This readme file was generated on 2025-06-07 by Masashi Ishii # GENERAL INFORMATION * Title of Dataset: International XAFS DB RDF and Ontology ## Author/Principal Investigator Information Name: Masashi Ishii ORCID: 0000-0003-0357-2832 Institution: Center for Basic Research on Materials, National Institute for Materials Science (NIMS) Address: 1-2-1, Sengen, Tsukuba, Ibaraki, 305-0047, Japan Email: ISHII.Masashi@nims.go.jp ## Author/Associate or Co-investigator Information Name: Asahiko Matsuda ORCID: 0000-0001-5989-027X Institution: Materials Data Platform, National Institute for Materials Science (NIMS) Address: 1-1, Namiki, Tsukuba, Ibaraki, 305-0044, Japan Email: MATSUDA.Asahiko@nims.go.jp Name: Koichi Sakamoto ORCID: Institution: Center for Basic Research on Materials, National Institute for Materials Science (NIMS) Address: 1-2-1, Sengen, Tsukuba, Ibaraki, 305-0047, Japan Email: SAKAMOTO.Koichi@nims.go.jp Name: Shohei Yamashita ORCID: Institution: Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK) Address: 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan Email: yamasho@post.kek.jp Name: Yasuhiro Niwa ORCID: Institution: Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK) Address: 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan Email: yasuhiro.niwa@kek.jp Name: Yasuhiro Inada ORCID: 0000-0001-5772-4788 Institution: College of Life Sciences, Ritsumeikan University Address: 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan Email: yinada@fc.ritsumei.ac.jp * Date of data collection: 2025-04-07 * Geographic location of data collection: Tsukuba city, Ibaraki, Japan * Information about funding sources that supported the collection of the data: This work is partly supported by the MEXT Program: Data Creation and Utilization-Type Material Research and Development Project (Digital Transformation Initiative Center for Magnetic Materials), Grant Number JPMXP1122715503, and by the Council for Science, Technology and Innovation (CSTI), Cross-ministerial Strategic Innovation Promotion Program (SIP), the 3rd period of SIP 'Materials Informatics Infrastructure Linkage and Human Resource Development for Fostering Material Unicorns' (Funding agency: NIMS). # SHARING/ACCESS INFORMATION * Licenses/restrictions placed on the data: Creative Commons BY Attribution 4.0 International * Links to publications that cite or use the data: https://ixdb.jxafs.org/ * Links to other publicly accessible locations of the data: https://materials-open-rdf.nims.go.jp/sparql * Links/relationships to ancillary data sets: By using the RDF datasets and ontology, links to XAFS data worldwide can be established. * Was data derived from another source? No * If yes, list source(s): * Recommended citation for this dataset: The International XAFS DB RDF and Ontology were created based on the content of the following paper [1] by the authors group. [1] M. Ishii, A. Matsuda, K. Sakamoto, S. Yamashita, Y. Niwa, and Y. Inada, Global cross-database search system for X-ray absorption spectra, Journal of Synchrotron Radiation, Volume 32, Part 3, pages 661-668. https://doi.org/10.1107/S1600577525002206 The DOI for the downloadable dataset is as follows, https://doi.org/10.48505/nims.5513 # DATA & FILE OVERVIEW ## File List: 1) mdr-xafs-ont.ttl Ontology summarizing the class concepts of RDF nodes 2) Open_CLS_rdf.ttl RDF of Canadian Light Source data normalized using the common schema 3) Open_ESRF_P_rdf.ttl RDF of ESRF ID21 Phosphorus data normalized using the common schema 4) Open_ESRF_S_rdf.ttl RDF of ESRF ID21 Sulfur data normalized using the common schema 5) Open_FAME_rdf.ttl RDF of SSHADE/FAME data normalized using the common schema 6) Open_IHEP_rdf.ttl RDF of Experimental XAS DB data normalized using the common schema 7) Open_LISA_rdf.ttl RDF of LISA XAS DB data normalized using the common schema 8) Open_RDF_AbsEdge.ttl RDF conceptualizing absorption edges commonly measured in XAFS experiments 9) Open_RDF_Connection_IXDB.ttl RDF linking attribute information and XAFS information in each database 10) Open_RDF_MdrWork.ttl RDF of MDR XAFS DB data normalized using the common schema 11) Open_XASLIB_rdf.ttl RDF of XASLIB data normalized using the common schema * Relationship between files, if important: RDF files link data attributes and XAFS concepts through the relationship below. The numbers here correspond to the numbers of the above files. { 2) 3) 4) 5) 6) 7) 10) 11) } - { 9) } - { 8) } The ontology 1) defines the overall classes. * Additional related data collected that was not included in the current data package: Nothing * Are there multiple versions of the dataset? Yes * If yes, name of file(s) that was updated: New RDF of other databases may be added in the future. * Why was the file updated? * When was the file updated? # METHODOLOGICAL INFORMATION ## Description of methods used for collection/generation of data: The dataset was created using the following steps. 1. Collected material names, absorption endpoints, link information, etc. from databases around the world. 2. Normalized and registered the information in a dictionary. Please refer to the following MatVoc website for the created dictionary: https://matvoc.nims.go.jp/explore/en/results/Q713 3. Generated RDF using a schema. 4. Verified operation using a local RDF store. For details on the creation of the dataset, please refer to the following paper: Global cross-database search system for X-ray absorption spectra Journal of Synchrotron Radiation, Volume 32, Part 3, pages 661-668. https://doi.org/10.1107/S1600577525002206 ## Methods for processing the data: Various collected information was organized into tables and imported into schema-based RDF templates using Python programs. The RDF templates are not included in this dataset. However, the schema is summarized in the above paper, so it should not be difficult to create a templates from it. Templates can also be created from the RDF available here. ## Instrument- or software-specific information needed to interpret the data: The following are examples of how this dataset can be used, but these are not intended to limit the uses of the dataset. 1. Applications in closed systems, such as semantic data search on local servers 2. Understanding RDF structures and query design when using the above public SPARQL endpoints 3. Use of the XAFS ontology 4. Building custom applications using the database The following softwares are useful for each of the applications listed in 1-4 above. 1. RDF triple store. You don't need to use any special triple store, but Virtuoso is one of the well-known ones. https://vos.openlinksw.com/owiki/wiki/VOS/VOSRDF There are many documents and examples available regarding installation and usage, so please refer to those. 2. No special software is required. For information on RDF and SPARQL specifications, please refer to the W3C website and related books. Resource Description Framework (RDF) https://www.w3.org/RDF/ SPARQL 1.2 Query Language https://www.w3.org/TR/sparql12-query/ Typical SPARQL examples using the following endpoint are listed in the appendix of the paper. https://materials-open-rdf.nims.go.jp/sparql However, the graph ID published here is the latest as of June 2025, and you will need to use the following IRI: https://ixdb-rdf_6.nims.go.jp/ The designation of data resources indicated in the paper needs to be revised as follows. from 3. Ontology editors are useful for viewing and searching concept hierarchies. Protege is a well-known editor. Welcome to the Protégé wiki! https://protegewiki.stanford.edu/wiki/Main_Page 4. Actually, the most effective way to utilize this resource is to build your own customized application that calls these data. Using Python Flask, etc. you can quickly and economically build services that are useful to the XAFS community. In fact, IXDB was created in this way. https://ixdb.jxafs.org/ Your system does not need to perform time-consuming and costly data management. By accessing endpoints, you can use the latest data in applications that suit your needs. * Standards and calibration information, if appropriate: No special adjustments are necessary. You can upload these files to your triple store as is. * Environmental/experimental conditions: The environment necessary for semantic data utilization can be constructed at low cost. Many systems do not require specific operating systems or construction platforms. * Describe any quality-assurance procedures performed on the data: The accuracy of this dataset is not guaranteed. Please use it at your own risk. * People involved with sample collection, processing, analysis and/or submission: We would like to express our gratitude to the following databases and their representatives for their understanding and cooperation: LISA XAS Database (Alessandro Puri, University of Bologna; CNR-IOM-OGG c/o ESRF LISA CRG) ESRF ID21 XANES Spectra Databases (Marine Cotte, ESRF ID21) Experimental XAS database (Xueqi Song and Haifeng Zhao, Institute of High Energy Physics, Chinese Academy of Science) XASLIB (Matthew Newville, University of Chicago) SSHADE/FAME (Isabelle Kieffer and Denis Testemale, SSHADE (OSUG Data Center)) CLS XAS Database (Denis Spasyuk, Canadian Light Source Inc.) MDR XAFS DB (Masashi Ishii, NIMS) # DATA-SPECIFIC INFORMATION FOR: [FILENAME] * Number of variables: Regarding ontology, we have defined 28 classes. * Number of cases/rows: This data is described in RDF (Turtle format). The number of triples in each file is summarized below. 1) mdr-xafs-ont.ttl 12.0kb 167 triples 2) Open_CLS_rdf.ttl 297.4kb 7711 triples 3) Open_ESRF_P_rdf.ttl 33.9kb 470 triples 4) Open_ESRF_S_rdf.ttl 39.3kb 631 triples 5) Open_FAME_rdf.ttl 275.7kb 4650 triples 6) Open_IHEP_rdf.ttl 49.7kb 1278 triples 7) Open_LISA_rdf.ttl 19.2kb 432 triples 8) Open_RDF_AbsEdge.ttl 84.6kb 2357 triples 9) Open_RDF_Connection_IXDB.ttl 271.4kb 4528 triples 10) Open_RDF_MdrWork.ttl 1.4mb 29517 triples 11) Open_XASLIB_rdf.ttl 130.8kb 2499 triples * Variable List: This data is machine-readable. For class definitions, please refer to the ontology. * Missing data codes: Nothing * Specialized formats or other abbreviations used: DB: Database IXDB: International XAFS Database MDR: Materials Data Repository RDF: Resource Description Framework SPARQL: SPARQL Protocol and RDF Query Language XAFS: X-ray Absorption Fine Structure