ChEBI dataset in Turtle, N-Triples, JSON-LD, and RDF/XML. https://www.ebi.ac.uk/chebi/

This is the trajectory file meant to work with the rdf2d-example example folder of d-SEAMS. Check Github to navigate the source code in the browser. The filename needs to be preserved to run without any changes.

The MNXref reconciliation of metabolites and biochemical reactions namespace

ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data). The data is abstracted and curated from the primary scientific literature, and cover a significant fraction of the SAR and discovery of modern drugs. It is available in RDF form through EMBL-EBI's RDF Platform.

The Molecular Entities in Linked Data (MEiLD) dataset comprises data of distinct atoms, molecules, ions, ion pairs, radicals, radical ions, and others that can be identifiable as separately distinguishable chemical entities. The dataset is provided in a JSON-LD format and was generated by the SDFEater, a tool that allows parsing atoms, bonds, and other molecule data. MEiLD contains 349,960 of 'small' chemical entities. Our dataset is based on the SDF files and is enriched with additional ontologies and line notation data. As a basis, the Molecular Entities in Linked Data dataset uses the Resource Description Framework (RDF) data model. Saving the data in such a model allows preserving the semantic relations, like hierarchical and associative, between them. To describe chemical molecules, vocabularies such as Chemical Vocabulary for Molecular Entities (CVME) and Simple Knowledge Organization System (SKOS) are used. The dataset can be beneficial, among others, for people concerned with research and development tools for cheminformatics and bioinformatics. In this paper, we describe various methods of access to our dataset. In addition to the MEiLD dataset, we publish the Shapes Constraint Language (SHACL) schema of our dataset and the CVME ontology. The data is available in Mendeley Data.

Theoretical calculations at the B3LYP/CC-pVDZ level were used to find the IR, Raman, VCD, and various molecular properties of a terphenyl derivative. Experimental and theoretical spectra agree within their respective limits. Partial density of states shows which parts of the molecules have the most important contribution to the FMO. Fluorine, sulfur, oxygen, and nitrogen atoms have practically insignificant contribution to the HOMO. Time dependent DFT calculations were used to study excitations, while natural transition orbitals were used to study the charge transfer in the strongest excitation. The experimentally observed FTIR modes are compared with calculated wavenumbers. Natural bond orbital analysis gives the idea about stability of molecules. MD simulations are used for calculating solubility parameters. Autoxidation and bond dissociation studies indicate stability of the compound. The docked ligands form secure complexes with the receptor methionyl-tRNA synthetase which indicates new anti-protozoan drugs.

This data set accompanies the manuscript Differential-Mobility Spectrometry of 1-deoxysphingosine Isomers: New Insights into the Gas Phase Structures of Ionized Lipids by Berwyck L. J. Poad, Alan T. Maccarone, Haibo Yu, Todd W. Mitchell, Essa M. Saied, Christoph Arenz, Thorsten Hornemann, James N. Bull, Evan J. Bieske, Stephen J. Blanksby.

ABSTRACT: Separation and structural identification of lipids remains a major challenge for contemporary lipidomics. Regioisomeric lipids differing only in position(s) of unsaturation are not differentiated by conventional liquid chromatography-mass spectrometry approaches leading to the incomplete, or sometimes incorrect, assignation of molecular structure. Here we describe an investigation of the gas phase separations by differential mobility spectrometry (DMS) of a series of synthetic analogues of the recently described 1-deoxysphingosine. The dependence of the DMS behavior on the position of the carbon-carbon double bond within the ionized lipid is systematically explored and compared to trends from complementary investigations, including collision cross sections measured by drift tube ion mobility, reaction efficiency with ozone, and molecular dynamics simulations. Consistent trends across these modes of interrogation point to the importance of direct, through-space interactions between the charge site and the carbon-carbon double bond. Differences in the geometry and energetics of this intra-molecular interaction underpin DMS separations and influence reactivity trends between regioisomers. Importantly, the disruption and reformation of these intra-molecular solvation interactions during DMS are proposed to be the causative factor in the observed separations of ionized lipids which are shown to have otherwise identical collision cross sections. These findings provide key insights into the strengths and limitations of current ion-mobility technologies for lipid isomer separations and can thus guide a more systematic approach to improved analytical separations in lipidomics.

This data set accompanies the manuscript Combining Charge-Switch Derivatisation with Ozone-Induced Dissociation for Facile Fatty Acid Analysis by Berwyck L.J. Poad, David L. Marshall,Eva Harazim, Rajesh Gupta,Venkateswarra R. Narreddula, Reuben S. E. Young, Todd W. Mitchell, Eva Duchoslav, J. Larry Campbell, James A. Broadbent, Josef Cvačka and Stephen J. Blanksby (In Press).

Abstract: The specific positions of carbon-carbon double bond(s) within an unsaturated fatty acid exert a significant effect on the physical and chemical properties of the lipid that ultimately inform its biological function(s). Contemporary liquid-chromatography mass spectrometry (MS) strategies based on electrospray ionisation coupled to tandem MS can easily detect fatty acyl lipids but generally cannot reveal those specific site(s) of unsaturation. Herein, we describe a novel and versatile workflow whereby fatty acids are first converted to fixed charge N-(4-aminomethylphenyl) pyridinium (AMPP) derivatives and subsequently subjected to ozone-induced dissociation (OzID) on a modified triple quadrupole mass spectrometer. The AMPP modification enhances the detection of fatty acids introduced by direct infusion. Fragmentation of the derivatised fatty acids also provides diagnostic fragment ions upon collision-induced dissociation that can be targeted in precursor ion scans to subsequently trigger OzID analyses in an automated data-dependent workflow. It is these OzID analyses that provide unambiguous assignment of carbon-carbon double bond locations in the AMPP-derivatized fatty acids. The performance of this analysis pipeline is assessed in profiling the patterns of unsaturation in fatty acids within the complex biological secretion vernix caseosa. This analysis uncovers significant isomeric diversity within the fatty acid pool of this sample, including a number of hitherto unreported double bond-positional isomers that hint at the activity of potentially new metabolic pathways.

Data file types consist of SCIEX Analyst (.wiff) files, and Python (.py) files.

An Open Context "predicates" dataset item. Open Context publishes structured data as granular, URL identified Web resources. This "Variables" record is part of the "Andean Geochemistry Visualization Project" data publication.

This is the datasets used for Linked Open Data instant level quality analysis for cultural heritage (2020). 7Z and ZIP versions are available for both Excel 2006 and R 4.0.3. The compressed files include, Excel spreadsheets (.xlsx, .csv), VBA scripts (.bas), and R scripts (.r). Please read the full documentation in Linked_Open_Data_Instance_Level_Analysis_Procedure.pdf.

Ongoing modeling efforts with respect to Graphene-oriented substrates.

This statistic shows the total value of chemical imports to North American countries from 2005 to 2019. In 2019, the total import value of the chemical industry in North America stood at around 165.7 billion U.S. dollars.

This data archive accompanies the article Introduction of a fixed-charge, photolabile derivative for enhanced structural elucidation of fatty acids by Venkateswara R. Narreddula, Nathan R. Boase, Ramesh Ailuri, David L. Marshall, Berwyck L. J. Poad, Michael J. Kelso, Adam J. Trevitt, Todd W. Mitchell and Stephen J. Blanksby.

ABSTRACT: Fatty acids are a structurally diverse category of lipids with a myriad of biochemical functions, which includes their role as building blocks of more complex lipids (e.g., glycerophospholipids and triacylglycerols). Increasingly, the analysis of fatty acids is undertaken using liquid chromatography-mass spectrometry (LC-MS), due to its versatility in the detection of lipids across a wide range of concentrations and diversity of molecular structures and masses. Previous work has shown that fixed-charge pyridinium derivatives are effective in enhancing the detection of fatty acids in LC-MS workflows. Herein, we describe the development of two novel pyridinium fixed-charged derivatization reagents that incorporate a photolabile aryl iodide that is selectively activated by laser irradiation inside the mass spectrometer. Photodissociation mass spectra of fatty acids conjugated to 1-(3-(aminomethyl)-4-iodophenyl)pyridin-1-ium(4-I-AMPP+)and 1-(4-(aminomethyl)-3-iodophenyl)pyridin-1-ium (3-I-AMPP+) derivatives reveal structurally diagnostic product ions. These spectra feature radical-directed dissociation of the carbon-carbon bonds within the fatty acyl chain, enabling structural assignments of fatty acids and discrimination of isomers that differ in site(s) of unsaturation, methyl branching or cyclopropanation. These derivatives are shown to be suitable for hyphenated LC-MS methods and their predictable photodissociation behavior allows de novoidentification of unusual fatty acids within a biological context.

This 'PoLyInfo Ontology' summarizes the concept classes, predicates, instances, etc. necessary for machine-readable representation of the polymer knowledge in PoLyInfo. It is an essential concept system for semantic search of PoLyInfoRDF, which is published in an authentication endpoint. In other words, by using these definitions, rules of thumb and new discoveries also become polymer knowledge shareable with PoLyInfo. On the other hand, the PoLyInfo ontology is consistent with the internationally known upper ontology BFO. This means that it can be linked to many other disciplines that are conforming to BFO, and PoLyInfo is now part of a huge body of knowledge that goes beyond polymer chemistry to address major societal issues such as environmental problems. Based on these considerations, possible uses of the PoLyInfo ontology include the following. ・ Machine-readable understanding of the polymer knowledge contained in PoLyInfoRDF and its use for semantic search (for use inside PoLyInfo) ・ Designing linkage methods for cross-search between your dataset and PoLyInfoRDF (for use inside Polymer Chemistry, including PoLyInfo). ・ Design of ontology linking external databases and PoLyInfoRDF (for use outside of Polymer Chemistry)

Information for Data Use Namespace http://dice.nims.go.jp/ontology/PoLyInfo-ont/Schema# SPARQL endpoint https://materials-open-rdf.nims.go.jp/sparql Public ontology viewer https://materiage.org/pli/

The PoLyInfo ontology will be detailed in a forthcoming paper. The bibliographic information of the papers will be published on this site and the papers will also be registered in the MDR. The license for use of this ontology is CC BY. Please include the author and DOI of the version you are citing: (Example Sentence) 'This data structure conforms to the PoLyInfo ontology Version 1.0 [1]. [1] Masashi Ishii and Koichi Sakamoto, PoLyInfo Ontology Version 1.0, https://doi.org/10.48505/nims.4414 (2024)' If you wish to cite the ontology and conceptual schema together, the latest version or in general, please refer to the citation instructions provided at collection site (https://doi.org/10.48505/nims.4413).

Abbreviation List BFO: Basic Formal Ontology RDF: Resource Description Framework SPARQL: SPARQL Protocol And RDF Query Language

本「PoLyInfo オントロジー」は、PoLyInfoの高分子知識を機械可読に表現する上で必要な概念クラス、述語、インスタンス等をまとめたものです。別途認証エンドポイント公開しているPoLyInfoRDFのセマンティックな検索を実現する上で、必須の概念体系となります。言い換えると、これらの定義を使うことで、経験則や新しい発見もPoLyInfoと高分子知識を共有できることになります。一方で、PoLyInfo オントロジーは、国際的に知られた上位オントロジーBFOと整合しています。すなわちBFOに準拠する多くの分野と連携が可能になっており、今やPoLyInfoは高分子化学を越えて、環境問題など大きな社会課題に取り組むための巨大知識の一部を担っています。これらのことから、PoLyInfo オントロジーの使い方として、以下のことが考えられます。 ・ PoLyInfoRDFに含まれる高分子知識の機械可読な理解と、セマンティックな検索への利用（PoLyInfo内での利用） ・ ご自身がお持ちのデータセットとPoLyInfoRDFの横断検索のためのリンク方法の設計（PoLyInfoを含む高分子化学内での利用） ・ 外部データベースとPoLyInfoRDFの連携オントロジーの設計（高分子化学外での利用）

データ利用の情報 名前空間 http://dice.nims.go.jp/ontology/PoLyInfo-ont/Schema# SPARQLエンドポイント https://materials-open-rdf.nims.go.jp/sparql Ontology ビューアー https://materiage.org/pli/

PoLyInfo オントロジーの内容は、近刊の論文の中で詳述します。論文書誌情報はこのサイトで公開し、また論文もMDRに登録予定です。 本オントロジーの利用ライセンスはCC BYです。引用するバージョンの著者とDOIの記載をお願いします： （文例） 「本データ構造はPoLyInfo オントロジー[1]に準拠した。 [1] Masashi Ishii and Koichi Sakamoto, PoLyInfo オントロジー, https://doi.org/10.48505/nims.4414 (2024)」 オントロジーと概念スキーマを一緒に引用する場合、最新版や一般的に引用する場合は、コレクションサイトに記載の引用方法をご参照ください(https://doi.org/10.48505/nims.4413)。

略語一覧： BFO: Basic Formal Ontology RDF: Resource Description Framework SPARQL: SPARQL Protocol And RDF Query Language

This data set contains:

1. Trajectories of glass and liquid Ge2Sb2Te5 models generated with the GAP. There are 5 models labeled 001-005 of 315 atoms and one large model of 7,200 atoms labeled 7K.

2. Structural analysis data including: radial distribution functions, rings, voids, tetrahedral angular order parameters.

3. The inter-atomic potential used to carry out the simulations.

4. The crystallization trajectory of one of the GAP models is provided separately due to the size.

The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.

Chemical Block Layered Alignment of Substructure or Chem-BLAST uses a method for finding chemical compounds within a large collection. In this method, all chemical compounds are annotated in terms of standard chemical structural fragments. These fragments are then organized into a data tree based on their chemical substructures. Search engines have been developed to use this data tree. These search engines use the Chem-BLAST technique to search on the fragments and look for their chemical structural neighbors. The technique was originally developed in the context of the HIV Structural database to enable a query on inhibitors of HIV protease. (See http://xpdb.nist.gov/hivsdb/hivsdb.html.) Recently the method has been significantly improved to extend to the ligands found in the Protein Data Bank (PDB). (See http://xpdb.nist.gov/chemblast/pdb.html.) The method establishes a tree-like relationship between the rings found in three-letter codes that denote ligands of the structures found in the PDB. Semantic Web relations are established between the structural scaffolds of the ligands and organizes them in an XML database utilizing the Web's Resource Description Framework (RDF). An Adobe Flex-based interface is used to present this information on the Web. Plans are under way to extend this work to non-ring type scaffolds as well. Chem-BLAST has also been extended to structures in PubChem. http://xpdb.nist.gov/chemblast/pdb.pl which includes several non-ring standard reused groups such as sulfates. Efforts are under way to use the underlying principles of Chem-BLAST to enable query on non-structural data, such as cell image data http://xpdb.nist.gov/cell/image.pl.

This is an RDFied version of the dataset published in Choi, JS., Ha, M.K., Trinh, T.X. et al. Towards a generalized toxicity prediction model for oxide nanomaterials using integrated data from different sources. Sci Rep 8, 6110 (2018)

The original dataset publication DOI: https://doi.org/10.1038/s41598-018-24483-z

The Original publication authors: Jang-Sik Choi, My Kieu Ha, Tung Xuan Trinh, Tae Hyun Yoon & Hyung-Gi Byun

Pendimethalin at IL_EPA-RDF-1