Exploring Structural Database Use in Crystallography: A USNC/Cr Workshop Series

Crystallography Open Database (COD) and Theoretical Crystallography Open Database (TCOD) - Session III

April 14, 2022

10:00 AM - 2:00 PM (ET)

Past

About

Please note that there has been a change to the order of the sessions being presented. Session I will now be "Depositing and managing data in the COD and the TCOD," and Session II will be "Using COD and TCOD, searching and getting data."

Using an open-access distribution model, the Crystallography Open Database (COD) collects all known ‘small molecule / small to medium sized unit cell’ crystal structures and makes them available freely on the Internet. As of today, the COD has aggregated over 480,000 structures, offering basic search capabilities and the possibility to download the whole database, or parts thereof using a variety of standard open communication protocols. A website provides capabilities for all registered users to deposit published and so far unpublished structures as personal communications or pre-publication depositions. Such a setup enables extension of the COD database by many users simultaneously. This increases the possibilities for growth of the COD database, and is the first step towards establishing a world wide Internet-based collaborative platform dedicated to the collection and curation of structural knowledge.

Session 1: "Depositing and managing data in the COD and the TCOD"

Learning Objectives

Participants will learn how to deposit their data into the database including what information is needed and how to deposit raw data.
Participants will learn how to maintain their data records in COD and TCOD.
Participants will be informed of quality standards such as: how personal data is used, how on-hold records are released to the public, and how records are peer reviewed.

Take Away Skills

Ability to upload and manage data records in the COD and TCOD.

Session 2: "Using COD and TCOD, searching and getting data"

Learning Objectives

Participants will gain a basic understanding of the structure of the COD including contents, scope, versioning, curation and identification principles of the COD.
Participants will understand how computations and queries are performed in COD.
Participants will learn how COD integrates with other databases.

Take Away Skills

Ability to use the basic computations and queries of COD

Session 3: "Under the hood: rolling out your own scientific database"

Learning Objectives

Participants will learn the basics of preparing their own database including choosing stable identifiers, versioning, using sensitive data, the use of relational models, and data curation.
Participants will learn the nuts and bolts of databases such as data formats, low-level data encoding, and data dictionaries.
Participants will learn logistical issues such as web access and web security.

Take Away Skills

Ability to work toward the preparation of a database with awareness of potential issues that must be addressed

Contact

Ana Ferreras

(202) 334-1697
aferreras@nas.edu

Disclaimer

It is essential to the National Academies mission of providing evidence-based advice that participants in any of our meetings or events avoid political or partisan statements or commentary and maintain a culture of mutual respect. The statements and presentations during our meetings or events are solely those of the individual participants and do not necessarily represent the views of other participants or the National Academy of Sciences, which is a non-partisan, tax exempt organization that includes under its Charter the National Academy of Engineering and National Academy of Medicine, and that operates the National Research Council.

Cambridge Structural Database (CSD) - Session II

April 13, 2022

11:00 AM - 2:00 PM (ET)

Past

About

This is session two of a two day workshop. We encourage all participants to register for both sessions (days).

The Cambridge Crystallographic Data Centre (CCDC) is the curator of the Cambridge Structural Database (CSD), the world’s largest repository of fully curated organic and organometallic experimental crystal structures. The large amount of reliable data makes the CSD an excellent place to gather insights into chemical and structural space.

2-day series: Working with the Cambridge Structural Database (CSD): searching, analyzing and depositing data using Cambridge Crystallographic Data Centre (CCDC) tools

Learning Objectives

Participants will explore how the CCDC’s tools allow users to search for structures of interest.
Participants will learn how to generate knowledge from statistical trends.
Participants will understand how to submit their own data to the database.

Take Away Skills

Ability to search structures and statistical trends within the database
Ability to submit their own data to the database

*Note: Graphical user interfaces and Python-based scripting will both be demonstrated.

Contact

Ana Ferreras

(202) 334-1697
aferreras@nas.edu

Disclaimer

It is essential to the National Academies mission of providing evidence-based advice that participants in any of our meetings or events avoid political or partisan statements or commentary and maintain a culture of mutual respect. The statements and presentations during our meetings or events are solely those of the individual participants and do not necessarily represent the views of other participants or the National Academy of Sciences, which is a non-partisan, tax exempt organization that includes under its Charter the National Academy of Engineering and National Academy of Medicine, and that operates the National Research Council.

Cambridge Structural Database (CSD) - Session I

April 12, 2022

11:00 AM - 2:00 PM (ET)

Past

About

This is session one of a two day workshop. We encourage all participants to register for both sessions (days).
The Cambridge Crystallographic Data Centre (CCDC) is the curator of the Cambridge Structural Database (CSD), the world’s largest repository of fully curated organic and organometallic experimental crystal structures. The large amount of reliable data makes the CSD an excellent place to gather insights into chemical and structural space.

2-day series: Working with the Cambridge Structural Database (CSD): searching, analyzing and depositing data using Cambridge Crystallographic Data Centre (CCDC) tools

Learning Objectives

Participants will explore how the CCDC’s tools allow users to search for structures of interest.
Participants will learn how to generate knowledge from statistical trends.
Participants will understand how to submit their own data to the database.

Take Away Skills

Ability to search structures and statistical trends within the database
Ability to submit their own data to the database

*Note: Graphical user interfaces and Python-based scripting will both be demonstrated.

Contact

Ana Ferreras

(202) 334-1697
aferreras@nas.edu

Disclaimer

It is essential to the National Academies mission of providing evidence-based advice that participants in any of our meetings or events avoid political or partisan statements or commentary and maintain a culture of mutual respect. The statements and presentations during our meetings or events are solely those of the individual participants and do not necessarily represent the views of other participants or the National Academy of Sciences, which is a non-partisan, tax exempt organization that includes under its Charter the National Academy of Engineering and National Academy of Medicine, and that operates the National Research Council.

Crystallography Open Database (COD) and Theoretical Crystallography Open Database (TCOD) - Session II

April 11, 2022

10:00 AM - 2:00 PM (ET)

Past

About

Please note that there has been a change to the order of the sessions being presented. Session I will now be "Depositing and managing data in the COD and the TCOD," and Session II will be "Using COD and TCOD, searching and getting data."

Using an open-access distribution model, the Crystallography Open Database (COD) collects all known ‘small molecule / small to medium sized unit cell’ crystal structures and makes them available freely on the Internet. As of today, the COD has aggregated over 480,000 structures, offering basic search capabilities and the possibility to download the whole database, or parts thereof using a variety of standard open communication protocols. A website provides capabilities for all registered users to deposit published and so far unpublished structures as personal communications or pre-publication depositions. Such a setup enables extension of the COD database by many users simultaneously. This increases the possibilities for growth of the COD database, and is the first step towards establishing a world wide Internet-based collaborative platform dedicated to the collection and curation of structural knowledge.

Session 1: "Depositing and managing data in the COD and the TCOD"

Learning Objectives

Participants will learn how to deposit their data into the database including what information is needed and how to deposit raw data.
Participants will learn how to maintain their data records in COD and TCOD.
Participants will be informed of quality standards such as: how personal data is used, how on-hold records are released to the public, and how records are peer reviewed.

Take Away Skills

Ability to upload and manage data records in the COD and TCOD.

Session 2: "Using COD and TCOD, searching and getting data"

Learning Objectives

Participants will gain a basic understanding of the structure of the COD including contents, scope, versioning, curation and identification principles of the COD.
Participants will understand how computations and queries are performed in COD.
Participants will learn how COD integrates with other databases.

Take Away Skills

Ability to use the basic computations and queries of COD

Session 3: "Under the hood: rolling out your own scientific database"

Learning Objectives

Participants will learn the basics of preparing their own database including choosing stable identifiers, versioning, using sensitive data, the use of relational models, and data curation.
Participants will learn the nuts and bolts of databases such as data formats, low-level data encoding, and data dictionaries.
Participants will learn logistical issues such as web access and web security.

Take Away Skills

Ability to work toward the preparation of a database with awareness of potential issues that must be addressed

Contact

Ana Ferreras

(202) 334-1697
aferreras@nas.edu

Disclaimer

It is essential to the National Academies mission of providing evidence-based advice that participants in any of our meetings or events avoid political or partisan statements or commentary and maintain a culture of mutual respect. The statements and presentations during our meetings or events are solely those of the individual participants and do not necessarily represent the views of other participants or the National Academy of Sciences, which is a non-partisan, tax exempt organization that includes under its Charter the National Academy of Engineering and National Academy of Medicine, and that operates the National Research Council.

Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC)

April 7, 2022

11:00 AM - 2:00 PM (ET)

Past

About

The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) includes a repository system and website designed to make the raw data of protein crystallography more widely available. Its focus is on identifying, cataloging and providing the metadata related to datasets, which could be used to reprocess the original diffraction data. The intent behind this project is to make the resulting three dimensional structures more reproducible and easier to modify and improve as processing methods advance.

Session title: Access to experimental data is crucial for scientific reproducibility

Learning Objectives

Participants will learn about the proteindiffraction.org repository of diffraction experiments used to determine structures that are din the protein data bank
Learn about the IRRMC tools used for working with data from the archive
Learn about progress in using neural networks to find anomalies in diffraction images and malfunctions of experimental systems
Learn about wwPDB plans for archival of integrative structures, whose models rely on combining information from multiple techniques and sources. The experimental data supporting the models may come from techniques such as X-ray crystallography (X-ray), nuclear magnetic resonance (NMR) spectroscopy, three-dimensional electron microscopy (3DEM), small-angle solution scattering (SAS), chemical cross-linking mass spectrometry (CX-MS), Förster resonance energy transfer (FRET), electron paramagnetic resonance spectroscopy (EPR), hydrogen-deuterium exchange mass spectrometry (HDX-MS), and other biophysical and proteomics methods.
Learn how access to unprocessed experimental data impacts scientific reproducibility.

Contact

Ana Ferreras

(202) 334-1697
aferreras@nas.edu

Disclaimer

It is essential to the National Academies mission of providing evidence-based advice that participants in any of our meetings or events avoid political or partisan statements or commentary and maintain a culture of mutual respect. The statements and presentations during our meetings or events are solely those of the individual participants and do not necessarily represent the views of other participants or the National Academy of Sciences, which is a non-partisan, tax exempt organization that includes under its Charter the National Academy of Engineering and National Academy of Medicine, and that operates the National Research Council.

Crystallography Open Database (COD) and Theoretical Crystallography Open Database (TCOD) - Session I

April 6, 2022

10:00 AM - 2:00 PM (ET)

Past

About

Please note that there has been a change to the order of the sessions being presented. Session I will now be "Depositing and managing data in the COD and the TCOD," and Session II will be "Using COD and TCOD, searching and getting data."
Using an open-access distribution model, the Crystallography Open Database (COD) collects all known ‘small molecule / small to medium sized unit cell’ crystal structures and makes them available freely on the Internet. As of today, the COD has aggregated over 480,000 structures, offering basic search capabilities and the possibility to download the whole database, or parts thereof using a variety of standard open communication protocols. A website provides capabilities for all registered users to deposit published and so far unpublished structures as personal communications or pre-publication depositions. Such a setup enables extension of the COD database by many users simultaneously. This increases the possibilities for growth of the COD database, and is the first step towards establishing a world wide Internet-based collaborative platform dedicated to the collection and curation of structural knowledge.

Session 1:

"Depositing and managing data in the COD and the TCOD"

Learning Objectives

Participants will learn how to deposit their data into the database including what information is needed and how to deposit raw data.
Participants will learn how to maintain their data records in COD and TCOD.
Participants will be informed of quality standards such as: how personal data is used, how on-hold records are released to the public, and how records are peer reviewed.

Take Away Skills

Ability to upload and manage data records in the COD and TCOD.

Session 2:

"Using COD and TCOD, searching and getting data"

Learning Objectives

Participants will gain a basic understanding of the structure of the COD including contents, scope, versioning, curation and identification principles of the COD.
Participants will understand how computations and queries are performed in COD.
Participants will learn how COD integrates with other databases.

Take Away Skills

Ability to use the basic computations and queries of COD

Session 3: "Under the hood: rolling out your own scientific database"

Learning Objectives

Participants will learn the basics of preparing their own database including choosing stable identifiers, versioning, using sensitive data, the use of relational models, and data curation.
Participants will learn the nuts and bolts of databases such as data formats, low-level data encoding, and data dictionaries.
Participants will learn logistical issues such as web access and web security.

Take Away Skills

Ability to work toward the preparation of a database with awareness of potential issues that must be addressed

Contact

Ana Ferreras

(202) 334-1697
aferreras@nas.edu

Disclaimer

It is essential to the National Academies mission of providing evidence-based advice that participants in any of our meetings or events avoid political or partisan statements or commentary and maintain a culture of mutual respect. The statements and presentations during our meetings or events are solely those of the individual participants and do not necessarily represent the views of other participants or the National Academy of Sciences, which is a non-partisan, tax exempt organization that includes under its Charter the National Academy of Engineering and National Academy of Medicine, and that operates the National Research Council.

SBGrid Consortium

April 5, 2022

11:00 AM - 2:00 PM (ET)

Past

About

SBGrid (www.sbgrid.org) is a consortium of 427 structural biology groups that utilize homogeneous stacks of scientific applications. SBGrid “Factory” at Harvard Medical School, which is led by Dr. Sliz actively curates over 1000 software titles ranging from tools used in crystallography, electron microscopy, computational chemistry to computational biology (biogrids.org). Multiple versions of all applications, the supporting libraries, and configuration files are maintained. The SBGrid consortium members use the extensive software collection, and work with the Factory to improve the quality SBGrid environment.
With software support activities dating back to 2001, the SBGrid collection is the largest global library of ready-to-execute scientific software. As part of its activities, SBGrid also maintains training materials (https://www.youtube.com/user/SBGridTV), software metadata, scientific source code and information about software citations, which is available through the SBGrid AppCiter (https://sbgrid.org/software/). More recently, we also developed a data bank to archive and validate X-ray diffraction, MicroED and LLSM datasets from SBGrid laboratories (data.sbgrid.org).
Session: Using the SBGrid Software Installer, AppCiter, and SBGrid Data Bank on PCs, HPC clusters and AWS cloud.

Learning Objectives

Learn how to use SBGrid Software Installer, AppCiter, and SBGrid Data Bank
Learn how to deploy SBGrid applications and experimental data on personal computers, HPC clusters, and in AWS.
Learn how to effectively utilize SBGrid applications in support of CryoEM, small-molecule docking and structure prediction.
Scientific software curation process - skills and expertise required to compile scientific software.

Take Away Skills

Ability to effectively utilize SBGrid open resources (SBGrid Data Bank, SBGrid TV, AppCiter, Scientific Software Database)
Ability to effectively utilize consortium-supported software (SBGrid and BioGrids stacks of applications), and to contribute to SBGrid
Basic understanding of software curation process and setting computing environment in AWS.

Contact

Ana Ferreras

(202) 334-1697
aferreras@nas.edu

Disclaimer

It is essential to the National Academies mission of providing evidence-based advice that participants in any of our meetings or events avoid political or partisan statements or commentary and maintain a culture of mutual respect. The statements and presentations during our meetings or events are solely those of the individual participants and do not necessarily represent the views of other participants or the National Academy of Sciences, which is a non-partisan, tax exempt organization that includes under its Charter the National Academy of Engineering and National Academy of Medicine, and that operates the National Research Council.

Electron Microscopy Data Bank (EMDB)

April 4, 2022

11:00 AM - 2:00 PM (ET)

Past

About

The Electron Microscopy Data Bank (EMDB) is a public repository for electron cryo-microscopy volume maps and tomograms of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron crystallography

Learning Objectives:

Participants will come away with knowledge of the different methods used to produce high resolution EM structures.
Participants will learn how to use the EMDB website to browse for EM structures of interest.
Participants will be introduced to validation metrics that allow them to assess the quality of EM data both in the EMDB archive and more generally.
Participants will be introduced to EM visualization software.
Participants will be briefly introduced to EMPIAR and AlphaFold DB.
Participants will embark on interactive, assisted, exercises to learn and reinforce their understanding of EM and the EMDB.

Take Away Skills:

Ability to search the EMDB archive
Ability to interpret the validation metrics of entries in the EMDB archive
Ability to visualize EM data

Contact

Ana Ferreras

(202) 334-1697
aferreras@nas.edu

Disclaimer

It is essential to the National Academies mission of providing evidence-based advice that participants in any of our meetings or events avoid political or partisan statements or commentary and maintain a culture of mutual respect. The statements and presentations during our meetings or events are solely those of the individual participants and do not necessarily represent the views of other participants or the National Academy of Sciences, which is a non-partisan, tax exempt organization that includes under its Charter the National Academy of Engineering and National Academy of Medicine, and that operates the National Research Council.

Protein Data Bank (PDB) - Session II

March 31, 2022

7:00 AM - 2:00 PM (ET)

Past

About

This is session two of a two day workshop. We encourage all participants to register for both sessions (days).

The Protein Data Bank (PDB; https://www.wwpdb.org) is the single global archive for preserving and disseminating information about the experimentally-determined three-dimensional (3D) structures/shapes of proteins, nucleic acids, and complex assemblies. Structural biologists working on every inhabited continent have contributed more than 185,000 experimentally determined structures to the PDB since it was established in 1971 as the first open-access digital data resource in biology. PDB data inform our understanding of fundamental biology, biomedicine, bioenergy, and bioengineering/biotechnology. The information is used by many millions of basic and applied researchers, educators, and students working and learning in every sovereign country recognized by the United Nations. Since 2003, the archive has been managed by the Worldwide Protein Data Bank (wwPDB) partnership, which includes PDB data centers in the US (RCSB PDB; https://www.rcsb.org), UK/Europe (PDBe; https://www.pdbe.org), and Asia (PDBj; https://www.pdbj.org) plus two specialty data archives for electron microscopy (EMDB; https://www.emdb.org) and NMR spectroscopy (BMRB; https://www.bmrb.io). This two-day workshop, sponsored by the RCSB Protein Data Bank (US PDB data center), will introduce participants to the science and technology of 3D macromolecular structure data deposition, validation, biocuration, archiving, and delivery.
2-day Series: Introducing the Protein Data Bank: 3D Macromolecular Structure Data Deposition, Validation, Biocuration, Archiving, and Delivery for Researchers, Educators, and Students Worldwide

Learning Objectives

Appreciate the importance of the PDBx/mmCIF data standard that underpins organization of all PDB archival data
Access and appropriately use the wwPDB OneDep system for macromolecular structure deposition
Understand how small molecule data in the PDB are organized and how to access it
Evaluate the quality and accuracy of a PDB structure using the wwPDB validation report
Understand how to use the Mol* molecular viewer to visualize PDB structures
Appreciate wwPDB plans for establishing a Next Generation PDB Archive
Participants will learn about the science and technology of 3D macromolecular structure data deposition, validation, biocuration, archiving, and delivery.

Contact

Ana Ferreras

(202) 334-1697
aferreras@nas.edu

Disclaimer

It is essential to the National Academies mission of providing evidence-based advice that participants in any of our meetings or events avoid political or partisan statements or commentary and maintain a culture of mutual respect. The statements and presentations during our meetings or events are solely those of the individual participants and do not necessarily represent the views of other participants or the National Academy of Sciences, which is a non-partisan, tax exempt organization that includes under its Charter the National Academy of Engineering and National Academy of Medicine, and that operates the National Research Council.

International Centre for Diffraction Data (ICDD) - Session II

March 30, 2022

11:00 AM - 2:00 PM (ET)

Past

About

This is session two of a two day workshop. We encourage all participants to register for both sessions (days).

Crystallographic databases play a vital role in materials research, influencing materials development and providing a reference for materials characterization. Design, data curation, and data management are all critical factors in developing a successful and useful database. This presentation will (1) focus on the processes used in creating the Powder Diffraction File (PDF®) including quality, reliability, management and accessibility of data and (2) highlight materials analysis applications.
The International Centre for Diffraction Data (ICDD®) Powder Diffraction File (PDF®) is a powerful database for materials characterization that has been used extensively by the scientific community. Starting with 1000 cards in 1941, the database has grown to contain over 1 million unique material data sets. The Powder Diffraction File has a wealth of information that a materials scientist can take advantage of in various ways, from materials identification, characterization, computation to design. The Powder Diffraction File in Relational Database Format (RDB) format contains extensive chemical, physical, bibliographic and crystallographic data including atomic coordinates enabling characterization and computational analysis.
Proper database structure, data validations and phase-type classifications are crucial in making any database useful and reliable. Various structural and chemical classifications implemented in the database will be presented in detail. These classifications are important in data mining studies and optimizing diffraction pattern search/match methods. While using a database, it is important to know the quality of the crystal structure, diffraction pattern data and any data field of interest found in the database. With the varying quality of published data in the literature, the PDF database editorial review processes require rigorous data evaluation methods to define data based on its quality. This critical evaluation is the rate determining step in populating a curated PDF database. Once the database has been established it is important to explore how the database can best be applied to solve problems in materials science. In the second part of this workshop, various database applications from phase identification, quantitative analysis and materials characterization using datamining applications will be presented. Advanced features in the PDF including atomic coordinates for Rietveld refinement techniques; amorphous and nano material references; digital simulation tools for evaluating X-ray, synchrotron, electron and neutron diffraction data as well as crystallite size and analysis of two-dimensional diffraction data will also be discussed.
2-day Series: The ICDD® Powder Diffraction File™: Database Concepts And Applications

Learning Objectives

Participants will learn about the processes used in creating the Powder Diffraction File (PDF®) including quality, reliability, management and accessibility of data.
Participants will learn how to use the ICDD for materials analysis applications.Participants will learn various database applications from phase identification, quantitative analysis and materials characterization using datamining applications.
Participants will be exposed to advanced features in the PDF including atomic coordinates for Rietveld refinement techniques, amorphous and nano material references, digital simulation tools for evaluating X-ray, synchrotron, electron and neutron diffraction data, and crystallite size and analysis of two-dimensional diffraction data.

Take Away Skills

Ability to use the ICDD for materials analysis applications
Ability to use multiple database applications including advanced features.

Contact

Ana Ferreras

(202) 334-1697
aferreras@nas.edu

Disclaimer

It is essential to the National Academies mission of providing evidence-based advice that participants in any of our meetings or events avoid political or partisan statements or commentary and maintain a culture of mutual respect. The statements and presentations during our meetings or events are solely those of the individual participants and do not necessarily represent the views of other participants or the National Academy of Sciences, which is a non-partisan, tax exempt organization that includes under its Charter the National Academy of Engineering and National Academy of Medicine, and that operates the National Research Council.

Protein Data Bank (PDB) - Session I

March 29, 2022

11:00 AM - 1:00 PM (ET)

Past

About

This is session one of a two day workshop. We encourage all participants to register for both sessions (days).

The Protein Data Bank (PDB; https://www.wwpdb.org) is the single global archive for preserving and disseminating information about the experimentally-determined three-dimensional (3D) structures/shapes of proteins, nucleic acids, and complex assemblies. Structural biologists working on every inhabited continent have contributed more than 185,000 experimentally determined structures to the PDB since it was established in 1971 as the first open-access digital data resource in biology. PDB data inform our understanding of fundamental biology, biomedicine, bioenergy, and bioengineering/biotechnology. The information is used by many millions of basic and applied researchers, educators, and students working and learning in every sovereign country recognized by the United Nations. Since 2003, the archive has been managed by the Worldwide Protein Data Bank (wwPDB) partnership, which includes PDB data centers in the US (RCSB PDB; https://www.rcsb.org), UK/Europe (PDBe; https://www.pdbe.org), and Asia (PDBj; https://www.pdbj.org) plus two specialty data archives for electron microscopy (EMDB; https://www.emdb.org) and NMR spectroscopy (BMRB; https://www.bmrb.io). This two-day workshop, sponsored by the RCSB Protein Data Bank (US PDB data center), will introduce participants to the science and technology of 3D macromolecular structure data deposition, validation, biocuration, archiving, and delivery.
2-day Series: Introducing the Protein Data Bank: 3D Macromolecular Structure Data Deposition, Validation, Biocuration, Archiving, and Delivery for Researchers, Educators, and Students Worldwide

Learning Objectives

Appreciate the importance of the PDBx/mmCIF data standard that underpins organization of all PDB archival data
Access and appropriately use the wwPDB OneDep system for macromolecular structure deposition
Understand how small molecule data in the PDB are organized and how to access it
Evaluate the quality and accuracy of a PDB structure using the wwPDB validation report
Understand how to use the Mol* molecular viewer to visualize PDB structures
Appreciate wwPDB plans for establishing a Next Generation PDB Archive
Participants will learn about the science and technology of 3D macromolecular structure data deposition, validation, biocuration, archiving, and delivery.

Contact

Ana Ferreras

(202) 334-1697
aferreras@nas.edu

Disclaimer

It is essential to the National Academies mission of providing evidence-based advice that participants in any of our meetings or events avoid political or partisan statements or commentary and maintain a culture of mutual respect. The statements and presentations during our meetings or events are solely those of the individual participants and do not necessarily represent the views of other participants or the National Academy of Sciences, which is a non-partisan, tax exempt organization that includes under its Charter the National Academy of Engineering and National Academy of Medicine, and that operates the National Research Council.

International Centre for Diffraction Data (ICDD) - Session I

March 28, 2022

11:00 AM - 2:00 PM (ET)

Past

About

This is session one of a two day workshop. We encourage all participants to register for both sessions (days).

Crystallographic databases play a vital role in materials research, influencing materials development and providing a reference for materials characterization. Design, data curation, and data management are all critical factors in developing a successful and useful database. This presentation will (1) focus on the processes used in creating the Powder Diffraction File (PDF®) including quality, reliability, management and accessibility of data and (2) highlight materials analysis applications.
The International Centre for Diffraction Data (ICDD®) Powder Diffraction File (PDF®) is a powerful database for materials characterization that has been used extensively by the scientific community. Starting with 1000 cards in 1941, the database has grown to contain over 1 million unique material data sets. The Powder Diffraction File has a wealth of information that a materials scientist can take advantage of in various ways, from materials identification, characterization, computation to design. The Powder Diffraction File in Relational Database Format (RDB) format contains extensive chemical, physical, bibliographic and crystallographic data including atomic coordinates enabling characterization and computational analysis.
Proper database structure, data validations and phase-type classifications are crucial in making any database useful and reliable. Various structural and chemical classifications implemented in the database will be presented in detail. These classifications are important in data mining studies and optimizing diffraction pattern search/match methods. While using a database, it is important to know the quality of the crystal structure, diffraction pattern data and any data field of interest found in the database. With the varying quality of published data in the literature, the PDF database editorial review processes require rigorous data evaluation methods to define data based on its quality. This critical evaluation is the rate determining step in populating a curated PDF database. Once the database has been established it is important to explore how the database can best be applied to solve problems in materials science. In the second part of this workshop, various database applications from phase identification, quantitative analysis and materials characterization using datamining applications will be presented. Advanced features in the PDF including atomic coordinates for Rietveld refinement techniques; amorphous and nano material references; digital simulation tools for evaluating X-ray, synchrotron, electron and neutron diffraction data as well as crystallite size and analysis of two-dimensional diffraction data will also be discussed.
2-day Series: The ICDD® Powder Diffraction File™: Database Concepts And Applications

Learning Objectives

Participants will learn about the processes used in creating the Powder Diffraction File (PDF®) including quality, reliability, management and accessibility of data.
Participants will learn how to use the ICDD for materials analysis applications.Participants will learn various database applications from phase identification, quantitative analysis and materials characterization using datamining applications.
Participants will be exposed to advanced features in the PDF including atomic coordinates for Rietveld refinement techniques, amorphous and nano material references, digital simulation tools for evaluating X-ray, synchrotron, electron and neutron diffraction data, and crystallite size and analysis of two-dimensional diffraction data.

Take Away Skills

Ability to use the ICDD for materials analysis applications
Ability to use multiple database applications including advanced features.

Contact

Ana Ferreras

(202) 334-1697
aferreras@nas.edu

Disclaimer

It is essential to the National Academies mission of providing evidence-based advice that participants in any of our meetings or events avoid political or partisan statements or commentary and maintain a culture of mutual respect. The statements and presentations during our meetings or events are solely those of the individual participants and do not necessarily represent the views of other participants or the National Academy of Sciences, which is a non-partisan, tax exempt organization that includes under its Charter the National Academy of Engineering and National Academy of Medicine, and that operates the National Research Council.

Inorganic Crystal Structure Database (ICSD) - Session II

March 24, 2022

11:00 AM - 1:00 PM (ET)

Past

About

This is session two of a two day workshop. We encourage all participants to register for both sessions (days).

The Inorganic Crystal Structure Database (ICSD) is the world’s largest database for fully determined inorganic crystal structures. It is made available to the scientific community and industry by FIZ Karlsruhe. ICSD contains the crystallographic data of all published crystalline inorganic structures, including atom coordinates, dating back to 1913. Organometallic and theoretical structures have been added within the past years. The ICSD data are of excellent quality. Only data that have passed thorough quality checks are included. As the world’s leading provider of scientific information on inorganic crystal structures, we take full responsibility for database production, maintenance and quality control, and we ensure that the ICSD database and our software solutions meet the highest possible quality standards.

In this 2 part tutorial, we will give a detailed overview of the search masks in ICSD and explain tips and tricks on how to best use them. We will also give an overview of the different ways to search in ICSD - from simple searches to more complex searches with the tools for combining searches in ICSD or with the "Expert Search" command line tool.
The tutorial session will include some questions that participants can work on using the ICSD. We will be around to give tips or further help if needed. Of course, we will also be happy to help with problems posed by participants.
Both parts are designed for beginners, but will also include some advanced tips and tricks for more familiar users of the database. There will also be plenty of time to ask questions about your specific challenges.

2-day series: The ICSD®: Concepts And Applications

Learning Objectives

Participants will be provided an overview of the search masks in ICSD including tips and tricks on how to best use them.
Participants will learn different ways to search in ICSD - from simple searches to more complex searches with the tools for combining searches in ICSD or with the "Expert Search" command line tool.

Take Away Skills

Ability to use the ICSD to answer interesting problems as modeled through practice problems.

Contact

Ana Ferreras

(202) 334-1697
aferreras@nas.edu

Disclaimer

It is essential to the National Academies mission of providing evidence-based advice that participants in any of our meetings or events avoid political or partisan statements or commentary and maintain a culture of mutual respect. The statements and presentations during our meetings or events are solely those of the individual participants and do not necessarily represent the views of other participants or the National Academy of Sciences, which is a non-partisan, tax exempt organization that includes under its Charter the National Academy of Engineering and National Academy of Medicine, and that operates the National Research Council.

Inorganic Crystal Structure Database (ICSD) - Session I

March 23, 2022

11:00 AM - 1:00 PM (ET)

Past

About

This is session one of a two day workshop. We encourage all participants to register for both sessions (days).

The Inorganic Crystal Structure Database (ICSD) is the world’s largest database for fully determined inorganic crystal structures. It is made available to the scientific community and industry by FIZ Karlsruhe. ICSD contains the crystallographic data of all published crystalline inorganic structures, including atom coordinates, dating back to 1913. Organometallic and theoretical structures have been added within the past years. The ICSD data are of excellent quality. Only data that have passed thorough quality checks are included. As the world’s leading provider of scientific information on inorganic crystal structures, we take full responsibility for database production, maintenance and quality control, and we ensure that the ICSD database and our software solutions meet the highest possible quality standards.

In this 2 part tutorial, we will give a detailed overview of the search masks in ICSD and explain tips and tricks on how to best use them. We will also give an overview of the different ways to search in ICSD - from simple searches to more complex searches with the tools for combining searches in ICSD or with the "Expert Search" command line tool.
The tutorial session will include some questions that participants can work on using the ICSD. We will be around to give tips or further help if needed. Of course, we will also be happy to help with problems posed by participants.
Both parts are designed for beginners, but will also include some advanced tips and tricks for more familiar users of the database. There will also be plenty of time to ask questions about your specific challenges.

2-day series: The ICSD®: Concepts And Applications

Learning Objectives

Participants will be provided an overview of the search masks in ICSD including tips and tricks on how to best use them.
Participants will learn different ways to search in ICSD - from simple searches to more complex searches with the tools for combining searches in ICSD or with the "Expert Search" command line tool.

Take Away Skills

Ability to use the ICSD to answer interesting problems as modeled through practice problems.

Contact

Ana Ferreras

(202) 334-1697
aferreras@nas.edu

Disclaimer

It is essential to the National Academies mission of providing evidence-based advice that participants in any of our meetings or events avoid political or partisan statements or commentary and maintain a culture of mutual respect. The statements and presentations during our meetings or events are solely those of the individual participants and do not necessarily represent the views of other participants or the National Academy of Sciences, which is a non-partisan, tax exempt organization that includes under its Charter the National Academy of Engineering and National Academy of Medicine, and that operates the National Research Council.

Webinar

Keynote: The Exemplary Crystallography and Structural Databases

March 21, 2022

11:00 AM - 12:15 PM (ET)

Past

About

Crystallographers and structural scientists have long accepted the maxim “Take nobody’s word for it” because “the science is in the data”. Indeed, from the outset in the first crystal structure report (Bragg 1913), the diffraction data were included. Moreover, they have been among the first scientific communities to exploit technology developments for expanding their data archiving scope. The International Science Council accords great importance to data and has a dedicated committee on data, known simply as CODATA, with many decades of experience of good policy and practice. Likewise, the National Academies of Sciences, Engineering, and Medicine reports include a cogent, recent, description of the reproducibility and replicability of science within which scientific data are a solid foundation. This excellent educational course will describe the diverse and thriving ecosystem of crystallographic and structural databases. This ecosystem is underpinned by data exchange standards, the crystallographic information framework “cif ”, and the desire to ensure the highest achievable quality, making a strong world-wide data infrastructure. There is then an exemplary provision for molecular structure scientists of collections of their data in these databases, be they for biology, chemistry or materials science, which is widely admired. Indeed, the use of these vast collections of data is extremely broad, and yield strong basic science and high societal impacts, which the course contributors will each describe.
Speaker: John R Helliwell, Emeritus Professor of Chemistry, University of Manchester, UK and DSc in Physics, University of York, UK; International Union of Crystallography Chairman of the Committee on Data and its Representative to CODATA.
Bragg, W.L. (1913) The structure of some crystals as indicated by their diffraction of X-rays Proc. R. Soc. London, Ser. A89, 248–277.
National Academies of Sciences, Engineering, and Medicine 2019. Reproducibility and Replicability in Science. Washington, DC: The National Academies Press. https://doi.org/10.17226/25303.

Contact

Ana Ferreras

(202) 334-1697
aferreras@nas.edu

Disclaimer

It is essential to the National Academies mission of providing evidence-based advice that participants in any of our meetings or events avoid political or partisan statements or commentary and maintain a culture of mutual respect. The statements and presentations during our meetings or events are solely those of the individual participants and do not necessarily represent the views of other participants or the National Academy of Sciences, which is a non-partisan, tax exempt organization that includes under its Charter the National Academy of Engineering and National Academy of Medicine, and that operates the National Research Council.

Log In

Sign in to access your saved publications, downloads, and email preferences.

Former MyNAP users: You'll need to reset your password on your first login to MyAcademies. Click "Forgot password" below to receive a reset link via email. Having trouble? Visit our FAQ page to contact support.

Members of the National Academy of Sciences, National Academy of Engineering, or National Academy of Medicine should log in through their respective Academy portals.

Email (required)
Password (required)

Don't have an account?

Register

Email (required)
New password (required)
Retype password (required) Password must be at least 8 characters
I accept the terms of use
terms of use

Thank You

Thank you for creating a MyAcademies account!

Enjoy free access to thousands of National Academies' publications, a 10% discount off every purchase, and build your personal library.

Forgot Password

Enter the email address for your MyAcademies (formerly MyNAP) account to receive password reset instructions.

Reset Requested

We sent password reset instructions to your email . Follow the link in that email to create a new password. Didn't receive it? Check your spam folder or contact us for assistance.

Reset Password

New password (required)
Retype password (required) Password must be at least 8 characters

Reset Password

Your password has been reset.

Log In

Verify email

Verify Your Email Address

We sent a verification link to your email. Please check your inbox (and spam folder) and follow the link to verify your email address. If you did not receive the email, you can request a new verification link below

Subscribe

First Name
Last Name
Email (required)
I agree to receive emails from the National Academies (required)

We respect your privacy and will never share your information.

My Academies

Exploring Structural Database Use in Crystallography: A USNC/Cr Workshop Series

Dropdown items

Crystallography Open Database (COD) and Theoretical Crystallography Open Database (TCOD) - Session III

Cambridge Structural Database (CSD) - Session II

Cambridge Structural Database (CSD) - Session I

Crystallography Open Database (COD) and Theoretical Crystallography Open Database (TCOD) - Session II

Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC)

Crystallography Open Database (COD) and Theoretical Crystallography Open Database (TCOD) - Session I

SBGrid Consortium

Electron Microscopy Data Bank (EMDB)

Protein Data Bank (PDB) - Session II

International Centre for Diffraction Data (ICDD) - Session II

Protein Data Bank (PDB) - Session I

International Centre for Diffraction Data (ICDD) - Session I

Inorganic Crystal Structure Database (ICSD) - Session II

Inorganic Crystal Structure Database (ICSD) - Session I

Keynote: The Exemplary Crystallography and Structural Databases