound cysteine detection" }, { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_3071", "term": "Biological databases" }, { "uri": "http://edamontology.org/topic_0593", "term": "NMR" }, { "uri": "http://edamontology.org/topic_2828", "term": "X-ray diffraction" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" } ], "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/GKAD1009", "pmid": "37941148", "pmcid": "PMC10767821", "type": [], "version": null, "note": null, "metadata": { "title": "MESPEUS:ã database of metal coordination groups in proteins", "abstract": "MESPEUS isã freelyãccessible database which uses carefully selected metal coordination groups found in metalloprotein str uct ures taken from the Protein Data Bãnk. T he datãbase contãins geometrical information of metal sites within proteins, including 40 metãl t ypes. In order to completely determine the metal coordination, the symmetry-related units ofã given protein str uct ureãre taken intoãccountãndãre generated using theãppropriate space group symmetry operations. This permitsã more complete description of the metal coordination geometry by includingãll coordinatingãtoms. The user-friendly web interfaceãllows users to directly search forã metal site of interest using se v eral useful options, including searching for metal elements, metal-donor distances, coordination number, donor residue group,ãnd str uct ural resolution. These searches can be carried out singly or in combination. The details ofã metal siteãnd the metal site(s) in the whole str uct ure can be graphically displa y ed using the interactiv e w eb interfãce. MESPEUS isãutomatically updated monthly b y synchronizing with the PDB database. An in v estigation f or the Mg-ATP interaction is giv en to demonstrate how MESPEUS can be used to e xtract inf ormationãbout metal sites by selecting str uct ureãnd coordination feat ures. MESPEUS isã vãilableãt ht tp://mespeus.nc hu.edu.tw/.", "date": "2024-01-05T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Lin G.-Y." }, { "name": "Su Y.-C." }, { "name": "Huang Y.L." }, { "name": "Hsin K.-Y." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Kun-Yi Hsin", "email": "kunyi.hsin@nchu.edu.tw", "url": null, "orcidid": "https://orcid.org/0000-0001-7220-3454", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Geng-Yu Lin", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-19T10:09:48.151582Z", "lastUpdate": "2024-04-19T10:09:48.154041Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "DeepHLAPred", "description": "Deep learning-based method for non-classical HLA binder prediction.", "homepage": "http://www.biolscience.cn/DeepHLApred/", "biotoolsID": "deephlapred", "biotoolsCURIE": "biotools:deephlapred", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0252", "term": "Peptide immunogenicity prediction" }, { "uri": "http://edamontology.org/operation_0440", "term": "Promoter prediction" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2830", "term": "Immunoproteins and antigens" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/tangxingyu0/DeepHLApred", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/S12864-023-09796-2", "pmid": "37993812", "pmcid": "PMC10666343", "type": [], "version": null, "note": null, "metadata": { "title": "DeepHLAPred: a deep learning-based method for non-classical HLA binder prediction", "abstract": "Human leukocyte antigen (HLA) is closely involved in regulating the human immune system. Despite great advance in detecting classical HLA Class I binders, there are few methods or toolkits for recognizing non-classical HLA Class I binders. To fill in this gap, we have developed a deep learning-based tool called DeepHLAPred. The DeepHLAPred used electron-ion interaction pseudo potential, integer numerical mapping and accumulated amino acid frequency as initial representation of non-classical HLA binder sequence. The deep learning module was used to further refine high-level representations. The deep learning module comprised two parallel convolutional neural networks, each followed by maximum pooling layer, dropout layer, and bi-directional long short-term memory network. The experimental results showed that the DeepHLAPred reached the state-of-the-art performanceson the cross-validation test and the independent test. The extensive test demonstrated the rationality of the DeepHLAPred. We further analyzed sequence pattern of non-classical HLA class I binders by information entropy. The information entropy of non-classical HLA binder sequence implied sequence pattern to a certain extent. In addition, we have developed a user-friendly webserver for convenient use, which is available at http://www.biolscience.cn/DeepHLApred/ . The tool and the analysis is helpful to detect non-classical HLA Class I binder. The source code and data is available at https://github.com/tangxingyu0/DeepHLApred .", "date": "2023-12-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Huang G." }, { "name": "Tang X." }, { "name": "Zheng P." } ], "journal": "BMC Genomics" } } ], "credit": [ { "name": "Guohua Huang", "email": "guohuahhn@163.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Xingyu Tang", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Peijie Zheng", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-19T10:04:52.539998Z", "lastUpdate": "2024-04-19T10:04:52.542062Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "RefMetaPlant", "description": "Reference metabolome database for plants across five major phyla.", "homepage": "https://www.biosino.org/RefMetaDB/", "biotoolsID": "refmetaplant", "biotoolsCURIE": "biotools:refmetaplant", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" }, { "uri": "http://edamontology.org/operation_3801", "term": "Spectral library search" }, { "uri": "http://edamontology.org/operation_2421", "term": "Database search" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3810", "term": "Agricultural science" } ], "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/GKAD980", "pmid": "37953341", "pmcid": "PMC10767953", "type": [], "version": null, "note": null, "metadata": { "title": "RefMetaPlant: a reference metabolome database for plants across five major phyla", "abstract": "Plants are unique with tremendous chemical diversity and metabolic complexity, which is highlighted by estimates that green plants collectively produce metabolites numbering in the millions. Plant metabolites play crucial roles in all aspects of plant biology, like growth, development, stress responses, etc. However, the lack of a reference metabolome for plants, and paucity of high-quality standard compound spectral libraries and related analytical tools, have hindered the discovery and functional study of phytochemicals in plants. Here, by leveraging an advanced LC–MS platform, we generated untargeted mass spectral data from >150 plant species collected across the five major phyla. Using a self-developed computation protocol, we constructed reference metabolome for 153 plant species. A ‘Reference Metabolome Database for Plants’ (RefMetaPlant) was built to encompass the reference metabolome, integrated standard compound mass spectral libraries for annotation, and related query and analytical tools like ‘LC–MS/MS Query’, ‘RefMetaBlast’ and ‘CompoundLibBlast’ for searches and profiling of plant metabolome and metabolite identification. Analogous to a reference genome in genomic research, RefMetaPlant provides a powerful platform to support plant genome-scale metabolite analysis to promote knowledge/data sharing and collaboration in the field of metabolomics. RefMetaPlant is freely available at https://www.biosino.org/RefMetaDB/.", "date": "2024-01-05T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Shi H." }, { "name": "Wu X." }, { "name": "Zhu Y." }, { "name": "Jiang T." }, { "name": "Wang Z." }, { "name": "Li X." }, { "name": "Liu J." }, { "name": "Zhang Y." }, { "name": "Chen F." }, { "name": "Gao J." }, { "name": "Xu X." }, { "name": "Zhang G." }, { "name": "Xiao N." }, { "name": "Feng X." }, { "name": "Zhang P." }, { "name": "Wu Y." }, { "name": "Li A." }, { "name": "Chen P." }, { "name": "Li X." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Ping Chen", "email": "pchen@cemps.ac.cn", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Xuan Li", "email": "lixuan@sippe.ac.cn", "url": null, "orcidid": "https://orcid.org/0000-0002-7435-9652", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-19T09:48:49.564191Z", "lastUpdate": "2024-04-19T09:48:49.566259Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "PPGR", "description": "Comprehensive perennial plant genomes and regulation database.", "homepage": "https://ngdc.cncb.ac.cn/ppgr/", "biotoolsID": "ppgr", "biotoolsCURIE": "biotools:ppgr", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2437", "term": "Gene regulatory network prediction" }, { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_0306", "term": "Text mining" }, { "uri": "http://edamontology.org/operation_0314", "term": "Gene expression profiling" }, { "uri": "http://edamontology.org/operation_0308", "term": "PCR primer design" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" }, { "uri": "http://edamontology.org/topic_0204", "term": "Gene regulation" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_0749", "term": "Transcription factors and regulatory sites" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" } ], "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/GKAD963", "pmid": "37933857", "pmcid": "PMC10767873", "type": [], "version": null, "note": null, "metadata": { "title": "PPGR: a comprehensive perennial plant genomes and regulation database", "abstract": "Perennial woody plants hold vital ecological significance, distinguished by their unique traits. While significant progress has been made in their genomic and functional studies, a major challenge persists: the absence of a comprehensive reference platform for collection, integration and in-depth analysis of the vast amount of data. Here, we present PPGR (Resource for Perennial Plant Genomes and Regulation; https://ngdc.cncb.ac.cn/ppgr/) to address this critical gap, by collecting, integrating, analyzing and visualizing genomic, gene regulation and functional data of perennial plants. PPGR currently includes 60 species, 847 million protein–protein/TF (transcription factor)-target interactions, 9016 transcriptome samples under various environmental conditions and genetic backgrounds. Noteworthy is the focus on genes that regulate wood production, seasonal dormancy, terpene biosynthesis and leaf senescence representing a wealth of information derived from experimental data, literature mining, public databases and genomic predictions. Furthermore, PPGR incorporates a range of multi-omics search and analysis tools to facilitate browsing and application of these extensive datasets. PPGR represents a comprehensive and high-quality resource for perennial plants, substantiated by an illustrative case study that demonstrates its capacity in unraveling gene functions and shedding light on potential regulatory processes.", "date": "2024-01-05T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Yang S." }, { "name": "Zong W." }, { "name": "Shi L." }, { "name": "Li R." }, { "name": "Ma Z." }, { "name": "Ma S." }, { "name": "Si J." }, { "name": "Wu Z." }, { "name": "Zhai J." }, { "name": "Ma Y." }, { "name": "Fan Z." }, { "name": "Chen S." }, { "name": "Huang H." }, { "name": "Zhang D." }, { "name": "Bao Y." }, { "name": "Li R." }, { "name": "Xie J." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Yiming Bao", "email": "baoym@big.ac.cn", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Rujiao Li", "email": "lirj@big.ac.cn", "url": null, "orcidid": "https://orcid.org/0000-0002-3276-8335", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Jianbo Xie", "email": "jbxie@bjfu.edu.cn", "url": null, "orcidid": "https://orcid.org/0000-0002-8650-7675", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-19T09:34:52.013720Z", "lastUpdate": "2024-04-19T09:34:52.015995Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "UniProtExtractR", "description": "Shiny App and R package for easily extracting protein-specific UniProtKB information and fine-tuning organelle resolution.", "homepage": "https://harperlab.connect.hms.harvard.edu/uniprotextractR", "biotoolsID": "uniprotextractr", "biotoolsCURIE": "biotools:uniprotextractr", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" }, { "uri": "http://edamontology.org/operation_3096", "term": "Editing" }, { "uri": "http://edamontology.org/operation_3359", "term": "Splitting" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_0623", "term": "Gene and protein families" }, { "uri": "http://edamontology.org/topic_0601", "term": "Protein modifications" } ], "operatingSystem": [], "language": [ "R" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/alex-bio/UniProtExtractR", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/BIOADV/VBAD157", "pmid": "37953912", "pmcid": "PMC10636703", "type": [], "version": null, "note": null, "metadata": { "title": "UniProtExtractR: an app and R package for easily extracting protein-specific UniProtKB information and fine-tuning organelle resolution", "abstract": "UniProtKB is a publicly accessible database of annotated protein features for numerous organisms; however, globally extracting protein entry information for data visualization and categorization can be challenging. While the UniProtKB entry syntax maintains database consistency, it simultaneously obscures key terms within long character strings. To increase accessibility, UniProtExtractR is both an app and R package that extracts desired information across nine UniProtKB categories: DNA binding, Pathway, Transmembrane, Signal peptide, Protein families, Domain [FT], Motif, Involvement in disease, and Subcellular location [CC]. The app features interactive frequency tables that globally summarize both the original UniProtKB input query as well as the extracted/changed entry values. Moreover, UniProtExtractR includes a tractable mapping algorithm to define custom organelle-level resolution. UniProtExtractR exists as a freely accessible Shiny app that requires no coding experience as well as R package, the code of which is entirely open source.", "date": "2023-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Panov A." }, { "name": "Harper J.W." } ], "journal": "Bioinformatics Advances" } } ], "credit": [ { "name": "Alexandra Panov", "email": "alex@hms.harvard.edu", "url": null, "orcidid": "https://orcid.org/0000-0002-2960-0291", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "J Wade Harper", "email": "wade_harper@hms.harvard.edu", "url": null, "orcidid": "https://orcid.org/0000-0002-6944-7236", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-19T09:32:39.965113Z", "lastUpdate": "2024-04-19T09:33:09.634027Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "COMO", "description": "Pipeline for multi-omics data integration in metabolic modelling and drug discovery.", "homepage": "https://github.com/HelikarLab/COMO", "biotoolsID": "como", "biotoolsCURIE": "biotools:como", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3660", "term": "Metabolic network modelling" }, { "uri": "http://edamontology.org/operation_3929", "term": "Metabolic pathway prediction" }, { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression profiling" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3336", "term": "Drug discovery" }, { "uri": "http://edamontology.org/topic_3407", "term": "Endocrinology and metabolism" }, { "uri": "http://edamontology.org/topic_3375", "term": "Drug metabolism" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3379", "term": "Preclinical and clinical studies" } ], "operatingSystem": [], "language": [ "Python", "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/BIB/BBAD387", "pmid": "37930022", "pmcid": "PMC10627799", "type": [], "version": null, "note": null, "metadata": { "title": "COMO: a pipeline for multi-omics data integration in metabolic modeling and drug discovery", "abstract": "Identifying potential drug targets using metabolic modeling requires integrating multiple modeling methods and heterogeneous biological datasets, which can be challenging without efficient tools. We developed Constraint-based Optimization of Metabolic Objectives (COMO), a user-friendly pipeline that integrates multi-omics data processing, context-specific metabolic model development, simulations, drug databases and disease data to aid drug discovery. COMO can be installed as a Docker Image or with Conda and includes intuitive instructions within a Jupyter Lab environment. It provides a comprehensive solution for the integration of bulk and single-cell RNA-seq, microarrays and proteomics outputs to develop context-specific metabolic models. Using public databases, open-source solutions for model construction and a streamlined approach for predicting repurposable drugs, COMO enables researchers to investigate low-cost alternatives and novel disease treatments. As a case study, we used the pipeline to construct metabolic models of B cells, which simulate and analyze them to predict metabolic drug targets for rheumatoid arthritis and systemic lupus erythematosus, respectively. COMO can be used to construct models for any cell or tissue type and identify drugs for any human disease where metabolic inhibition is relevant. The pipeline has the potential to improve the health of the global community cost-effectively by providing high-confidence targets to pursue in preclinical and clinical studies. The source code of the COMO pipeline is available at https://github.com/HelikarLab/COMO. The Docker image can be pulled at https://github.com/HelikarLab/COMO/pkgs/container/como.", "date": "2023-11-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Bessell B." }, { "name": "Loecker J." }, { "name": "Zhao Z." }, { "name": "Aghamiri S.S." }, { "name": "Mohanty S." }, { "name": "Amin R." }, { "name": "Helikar T." }, { "name": "Puniya B.L." } ], "journal": "Briefings in Bioinformatics" } } ], "credit": [ { "name": "Tomáš Helikar", "email": "thelikar2@unl.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Bhanwar Lal Puniya", "email": "bpuniya2@unl.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-19T09:14:48.657400Z", "lastUpdate": "2024-04-19T09:14:48.659485Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "VarCards2", "description": "Integrated genetic and clinical database for ACMG-AMP variant-interpretation guidelines in the human whole genome.", "homepage": "http://www.genemed.tech/varcards2/", "biotoolsID": "varcards2", "biotoolsCURIE": "biotools:varcards2", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3461", "term": "Virulence prediction" }, { "uri": "http://edamontology.org/operation_3225", "term": "Variant classification" }, { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" }, { "uri": "http://edamontology.org/operation_3226", "term": "Variant prioritisation" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3320", "term": "RNA splicing" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_3295", "term": "Epigenetics" } ], "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/GKAD1061", "pmid": "37956311", "pmcid": "PMC10767961", "type": [], "version": null, "note": null, "metadata": { "title": "VarCards2: an integrated genetic and clinical database for ACMG-AMP variant-interpretation guidelines in the human whole genome", "abstract": "VarCards, an online database, combines comprehensive variant- and gene-level annotation data to streamline genetic counselling for coding variants. Recognising the increasing clinical relevance of non-coding variations, there has been an accelerated development of bioinformatics tools dedicated to interpreting non-coding variations, including single-nucleotide variants and copy number variations. Regrettably, most tools remain as either locally installed databases or command-line tools dispersed across diverse online platforms. Such a landscape poses inconveniences and challenges for genetic counsellors seeking to utilise these resources without advanced bioinformatics expertise. Consequently, we developed VarCards2, which incorporates nearly nine billion artificially generated single-nucleotide variants (including those from mitochondrial DNA) and compiles vital annotation information for genetic counselling based on ACMG-AMP variant-interpretation guidelines. These annotations include (I) functional effects; (II) minor allele frequencies; (III) comprehensive function and pathogenicity predictions covering all potential variants, such as non-synonymous substitutions, non-canonical splicing variants, and non-coding variations and (IV) gene-level information. Furthermore, VarCards2 incorporates 368 820 266 documented short insertions and deletions and 2 773 555 documented copy number variations, complemented by their corresponding annotation and prediction tools. In conclusion, VarCards2, by integrating over 150 variant- and gene-level annotation sources, significantly enhances the efficiency of genetic counselling and can be freely accessed at http://www.genemed.tech/varcards2/.", "date": "2024-01-05T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Wang Z." }, { "name": "Zhao G." }, { "name": "Zhu Z." }, { "name": "Wang Y." }, { "name": "Xiang X." }, { "name": "Zhang S." }, { "name": "Luo T." }, { "name": "Zhou Q." }, { "name": "Qiu J." }, { "name": "Tang B." }, { "name": "Xia K." }, { "name": "Li B." }, { "name": "Li J." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Guihu Zhao", "email": "ghzhao@csu.edu.cn", "url": null, "orcidid": "https://orcid.org/0000-0003-4033-1843", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Bin Li", "email": "lijinchen@csu.edu.cn", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Jinchen Li", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-3335-9303", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-19T09:11:21.895049Z", "lastUpdate": "2024-04-19T09:11:21.897336Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "PGS-Depot", "description": "Comprehensive resource for polygenic scores constructed by summary statistics based methods.", "homepage": "http://www.pgsdepot.net", "biotoolsID": "pgs-depot", "biotoolsCURIE": "biotools:pgs-depot", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" }, { "uri": "http://edamontology.org/operation_3659", "term": "Regression analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_3517", "term": "GWAS study" }, { "uri": "http://edamontology.org/topic_3337", "term": "Biobank" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R", "Shell" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/biostat0903/PGS-Depot", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/NAR/GKAD1029", "pmid": "37953384", "pmcid": "PMC10767792", "type": [], "version": null, "note": null, "metadata": { "title": "PGS-Depot:ã comprehensive resource for polygenic scores constructed by summary statistics based methods", "abstract": "Polygenic score (PGS) isãn important tool for the genetic prediction of comple x traits. Ho w e v er, thereãre currently no resources pro viding comprehensive PGSs computed from published summary statistics,ãnd it is difficult to implementãnd run different PGS methods due to the complexity of their pipelinesãnd parameter settings. Toãddress these issues, we introduceã new resource called PGS-Depot containing the most comprehensive set of publiclyã vãilable disease-related GWAS summary statistics. PGS-Depot includes 5585 high quality summary stãtistics (1933 quantitãtiveãnd 3652 binary trait statistics) curated from 1564 traits in Europeanãnd East Asian populations. A standardized best-practice pipeline is used to implement 11 summary statistics-based PGS methods, each with different modelãssumptionsãnd estimation procedures. T he prediction perf ormance of each method can be compared for both in-ãnd cross-ancestry populations,ãnd users canãlso submit their own summary statistics to obtain custom PGS with theã vãilable methods. Other features include searching for PGSs by trait name, publication, cohort information, population, or the MeSH ontology treeãnd searching for trait descriptions with the e xperimental fãctor ontology (EFO). All scores, SNP effect sizesãnd summary statistics can be downloaded via FTP. PGS-Depot is freelyã vãilableãt http://www.pgsdepot.net .", "date": "2024-01-05T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Cao C." }, { "name": "Zhang S." }, { "name": "Wang J." }, { "name": "Tian M." }, { "name": "Ji X." }, { "name": "Huang D." }, { "name": "Yang S." }, { "name": "Gu N." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Dandan Huang", "email": "mikey.huang2011@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Sheng Yang", "email": "yangsheng@njmu.edu.cn", "url": null, "orcidid": "https://orcid.org/0000-0003-3657-8771", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-19T08:45:10.333820Z", "lastUpdate": "2024-04-19T08:45:10.336582Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" } ] }