Pub. Chem. RDF Release Notes. Semantic Web. technologies are emerging as an increasingly important approach to distribute and integrate scientific data. These technologies include the trio of the Resource Description Framework (RDF), Web Ontology Language. OWL), and SPARQL query language. The Pub. Chem. RDF project provides RDF formatted information for the Pub. Chem Compound, Substance, and Bioassay databases. RDF constitutes a family of World Wide Web Consortium (W3. C) specifications for data interchange on the Web. RDF breaks down knowledge into machine- readable. Each “triple” is organized as a trio of ‘subject- predicate- object’. For example, in the phrase “atorvastatin may treat hypercholesterolemia,” the subject is “atorvastatin”, the predicate is “may treat”, and the object is “cholesterol.” RDF uses a. Uniform Resource Identifier (URI) to name each part of the. A URI looks just like a typical web URL. RDF is a. core part of semantic web standards. As an extension of the existing World Wide Web, the semantic web attempts to make it easier for users to find, share, and combine. Semantic web leverages the following technologies: extensible markup language (XML), which. RDF; web ontology language (OWL), which extends the ability of RDF to. RDF), which expresses knowledge; and RDF query language (SPARQL), which enables query and manipulation of RDF content. Pub. Chem users have frequently expressed interest in having a downloadable database. Apache First Beta Update Installed AppsToday, we are happy to announce the release of Visual Studio 2015 Update 1. This release includes our latest feature and functionality updates. Developers using the. Using Pub. Chem. RDF, one can download the desired RDF formatted data files. Pub. Chem FTP site, import them into a triplestore, and query using a SPARQL query interface. Together these tools enable the schema- less database access and query. There. are a number of open- source and commercial triplestores such as the Apache Jena TDB and Open. Link Virtuoso (a list can be found here: http: //en. Triplestore). Other than triplestores, Pub. Apache Hadoop ( / h ə ˈ d uː p /) is an open-source software framework used for distributed storage and processing of dataset of big data using the MapReduce. But now that the breach is known to be CVE-2017-5638, the software company isn’t pulling punches. In a statement, Apache Struts wrote, “This vulnerability was. Chem. RDF data can also be. RDF- aware graph databases such as Neo. RDF graphs. At last but not least, the. Apache First Beta Update Installed DriversPub. Chem knowledge base allows logical inference, such as forward/backward chaining. The RDF data on the Pub. Chem FTP site. is arranged in such a way that you only need to download the type of information in which you. Pub. Chem data you will not use. For example, if you are just interested in computed chemical. Pub. Chem. RDF data in the compound descriptor directory. In addition to bulk download, Pub. Chem. RDF also. provides programmatic data access through RESTful interface. This document provides detailed technical information (release notes) about the Pub. Chem. RDF project. Additional information is available as follows. Pub. Chem. RDF graphs. As depicted in Figure 1, the Pub. Chem. RDF content. Whenever possible, pre- existing ontological frameworks were used to semantically describe information available in the Pub. Chem archive, rather than creating new ones. However, in some cases, no suitable types or relations were. Pub. Chem vocabulary was created to define these terms. The set of standardized ontologies used to define the domain- specific knowledge are found in Table 1 and includes: Chemical Entities of Biological Interest (Ch. EBI), CHEMical INFormation ontology (CHEMINF), Protein Ontology (PRO), Gene Ontology (GO), Semanticscience Integrated Ontology (SIO), Basic Formal Ontology (BFO), Ontology for Biomedical Investigations (OBI), Information Artifact Ontology (IAO), Bio. Assay Ontology (BAO), Units of Measurement (UO), Citation Typing Ontology (Ci. TO), FRBR- aligned Bibliographic Ontology (Fa. Bi. O), Dublin Core Metadata Initiative (DCMI) Terms, Simple Knowledge Organization System (SKOS), Bio. PAX, National Drug File- Reference Terminology (NDF- RT), and National Center Institute thesaurus (NCIt). All of the biomedical ontologies, such as Ch. EBI, CHEMINF, PRO, GO, BFO. SIO, and BAO, are interfaced by the NIH Roadmap National Center for Biomedical Ontology (NCBO) through its Bio. Portal, and comply with an evolving set of shared principles established by the Open Biomedical Ontologies (OBO) foundry. Adoption of these core ontologies helps to ensure that the mapping of. Semantic Web resources. The prefixes and corresponding namespaces of standardized ontologies used in Pub. Chem. RDF. Expand all. Collapse all. Vocabulary. Namespace. Prefix. RDF Schemahttp: //www. Vocabulary predicate used in Pub. Chem. RDF. RDFhttp: //www. Vocabulary predicate used in Pub. Chem. RDF. OWLhttp: //www. OWL is mainly used to define the classes and predicates in Pub. Chem. RDF vocabulay that has namespace: http: //rdf. XML Schemahttp: //www. XMLSchema#xsd. XML Schema is used to define the data type of literals; typical data types used in Pub. Chem. RDF includes integer, float, date, and so on. NDF- RThttp: //evs. NDF- RT/NDF- RT. owl#ndfrt. The National Drug File - Reference Terminology (NDF- RT) classfication of drugs and drug ingredients is used to annotate Pub. Chem. RDF compounds. NCIthttp: //ncicb. EVS/Thesaurus. owl#ncit. National Cancer Institute Thesaurus (NCIt) classification of chemicals and drugs is used to annotate Pub. Chem. RDF compounds. SIOhttp: //semanticscience. Semanticscience Integrated Ontology (SIO) predicates used in Pub. Chem. RDF. sio: has- valuesio: has- attributesio: has- unitsio: is- output- ofsio: has- measurement- valuesio: refers- to. CHEMINFhttp: //semanticscience. Chemical Information Ontology (CHEMINF) predicates used in Pub. Chem. RDF. cheminf: CHEMINF_0. Pub. Chem normalized counterpartcheminf: CHEMINF_0. CHEMINF_0. 00. 45. CHEMINF_0. 00. 46. CHEMINF_0. 00. 46. CHEMINF_0. 00. 48. Pub. Chem 2- D similarity algorithmcheminf: CHEMINF_0. Pub. Chem 3- D similarity algorithm. Chemical Information Ontology (CHEMINF) classes used in Pub. Chem. RDF. cheminf: CHEMINF_0. Molecular Weightcheminf: CHEMINF_0. Molecular Formulacheminf: CHEMINF_0. Total Formal Chargecheminf: CHEMINF_0. Mono Isotopic Weightcheminf: CHEMINF_0. Exact Masscheminf: CHEMINF_0. Compound Identifiercheminf: CHEMINF_0. Covalent Unit Countcheminf: CHEMINF_0. Defined Atom Stereocenter Countcheminf: CHEMINF_0. Defined Bond Stereocenter Countcheminf: CHEMINF_0. Isotope Atom Countcheminf: CHEMINF_0. Heavy Atome Countcheminf: CHEMINF_0. Undefined Atom Stereocenter Countcheminf: CHEMINF_0. Undefined Bond Stereocenter Countcheminf: CHEMINF_0. Canonical SMILEScheminf: CHEMINF_0. Isomeric SMILEScheminf: CHEMINF_0. Preferred IUPAC Namecheminf: CHEMINF_0. Hydrogen Bond Donor Countcheminf: CHEMINF_0. Hydrogen Bond Acceptor Countcheminf: CHEMINF_0. Rotatable Bond Countcheminf: CHEMINF_0. Structure Complexitycheminf: CHEMINF_0. Tautomer Countcheminf: CHEMINF_0. TPSAcheminf: CHEMINF_0. XLog. P3cheminf: CHEMINF_0. IUPAC In. Ch. Icheminf: CHEMINF_0. IUPAC In. Ch. IKeycheminf: CHEMINF_0. Ch. EMBL identifiercheminf: CHEMINF_0. KEGG identifiercheminf: CHEMINF_0. Human Metabolome Database identifiercheminf: CHEMINF_0. Chem. Spider identifiercheminf: CHEMINF_0. Drug. Bank identifiercheminf: CHEMINF_0. Ch. EBI identifiercheminf: CHEMINF_0. CAS registry numbercheminf: CHEMINF_0. EC number (A seven- digit identifier for regulatory purposes within the European Union)cheminf: CHEMINF_0. Lipid. Maps identifiercheminf: CHEMINF_0. National service center numbercheminf: CHEMINF_0. Unique ingredient identifiercheminf: CHEMINF_0. Validated chemical database identifier (superclass of other database identifiers)cheminf: CHEMINF_0. Drug trade name (brand name)cheminf: CHEMINF_0. International nonproprietary name (INN)cheminf: CHEMINF_0. Pub. Chem depositor- supplied name. SKOShttp: //www. w. Simple Knowledge Organization System (SKOS) predicates used in Pub. Chem. RDF. skos: exact. Matchused for depositor- provided external linksskos: close. Matchused for similarity links derived from structure- /sequence- based calculations. BFO, OBI, IAO, SO, UOhttp: //purl. Basic Formal Ontology (BFO), Ontology for biomedical Investigations (OBI), Information Artifact Ontology (IAO) predicates used in Pub. Chem. RDF. obo: BFO_0. BFO_0. 00. 00. 56participates in at some timeobo: OBI_0. IAO_0. 00. 01. 36is aboutobo: BFO_0. BFO_0. 00. 01. 71located in at all timesobo: BFO_0. Sequence Ontology (SO), Gene Ontology (GO), Basic Formal Ontology (BFO), Unit Ontology (UO) classes used in Pub. Chem. RDF. obo: SO_0. GO_0. 00. 15. 16prostaglandin biosynthetic processobo: GO_0. BFO_0. 00. 00. 34functionobo: UO_0. UO_0. 00. 03. 24square angstromobo: UO_0. Ch. EBI, PR, GOhttp: //purl. Chemical Entities of Biological Interest (Ch. EBI) classifcation is used to annotate Pub.
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