From 2df1b0ca2ea1f1ed53217af510997e4fd98bf21a Mon Sep 17 00:00:00 2001 From: Andrea Mannocci Date: Mon, 14 Feb 2022 12:26:36 +0100 Subject: [PATCH] new dump from fairsharing --- data/raw/fairsharing_dump_api_02_2022.json | 1853 ++++++++++++++++++++ 1 file changed, 1853 insertions(+) create mode 100644 data/raw/fairsharing_dump_api_02_2022.json diff --git a/data/raw/fairsharing_dump_api_02_2022.json b/data/raw/fairsharing_dump_api_02_2022.json new file mode 100644 index 0000000..0b5e0ee --- /dev/null +++ b/data/raw/fairsharing_dump_api_02_2022.json @@ -0,0 +1,1853 @@ +{"id": "3226", "type": "fairsharing-records", "attributes": {"created-at": "2020-12-09T11:53:44.000Z", "updated-at": "2022-02-08T10:42:36.452Z", "metadata": {"doi": "10.25504/FAIRsharing.d6423b", "name": "WDC Sunspot Index and Long-term Solar Observations", "status": "ready", "contacts": [{"contact-name": "Fr\u00e9d\u00e9ric Clette", "contact-email": "silso.info@oma.be", "contact-orcid": "0000-0002-3343-5153"}], "homepage": "http://sidc.be/silso/home", "identifier": 3226, "description": "The WDC-SILSO is an activity of the Operational Directorate \u201cSolar Physics and Space Weather\u201d also known internationally as the Solar Influences Data analysis Center (SIDC). 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To promote biodiversity and health big data sharing around the world, the Open Biodiversity and Health Big Data (BHBD) initiative is introduced. 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Please link to https://fairsharing.org and https://api.fairsharing.org/img/fairsharing-attribution.svg for attribution.", "description": "This FAIRsharing record describes: The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of multi-omics data generated at unprecedented scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big data integration and value-added curation. 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Software vendors provide a variety of individual documentation forms according to their standard contracts, which function as isolated applications. Furthermore, free availability of those forms is rarely the case. Currently less than 5 % of medical forms are freely accessible. Based on this lack of transparency harmonization of data models in health care is extremely cumbersome, thus work and know-how of completed clinical trials and routine documentation in hospitals are hard to be re-used. The MDM-Portal serves as an infrastructure for academic (non-commercial) medical research to contribute a solution to this problem. It already contains more than 6,000 system-independent forms (CDISC ODM Format, www.cdisc.org, Operational Data Model) with more than 470,000 data-elements. This enables researchers to view, discuss, download and export forms in most common technical formats such as PDF, CSV, Excel, SQL, SPSS, R, etc. A growing user community will lead to a growing database of medical forms. In this matter, we would like to encourage all medical researchers to register and add forms and discuss existing forms.", "publications": [{"id": 1159, "pubmed_id": 26868052, "title": "Portal of medical data models: information infrastructure for medical research and healthcare", "year": 2016, "url": "http://doi.org/10.1093/database/bav121", "authors": "Dugas M, Neuhaus P, Meidt A, Doods J, Storck M, Bruland P, Varghese J", "journal": "Database", "doi": "10.1093/database/bav121", "created_at": "2021-09-30T08:24:28.885Z", "updated_at": "2021-09-30T08:24:28.885Z"}], "licence-links": [{"licence-name": "Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)", "licence-id": 172, "link-id": 912, "relation": "undefined"}], "url-for-logo": null}} +{"id": "2477", "type": "fairsharing-records", "attributes": {"created-at": "2017-07-05T12:52:05.000Z", "updated-at": "2021-11-24T13:16:30.680Z", "metadata": {"doi": "10.25504/FAIRsharing.7tz5g8", "name": "Nonindigenous Aquatic Species NAS IPT - USGS", "status": "ready", "contacts": [{"contact-email": "bison@usgs.gov"}], "homepage": "https://nas.er.usgs.gov/ipt/", "identifier": 2477, "description": "The Nonindigenous Aquatic Species (NAS) information resource for the United States Geological Survey has been established as a central repository for spatially referenced biogeographic accounts of introduced aquatic species. 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Please link to https://fairsharing.org and https://api.fairsharing.org/img/fairsharing-attribution.svg for attribution.", "description": "This FAIRsharing record describes: The Mitochondrial Disease Sequence Data Resource (MSeqDR) is a centralized genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical diagnosis and research investigations of individual patient phenotypes, genomes, genes, and variants. It integrates community knowledge from expert\u2010curated databases with genomic and phenotype data shared by clinicians and researchers.", "publications": [{"id": 2575, "pubmed_id": 26919060, "title": "MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease.", "year": 2016, "url": "http://doi.org/10.1002/humu.22974", "authors": "Shen L, Diroma MA, Gonzalez M, Navarro-Gomez D, Leipzig J, Lott MT, van Oven M, Wallace DC, Muraresku CC, Zolkipli-Cunningham Z, Chinnery PF, Attimonelli M, Zuchner S, Falk MJ, Gai X", "journal": "Hum Mutationm", "doi": "10.1002/humu.22974", "created_at": "2021-09-30T08:27:15.845Z", "updated_at": "2021-09-30T08:27:15.845Z"}, {"id": 2736, "pubmed_id": 29539190, "title": "MSeqDR mvTool: A mitochondrial DNA Web and API resource for comprehensive variant annotation, universal nomenclature collation, and reference genome conversion", "year": 2018, "url": "http://doi.org/10.1002/humu.23422", "authors": "Lishuang Shen, Marcella Attimonelli, Bai Renkui, Marie T Lott, Douglas C Wallace, Marni J Falk, Xiaowu Gai.", "journal": "Human Mutation", "doi": "doi:10.1002/humu.23422", "created_at": "2021-09-30T08:27:35.950Z", "updated_at": "2021-09-30T08:27:35.950Z"}, {"id": 2737, "pubmed_id": 25542617, "title": "Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities.", "year": 2014, "url": "http://doi.org/10.1016/j.ymgme.2014.11.016", "authors": "Falk MJ, Shen L, Gonzalez M, Leipzig J, Lott MT, Stassen AP, Diroma MA, Navarro-Gomez D, Yeske P, Bai R, Boles RG, Brilhante V, Ralph D, DaRe JT, Shelton R, Terry SF, Zhang Z, Copeland WC, van Oven M, Prokisch H, Wallace DC, Attimonelli M, Krotoski D, Zuchner S, Gai X; MSeqDR Consortium Participants; MSeqDR Consortium participants: Sherri Bale, Jirair Bedoyan, Doron Behar, Penelope Bonnen, Lisa Brooks, Claudia Calabrese, Sarah Calvo, Patrick Chinnery, John Christodoulou, Deanna Church,; Rosanna Clima, Bruce H. Cohen, Richard G. Cotton, IFM de Coo, Olga Derbenevoa, Johan T. den Dunnen, David Dimmock, Gregory Enns, Giuseppe Gasparre,; Amy Goldstein, Iris Gonzalez, Katrina Gwinn, Sihoun Hahn, Richard H. Haas, Hakon Hakonarson, Michio Hirano, Douglas Kerr, Dong Li, Maria Lvova, Finley Macrae, Donna Maglott, Elizabeth McCormick, Grant Mitchell, Vamsi K. Mootha, Yasushi Okazaki,; Aurora Pujol, Melissa Parisi, Juan Carlos Perin, Eric A. Pierce, Vincent Procaccio, Shamima Rahman, Honey Reddi, Heidi Rehm, Erin Riggs, Richard Rodenburg, Yaffa Rubinstein, Russell Saneto, Mariangela Santorsola, Curt Scharfe,; Claire Sheldon, Eric A. Shoubridge, Domenico Simone, Bert Smeets, Jan A. Smeitink, Christine Stanley, Anu Suomalainen, Mark Tarnopolsky, Isabelle Thiffault, David R. 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Please link to https://fairsharing.org and https://api.fairsharing.org/img/fairsharing-attribution.svg for attribution.", "description": "This FAIRsharing record describes: Metabolic Atlas integrates open source genome-scale metabolic models (GEMs) of human and yeast for easy browsing and analysis. It also contains many more GEMs constructed by our organization. Detailed biochemical information is provided for individual model components, such as reactions, metabolites, and genes. These components are also associated with standard identifiers, facilitating integration with external databases, such as the Human Protein Atlas.", "publications": [{"id": 2910, "pubmed_id": 32209698, "title": "An atlas of human metabolism.", "year": 2020, "url": "http://doi.org/eaaz1482", "authors": "Robinson JL,Kocabas P,Wang H,Cholley PE,Cook D,Nilsson A,Anton M,Ferreira R,Domenzain I,Billa V,Limeta A,Hedin A,Gustafsson J,Kerkhoven EJ,Svensson LT,Palsson BO,Mardinoglu A,Hansson L,Uhlen M,Nielsen J", "journal": "Sci Signal", "doi": "10.1126/scisignal.aaz1482", "created_at": "2021-09-30T08:27:58.350Z", "updated_at": "2021-09-30T08:27:58.350Z"}], "licence-links": [{"licence-name": "GNU General Public License (GPL) 3.0", "licence-id": 356, "link-id": 1299, "relation": "undefined"}], "url-for-logo": null}} +{"id": "2274", "type": "fairsharing-records", "attributes": {"created-at": "2016-04-10T09:22:09.000Z", "updated-at": "2021-11-24T13:14:50.740Z", "metadata": {"doi": "10.25504/FAIRsharing.ennep4", "name": "Global Unique Device Identification Database", "status": "ready", "homepage": "https://accessgudid.nlm.nih.gov/", "identifier": 2274, "description": "The Global Unique Device Identification Database (GUDID - pronounced \"Good ID\") is a database administered by the FDA as part of the UDI system. 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Please link to https://fairsharing.org and https://api.fairsharing.org/img/fairsharing-attribution.svg for attribution.", "description": "This FAIRsharing record describes: The Global Unique Device Identification Database (GUDID - pronounced \"Good ID\") is a database administered by the FDA as part of the UDI system. The GUDID contains device identification information submitted by device companies to the FDA. The GUDID contains ONLY the Device Identifier (DI), which serves as the primary key to obtain information in the database. Production Identifiers (PI) are not submitted to or stored in the GUDID, but GUDID data indicates which PIs are on the device label. Many data elements in the GUDID correspond to information on the medical device label. The figure below shows a fictitious medical device label and identifies the GUDID data elements that appear on the label. 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Please link to https://fairsharing.org and https://api.fairsharing.org/img/fairsharing-attribution.svg for attribution.", "description": "This FAIRsharing record describes: Genomics England PanelApp is a publically-available knowledgebase that allows virtual gene panels related to human disorders to be created, stored and queried. It includes a crowdsourcing tool that allows genes to be added or reviewed by experts throughout the worldwide scientific community, providing an opportunity for the standardisation of gene panels, and a consensus on which genes have sufficient evidence for disease association. The diagnostic grade \u2018Green\u2019 genes and their modes of inheritance in the Version 1+ PanelApp virtual gene panels are used to direct the variant tiering process for the interpretation of genomes in the 100,000 Genomes Project and for the National Health Service England Genomic Medicine Service. As panels in PanelApp are publically available, they can also be utilised by others. Experts are asked to register (https://panelapp.genomicsengland.co.uk/accounts/registration/) in order to review and rate the genes on the panel to indicate whether there is a diagnostic-grade level of evidence for the gene to be implicated in a given disease. Bioinformaticians can access the data via the PanelApp API (https://panelapp.genomicsengland.co.uk/#!API). 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Also, the 3D visualization of the interface and interactions among hot spot residues are provided.", "publications": [{"id": 68, "pubmed_id": 20437205, "title": "Analysis of hot region organization in hub proteins.", "year": 2010, "url": "http://doi.org/10.1007/s10439-010-0048-9", "authors": "Cukuroglu E., Gursoy A., Keskin O.,", "journal": "Ann Biomed Eng", "doi": "10.1007/s10439-010-0048-9", "created_at": "2021-09-30T08:22:27.571Z", "updated_at": "2021-09-30T08:22:27.571Z"}, {"id": 82, "pubmed_id": 15644221, "title": "Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues.", "year": 2005, "url": "http://doi.org/10.1016/j.jmb.2004.10.077", "authors": "Keskin O., Ma B., Nussinov R.,", "journal": "J. Mol. 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Before viewing the data, users have to agree that they will not seek any intellectual property protection over the data, including gene sequences contained in the database. The Information Access Agreement allows any cacao breeders and other researchers to freely use the genome information to develop new cacao varieties. 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Work continues on the refinement of the assembly and annotation, working toward a complete finished sequence. Public access to the genome is available permanently without patent via this resource. Before viewing the data, users have to agree that they will not seek any intellectual property protection over the data, including gene sequences contained in the database. The Information Access Agreement allows any cacao breeders and other researchers to freely use the genome information to develop new cacao varieties. This allows for a level playing field and a healthy competitive environment that will ultimately benefit the sustainability of cacao production in the long term.", "publications": [], "licence-links": [], "url-for-logo": null}} +{"id": "2146", "type": "fairsharing-records", "attributes": {"created-at": "2014-11-04T15:23:40.000Z", "updated-at": "2021-12-06T10:48:35.560Z", "metadata": {"doi": "10.25504/FAIRsharing.fssydn", "name": "DisGeNET", "status": "ready", "contacts": [{"contact-name": "Laura I. Furlong", "contact-email": "laura.furlong@upf.edu", "contact-orcid": "0000-0002-9383-528X"}], "homepage": "http://www.disgenet.org", "citations": [{"doi": null, "pubmed-id": null, "publication-id": 2593}], "identifier": 2146, "description": "DisGeNET is a discovery platform containing one of the largest collections available of genes and variants involved in human diseases. 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It is being built using the open-source Tripal database infrastructure. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, visualization and data retrieval of cotton research data. CottonGen contains annotated whole genome sequences, unigenes from expressed sequence tags (ESTs), markers, trait loci, genetic maps, genes, taxonomy, germplasm, publications and communication resources for the cotton community. 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Please link to https://fairsharing.org and https://api.fairsharing.org/img/fairsharing-attribution.svg for attribution.", "description": "This FAIRsharing record describes: CottonGen is a cotton community genomics, genetics and breeding database being developed to enable basic, translational and applied research in cotton. It is being built using the open-source Tripal database infrastructure. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, visualization and data retrieval of cotton research data. CottonGen contains annotated whole genome sequences, unigenes from expressed sequence tags (ESTs), markers, trait loci, genetic maps, genes, taxonomy, germplasm, publications and communication resources for the cotton community. Annotated whole genome sequences of Gossypium raimondii are available with aligned genetic markers and transcripts.", "publications": [{"id": 2085, "pubmed_id": 24203703, "title": "CottonGen: a genomics, genetics and breeding database for cotton research.", "year": 2013, "url": "http://doi.org/10.1093/nar/gkt1064", "authors": "Yu J,Jung S,Cheng CH,Ficklin SP,Lee T,Zheng P,Jones D,Percy RG,Main D", "journal": "Nucleic Acids Research", "doi": "10.1093/nar/gkt1064", "created_at": "2021-09-30T08:26:15.055Z", "updated_at": "2021-09-30T11:29:28.187Z"}], "licence-links": [], "url-for-logo": null}}