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"description": "Research Object RO-Crate of aggregated linksets used by Open PHACTS 2.1 IMS. \n\n2.1.1 is republished, previously on http://data.openphacts.org/2.1/ims/linksets/ by VU, which as of 2021-04-20 is offline. \n\nThe linksets can in theory be loaded in an Identity Mapping Service (IMS) instance using the modified load-relative.xml which has relative URIs within this RO-Crate, but this has not been tested.\n\nThe content of this RO-Crate has mixed licenses, deemed comparable with its own license CC-BY-SA-4.0 or as part of a collection. See this RO-Crate metadata for each nested Dataset entity, which attempts to reflect their authorative VoID files. Note the CC-BY-ND 3.0 restriction of derivative works for linksets/drugbank, linksets/disgenet, linksets/nextprot. ops-surechembl-linksets is licensed CC-BY-NC-SA-3.0 (not for commercial use), and therefore linked by reference through separate Zenodo DOI.",
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"alternateName": "Proceedings of the Second International Workshop on Linked Science 2012 - Tackling Big Data",
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"description": "Within complex scientific domains such as pharmacology, operational equivalence between two concepts is often context-, user- and task-specific. Existing Linked Data integration procedures and equivalence services do not take the context and task of the user into account. We present a vision for enabling users to control the notion of operational equivalence by applying scientific lenses over Linked Data. The scientific lenses vary the links that are activated between the datasets which affects the data returned to the user.\n\nFrom Proceedings of the Second International Workshop on Linked Science 2012 - Tackling Big Data.",
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"name": "HMDB 3.0--The Human Metabolome Database in 2013",
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"@type": "ScholarlyArticle",
"datePublished": "2015-11-17T10:00:00.000Z",
"description": "SureChEMBL is a publicly available large-scale resource containing compounds extracted from the full text, images and attachments of patent documents. The data are extracted from the patent literature according to an automated text and image-mining pipeline on a daily basis. SureChEMBL provides access to a previously unavailable, open and timely set of annotated compound-patent associations, complemented with sophisticated combined structure and keyword-based search capabilities against the compound repository and patent document corpus; given the wealth of knowledge hidden in patent documents, analysis of SureChEMBL data has immediate applications in drug discovery, medicinal chemistry and other commercial areas of chemical science. Currently, the database contains 17 million compounds extracted from 14 million patent documents. Access is available through a dedicated web-based interface and data downloads at: https://www.surechembl.org/.",
"name": "SureChEMBL: a large-scale, chemically annotated patent document database",
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"datePublished": "2014-01-01T11:00:00.000Z",
"description": "The discovery of new medicines requires pharmacologists to interact with a number of information sources ranging from tabular data to scientific papers, and other specialized formats. In this application report, we describe a linked data platform for integrating multiple pharmacology datasets that form the basis for several drug discovery applications. The functionality offered by the platform has been drawn from a collection of prioritised drug discovery business questions created as part of the Open PHACTS project, a collaboration of research institutions and major pharmaceutical companies. We describe the architecture of the platform focusing on seven design decisions that drove its development with the aim of informing others developing similar software in this or other domains. The utility of the platform is demonstrated by the variety of drug discovery applications being built to access the integrated data.\n",
"name": "Applying linked data approaches to pharmacology: Architectural decisions and implementation",
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"license": {
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"description": "HMDB is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (HMDB) and the original publication (see below). We ask that users who download significant portions of the database cite the HMDB paper in any resulting publications. For commercial licences, please consult with jreid3@ualberta.ca (Jennifer).\n\nPlease cite:\n\n Wishart DS, Tzur D, Knox C, et al., HMDB: the Human Metabolome Database. Nucleic Acids Res. 2007 Jan;35(Database issue):D521-6. 17202168\n Wishart DS, Knox C, Guo AC, et al., HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res. 2009 37(Database issue):D603-610. 18953024\n Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, et al., HMDB 3.0 — The Human Metabolome Database in 2013. Nucleic Acids Res. 2013. Jan 1;41(D1):D801-7. 23161693\n Wishart DS, Feunang YD, Marcu A, Guo AC, Liang K, et al., HMDB 4.0 — The Human Metabolome Database for 2018. Nucleic Acids Res. 2018. Jan 4;46(D1):D608-17. 29140435",
"name": "Citing the HMDB",
"citation": {
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},
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