{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T23:48:26Z","timestamp":1772322506127,"version":"3.50.1"},"reference-count":61,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2020,4,14]],"date-time":"2020-04-14T00:00:00Z","timestamp":1586822400000},"content-version":"vor","delay-in-days":104,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"publisher","award":["OT3TR002019"],"award-info":[{"award-number":["OT3TR002019"]}],"id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01GM089820"],"award-info":[{"award-number":["R01GM089820"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>Hypothesis generation is a critical step in research and a cornerstone in the rare disease field. Research is most efficient when those hypotheses are based on the entirety of knowledge known to date. Systematic review articles are commonly used in biomedicine to summarize existing knowledge and contextualize experimental data. But the information contained within review articles is typically only expressed as free-text, which is difficult to use computationally. Researchers struggle to navigate, collect and remix prior knowledge as it is scattered in several silos without seamless integration and access. This lack of a structured information framework hinders research by both experimental and computational scientists. To better organize knowledge and data, we built a structured review article that is specifically focused on NGLY1 Deficiency, an ultra-rare genetic disease first reported in 2012. We represented this structured review as a knowledge graph and then stored this knowledge graph in a Neo4j database to simplify dissemination, querying and visualization of the network. Relative to free-text, this structured review better promotes the principles of findability, accessibility, interoperability and reusability (FAIR). In collaboration with domain experts in NGLY1 Deficiency, we demonstrate how this resource can improve the efficiency and comprehensiveness of hypothesis generation. We also developed a read\u2013write interface that allows domain experts to contribute FAIR structured knowledge to this community resource. In contrast to traditional free-text review articles, this structured review exists as a living knowledge graph that is curated by humans and accessible to computational analyses. Finally, we have generalized this workflow into modular and repurposable components that can be applied to other domain areas. This NGLY1 Deficiency-focused network is publicly available at http:\/\/ngly1graph.org\/.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Database URL: http:\/\/ngly1graph.org\/. Network data files are at: https:\/\/github.com\/SuLab\/ngly1-graph and source code at: https:\/\/github.com\/SuLab\/bioknowledge-reviewer.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Contact<\/jats:title>\n                    <jats:p>asu@scripps.edu<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/database\/baaa015","type":"journal-article","created":{"date-parts":[[2020,2,14]],"date-time":"2020-02-14T15:11:23Z","timestamp":1581693083000},"source":"Crossref","is-referenced-by-count":8,"title":["Structured reviews for data and knowledge-driven research"],"prefix":"10.1093","volume":"2020","author":[{"given":"N\u00faria","family":"Queralt-Rosinach","sequence":"first","affiliation":[{"name":"Department of Integrative Structural and Computational Biology, Scripps Research, 10550 N Torrey Pines Rd. La Jolla, CA 92037, USA"}]},{"given":"Gregory S","family":"Stupp","sequence":"first","affiliation":[{"name":"Department of Integrative Structural and Computational Biology, Scripps Research, 10550 N Torrey Pines Rd. La Jolla, CA 92037, USA"}]},{"given":"Tong Shu","family":"Li","sequence":"first","affiliation":[{"name":"Department of Integrative Structural and Computational Biology, Scripps Research, 10550 N Torrey Pines Rd. La Jolla, CA 92037, USA"}]},{"given":"Michael","family":"Mayers","sequence":"first","affiliation":[{"name":"Department of Integrative Structural and Computational Biology, Scripps Research, 10550 N Torrey Pines Rd. La Jolla, CA 92037, USA"}]},{"given":"Maureen E","family":"Hoatlin","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Oregon Health and Science University, 3181 SW Sam Jackson Parkway, Portland, OR 97239, USA"}]},{"given":"Matthew","family":"Might","sequence":"first","affiliation":[{"name":"Department of Medicine, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, 510 20th St S, Birmingham, AL 35210, USA"}]},{"given":"Benjamin M","family":"Good","sequence":"first","affiliation":[{"name":"Department of Integrative Structural and Computational Biology, Scripps Research, 10550 N Torrey Pines Rd. La Jolla, CA 92037, USA"}]},{"given":"Andrew I","family":"Su","sequence":"first","affiliation":[{"name":"Department of Integrative Structural and Computational Biology, Scripps Research, 10550 N Torrey Pines Rd. La Jolla, CA 92037, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,4,11]]},"reference":[{"key":"2020041319352627400_ref1","doi-asserted-by":"crossref","first-page":"D529","DOI":"10.1093\/nar\/gky1079","article-title":"The BioGRID interaction database: 2019 update","volume":"47","author":"Oughtred","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020041319352627400_ref2","doi-asserted-by":"crossref","first-page":"D330","DOI":"10.1093\/nar\/gky1055","article-title":"The gene ontology resource: 20 years and still GOing strong","volume":"47","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020041319352627400_ref3","doi-asserted-by":"crossref","first-page":"D712","DOI":"10.1093\/nar\/gkw1128","article-title":"The monarch initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species","volume":"45","author":"Mungall","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2020041319352627400_ref4","doi-asserted-by":"crossref","first-page":"1338","DOI":"10.1093\/bioinformatics\/btt765","article-title":"The EBI RDF platform: linked open data for the life sciences","volume":"30","author":"Jupp","year":"2014","journal-title":"Bioinformatics"},{"key":"2020041319352627400_ref5","doi-asserted-by":"crossref","first-page":"e115460","DOI":"10.1371\/journal.pone.0115460","article-title":"The application of the open pharmacological concepts triple store (open PHACTS) to support drug discovery research","volume":"9","author":"Ratnam","year":"2014","journal-title":"PLOS ONE"},{"key":"2020041319352627400_ref6","doi-asserted-by":"crossref","first-page":"e1000215","DOI":"10.1371\/journal.pcbi.1000215","article-title":"Biomedical discovery acceleration, with applications to craniofacial development","volume":"5","author":"Leach","year":"2009","journal-title":"PLOS Comput. 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