{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,6,12]],"date-time":"2025-06-12T04:09:51Z","timestamp":1749701391298,"version":"3.41.0"},"reference-count":58,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,10,14]],"date-time":"2016-10-14T00:00:00Z","timestamp":1476403200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Cheminform"],"published-print":{"date-parts":[[2016,12]]},"DOI":"10.1186\/s13321-016-0168-9","type":"journal-article","created":{"date-parts":[[2016,10,14]],"date-time":"2016-10-14T09:07:04Z","timestamp":1476436024000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["SciData: a data model and ontology for semantic representation of scientific data"],"prefix":"10.1186","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0703-7776","authenticated-orcid":false,"given":"Stuart J.","family":"Chalk","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,10,14]]},"reference":[{"key":"168_CR1","unstructured":"Chalk S (2016) SciData: a scientific data model. http:\/\/stuchalk.github.io\/scidata\/ . Accessed 1 March 2016"},{"issue":"3","key":"168_CR2","doi-asserted-by":"publisher","first-page":"4","DOI":"10.3789\/isqv25no3.2013.02","volume":"25","author":"CL Bird","year":"2013","unstructured":"Bird CL, Willoughby C, Coles SJ, Frey JG (2013) Data curation issues in the chemical sciences. Inf Stand Q 25(3):4\u201312. doi: 10.3789\/isqv25no3.2013.02","journal-title":"Inf Stand Q"},{"key":"168_CR3","unstructured":"Murray-Rust P (2010) What is scientific data? http:\/\/blogs.ch.cam.ac.uk\/pmr\/2010\/07\/25\/pp01-what-is-scientific-data\/ . Accessed 1 March 2016"},{"key":"168_CR4","unstructured":"Hey T, Tansley S, Tolle K (2009) The fourth paradigm: data-intensive scientific discovery. ISBN: 978-0982544204. http:\/\/research.microsoft.com\/en-us\/collaboration\/fourthparadigm\/"},{"key":"168_CR5","unstructured":"W3C (2016) Resource Description Framework (RDF) The World Wide Web Consortium. http:\/\/www.w3.org\/RDF\/"},{"key":"168_CR6","unstructured":"W3C (2016) SPARQL query language for RDF The World Wide Web Consortium. http:\/\/www.w3.org\/TR\/rdf-sparql-query\/ . Accessed 1 March 2016"},{"key":"168_CR7","unstructured":"W3C (2016) JSON-LD 1.0: a JSON-based serialization for linked data. The World Wide Web Consortium. http:\/\/www.w3.org\/TR\/json-ld\/ Accessed March 1, 2016"},{"key":"168_CR8","unstructured":"Fredrich T (2016) What is REST? http:\/\/www.restapitutorial.com\/lessons\/whatisrest.html . Accessed 23 June 2016"},{"key":"168_CR9","doi-asserted-by":"crossref","unstructured":"Lanthaler M, G\u00fctl C (2012) On using JSON-LD to create evolvable RESTful services. In: Third international workshop on RESTful design, ACM, pp 25\u201332. http:\/\/dx.doi.org\/10.1145\/2307819.2307827","DOI":"10.1145\/2307819.2307827"},{"key":"168_CR10","unstructured":"W3C (2016) JSON-LD playground http:\/\/json-ld.org\/playground\/ . Accessed 1 March 2016"},{"key":"168_CR11","unstructured":"Gower B (1997) Scientific method: a historical and philosophical introduction. Routledge. ISBN: 978-0415122825. https:\/\/www.amazon.com\/dp\/0415122821"},{"key":"168_CR12","unstructured":"RSC (2016) Development of the periodic table http:\/\/www.rsc.org\/periodic-table\/history\/about . Accessed 23 June 2016"},{"key":"168_CR13","unstructured":"EOL (2016) What is biological classification? http:\/\/eol.org\/info\/461 . Accessed 23 June 2016"},{"key":"168_CR14","unstructured":"UCB (2016) Phylogenetic systematics, a.k.a. evolutionary trees: reading trees\u2014a quick review. http:\/\/evolution.berkeley.edu\/evolibrary\/article\/phylogenetics_02 . Accessed 23 June 2016"},{"issue":"10","key":"168_CR15","doi-asserted-by":"publisher","first-page":"11419","DOI":"10.4249\/scholarpedia.11419","volume":"7","author":"P Langacker","year":"2012","unstructured":"Langacker P (2012) Grand unification. Scholarpedia 7(10):11419","journal-title":"Scholarpedia"},{"key":"168_CR16","doi-asserted-by":"crossref","unstructured":"Lysakowski R, Gragg CE (eds) (1994) Computerized chemical data standards: databases, data interchange, and information systems, ASTM. ISBN: 978-0-8031-1876-8. http:\/\/www.astm.org\/DIGITAL_LIBRARY\/STP\/SOURCE_PAGES\/STP1214.htm","DOI":"10.1520\/STP1214-EB"},{"issue":"1","key":"168_CR17","first-page":"1","volume":"31","author":"JA Perkins","year":"2005","unstructured":"Perkins JA (2005) A history of molecular representation. Part one: 1800 to the 1960s. J Biocommun 31(1):1","journal-title":"J Biocommun"},{"key":"168_CR18","doi-asserted-by":"crossref","unstructured":"Apodaca R (2007) Everything old is new again\u2014Wiswesser Line Notation (WLN). http:\/\/depth-first.com\/articles\/2007\/07\/20\/everything-old-is-new-again-wiswesser-line-notation-wln\/ . Accessed 23 June 2016","DOI":"10.59350\/1rckp-m1m66"},{"key":"168_CR19","unstructured":"DCIS (2016) SMILES: a simplified chemical language daylight chemical information systems. http:\/\/www.daylight.com\/dayhtml\/doc\/theory\/theory.smiles.html . Accessed 23 June 2016"},{"key":"168_CR20","unstructured":"InChI Trust (2016) InChI and InChIKeys for chemical structures. http:\/\/www.inchi-trust.org\/ . Accessed 23 June 2016"},{"key":"168_CR21","unstructured":"OC (2016) OpenBabel: supported file formats and options OpenBabel community. http:\/\/openbabel.org\/docs\/2.3.0\/FileFormats\/Overview.html . Accessed 23 June 2016"},{"key":"168_CR22","unstructured":"Hanson R (2016) Jmol\/JSmol file formats\/coordinates http:\/\/wiki.jmol.org\/index.php\/File_formats\/Coordinates-MOL_and_SD_.28Symyx_MDL.29 . Accessed 23 June 2016"},{"key":"168_CR23","unstructured":"Murray-Rust P, Rzepa H (2012) Chemical markup language\u2014CML. http:\/\/xml-cml.org\/ . Accessed 23 June 2016"},{"key":"168_CR24","unstructured":"W3C (2016) Extensible Markup Language (XML) https:\/\/www.w3.org\/TR\/xml\/"},{"key":"168_CR25","doi-asserted-by":"crossref","unstructured":"Bernstein HJ, Bollinger JC, Brown ID, Grazulis S, Hester JR, McMahon B, Spadaccini N, Westbrook JD, Westrip SP (2016) Specification of the crystallographic information file format, version 2.0. J Appl Crystallogr 49(1). http:\/\/dx.doi.org\/10.1107\/S1600576715021871","DOI":"10.1107\/S1600576715021871"},{"key":"168_CR26","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1107\/S010876739101067X","volume":"47","author":"SR Hall","year":"1991","unstructured":"Hall SR, Allen FH, Brown ID (1991) The crystallographic Information File (Cif): a new standard archive file for crystallography. Acta Cryst A 47:655\u2013685","journal-title":"Acta Cryst A"},{"key":"168_CR27","unstructured":"IUCr (2016) CIF international union of crystallography. http:\/\/www.iucr.org\/resources\/cif . Accessed 23 June 2016"},{"issue":"2","key":"168_CR28","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1021\/ci00002a020","volume":"31","author":"SR Hall","year":"1991","unstructured":"Hall SR (1991) The Star file: a new format for electronic data transfer and archiving. J Chem Inf Comput Sci 31(2):326\u2013333. doi: 10.1021\/ci00002a020","journal-title":"J Chem Inf Comput Sci"},{"key":"168_CR29","unstructured":"IUPAC (2016) IUPAC subcommittee on electronic data standards. http:\/\/jcamp-dx.org\/ . Accessed 1 March 2016"},{"key":"168_CR30","unstructured":"UCAR (2016) Network common data form (NetCDF) http:\/\/www.unidata.ucar.edu\/software\/netcdf\/ . Accessed 23 June 2016"},{"key":"168_CR31","doi-asserted-by":"crossref","unstructured":"ASTM (2016) Standard guide for analytical data interchange protocol for mass spectrometric data\u2014E2078\u201400(2016) http:\/\/dx.doi.org\/10.1520\/E2078-00R16 . Accessed 23 June 2016","DOI":"10.1520\/E2078-00R16"},{"key":"168_CR32","doi-asserted-by":"crossref","unstructured":"ASTM (2016) Standard specification for analytical data interchange protocol for chromatographic data\u2014E1947\u201498(2014) http:\/\/dx.doi.org\/10.1520\/E1947-98R14 . Accessed 23 June 2016","DOI":"10.1520\/E1947-98R14"},{"key":"168_CR33","unstructured":"ASTM (2016) The analytical information markup language (AnIML) AnIML working group. https:\/\/www.animl.org\/"},{"key":"168_CR34","unstructured":"Oracle (2016) MySQL open-source database oracle corporation. http:\/\/www.mysql.com\/ . Accessed 1 March 2016"},{"key":"168_CR35","unstructured":"Microsoft (2014) SQL server 2014 microsoft corporation. http:\/\/www.microsoft.com\/en-us\/server-cloud\/products\/sql-server\/ . Accessed 1 March 2016"},{"key":"168_CR36","unstructured":"Oracle (2016) Oracle database oracle corporation. https:\/\/www.oracle.com\/database\/index.html . Accessed 1 March 2016"},{"key":"168_CR37","unstructured":"Reeve A (2012) Big Data and NoSQL: the problem with relational databases EMC corporation. https:\/\/infocus.emc.com\/april_reeve\/big-data-and-nosql-the-problem-with-relational-databases\/ . Accessed 1 March 2016"},{"key":"168_CR38","unstructured":"Sequeda J (2013) Introduction to: Triplestores Dataversity. http:\/\/www.dataversity.net\/introduction-to-triplestores\/ . Accessed 1 March 2016"},{"key":"168_CR39","unstructured":"Dodds L, Davis I (2012) Linked data patterns. Data management patterns: named graph. http:\/\/patterns.dataincubator.org\/book\/named-graphs.html"},{"key":"168_CR40","unstructured":"NLM (2016) PubChem National Institutes of Health. http:\/\/pubchem.ncbi.nlm.nih.gov\/ Accessed June 23, 2016"},{"key":"168_CR41","unstructured":"RSC (2016) ChemSpider: search and share chemistry. http:\/\/www.chemspider.com\/ . Accessed 23 June 2016"},{"key":"168_CR42","unstructured":"DDB (2016) Dortmund Data Bank DDBST GmbH. http:\/\/www.ddbst.com\/ . Accessed 23 June 2016"},{"key":"168_CR43","unstructured":"CCDC (2016) Cambridge Crystallographic Data Centre Cambridge, UK http:\/\/www.ccdc.cam.ac.uk\/ . Accessed 23 June 2016"},{"key":"168_CR44","unstructured":"Noy NF, McGuinness DL (2012) Ontology development 101: a guide to creating your first ontology Stanford University. http:\/\/protege.stanford.edu\/publications\/ontology_development\/ontology101-noy-mcguinness.html . Accessed 1 March 2016"},{"key":"168_CR45","unstructured":"W3C (2016) OWL 2 Web Ontology Language. The World Wide Web Consortium. http:\/\/www.w3.org\/TR\/owl-overview\/ . Accessed 1 March 2016"},{"key":"168_CR46","unstructured":"UNECE (2007) Globally harmonized system of classification and labelling of chemicals (GHS) (Rev.2). Geneva, Switzerland: United Nations Economic Commission for Europe. http:\/\/www.unece.org\/trans\/danger\/publi\/ghs\/ghs_rev02\/02files_e.html . Accessed 23 June 2016"},{"key":"168_CR47","unstructured":"IUPAC (1993) Nomenclature of organic chemistry. http:\/\/www.acdlabs.com\/iupac\/nomenclature\/ . Accessed 23 June 2016"},{"issue":"9\u201310","key":"168_CR48","doi-asserted-by":"publisher","first-page":"1039","DOI":"10.1515\/pac-2014-0718","volume":"87","author":"RM Hartshorn","year":"2015","unstructured":"Hartshorn RM, Hellwich KH, Yerin A, Damhus T, Hutton AT (2015) Brief guide to the nomenclature of inorganic chemistry. Pure Appl Chem 87(9\u201310):1039\u20131049. doi: 10.1515\/pac-2014-0718","journal-title":"Pure Appl Chem"},{"key":"168_CR49","unstructured":"FGED (2016) MIAME: minimum information about a microarray experiment. http:\/\/fged.org\/projects\/miame\/ . Accessed 23 June 2016"},{"key":"168_CR50","unstructured":"MIRAGE WG (2016) Minimum Information Required for a Glycomics Experiment Beilstein Institut. http:\/\/www.beilstein-institut.de\/en\/projects\/mirage"},{"key":"168_CR51","unstructured":"STRENDA Commission (2016) STRENDA: Standards for Reporting Enzymology Data Frankfurt Beilstein Institut. http:\/\/www.beilstein-institut.de\/en\/projects\/strenda . Accessed 23 June 2016"},{"key":"168_CR52","unstructured":"STRENDA Commission (2016) The STRENDA Guidelines Frankfurt Beilstein Institut. https:\/\/www.beilstein-strenda-db.org\/strenda\/public\/guidelines.xhtml . Accessed 23 June 2016"},{"key":"168_CR53","unstructured":"Hodgson R, Keller PJ, Hodges J, Spivak J (2014) QUDT: quantities, units, dimensions and data types ontologies TopQuadrant, Inc. http:\/\/www.qudt.org\/ . Accessed 1 March 2016"},{"key":"168_CR54","unstructured":"Chalk S (2016) Scientific data model ontology (SDMO) http:\/\/stuchalk.github.io\/scidata\/ontology\/scidata.owl . Accessed 23 June 2016"},{"key":"168_CR55","unstructured":"DCMI (2016) Dublin core metadata terms ASIS&T. http:\/\/dublincore.org\/documents\/dcmi-terms\/ . Accessed 1 March 2016"},{"key":"168_CR56","unstructured":"Chalk S (2016) SciData: example data files http:\/\/stuchalk.github.io\/scidata\/examples\/ . Accessed 23 June 2016"},{"key":"168_CR57","unstructured":"W3C (2016) JSON-LD 1.0: The Context The World Wide Web Consortium. http:\/\/www.w3.org\/TR\/json-ld\/-the-context . Accessed 1 March 2016"},{"key":"168_CR58","unstructured":"W3C (2016) The extensible stylesheet language family (XSL). https:\/\/www.w3.org\/Style\/XSL\/"}],"container-title":["Journal of Cheminformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-016-0168-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s13321-016-0168-9\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-016-0168-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,11]],"date-time":"2025-06-11T11:12:26Z","timestamp":1749640346000},"score":1,"resource":{"primary":{"URL":"https:\/\/jcheminf.biomedcentral.com\/articles\/10.1186\/s13321-016-0168-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,10,14]]},"references-count":58,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2016,12]]}},"alternative-id":["168"],"URL":"https:\/\/doi.org\/10.1186\/s13321-016-0168-9","relation":{},"ISSN":["1758-2946"],"issn-type":[{"type":"electronic","value":"1758-2946"}],"subject":[],"published":{"date-parts":[[2016,10,14]]},"assertion":[{"value":"18 March 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 October 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 October 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"54"}}