Journal of Synchrotron Radiation

research papers

A Challenge of Constructing an International XAFS Database
Kiyotaka Asakuraa*, Hitoshi Abebc and Masao KimurabcaInstitute for Catalysis, Hokkaido University, Kita 21-10 Kita, Sapporo, Hokkaido, 001-0021, Japanb

Photon Factory, Institute of Materials' Structure Science, High Energy Accelerator Research

Organization, Oho 1-1, Tsukuba, Ibaraki, 305-0801, Japanc

Department of Materials' Structure Science, School of High Energy Accelerator Science,

SOKENDAI(The Graduate University for Advanced Studies), Oho 1-1, Tsukuba, Ibaraki, 305-0801,
Japan
Correspondence email: askr@cat.hokudai.ac.jp

Abstract

This paper describes the present state of XAFS databases, particularly in Japan, andproposes future directions. International
collaboration is important for enlarging the

FeCl – doped PA

database for further development of XAFS
spectroscopy.

[NEt ][FeCl ]Keywords: XAFS database; automatic data
deposition; data repository system

database

X-ray absorption fine structure (XAFS)[Co(NH ) ][FeCl ]t / arb. units

1. Why we need an international XAFS

[NEt ] [FeCl ]2040

spectroscopy is a powerful technique for0

determining local structure in metals with no

Photon Energy / eV

60

long-range order (Iwasawa et al., 2016).

Figure 2 Fe K-edge XANES spectra of selected Fe

Because a continuum X-ray source is required,

chlorides. The pre-edge peak is set at 0 eV. The Fe

XAFS spectroscopy became a practicalchloride dopant was characterized by XAFS

characterization technique only after

spectroscopy. By comparing with reference

synchrotron radiation sources were developed.

compounds, the Fe species in the PA could be
identified as [FeCl4]-.

and t are absorption

coefficient and thickness of the sample. (reproduced
from (Asakura et al., 1985) with permission
Chemical Society of Japan copyright (1985)).
IMPORTANT: this document contains embedded data - to preserve data integrity, please ensure where possible that the IUCr
Word tools (available from http://journals.iucr.org/services/docxtemplate/) are installed when editing this document.

1

Journal of Synchrotron Radiation

research papers

Since the first measurements were
Synchrotron Radiation Lightsource(Kincaid & Eisenberger, 1975), large
quantities of XAFS data have beencollected. These data can be divided
into two groups: (1) referencecompounds with known structures andproperties and (2)unknown target
materials under investigation. The data
for the former group are important formaterials scientists who wish to
analyse the XAFS spectra of unknown
compounds by comparing them withthose of reference compounds. Figure 1
shows the XAFS spectra of different Fe

Edge peak intensity / arb. units

made by Eisenberger at the Stanford
5
1.0
3
0.5

2
E
B

H

4
F

I
G

D

C
1 A
0
50
100
150
200
250
Exchange reaction enthalpy / kJ m ol-1

Figure 1 Relationship between edge peakintensity for Ag (I) compounds and covalence(Miyamoto et al., 2010; Miyamoto et al.,2012). Reproduced with permission from
(Miyamoto et al. 2010). Copyright (2010)
American Chemical Society.

chloride compounds. Some compounds produce a remarkable pre-edge peak that can be assigned to a
1s-to-3d transition, which is dipole forbidden , though it becomes stronger when centrosymmetry is
broken in a tetrahedral structure (Asakura et al., 1985) (Shulman et al., 1976). Thus, the Fe chloride
species in FeCl3-doped polyacetylene (PA) can be identified by comparing to XAFS spectra ofreference compounds. A collection of some XAFS spectra may be especially important when XAFS
spectroscopy is performed by non-specialists. Collections of typical XAFS spectra are published in apaper form such as books. The Catalysis Society of Japan has published the Catalyst Handbook,which includes XAFS spectra of reference compounds containing catalytically important elements(Japan, 2008).
An open-access, Internet-based database of XAFS spectra in a digital form is more convenient for
all researchers to update and search data. Such a large, comprehensive database would be useful not
only for XAFS non-specialists but also for specialists who want to elucidate general concepts fromXAFS spectra. Figure 2 shows the relationship between the intensity of edge-peak of Ag+ L3 X-ray
absorption near edge structure (XANES) and the covalence of Ag compounds (Miyamoto et al., 2010;
Miyamoto et al., 2012), which demonstrates a positive correlation. Such examples can be found inother studies, such as Lytle’s white line analysis and Wong’s V oxide pre-edge and edge shift analysis(Lytle et al., 1979; Wong et al., 1984). Eventually, deep learning methods could derive such relations
easily and automatically if a large database of XAFS spectra was available and related to othermaterial databases (Takigawa et al., 2016).
2. Overview of currently available XAFS databases

2

Journal of Synchrotron Radiation

research papers

Several databases of XAFS spectra have been developed, as shown in Table 1. These databases are
free, and they generally permit open access. F.W. Lytle database has a long history, which is thelargest and perhaps most well-known XAFS database. SPring-8 BL14 database, which requires a user
ID and password to view and search data, has ample data (more than 800) for reference compounds.
Recently, “Photon Beam Platform”, a national project in Japan to promote the collaboration among
synchrotron radiation and laser facilities is carrying out round robin tests for XAFS data in a data
format of XML(eXtensible Markup Language). International proposal of round robin tests of
XAFS data has also been proposed (Chantller et al., 2018)
This paper focuses on the XAFS database developed as a collaboration between the Hokkaido
University Institute for Catalysis (ICAT) and the Japanese XAFS Society (JXS). We would like topropose an international collaboration to make a new big and open database for XAFS.
Table 1 Available XAFS databases (as of Dec. 31, 2017)
Database
F.W. Lytle
database

URL
http://ixs.iit.edu/database/Features
Text format with periodic table interface
All data obtained by F.W. Lytle
19,307 records covering 74 elements

CARS

http://cars.uchicago.edu/
xaslib/search

Text (XDI) format with periodic table interface andgraphical output of spectra (Newville et al., 2015)
171 records covering 13 elements
Measured at the Advanced Photon Source, SSRL, andNational Synchrotron Light Source
Includes suites (tagging-related spectra) and user ratings

SPring-8 BL14

https://sp8dr.spring8.or.jp/
portal/dspace

Only available to SPring-8 users
725 records
Compressed text file (ZIP) format with metadata that
contains vendor and lot number

EuropeanSynchrotron
Radiation
Facility, ID21
group

http://www.esrf.eu/home/
UsersAndScience

Hokkaido
University ICAT
and JXS

https://www.cat.hokudai.ac.
jp/catdb/index.php?
action=xafs_login_form&
opnid=2/Experiments/XNP/ID21/
php.html

Sulphur database
41 (inorganic) and 26 (organic) records for S compounds
Graphical output, but text format is available
User name is included
209 records and 24 elements
Text format with metadata
Includes user name, beam line, and facility
Open access, but data uploading is restricted to users with
ID and password

3

Journal of Synchrotron Radiation

research papers

3. ICAT XAFS database in Japan
3.1. History

The Hokkaido University ICAT started to build the XAFS database in 2011 as a project of the Joint
Usage/Research Center for catalysis, in collaboration with JXS. The database is accessible to anyone
through the Internet. Volunteers working in the XAFS field can register for an ID and password to
upload their data to the database. For security and traceability, data files contain the name of theperson who uploaded the data. The website is managed by ICAT.
3.2. Fundamental ICAT data policies

The basic policies of the ICAT XAFS database are as follows:
Volunteer base – Anyone who is registered can upload their data.
Open-access database – Anyone can see and use the data. They are asked include a citation in
published work if they used the data.
Simple dataset format – The data have a text-based format, and only the energy and t of theraw spectrum are recorded, in addition to some metadata.
Compatibility – Foil XAFS data that are measured at the same beam time and beam line aredeposited simultaneously to make energy calibration possible. Consequently, we can compare
the data measured at different beam times, beam lines, and facilities.
Target – Dataset includes primarily standard compounds with known structures.
Guarantee of accuracy – A “majority rule” approach is used to improve accuracy. The
database allows deposition of multiple records for the same compounds.
Each data file has a metadata area and a data area, as shown in Fig. 3. Table 2 lists the available
metadata fields in the ICAT database. Although detailed metadata are helpful, too many required
inputs will reduce the motivation of volunteers, so the number of metadata fields are kept as small as
possible.

4

Journal of Synchrotron Radiation

Table 2

research papers

Available metadata fields in ICAT database

Sample name
Structural details (powder, foil, solution)
Absorption atom
Edge
Reference sample (usually foil)
Date of measurement
Monochromator (crystal)
Facility
Beam line

Beam current (mA)
Beam energy of storage ring (GeV)
Higher harmonics rejection method
Focus
Detection method
I｡ and I gases if ionization chamber was used
Measurement temperature
Comments

Figure 3 ICAT data file structure5

Journal of Synchrotron Radiation

research papers

One of the most important policies is compatibility. Although absolute angle of eachmonochromator can be determined by Pettier’s method or other{Pettifer, 1985 #2007}, it is moreconvenient to calibrate each data using foil measured at the same time. The data are uploaded withthe foil data measured at the same time. It benefit us to obtain the signal-to-noise ratio (S/N) and theenergy resolution of the XAFS measurement systems by comparison with the foil XAFS data in
addition to adjust the energy scale from different files by comparison with the foil XAFS spectra.
Another important policy is the guarantee of accuracy, that is, the quality of each XAFS spectrum.
One way to guarantee accuracy is to permit only highly qualified researchers to measure spectra undera strict, specific protocol and upload the data in a rigorously controlled way. However, this would
require more qualified researchers, time, and money than are not generally available. Also, theamount of data stored per day would be limited and it would be hard to construct a large database.
ICAT uses another strategy for data quality, that is, majority rule. The volunteers, who are expected
to have average skill for measuring XAFS spectra and preparing datasets, measure the spectra andupload the data with the metadata. When many volunteers randomly and independently upload spectra,
eventually different versions of the same reference spectra are collected. These data points are
statistically distributed so that the average spectra and their error bars can be determined. Data that lie
within the error bars are reliable, but a spectrum lying outside this range is either wrong or represents
a different phase . Thus, multiple spectra of the same compound improve the quality of the database.
Once the several spectra of the same compound available, users check the accuracy by comparing thespectra by themselves.
4. Problems with existing ICAT database

Despite its usefulness, the ICAT database has several drawbacks. The first problem is the small
number of data files in the database. This makes it difficult to apply majority rule and derive effective
relationships between spectral features and material properties. A way is needed to get more data
effectively. The second problem is that the database is not linked to other material databases, such as
X-ray diffraction, optical spectra, and other physical and chemical properties. The third problem isthe format. ICAT database uses simple the text-base format. Several data formats have been proposed,such as CIF XAFS, XDI (eXtensible Data Interchange), JASON(JavaScript Object Notation), NeXus,
and HDF5 (Ascone et al., 2012; Ravel & Newville, 2016; Konnecke et al., 2015 ). The NeXus andHDF5 formats can store and manage imaging data written in a binary format. Adoption of NeXus or
HDF5 may be a good choice for a flexible database, but it must first be designed well after longdeliberation. Nevertheless, the text format with only energy and t data is simple, easy to implement,
and transferrable to other formats. Although continued discussion of the XAFS database format isneeded, it might be expedient to start database construction in a text format and convert the data to aunified format later.
6

Journal of Synchrotron Radiation

research papers

5. Future database development – Bigger is betterIn the future, computers will be able to automatically evaluate the correctness of spectra based on
majority rule. Even if information about a sample is inadequate, the computer could classify the
samples into several subsets. For example, if the sample name is entered only as TiO2, the spectra
would need to be associated with one of the three different crystalline forms of TiO2 – Rutile, Anatase,and Brookite. Thus, the computer would need to assign the spectra to one of these crystal forms using
other spectra data. Some spectra may be located between two of the groups, indicating a mixture, so it
is better to have more data of the same compounds available for comparison. A large database will
reduce the probability of misinterpretation and improve our understanding of the spectra. The future
direction of the XAFS database is to be bigger and more open. The majority rule, in combination withadvanced computing, such as artificial intelligence(AI), can work to reinforce data quality andreliability and to elucidate meaningful new concepts through deep learning. The problem is how toconstruct a larger database as mentioned above. Since we collect data manually at the moment, theICAT database only contains a limited number of data files. If the data were automatically stored in
an appropriate way, all measured data could be included in the database. Manual input would be
limited to metadata and clarification and categorization of data into spectra for reference or unknown
compounds.
Since most XAFS spectra are measured at synchrotron radiation facilities, we propose thefollowing system:
Store all data measured at these facilities automatically in the facility’s computer inappropriate formats and with metadata. Thus, each facility can constructthe larger database.
Then combine the databases from each facility by connection to the internet. Before thatcan be done, however, we need to decide on rules for data disclosure. The fundamental
principle should be that all scientific data must be open to the public eventually, but thedata owner rights and originality should be reserved.
Using these basic ideas, the data can be made accessible to the public but only after the agreement of
the data owners. This will allow data owners choose to keep their data confidential, but it is hopedthat they would release the data after the associated studies are published in the literature.
Data disclosure would be beneficial to our society in two ways: (1) the quantity of data in the
XAFS database would increase, improving its quality and accessibility for everyone and (2) the
quality and transparency of published research would be improved by disclosing the raw data. The
cooperation of publishers would be important, and it is hoped that they would require disclosure of the
raw XAFS data when a paper is accepted. Facilities could provide further support by making data
7

Journal of Synchrotron Radiation

research papers

disclosure contracts with all users before they start experiments. The raw data should also be madeavailable when a patent is established. In addition to these rules, all data should be disclosed after acertain period (10 years for example). Facilities should retain responsibility for data security andprotection; otherwise, users would not allow facilities to store their data.
One more important suggestion is to define a unique digital data number, similar to the digital
object identifier (DOI) for a published paper. A data identifier would allow the data to be cited when
it is used in a publication. This would increase the incentive for owners to upload and to open theirdata. Like the citation index for a paper, a user could benefit from the number of citations of their data.
This would provide further motivation to perform precise measurements and develop higher-quality
data. A suggested format for the data identifier is as follows:
XAFS_ATOM_EDGE_Measure_Time_ContactPerson (Name & ResearcherID or
ORCID)_Facility_BeamLine.
Note that the identifier must be automatically determined and unique.
The linkage of facility databases will be another important task, since XAFS data are notstandalone. To derive structure-property relationships, XAFS data need to be considered in thecontext of the physical and chemical properties of the measured material. To do this, a clear sample
name must be determined uniquely and universally. If the sample is a standard reference compound,
this should be clearly conveyed by some unique sample identifier. The Chemical Abstracts Service(CAS) number is the best choice the sample identifier because it will be comprehensive and make iteasier to associate the sample with physical and chemical properties. Moreover, the majority rule will
work more effectively because different files for the same material can be linked easily, possibly
automatically. The facilities could encourage input of the CAS number into the metadata by providing
a CAS number dictionary to users. The data owner should provide their own data name according tosome rule, such as:
CAS_Number_ChemicalComposition_Phase_DataOwner (ResearcherID or ORCID)_Comment (Origin) (13463-67-7_TiO2_Rutile_G-6052-2010_PurchaseFromWakoLotNo0001).
6. What to Do Next

We believe that an open XAFS database is necessary but also very useful. Some issues should be
set aside for now, and each facility should start to construct a database or repository of its own data,with the goal of eventual linkage to a larger database. We propose the following actions:
1. Ask all facilities to start collecting XAFS data.
2. Decide on simple naming rules for linkage to other databases.
3. Decide on naming rules for data files, along the lines of the DOI.
8

Journal of Synchrotron Radiation

research papers

4. Start the discussion for determining data release rules.
We hope we can discuss my proposal at the next Q2XAFS and at other meetings.

Acknowledgment
This work was supported by MEXT Joint Usage/Research Center Program (2010-2015, 2016-2011)
and the Accelerator Science Support Fund from the High Energy Accelerator Research Organization(KEK) (2010-2017) and CREST JST “Resolution Catalyst”. One of the author (KA) thanks to

the fruitful discussion with Committee of manufacturing process innovation by materials
informatics( Chair : Prof.Toyohiro Chikyo in NIMS)

7. References

Asakura, K., Ikemoto, I., Kuroda, H., Kobayashi, T. & Shirakawa, H. (1985). Bull.Chem.Soc.Jpn. 58,
2113-2120.
Ascone, I., Asakura, K., George, G. N. & Wakatsuki, S. (2012). J.Synchro.Rad 19, 349-350.
Chantller, C., T,, Bunker , B. A., Abe, H., Kimura, M., Newville, M. & Weltere, E. (2018).
J.Synchro.Rad submitted to the same issue
Iwasawa, Y., Asakura, K. & Tada, M. (2016). Editor. XAFS techniques for catalysts, nanomaterials,
and surfaces, Springer.
Japan, C. S. o. (2008). Editor. Catalyst Handbook, 1 ed. Tokyo: Kodan-sha Scientific.
Kincaid, B. M. & Eisenberger, P. (1975). Phys. Rev. Lett. 34, 1361-1364.
Konnecke, M., Akeroyd, F. A., Bernstein, H. J., Brewster, A. S., Campbell, S. I., Clausen, B., Cottrell,S., Hoffmann, J. U., Jemian, P. R., Mannicke, D., Osborn, R., Peterson, P. F., Richter, T.,
Suzuki, J., Watts, B., Wintersberger, E. & Wuttke, J. (2015). J.Appl.Crystallo. 48, 301-305.
Lytle, F. W., Wei, P. S. P., Greegor, R. B., Via, G. H. & Sinfelt, J. H. (1979). J.Chem.Phys. 70, 4849.
Miyamoto , T., Kitajima, Y. & Asakura, K. (2012). e-J. Surf. Sci. Nanotech. 10, 609-612.
Miyamoto, T., Niimi, H., Kitajima, Y., Naito, T. & Asakura, K. (2010). J.Phys.Chem. A 114, 40934098.
Newville, M., Ravel, B., Sole, V. A. & Wellenreuther, G. (2015). XAS-DataInterchange/specification/spec.md, https://github.com/XraySpectroscopy/XAS-DataInterchange/blob/master/specification/spec.md.
Ravel, B. & Newville, M. (2016). J.Phys.Conf.Ser., pp. 12148-12151. IOP Publishing.
Shulman, G. R., Yafet, Y., Eisenberger, P. & Blumberg, W. E. (1976). Proc. Natl. Acad. Sci. USA 73,
1384-1388.
Takigawa, I., Shimizu, K.-i., Tsuda, K. & Takakusagi, S. (2016). RSC Adv. 6, 52587-52595.
Wong, J., Lytle, F. W., Messmer, R. P. & Maylotte, D. H. (1984). Phys. Rev. B 30, 5596.

9

Journal of Synchrotron Radiation

research papers

A Challenge of Constructing an International XAFS Database
Kiyotaka Asakuraa*, Hitoshi Abebc and Masao KimurabcaInstitute for Catalysis, Hokkaido University, Kita 21-10 Kita, Sapporo, Hokkaido, 001-0021, Japanb

Photon Factory, Institute of Materials' Structure Science, High Energy Accelerator Research

Organization, Oho 1-1, Tsukuba, Ibaraki, 305-0801, Japanc

Department of Materials' Structure Science, School of High Energy Accelerator Science,

SOKENDAI(The Graduate University for Advanced Studies), Oho 1-1, Tsukuba, Ibaraki, 305-0801,
Japan
Correspondence email: askr@cat.hokudai.ac.jp

Abstract

This paper describes the present state of XAFS databases, particularly in Japan, andproposes future directions. International
collaboration is important for enlarging the

FeCl – doped PA

database for further development of XAFS
spectroscopy.

[NEt ][FeCl ]Keywords: XAFS database; automatic data
deposition; data repository system

database

X-ray absorption fine structure (XAFS)[Co(NH ) ][FeCl ]t / arb. units

1. Why we need an international XAFS

[NEt ] [FeCl ]2040

spectroscopy is a powerful technique for0

determining local structure in metals with no

Photon Energy / eV

60

long-range order (Iwasawa et al., 2016).

Figure 2 Fe K-edge XANES spectra of selected Fe

Because a continuum X-ray source is required,

chlorides. The pre-edge peak is set at 0 eV. The Fe

XAFS spectroscopy became a practicalchloride dopant was characterized by XAFS

characterization technique only after

spectroscopy. By comparing with reference

synchrotron radiation sources were developed.

compounds, the Fe species in the PA could be
identified as [FeCl4]-.

and t are absorption

coefficient and thickness of the sample. (reproduced
from (Asakura et al., 1985) with permission
Chemical Society of Japan copyright (1985)).
IMPORTANT: this document contains embedded data - to preserve data integrity, please ensure where possible that the IUCr
Word tools (available from http://journals.iucr.org/services/docxtemplate/) are installed when editing this document.

1

Journal of Synchrotron Radiation

research papers

Since the first measurements were
Synchrotron Radiation Lightsource(Kincaid & Eisenberger, 1975), large
quantities of XAFS data have beencollected. These data can be divided
into two groups: (1) referencecompounds with known structures andproperties and (2)unknown target
materials under investigation. The data
for the former group are important formaterials scientists who wish to
analyse the XAFS spectra of unknown
compounds by comparing them withthose of reference compounds. Figure 1
shows the XAFS spectra of different Fe

Edge peak intensity / arb. units

made by Eisenberger at the Stanford
5
1.0
3
0.5

2
E
B

H

4
F

I
G

D

C
1 A
0
50
100
150
200
250
Exchange reaction enthalpy / kJ m ol-1

Figure 1 Relationship between edge peakintensity for Ag (I) compounds and covalence(Miyamoto et al., 2010; Miyamoto et al.,2012). Reproduced with permission from
(Miyamoto et al. 2010). Copyright (2010)
American Chemical Society.

chloride compounds. Some compounds produce a remarkable pre-edge peak that can be assigned to a
1s-to-3d transition, which is dipole forbidden , though it becomes stronger when centrosymmetry is
broken in a tetrahedral structure (Asakura et al., 1985) (Shulman et al., 1976). Thus, the Fe chloride
species in FeCl3-doped polyacetylene (PA) can be identified by comparing to XAFS spectra ofreference compounds. A collection of some XAFS spectra may be especially important when XAFS
spectroscopy is performed by non-specialists. Collections of typical XAFS spectra are published in apaper form such as books. The Catalysis Society of Japan has published the Catalyst Handbook,which includes XAFS spectra of reference compounds containing catalytically important elements(Japan, 2008).
An open-access, Internet-based database of XAFS spectra in a digital form is more convenient for
all researchers to update and search data. Such a large, comprehensive database would be useful not
only for XAFS non-specialists but also for specialists who want to elucidate general concepts fromXAFS spectra. Figure 2 shows the relationship between the intensity of edge-peak of Ag+ L3 X-ray
absorption near edge structure (XANES) and the covalence of Ag compounds (Miyamoto et al., 2010;
Miyamoto et al., 2012), which demonstrates a positive correlation. Such examples can be found inother studies, such as Lytle’s white line analysis and Wong’s V oxide pre-edge and edge shift analysis(Lytle et al., 1979; Wong et al., 1984). Eventually, deep learning methods could derive such relations
easily and automatically if a large database of XAFS spectra was available and related to othermaterial databases (Takigawa et al., 2016).
2. Overview of currently available XAFS databases

2

Journal of Synchrotron Radiation

research papers

Several databases of XAFS spectra have been developed, as shown in Table 1. These databases are
free, and they generally permit open access. F.W. Lytle database has a long history, which is thelargest and perhaps most well-known XAFS database. SPring-8 BL14 database, which requires a user
ID and password to view and search data, has ample data (more than 800) for reference compounds.
Recently, “Photon Beam Platform”, a national project in Japan to promote the collaboration among
synchrotron radiation and laser facilities is carrying out round robin tests for XAFS data in a data
format of XML(eXtensible Markup Language). International proposal of round robin tests of
XAFS data has also been proposed (Chantller et al., 2018)
This paper focuses on the XAFS database developed as a collaboration between the Hokkaido
University Institute for Catalysis (ICAT) and the Japanese XAFS Society (JXS). We would like topropose an international collaboration to make a new big and open database for XAFS.
Table 1 Available XAFS databases (as of Dec. 31, 2017)
Database
F.W. Lytle
database

URL
http://ixs.iit.edu/database/Features
Text format with periodic table interface
All data obtained by F.W. Lytle
19,307 records covering 74 elements

CARS

http://cars.uchicago.edu/
xaslib/search

Text (XDI) format with periodic table interface andgraphical output of spectra (Newville et al., 2015)
171 records covering 13 elements
Measured at the Advanced Photon Source, SSRL, andNational Synchrotron Light Source
Includes suites (tagging-related spectra) and user ratings

SPring-8 BL14

https://sp8dr.spring8.or.jp/
portal/dspace

Only available to SPring-8 users
725 records
Compressed text file (ZIP) format with metadata that
contains vendor and lot number

EuropeanSynchrotron
Radiation
Facility, ID21
group

http://www.esrf.eu/home/
UsersAndScience

Hokkaido
University ICAT
and JXS

https://www.cat.hokudai.ac.
jp/catdb/index.php?
action=xafs_login_form&
opnid=2/Experiments/XNP/ID21/
php.html

Sulphur database
41 (inorganic) and 26 (organic) records for S compounds
Graphical output, but text format is available
User name is included
209 records and 24 elements
Text format with metadata
Includes user name, beam line, and facility
Open access, but data uploading is restricted to users with
ID and password

3

Journal of Synchrotron Radiation

research papers

3. ICAT XAFS database in Japan
3.1. History

The Hokkaido University ICAT started to build the XAFS database in 2011 as a project of the Joint
Usage/Research Center for catalysis, in collaboration with JXS. The database is accessible to anyone
through the Internet. Volunteers working in the XAFS field can register for an ID and password to
upload their data to the database. For security and traceability, data files contain the name of theperson who uploaded the data. The website is managed by ICAT.
3.2. Fundamental ICAT data policies

The basic policies of the ICAT XAFS database are as follows:
Volunteer base – Anyone who is registered can upload their data.
Open-access database – Anyone can see and use the data. They are asked include a citation in
published work if they used the data.
Simple dataset format – The data have a text-based format, and only the energy and t of theraw spectrum are recorded, in addition to some metadata.
Compatibility – Foil XAFS data that are measured at the same beam time and beam line aredeposited simultaneously to make energy calibration possible. Consequently, we can compare
the data measured at different beam times, beam lines, and facilities.
Target – Dataset includes primarily standard compounds with known structures.
Guarantee of accuracy – A “majority rule” approach is used to improve accuracy. The
database allows deposition of multiple records for the same compounds.
Each data file has a metadata area and a data area, as shown in Fig. 3. Table 2 lists the available
metadata fields in the ICAT database. Although detailed metadata are helpful, too many required
inputs will reduce the motivation of volunteers, so the number of metadata fields are kept as small as
possible.

4

Journal of Synchrotron Radiation

Table 2

research papers

Available metadata fields in ICAT database

Sample name
Structural details (powder, foil, solution)
Absorption atom
Edge
Reference sample (usually foil)
Date of measurement
Monochromator (crystal)
Facility
Beam line

Beam current (mA)
Beam energy of storage ring (GeV)
Higher harmonics rejection method
Focus
Detection method
I｡ and I gases if ionization chamber was used
Measurement temperature
Comments

Figure 3 ICAT data file structure5

Journal of Synchrotron Radiation

research papers

One of the most important policies is compatibility. Although absolute angle of eachmonochromator can be determined by Pettier’s method or other{Pettifer, 1985 #2007}, it is moreconvenient to calibrate each data using foil measured at the same time. The data are uploaded withthe foil data measured at the same time. It benefit us to obtain the signal-to-noise ratio (S/N) and theenergy resolution of the XAFS measurement systems by comparison with the foil XAFS data in
addition to adjust the energy scale from different files by comparison with the foil XAFS spectra.
Another important policy is the guarantee of accuracy, that is, the quality of each XAFS spectrum.
One way to guarantee accuracy is to permit only highly qualified researchers to measure spectra undera strict, specific protocol and upload the data in a rigorously controlled way. However, this would
require more qualified researchers, time, and money than are not generally available. Also, theamount of data stored per day would be limited and it would be hard to construct a large database.
ICAT uses another strategy for data quality, that is, majority rule. The volunteers, who are expected
to have average skill for measuring XAFS spectra and preparing datasets, measure the spectra andupload the data with the metadata. When many volunteers randomly and independently upload spectra,
eventually different versions of the same reference spectra are collected. These data points are
statistically distributed so that the average spectra and their error bars can be determined. Data that lie
within the error bars are reliable, but a spectrum lying outside this range is either wrong or represents
a different phase . Thus, multiple spectra of the same compound improve the quality of the database.
Once the several spectra of the same compound available, users check the accuracy by comparing thespectra by themselves.
4. Problems with existing ICAT database

Despite its usefulness, the ICAT database has several drawbacks. The first problem is the small
number of data files in the database. This makes it difficult to apply majority rule and derive effective
relationships between spectral features and material properties. A way is needed to get more data
effectively. The second problem is that the database is not linked to other material databases, such as
X-ray diffraction, optical spectra, and other physical and chemical properties. The third problem isthe format. ICAT database uses simple the text-base format. Several data formats have been proposed,such as CIF XAFS, XDI (eXtensible Data Interchange), JASON(JavaScript Object Notation), NeXus,
and HDF5 (Ascone et al., 2012; Ravel & Newville, 2016; Konnecke et al., 2015 ). The NeXus andHDF5 formats can store and manage imaging data written in a binary format. Adoption of NeXus or
HDF5 may be a good choice for a flexible database, but it must first be designed well after longdeliberation. Nevertheless, the text format with only energy and t data is simple, easy to implement,
and transferrable to other formats. Although continued discussion of the XAFS database format isneeded, it might be expedient to start database construction in a text format and convert the data to aunified format later.
6

Journal of Synchrotron Radiation

research papers

5. Future database development – Bigger is betterIn the future, computers will be able to automatically evaluate the correctness of spectra based on
majority rule. Even if information about a sample is inadequate, the computer could classify the
samples into several subsets. For example, if the sample name is entered only as TiO2, the spectra
would need to be associated with one of the three different crystalline forms of TiO2 – Rutile, Anatase,and Brookite. Thus, the computer would need to assign the spectra to one of these crystal forms using
other spectra data. Some spectra may be located between two of the groups, indicating a mixture, so it
is better to have more data of the same compounds available for comparison. A large database will
reduce the probability of misinterpretation and improve our understanding of the spectra. The future
direction of the XAFS database is to be bigger and more open. The majority rule, in combination withadvanced computing, such as artificial intelligence(AI), can work to reinforce data quality andreliability and to elucidate meaningful new concepts through deep learning. The problem is how toconstruct a larger database as mentioned above. Since we collect data manually at the moment, theICAT database only contains a limited number of data files. If the data were automatically stored in
an appropriate way, all measured data could be included in the database. Manual input would be
limited to metadata and clarification and categorization of data into spectra for reference or unknown
compounds.
Since most XAFS spectra are measured at synchrotron radiation facilities, we propose thefollowing system:
Store all data measured at these facilities automatically in the facility’s computer inappropriate formats and with metadata. Thus, each facility can constructthe larger database.
Then combine the databases from each facility by connection to the internet. Before thatcan be done, however, we need to decide on rules for data disclosure. The fundamental
principle should be that all scientific data must be open to the public eventually, but thedata owner rights and originality should be reserved.
Using these basic ideas, the data can be made accessible to the public but only after the agreement of
the data owners. This will allow data owners choose to keep their data confidential, but it is hopedthat they would release the data after the associated studies are published in the literature.
Data disclosure would be beneficial to our society in two ways: (1) the quantity of data in the
XAFS database would increase, improving its quality and accessibility for everyone and (2) the
quality and transparency of published research would be improved by disclosing the raw data. The
cooperation of publishers would be important, and it is hoped that they would require disclosure of the
raw XAFS data when a paper is accepted. Facilities could provide further support by making data
7

Journal of Synchrotron Radiation

research papers

disclosure contracts with all users before they start experiments. The raw data should also be madeavailable when a patent is established. In addition to these rules, all data should be disclosed after acertain period (10 years for example). Facilities should retain responsibility for data security andprotection; otherwise, users would not allow facilities to store their data.
One more important suggestion is to define a unique digital data number, similar to the digital
object identifier (DOI) for a published paper. A data identifier would allow the data to be cited when
it is used in a publication. This would increase the incentive for owners to upload and to open theirdata. Like the citation index for a paper, a user could benefit from the number of citations of their data.
This would provide further motivation to perform precise measurements and develop higher-quality
data. A suggested format for the data identifier is as follows:
XAFS_ATOM_EDGE_Measure_Time_ContactPerson (Name & ResearcherID or
ORCID)_Facility_BeamLine.
Note that the identifier must be automatically determined and unique.
The linkage of facility databases will be another important task, since XAFS data are notstandalone. To derive structure-property relationships, XAFS data need to be considered in thecontext of the physical and chemical properties of the measured material. To do this, a clear sample
name must be determined uniquely and universally. If the sample is a standard reference compound,
this should be clearly conveyed by some unique sample identifier. The Chemical Abstracts Service(CAS) number is the best choice the sample identifier because it will be comprehensive and make iteasier to associate the sample with physical and chemical properties. Moreover, the majority rule will
work more effectively because different files for the same material can be linked easily, possibly
automatically. The facilities could encourage input of the CAS number into the metadata by providing
a CAS number dictionary to users. The data owner should provide their own data name according tosome rule, such as:
CAS_Number_ChemicalComposition_Phase_DataOwner (ResearcherID or ORCID)_Comment (Origin) (13463-67-7_TiO2_Rutile_G-6052-2010_PurchaseFromWakoLotNo0001).
6. What to Do Next

We believe that an open XAFS database is necessary but also very useful. Some issues should be
set aside for now, and each facility should start to construct a database or repository of its own data,with the goal of eventual linkage to a larger database. We propose the following actions:
1. Ask all facilities to start collecting XAFS data.
2. Decide on simple naming rules for linkage to other databases.
3. Decide on naming rules for data files, along the lines of the DOI.
8

Journal of Synchrotron Radiation

research papers

4. Start the discussion for determining data release rules.
We hope we can discuss my proposal at the next Q2XAFS and at other meetings.

Acknowledgment
This work was supported by MEXT Joint Usage/Research Center Program (2010-2015, 2016-2011)
and the Accelerator Science Support Fund from the High Energy Accelerator Research Organization(KEK) (2010-2017) and CREST JST “Resolution Catalyst”. One of the author (KA) thanks to

the fruitful discussion with Committee of manufacturing process innovation by materials
informatics( Chair : Prof.Toyohiro Chikyo in NIMS)

7. References

Asakura, K., Ikemoto, I., Kuroda, H., Kobayashi, T. & Shirakawa, H. (1985). Bull.Chem.Soc.Jpn. 58,
2113-2120.
Ascone, I., Asakura, K., George, G. N. & Wakatsuki, S. (2012). J.Synchro.Rad 19, 349-350.
Chantller, C., T,, Bunker , B. A., Abe, H., Kimura, M., Newville, M. & Weltere, E. (2018).
J.Synchro.Rad submitted to the same issue
Iwasawa, Y., Asakura, K. & Tada, M. (2016). Editor. XAFS techniques for catalysts, nanomaterials,
and surfaces, Springer.
Japan, C. S. o. (2008). Editor. Catalyst Handbook, 1 ed. Tokyo: Kodan-sha Scientific.
Kincaid, B. M. & Eisenberger, P. (1975). Phys. Rev. Lett. 34, 1361-1364.
Konnecke, M., Akeroyd, F. A., Bernstein, H. J., Brewster, A. S., Campbell, S. I., Clausen, B., Cottrell,S., Hoffmann, J. U., Jemian, P. R., Mannicke, D., Osborn, R., Peterson, P. F., Richter, T.,
Suzuki, J., Watts, B., Wintersberger, E. & Wuttke, J. (2015). J.Appl.Crystallo. 48, 301-305.
Lytle, F. W., Wei, P. S. P., Greegor, R. B., Via, G. H. & Sinfelt, J. H. (1979). J.Chem.Phys. 70, 4849.
Miyamoto , T., Kitajima, Y. & Asakura, K. (2012). e-J. Surf. Sci. Nanotech. 10, 609-612.
Miyamoto, T., Niimi, H., Kitajima, Y., Naito, T. & Asakura, K. (2010). J.Phys.Chem. A 114, 40934098.
Newville, M., Ravel, B., Sole, V. A. & Wellenreuther, G. (2015). XAS-DataInterchange/specification/spec.md, https://github.com/XraySpectroscopy/XAS-DataInterchange/blob/master/specification/spec.md.
Ravel, B. & Newville, M. (2016). J.Phys.Conf.Ser., pp. 12148-12151. IOP Publishing.
Shulman, G. R., Yafet, Y., Eisenberger, P. & Blumberg, W. E. (1976). Proc. Natl. Acad. Sci. USA 73,
1384-1388.
Takigawa, I., Shimizu, K.-i., Tsuda, K. & Takakusagi, S. (2016). RSC Adv. 6, 52587-52595.
Wong, J., Lytle, F. W., Messmer, R. P. & Maylotte, D. H. (1984). Phys. Rev. B 30, 5596.

9

Journal of Synchrotron Radiation

research papers

A Challenge of Constructing an International XAFS Database
Kiyotaka Asakuraa*, Hitoshi Abebc and Masao KimurabcaInstitute for Catalysis, Hokkaido University, Kita 21-10 Kita, Sapporo, Hokkaido, 001-0021, Japanb

Photon Factory, Institute of Materials' Structure Science, High Energy Accelerator Research

Organization, Oho 1-1, Tsukuba, Ibaraki, 305-0801, Japanc

Department of Materials' Structure Science, School of High Energy Accelerator Science,

SOKENDAI(The Graduate University for Advanced Studies), Oho 1-1, Tsukuba, Ibaraki, 305-0801,
Japan
Correspondence email: askr@cat.hokudai.ac.jp

Abstract

This paper describes the present state of XAFS databases, particularly in Japan, andproposes future directions. International
collaboration is important for enlarging the

FeCl – doped PA

database for further development of XAFS
spectroscopy.

[NEt ][FeCl ]Keywords: XAFS database; automatic data
deposition; data repository system

database

X-ray absorption fine structure (XAFS)[Co(NH ) ][FeCl ]t / arb. units

1. Why we need an international XAFS

[NEt ] [FeCl ]2040

spectroscopy is a powerful technique for0

determining local structure in metals with no

Photon Energy / eV

60

long-range order (Iwasawa et al., 2016).

Figure 2 Fe K-edge XANES spectra of selected Fe

Because a continuum X-ray source is required,

chlorides. The pre-edge peak is set at 0 eV. The Fe

XAFS spectroscopy became a practicalchloride dopant was characterized by XAFS

characterization technique only after

spectroscopy. By comparing with reference

synchrotron radiation sources were developed.

compounds, the Fe species in the PA could be
identified as [FeCl4]-.

and t are absorption

coefficient and thickness of the sample. (reproduced
from (Asakura et al., 1985) with permission
Chemical Society of Japan copyright (1985)).
IMPORTANT: this document contains embedded data - to preserve data integrity, please ensure where possible that the IUCr
Word tools (available from http://journals.iucr.org/services/docxtemplate/) are installed when editing this document.

1

Journal of Synchrotron Radiation

research papers

Since the first measurements were
Synchrotron Radiation Lightsource(Kincaid & Eisenberger, 1975), large
quantities of XAFS data have beencollected. These data can be divided
into two groups: (1) referencecompounds with known structures andproperties and (2)unknown target
materials under investigation. The data
for the former group are important formaterials scientists who wish to
analyse the XAFS spectra of unknown
compounds by comparing them withthose of reference compounds. Figure 1
shows the XAFS spectra of different Fe

Edge peak intensity / arb. units

made by Eisenberger at the Stanford
5
1.0
3
0.5

2
E
B

H

4
F

I
G

D

C
1 A
0
50
100
150
200
250
Exchange reaction enthalpy / kJ m ol-1

Figure 1 Relationship between edge peakintensity for Ag (I) compounds and covalence(Miyamoto et al., 2010; Miyamoto et al.,2012). Reproduced with permission from
(Miyamoto et al. 2010). Copyright (2010)
American Chemical Society.

chloride compounds. Some compounds produce a remarkable pre-edge peak that can be assigned to a
1s-to-3d transition, which is dipole forbidden , though it becomes stronger when centrosymmetry is
broken in a tetrahedral structure (Asakura et al., 1985) (Shulman et al., 1976). Thus, the Fe chloride
species in FeCl3-doped polyacetylene (PA) can be identified by comparing to XAFS spectra ofreference compounds. A collection of some XAFS spectra may be especially important when XAFS
spectroscopy is performed by non-specialists. Collections of typical XAFS spectra are published in apaper form such as books. The Catalysis Society of Japan has published the Catalyst Handbook,which includes XAFS spectra of reference compounds containing catalytically important elements(Japan, 2008).
An open-access, Internet-based database of XAFS spectra in a digital form is more convenient for
all researchers to update and search data. Such a large, comprehensive database would be useful not
only for XAFS non-specialists but also for specialists who want to elucidate general concepts fromXAFS spectra. Figure 2 shows the relationship between the intensity of edge-peak of Ag+ L3 X-ray
absorption near edge structure (XANES) and the covalence of Ag compounds (Miyamoto et al., 2010;
Miyamoto et al., 2012), which demonstrates a positive correlation. Such examples can be found inother studies, such as Lytle’s white line analysis and Wong’s V oxide pre-edge and edge shift analysis(Lytle et al., 1979; Wong et al., 1984). Eventually, deep learning methods could derive such relations
easily and automatically if a large database of XAFS spectra was available and related to othermaterial databases (Takigawa et al., 2016).
2. Overview of currently available XAFS databases

2

Journal of Synchrotron Radiation

research papers

Several databases of XAFS spectra have been developed, as shown in Table 1. These databases are
free, and they generally permit open access. F.W. Lytle database has a long history, which is thelargest and perhaps most well-known XAFS database. SPring-8 BL14 database, which requires a user
ID and password to view and search data, has ample data (more than 800) for reference compounds.
Recently, “Photon Beam Platform”, a national project in Japan to promote the collaboration among
synchrotron radiation and laser facilities is carrying out round robin tests for XAFS data in a data
format of XML(eXtensible Markup Language). International proposal of round robin tests of
XAFS data has also been proposed (Chantller et al., 2018)
This paper focuses on the XAFS database developed as a collaboration between the Hokkaido
University Institute for Catalysis (ICAT) and the Japanese XAFS Society (JXS). We would like topropose an international collaboration to make a new big and open database for XAFS.
Table 1 Available XAFS databases (as of Dec. 31, 2017)
Database
F.W. Lytle
database

URL
http://ixs.iit.edu/database/Features
Text format with periodic table interface
All data obtained by F.W. Lytle
19,307 records covering 74 elements

CARS

http://cars.uchicago.edu/
xaslib/search

Text (XDI) format with periodic table interface andgraphical output of spectra (Newville et al., 2015)
171 records covering 13 elements
Measured at the Advanced Photon Source, SSRL, andNational Synchrotron Light Source
Includes suites (tagging-related spectra) and user ratings

SPring-8 BL14

https://sp8dr.spring8.or.jp/
portal/dspace

Only available to SPring-8 users
725 records
Compressed text file (ZIP) format with metadata that
contains vendor and lot number

EuropeanSynchrotron
Radiation
Facility, ID21
group

http://www.esrf.eu/home/
UsersAndScience

Hokkaido
University ICAT
and JXS

https://www.cat.hokudai.ac.
jp/catdb/index.php?
action=xafs_login_form&
opnid=2/Experiments/XNP/ID21/
php.html

Sulphur database
41 (inorganic) and 26 (organic) records for S compounds
Graphical output, but text format is available
User name is included
209 records and 24 elements
Text format with metadata
Includes user name, beam line, and facility
Open access, but data uploading is restricted to users with
ID and password

3

Journal of Synchrotron Radiation

research papers

3. ICAT XAFS database in Japan
3.1. History

The Hokkaido University ICAT started to build the XAFS database in 2011 as a project of the Joint
Usage/Research Center for catalysis, in collaboration with JXS. The database is accessible to anyone
through the Internet. Volunteers working in the XAFS field can register for an ID and password to
upload their data to the database. For security and traceability, data files contain the name of theperson who uploaded the data. The website is managed by ICAT.
3.2. Fundamental ICAT data policies

The basic policies of the ICAT XAFS database are as follows:
Volunteer base – Anyone who is registered can upload their data.
Open-access database – Anyone can see and use the data. They are asked include a citation in
published work if they used the data.
Simple dataset format – The data have a text-based format, and only the energy and t of theraw spectrum are recorded, in addition to some metadata.
Compatibility – Foil XAFS data that are measured at the same beam time and beam line aredeposited simultaneously to make energy calibration possible. Consequently, we can compare
the data measured at different beam times, beam lines, and facilities.
Target – Dataset includes primarily standard compounds with known structures.
Guarantee of accuracy – A “majority rule” approach is used to improve accuracy. The
database allows deposition of multiple records for the same compounds.
Each data file has a metadata area and a data area, as shown in Fig. 3. Table 2 lists the available
metadata fields in the ICAT database. Although detailed metadata are helpful, too many required
inputs will reduce the motivation of volunteers, so the number of metadata fields are kept as small as
possible.

4

Journal of Synchrotron Radiation

Table 2

research papers

Available metadata fields in ICAT database

Sample name
Structural details (powder, foil, solution)
Absorption atom
Edge
Reference sample (usually foil)
Date of measurement
Monochromator (crystal)
Facility
Beam line

Beam current (mA)
Beam energy of storage ring (GeV)
Higher harmonics rejection method
Focus
Detection method
I｡ and I gases if ionization chamber was used
Measurement temperature
Comments

Figure 3 ICAT data file structure5

Journal of Synchrotron Radiation

research papers

One of the most important policies is compatibility. Although absolute angle of eachmonochromator can be determined by Pettier’s method or other{Pettifer, 1985 #2007}, it is moreconvenient to calibrate each data using foil measured at the same time. The data are uploaded withthe foil data measured at the same time. It benefit us to obtain the signal-to-noise ratio (S/N) and theenergy resolution of the XAFS measurement systems by comparison with the foil XAFS data in
addition to adjust the energy scale from different files by comparison with the foil XAFS spectra.
Another important policy is the guarantee of accuracy, that is, the quality of each XAFS spectrum.
One way to guarantee accuracy is to permit only highly qualified researchers to measure spectra undera strict, specific protocol and upload the data in a rigorously controlled way. However, this would
require more qualified researchers, time, and money than are not generally available. Also, theamount of data stored per day would be limited and it would be hard to construct a large database.
ICAT uses another strategy for data quality, that is, majority rule. The volunteers, who are expected
to have average skill for measuring XAFS spectra and preparing datasets, measure the spectra andupload the data with the metadata. When many volunteers randomly and independently upload spectra,
eventually different versions of the same reference spectra are collected. These data points are
statistically distributed so that the average spectra and their error bars can be determined. Data that lie
within the error bars are reliable, but a spectrum lying outside this range is either wrong or represents
a different phase . Thus, multiple spectra of the same compound improve the quality of the database.
Once the several spectra of the same compound available, users check the accuracy by comparing thespectra by themselves.
4. Problems with existing ICAT database

Despite its usefulness, the ICAT database has several drawbacks. The first problem is the small
number of data files in the database. This makes it difficult to apply majority rule and derive effective
relationships between spectral features and material properties. A way is needed to get more data
effectively. The second problem is that the database is not linked to other material databases, such as
X-ray diffraction, optical spectra, and other physical and chemical properties. The third problem isthe format. ICAT database uses simple the text-base format. Several data formats have been proposed,such as CIF XAFS, XDI (eXtensible Data Interchange), JASON(JavaScript Object Notation), NeXus,
and HDF5 (Ascone et al., 2012; Ravel & Newville, 2016; Konnecke et al., 2015 ). The NeXus andHDF5 formats can store and manage imaging data written in a binary format. Adoption of NeXus or
HDF5 may be a good choice for a flexible database, but it must first be designed well after longdeliberation. Nevertheless, the text format with only energy and t data is simple, easy to implement,
and transferrable to other formats. Although continued discussion of the XAFS database format isneeded, it might be expedient to start database construction in a text format and convert the data to aunified format later.
6

Journal of Synchrotron Radiation

research papers

5. Future database development – Bigger is betterIn the future, computers will be able to automatically evaluate the correctness of spectra based on
majority rule. Even if information about a sample is inadequate, the computer could classify the
samples into several subsets. For example, if the sample name is entered only as TiO2, the spectra
would need to be associated with one of the three different crystalline forms of TiO2 – Rutile, Anatase,and Brookite. Thus, the computer would need to assign the spectra to one of these crystal forms using
other spectra data. Some spectra may be located between two of the groups, indicating a mixture, so it
is better to have more data of the same compounds available for comparison. A large database will
reduce the probability of misinterpretation and improve our understanding of the spectra. The future
direction of the XAFS database is to be bigger and more open. The majority rule, in combination withadvanced computing, such as artificial intelligence(AI), can work to reinforce data quality andreliability and to elucidate meaningful new concepts through deep learning. The problem is how toconstruct a larger database as mentioned above. Since we collect data manually at the moment, theICAT database only contains a limited number of data files. If the data were automatically stored in
an appropriate way, all measured data could be included in the database. Manual input would be
limited to metadata and clarification and categorization of data into spectra for reference or unknown
compounds.
Since most XAFS spectra are measured at synchrotron radiation facilities, we propose thefollowing system:
Store all data measured at these facilities automatically in the facility’s computer inappropriate formats and with metadata. Thus, each facility can constructthe larger database.
Then combine the databases from each facility by connection to the internet. Before thatcan be done, however, we need to decide on rules for data disclosure. The fundamental
principle should be that all scientific data must be open to the public eventually, but thedata owner rights and originality should be reserved.
Using these basic ideas, the data can be made accessible to the public but only after the agreement of
the data owners. This will allow data owners choose to keep their data confidential, but it is hopedthat they would release the data after the associated studies are published in the literature.
Data disclosure would be beneficial to our society in two ways: (1) the quantity of data in the
XAFS database would increase, improving its quality and accessibility for everyone and (2) the
quality and transparency of published research would be improved by disclosing the raw data. The
cooperation of publishers would be important, and it is hoped that they would require disclosure of the
raw XAFS data when a paper is accepted. Facilities could provide further support by making data
7

Journal of Synchrotron Radiation

research papers

disclosure contracts with all users before they start experiments. The raw data should also be madeavailable when a patent is established. In addition to these rules, all data should be disclosed after acertain period (10 years for example). Facilities should retain responsibility for data security andprotection; otherwise, users would not allow facilities to store their data.
One more important suggestion is to define a unique digital data number, similar to the digital
object identifier (DOI) for a published paper. A data identifier would allow the data to be cited when
it is used in a publication. This would increase the incentive for owners to upload and to open theirdata. Like the citation index for a paper, a user could benefit from the number of citations of their data.
This would provide further motivation to perform precise measurements and develop higher-quality
data. A suggested format for the data identifier is as follows:
XAFS_ATOM_EDGE_Measure_Time_ContactPerson (Name & ResearcherID or
ORCID)_Facility_BeamLine.
Note that the identifier must be automatically determined and unique.
The linkage of facility databases will be another important task, since XAFS data are notstandalone. To derive structure-property relationships, XAFS data need to be considered in thecontext of the physical and chemical properties of the measured material. To do this, a clear sample
name must be determined uniquely and universally. If the sample is a standard reference compound,
this should be clearly conveyed by some unique sample identifier. The Chemical Abstracts Service(CAS) number is the best choice the sample identifier because it will be comprehensive and make iteasier to associate the sample with physical and chemical properties. Moreover, the majority rule will
work more effectively because different files for the same material can be linked easily, possibly
automatically. The facilities could encourage input of the CAS number into the metadata by providing
a CAS number dictionary to users. The data owner should provide their own data name according tosome rule, such as:
CAS_Number_ChemicalComposition_Phase_DataOwner (ResearcherID or ORCID)_Comment (Origin) (13463-67-7_TiO2_Rutile_G-6052-2010_PurchaseFromWakoLotNo0001).
6. What to Do Next

We believe that an open XAFS database is necessary but also very useful. Some issues should be
set aside for now, and each facility should start to construct a database or repository of its own data,with the goal of eventual linkage to a larger database. We propose the following actions:
1. Ask all facilities to start collecting XAFS data.
2. Decide on simple naming rules for linkage to other databases.
3. Decide on naming rules for data files, along the lines of the DOI.
8

Journal of Synchrotron Radiation

research papers

4. Start the discussion for determining data release rules.
We hope we can discuss my proposal at the next Q2XAFS and at other meetings.

Acknowledgment
This work was supported by MEXT Joint Usage/Research Center Program (2010-2015, 2016-2011)
and the Accelerator Science Support Fund from the High Energy Accelerator Research Organization(KEK) (2010-2017) and CREST JST “Resolution Catalyst”. One of the author (KA) thanks to

the fruitful discussion with Committee of manufacturing process innovation by materials
informatics( Chair : Prof.Toyohiro Chikyo in NIMS)

7. References

Asakura, K., Ikemoto, I., Kuroda, H., Kobayashi, T. & Shirakawa, H. (1985). Bull.Chem.Soc.Jpn. 58,
2113-2120.
Ascone, I., Asakura, K., George, G. N. & Wakatsuki, S. (2012). J.Synchro.Rad 19, 349-350.
Chantller, C., T,, Bunker , B. A., Abe, H., Kimura, M., Newville, M. & Weltere, E. (2018).
J.Synchro.Rad submitted to the same issue
Iwasawa, Y., Asakura, K. & Tada, M. (2016). Editor. XAFS techniques for catalysts, nanomaterials,
and surfaces, Springer.
Japan, C. S. o. (2008). Editor. Catalyst Handbook, 1 ed. Tokyo: Kodan-sha Scientific.
Kincaid, B. M. & Eisenberger, P. (1975). Phys. Rev. Lett. 34, 1361-1364.
Konnecke, M., Akeroyd, F. A., Bernstein, H. J., Brewster, A. S., Campbell, S. I., Clausen, B., Cottrell,S., Hoffmann, J. U., Jemian, P. R., Mannicke, D., Osborn, R., Peterson, P. F., Richter, T.,
Suzuki, J., Watts, B., Wintersberger, E. & Wuttke, J. (2015). J.Appl.Crystallo. 48, 301-305.
Lytle, F. W., Wei, P. S. P., Greegor, R. B., Via, G. H. & Sinfelt, J. H. (1979). J.Chem.Phys. 70, 4849.
Miyamoto , T., Kitajima, Y. & Asakura, K. (2012). e-J. Surf. Sci. Nanotech. 10, 609-612.
Miyamoto, T., Niimi, H., Kitajima, Y., Naito, T. & Asakura, K. (2010). J.Phys.Chem. A 114, 40934098.
Newville, M., Ravel, B., Sole, V. A. & Wellenreuther, G. (2015). XAS-DataInterchange/specification/spec.md, https://github.com/XraySpectroscopy/XAS-DataInterchange/blob/master/specification/spec.md.
Ravel, B. & Newville, M. (2016). J.Phys.Conf.Ser., pp. 12148-12151. IOP Publishing.
Shulman, G. R., Yafet, Y., Eisenberger, P. & Blumberg, W. E. (1976). Proc. Natl. Acad. Sci. USA 73,
1384-1388.
Takigawa, I., Shimizu, K.-i., Tsuda, K. & Takakusagi, S. (2016). RSC Adv. 6, 52587-52595.
Wong, J., Lytle, F. W., Messmer, R. P. & Maylotte, D. H. (1984). Phys. Rev. B 30, 5596.

9

Journal of Synchrotron Radiation

research papers

A Challenge of Constructing an International XAFS Database
Kiyotaka Asakuraa*, Hitoshi Abebc and Masao KimurabcaInstitute for Catalysis, Hokkaido University, Kita 21-10 Kita, Sapporo, Hokkaido, 001-0021, Japanb

Photon Factory, Institute of Materials' Structure Science, High Energy Accelerator Research

Organization, Oho 1-1, Tsukuba, Ibaraki, 305-0801, Japanc

Department of Materials' Structure Science, School of High Energy Accelerator Science,

SOKENDAI(The Graduate University for Advanced Studies), Oho 1-1, Tsukuba, Ibaraki, 305-0801,
Japan
Correspondence email: askr@cat.hokudai.ac.jp

Abstract

This paper describes the present state of XAFS databases, particularly in Japan, andproposes future directions. International
collaboration is important for enlarging the

FeCl – doped PA

database for further development of XAFS
spectroscopy.

[NEt ][FeCl ]Keywords: XAFS database; automatic data
deposition; data repository system

database

X-ray absorption fine structure (XAFS)[Co(NH ) ][FeCl ]t / arb. units

1. Why we need an international XAFS

[NEt ] [FeCl ]2040

spectroscopy is a powerful technique for0

determining local structure in metals with no

Photon Energy / eV

60

long-range order (Iwasawa et al., 2016).

Figure 2 Fe K-edge XANES spectra of selected Fe

Because a continuum X-ray source is required,

chlorides. The pre-edge peak is set at 0 eV. The Fe

XAFS spectroscopy became a practicalchloride dopant was characterized by XAFS

characterization technique only after

spectroscopy. By comparing with reference

synchrotron radiation sources were developed.

compounds, the Fe species in the PA could be
identified as [FeCl4]-.

and t are absorption

coefficient and thickness of the sample. (reproduced
from (Asakura et al., 1985) with permission
Chemical Society of Japan copyright (1985)).
IMPORTANT: this document contains embedded data - to preserve data integrity, please ensure where possible that the IUCr
Word tools (available from http://journals.iucr.org/services/docxtemplate/) are installed when editing this document.

1

Journal of Synchrotron Radiation

research papers

Since the first measurements were
Synchrotron Radiation Lightsource(Kincaid & Eisenberger, 1975), large
quantities of XAFS data have beencollected. These data can be divided
into two groups: (1) referencecompounds with known structures andproperties and (2)unknown target
materials under investigation. The data
for the former group are important formaterials scientists who wish to
analyse the XAFS spectra of unknown
compounds by comparing them withthose of reference compounds. Figure 1
shows the XAFS spectra of different Fe

Edge peak intensity / arb. units

made by Eisenberger at the Stanford
5
1.0
3
0.5

2
E
B

H

4
F

I
G

D

C
1 A
0
50
100
150
200
250
Exchange reaction enthalpy / kJ m ol-1

Figure 1 Relationship between edge peakintensity for Ag (I) compounds and covalence(Miyamoto et al., 2010; Miyamoto et al.,2012). Reproduced with permission from
(Miyamoto et al. 2010). Copyright (2010)
American Chemical Society.

chloride compounds. Some compounds produce a remarkable pre-edge peak that can be assigned to a
1s-to-3d transition, which is dipole forbidden , though it becomes stronger when centrosymmetry is
broken in a tetrahedral structure (Asakura et al., 1985) (Shulman et al., 1976). Thus, the Fe chloride
species in FeCl3-doped polyacetylene (PA) can be identified by comparing to XAFS spectra ofreference compounds. A collection of some XAFS spectra may be especially important when XAFS
spectroscopy is performed by non-specialists. Collections of typical XAFS spectra are published in apaper form such as books. The Catalysis Society of Japan has published the Catalyst Handbook,which includes XAFS spectra of reference compounds containing catalytically important elements(Japan, 2008).
An open-access, Internet-based database of XAFS spectra in a digital form is more convenient for
all researchers to update and search data. Such a large, comprehensive database would be useful not
only for XAFS non-specialists but also for specialists who want to elucidate general concepts fromXAFS spectra. Figure 2 shows the relationship between the intensity of edge-peak of Ag+ L3 X-ray
absorption near edge structure (XANES) and the covalence of Ag compounds (Miyamoto et al., 2010;
Miyamoto et al., 2012), which demonstrates a positive correlation. Such examples can be found inother studies, such as Lytle’s white line analysis and Wong’s V oxide pre-edge and edge shift analysis(Lytle et al., 1979; Wong et al., 1984). Eventually, deep learning methods could derive such relations
easily and automatically if a large database of XAFS spectra was available and related to othermaterial databases (Takigawa et al., 2016).
2. Overview of currently available XAFS databases

2

Journal of Synchrotron Radiation

research papers

Several databases of XAFS spectra have been developed, as shown in Table 1. These databases are
free, and they generally permit open access. F.W. Lytle database has a long history, which is thelargest and perhaps most well-known XAFS database. SPring-8 BL14 database, which requires a user
ID and password to view and search data, has ample data (more than 800) for reference compounds.
Recently, “Photon Beam Platform”, a national project in Japan to promote the collaboration among
synchrotron radiation and laser facilities is carrying out round robin tests for XAFS data in a data
format of XML(eXtensible Markup Language). International proposal of round robin tests of
XAFS data has also been proposed (Chantller et al., 2018)
This paper focuses on the XAFS database developed as a collaboration between the Hokkaido
University Institute for Catalysis (ICAT) and the Japanese XAFS Society (JXS). We would like topropose an international collaboration to make a new big and open database for XAFS.
Table 1 Available XAFS databases (as of Dec. 31, 2017)
Database
F.W. Lytle
database

URL
http://ixs.iit.edu/database/Features
Text format with periodic table interface
All data obtained by F.W. Lytle
19,307 records covering 74 elements

CARS

http://cars.uchicago.edu/
xaslib/search

Text (XDI) format with periodic table interface andgraphical output of spectra (Newville et al., 2015)
171 records covering 13 elements
Measured at the Advanced Photon Source, SSRL, andNational Synchrotron Light Source
Includes suites (tagging-related spectra) and user ratings

SPring-8 BL14

https://sp8dr.spring8.or.jp/
portal/dspace

Only available to SPring-8 users
725 records
Compressed text file (ZIP) format with metadata that
contains vendor and lot number

EuropeanSynchrotron
Radiation
Facility, ID21
group

http://www.esrf.eu/home/
UsersAndScience

Hokkaido
University ICAT
and JXS

https://www.cat.hokudai.ac.
jp/catdb/index.php?
action=xafs_login_form&
opnid=2/Experiments/XNP/ID21/
php.html

Sulphur database
41 (inorganic) and 26 (organic) records for S compounds
Graphical output, but text format is available
User name is included
209 records and 24 elements
Text format with metadata
Includes user name, beam line, and facility
Open access, but data uploading is restricted to users with
ID and password

3

Journal of Synchrotron Radiation

research papers

3. ICAT XAFS database in Japan
3.1. History

The Hokkaido University ICAT started to build the XAFS database in 2011 as a project of the Joint
Usage/Research Center for catalysis, in collaboration with JXS. The database is accessible to anyone
through the Internet. Volunteers working in the XAFS field can register for an ID and password to
upload their data to the database. For security and traceability, data files contain the name of theperson who uploaded the data. The website is managed by ICAT.
3.2. Fundamental ICAT data policies

The basic policies of the ICAT XAFS database are as follows:
Volunteer base – Anyone who is registered can upload their data.
Open-access database – Anyone can see and use the data. They are asked include a citation in
published work if they used the data.
Simple dataset format – The data have a text-based format, and only the energy and t of theraw spectrum are recorded, in addition to some metadata.
Compatibility – Foil XAFS data that are measured at the same beam time and beam line aredeposited simultaneously to make energy calibration possible. Consequently, we can compare
the data measured at different beam times, beam lines, and facilities.
Target – Dataset includes primarily standard compounds with known structures.
Guarantee of accuracy – A “majority rule” approach is used to improve accuracy. The
database allows deposition of multiple records for the same compounds.
Each data file has a metadata area and a data area, as shown in Fig. 3. Table 2 lists the available
metadata fields in the ICAT database. Although detailed metadata are helpful, too many required
inputs will reduce the motivation of volunteers, so the number of metadata fields are kept as small as
possible.

4

Journal of Synchrotron Radiation

Table 2

research papers

Available metadata fields in ICAT database

Sample name
Structural details (powder, foil, solution)
Absorption atom
Edge
Reference sample (usually foil)
Date of measurement
Monochromator (crystal)
Facility
Beam line

Beam current (mA)
Beam energy of storage ring (GeV)
Higher harmonics rejection method
Focus
Detection method
I｡ and I gases if ionization chamber was used
Measurement temperature
Comments

Figure 3 ICAT data file structure5

Journal of Synchrotron Radiation

research papers

One of the most important policies is compatibility. Although absolute angle of eachmonochromator can be determined by Pettier’s method or other{Pettifer, 1985 #2007}, it is moreconvenient to calibrate each data using foil measured at the same time. The data are uploaded withthe foil data measured at the same time. It benefit us to obtain the signal-to-noise ratio (S/N) and theenergy resolution of the XAFS measurement systems by comparison with the foil XAFS data in
addition to adjust the energy scale from different files by comparison with the foil XAFS spectra.
Another important policy is the guarantee of accuracy, that is, the quality of each XAFS spectrum.
One way to guarantee accuracy is to permit only highly qualified researchers to measure spectra undera strict, specific protocol and upload the data in a rigorously controlled way. However, this would
require more qualified researchers, time, and money than are not generally available. Also, theamount of data stored per day would be limited and it would be hard to construct a large database.
ICAT uses another strategy for data quality, that is, majority rule. The volunteers, who are expected
to have average skill for measuring XAFS spectra and preparing datasets, measure the spectra andupload the data with the metadata. When many volunteers randomly and independently upload spectra,
eventually different versions of the same reference spectra are collected. These data points are
statistically distributed so that the average spectra and their error bars can be determined. Data that lie
within the error bars are reliable, but a spectrum lying outside this range is either wrong or represents
a different phase . Thus, multiple spectra of the same compound improve the quality of the database.
Once the several spectra of the same compound available, users check the accuracy by comparing thespectra by themselves.
4. Problems with existing ICAT database

Despite its usefulness, the ICAT database has several drawbacks. The first problem is the small
number of data files in the database. This makes it difficult to apply majority rule and derive effective
relationships between spectral features and material properties. A way is needed to get more data
effectively. The second problem is that the database is not linked to other material databases, such as
X-ray diffraction, optical spectra, and other physical and chemical properties. The third problem isthe format. ICAT database uses simple the text-base format. Several data formats have been proposed,such as CIF XAFS, XDI (eXtensible Data Interchange), JASON(JavaScript Object Notation), NeXus,
and HDF5 (Ascone et al., 2012; Ravel & Newville, 2016; Konnecke et al., 2015 ). The NeXus andHDF5 formats can store and manage imaging data written in a binary format. Adoption of NeXus or
HDF5 may be a good choice for a flexible database, but it must first be designed well after longdeliberation. Nevertheless, the text format with only energy and t data is simple, easy to implement,
and transferrable to other formats. Although continued discussion of the XAFS database format isneeded, it might be expedient to start database construction in a text format and convert the data to aunified format later.
6

Journal of Synchrotron Radiation

research papers

5. Future database development – Bigger is betterIn the future, computers will be able to automatically evaluate the correctness of spectra based on
majority rule. Even if information about a sample is inadequate, the computer could classify the
samples into several subsets. For example, if the sample name is entered only as TiO2, the spectra
would need to be associated with one of the three different crystalline forms of TiO2 – Rutile, Anatase,and Brookite. Thus, the computer would need to assign the spectra to one of these crystal forms using
other spectra data. Some spectra may be located between two of the groups, indicating a mixture, so it
is better to have more data of the same compounds available for comparison. A large database will
reduce the probability of misinterpretation and improve our understanding of the spectra. The future
direction of the XAFS database is to be bigger and more open. The majority rule, in combination withadvanced computing, such as artificial intelligence(AI), can work to reinforce data quality andreliability and to elucidate meaningful new concepts through deep learning. The problem is how toconstruct a larger database as mentioned above. Since we collect data manually at the moment, theICAT database only contains a limited number of data files. If the data were automatically stored in
an appropriate way, all measured data could be included in the database. Manual input would be
limited to metadata and clarification and categorization of data into spectra for reference or unknown
compounds.
Since most XAFS spectra are measured at synchrotron radiation facilities, we propose thefollowing system:
Store all data measured at these facilities automatically in the facility’s computer inappropriate formats and with metadata. Thus, each facility can constructthe larger database.
Then combine the databases from each facility by connection to the internet. Before thatcan be done, however, we need to decide on rules for data disclosure. The fundamental
principle should be that all scientific data must be open to the public eventually, but thedata owner rights and originality should be reserved.
Using these basic ideas, the data can be made accessible to the public but only after the agreement of
the data owners. This will allow data owners choose to keep their data confidential, but it is hopedthat they would release the data after the associated studies are published in the literature.
Data disclosure would be beneficial to our society in two ways: (1) the quantity of data in the
XAFS database would increase, improving its quality and accessibility for everyone and (2) the
quality and transparency of published research would be improved by disclosing the raw data. The
cooperation of publishers would be important, and it is hoped that they would require disclosure of the
raw XAFS data when a paper is accepted. Facilities could provide further support by making data
7

Journal of Synchrotron Radiation

research papers

disclosure contracts with all users before they start experiments. The raw data should also be madeavailable when a patent is established. In addition to these rules, all data should be disclosed after acertain period (10 years for example). Facilities should retain responsibility for data security andprotection; otherwise, users would not allow facilities to store their data.
One more important suggestion is to define a unique digital data number, similar to the digital
object identifier (DOI) for a published paper. A data identifier would allow the data to be cited when
it is used in a publication. This would increase the incentive for owners to upload and to open theirdata. Like the citation index for a paper, a user could benefit from the number of citations of their data.
This would provide further motivation to perform precise measurements and develop higher-quality
data. A suggested format for the data identifier is as follows:
XAFS_ATOM_EDGE_Measure_Time_ContactPerson (Name & ResearcherID or
ORCID)_Facility_BeamLine.
Note that the identifier must be automatically determined and unique.
The linkage of facility databases will be another important task, since XAFS data are notstandalone. To derive structure-property relationships, XAFS data need to be considered in thecontext of the physical and chemical properties of the measured material. To do this, a clear sample
name must be determined uniquely and universally. If the sample is a standard reference compound,
this should be clearly conveyed by some unique sample identifier. The Chemical Abstracts Service(CAS) number is the best choice the sample identifier because it will be comprehensive and make iteasier to associate the sample with physical and chemical properties. Moreover, the majority rule will
work more effectively because different files for the same material can be linked easily, possibly
automatically. The facilities could encourage input of the CAS number into the metadata by providing
a CAS number dictionary to users. The data owner should provide their own data name according tosome rule, such as:
CAS_Number_ChemicalComposition_Phase_DataOwner (ResearcherID or ORCID)_Comment (Origin) (13463-67-7_TiO2_Rutile_G-6052-2010_PurchaseFromWakoLotNo0001).
6. What to Do Next

We believe that an open XAFS database is necessary but also very useful. Some issues should be
set aside for now, and each facility should start to construct a database or repository of its own data,with the goal of eventual linkage to a larger database. We propose the following actions:
1. Ask all facilities to start collecting XAFS data.
2. Decide on simple naming rules for linkage to other databases.
3. Decide on naming rules for data files, along the lines of the DOI.
8

Journal of Synchrotron Radiation

research papers

4. Start the discussion for determining data release rules.
We hope we can discuss my proposal at the next Q2XAFS and at other meetings.

Acknowledgment
This work was supported by MEXT Joint Usage/Research Center Program (2010-2015, 2016-2011)
and the Accelerator Science Support Fund from the High Energy Accelerator Research Organization(KEK) (2010-2017) and CREST JST “Resolution Catalyst”. One of the author (KA) thanks to

the fruitful discussion with Committee of manufacturing process innovation by materials
informatics( Chair : Prof.Toyohiro Chikyo in NIMS)

7. References

Asakura, K., Ikemoto, I., Kuroda, H., Kobayashi, T. & Shirakawa, H. (1985). Bull.Chem.Soc.Jpn. 58,
2113-2120.
Ascone, I., Asakura, K., George, G. N. & Wakatsuki, S. (2012). J.Synchro.Rad 19, 349-350.
Chantller, C., T,, Bunker , B. A., Abe, H., Kimura, M., Newville, M. & Weltere, E. (2018).
J.Synchro.Rad submitted to the same issue
Iwasawa, Y., Asakura, K. & Tada, M. (2016). Editor. XAFS techniques for catalysts, nanomaterials,
and surfaces, Springer.
Japan, C. S. o. (2008). Editor. Catalyst Handbook, 1 ed. Tokyo: Kodan-sha Scientific.
Kincaid, B. M. & Eisenberger, P. (1975). Phys. Rev. Lett. 34, 1361-1364.
Konnecke, M., Akeroyd, F. A., Bernstein, H. J., Brewster, A. S., Campbell, S. I., Clausen, B., Cottrell,S., Hoffmann, J. U., Jemian, P. R., Mannicke, D., Osborn, R., Peterson, P. F., Richter, T.,
Suzuki, J., Watts, B., Wintersberger, E. & Wuttke, J. (2015). J.Appl.Crystallo. 48, 301-305.
Lytle, F. W., Wei, P. S. P., Greegor, R. B., Via, G. H. & Sinfelt, J. H. (1979). J.Chem.Phys. 70, 4849.
Miyamoto , T., Kitajima, Y. & Asakura, K. (2012). e-J. Surf. Sci. Nanotech. 10, 609-612.
Miyamoto, T., Niimi, H., Kitajima, Y., Naito, T. & Asakura, K. (2010). J.Phys.Chem. A 114, 40934098.
Newville, M., Ravel, B., Sole, V. A. & Wellenreuther, G. (2015). XAS-DataInterchange/specification/spec.md, https://github.com/XraySpectroscopy/XAS-DataInterchange/blob/master/specification/spec.md.
Ravel, B. & Newville, M. (2016). J.Phys.Conf.Ser., pp. 12148-12151. IOP Publishing.
Shulman, G. R., Yafet, Y., Eisenberger, P. & Blumberg, W. E. (1976). Proc. Natl. Acad. Sci. USA 73,
1384-1388.
Takigawa, I., Shimizu, K.-i., Tsuda, K. & Takakusagi, S. (2016). RSC Adv. 6, 52587-52595.
Wong, J., Lytle, F. W., Messmer, R. P. & Maylotte, D. H. (1984). Phys. Rev. B 30, 5596.

9

Journal of Synchrotron Radiation

research papers

A Challenge of Constructing an International XAFS Database
Kiyotaka Asakuraa*, Hitoshi Abebc and Masao KimurabcaInstitute for Catalysis, Hokkaido University, Kita 21-10 Kita, Sapporo, Hokkaido, 001-0021, Japanb

Photon Factory, Institute of Materials' Structure Science, High Energy Accelerator Research

Organization, Oho 1-1, Tsukuba, Ibaraki, 305-0801, Japanc

Department of Materials' Structure Science, School of High Energy Accelerator Science,

SOKENDAI(The Graduate University for Advanced Studies), Oho 1-1, Tsukuba, Ibaraki, 305-0801,
Japan
Correspondence email: askr@cat.hokudai.ac.jp

Abstract

This paper describes the present state of XAFS databases, particularly in Japan, andproposes future directions. International
collaboration is important for enlarging the

FeCl – doped PA

database for further development of XAFS
spectroscopy.

[NEt ][FeCl ]Keywords: XAFS database; automatic data
deposition; data repository system

database

X-ray absorption fine structure (XAFS)[Co(NH ) ][FeCl ]t / arb. units

1. Why we need an international XAFS

[NEt ] [FeCl ]2040

spectroscopy is a powerful technique for0

determining local structure in metals with no

Photon Energy / eV

60

long-range order (Iwasawa et al., 2016).

Figure 2 Fe K-edge XANES spectra of selected Fe

Because a continuum X-ray source is required,

chlorides. The pre-edge peak is set at 0 eV. The Fe

XAFS spectroscopy became a practicalchloride dopant was characterized by XAFS

characterization technique only after

spectroscopy. By comparing with reference

synchrotron radiation sources were developed.

compounds, the Fe species in the PA could be
identified as [FeCl4]-.

and t are absorption

coefficient and thickness of the sample. (reproduced
from (Asakura et al., 1985) with permission
Chemical Society of Japan copyright (1985)).
IMPORTANT: this document contains embedded data - to preserve data integrity, please ensure where possible that the IUCr
Word tools (available from http://journals.iucr.org/services/docxtemplate/) are installed when editing this document.

1

Journal of Synchrotron Radiation

research papers

Since the first measurements were
Synchrotron Radiation Lightsource(Kincaid & Eisenberger, 1975), large
quantities of XAFS data have beencollected. These data can be divided
into two groups: (1) referencecompounds with known structures andproperties and (2)unknown target
materials under investigation. The data
for the former group are important formaterials scientists who wish to
analyse the XAFS spectra of unknown
compounds by comparing them withthose of reference compounds. Figure 1
shows the XAFS spectra of different Fe

Edge peak intensity / arb. units

made by Eisenberger at the Stanford
5
1.0
3
0.5

2
E
B

H

4
F

I
G

D

C
1 A
0
50
100
150
200
250
Exchange reaction enthalpy / kJ m ol-1

Figure 1 Relationship between edge peakintensity for Ag (I) compounds and covalence(Miyamoto et al., 2010; Miyamoto et al.,2012). Reproduced with permission from
(Miyamoto et al. 2010). Copyright (2010)
American Chemical Society.

chloride compounds. Some compounds produce a remarkable pre-edge peak that can be assigned to a
1s-to-3d transition, which is dipole forbidden , though it becomes stronger when centrosymmetry is
broken in a tetrahedral structure (Asakura et al., 1985) (Shulman et al., 1976). Thus, the Fe chloride
species in FeCl3-doped polyacetylene (PA) can be identified by comparing to XAFS spectra ofreference compounds. A collection of some XAFS spectra may be especially important when XAFS
spectroscopy is performed by non-specialists. Collections of typical XAFS spectra are published in apaper form such as books. The Catalysis Society of Japan has published the Catalyst Handbook,which includes XAFS spectra of reference compounds containing catalytically important elements(Japan, 2008).
An open-access, Internet-based database of XAFS spectra in a digital form is more convenient for
all researchers to update and search data. Such a large, comprehensive database would be useful not
only for XAFS non-specialists but also for specialists who want to elucidate general concepts fromXAFS spectra. Figure 2 shows the relationship between the intensity of edge-peak of Ag+ L3 X-ray
absorption near edge structure (XANES) and the covalence of Ag compounds (Miyamoto et al., 2010;
Miyamoto et al., 2012), which demonstrates a positive correlation. Such examples can be found inother studies, such as Lytle’s white line analysis and Wong’s V oxide pre-edge and edge shift analysis(Lytle et al., 1979; Wong et al., 1984). Eventually, deep learning methods could derive such relations
easily and automatically if a large database of XAFS spectra was available and related to othermaterial databases (Takigawa et al., 2016).
2. Overview of currently available XAFS databases

2

Journal of Synchrotron Radiation

research papers

Several databases of XAFS spectra have been developed, as shown in Table 1. These databases are
free, and they generally permit open access. F.W. Lytle database has a long history, which is thelargest and perhaps most well-known XAFS database. SPring-8 BL14 database, which requires a user
ID and password to view and search data, has ample data (more than 800) for reference compounds.
Recently, “Photon Beam Platform”, a national project in Japan to promote the collaboration among
synchrotron radiation and laser facilities is carrying out round robin tests for XAFS data in a data
format of XML(eXtensible Markup Language). International proposal of round robin tests of
XAFS data has also been proposed (Chantller et al., 2018)
This paper focuses on the XAFS database developed as a collaboration between the Hokkaido
University Institute for Catalysis (ICAT) and the Japanese XAFS Society (JXS). We would like topropose an international collaboration to make a new big and open database for XAFS.
Table 1 Available XAFS databases (as of Dec. 31, 2017)
Database
F.W. Lytle
database

URL
http://ixs.iit.edu/database/Features
Text format with periodic table interface
All data obtained by F.W. Lytle
19,307 records covering 74 elements

CARS

http://cars.uchicago.edu/
xaslib/search

Text (XDI) format with periodic table interface andgraphical output of spectra (Newville et al., 2015)
171 records covering 13 elements
Measured at the Advanced Photon Source, SSRL, andNational Synchrotron Light Source
Includes suites (tagging-related spectra) and user ratings

SPring-8 BL14

https://sp8dr.spring8.or.jp/
portal/dspace

Only available to SPring-8 users
725 records
Compressed text file (ZIP) format with metadata that
contains vendor and lot number

EuropeanSynchrotron
Radiation
Facility, ID21
group

http://www.esrf.eu/home/
UsersAndScience

Hokkaido
University ICAT
and JXS

https://www.cat.hokudai.ac.
jp/catdb/index.php?
action=xafs_login_form&
opnid=2/Experiments/XNP/ID21/
php.html

Sulphur database
41 (inorganic) and 26 (organic) records for S compounds
Graphical output, but text format is available
User name is included
209 records and 24 elements
Text format with metadata
Includes user name, beam line, and facility
Open access, but data uploading is restricted to users with
ID and password

3

Journal of Synchrotron Radiation

research papers

3. ICAT XAFS database in Japan
3.1. History

The Hokkaido University ICAT started to build the XAFS database in 2011 as a project of the Joint
Usage/Research Center for catalysis, in collaboration with JXS. The database is accessible to anyone
through the Internet. Volunteers working in the XAFS field can register for an ID and password to
upload their data to the database. For security and traceability, data files contain the name of theperson who uploaded the data. The website is managed by ICAT.
3.2. Fundamental ICAT data policies

The basic policies of the ICAT XAFS database are as follows:
Volunteer base – Anyone who is registered can upload their data.
Open-access database – Anyone can see and use the data. They are asked include a citation in
published work if they used the data.
Simple dataset format – The data have a text-based format, and only the energy and t of theraw spectrum are recorded, in addition to some metadata.
Compatibility – Foil XAFS data that are measured at the same beam time and beam line aredeposited simultaneously to make energy calibration possible. Consequently, we can compare
the data measured at different beam times, beam lines, and facilities.
Target – Dataset includes primarily standard compounds with known structures.
Guarantee of accuracy – A “majority rule” approach is used to improve accuracy. The
database allows deposition of multiple records for the same compounds.
Each data file has a metadata area and a data area, as shown in Fig. 3. Table 2 lists the available
metadata fields in the ICAT database. Although detailed metadata are helpful, too many required
inputs will reduce the motivation of volunteers, so the number of metadata fields are kept as small as
possible.

4

Journal of Synchrotron Radiation

Table 2

research papers

Available metadata fields in ICAT database

Sample name
Structural details (powder, foil, solution)
Absorption atom
Edge
Reference sample (usually foil)
Date of measurement
Monochromator (crystal)
Facility
Beam line

Beam current (mA)
Beam energy of storage ring (GeV)
Higher harmonics rejection method
Focus
Detection method
I｡ and I gases if ionization chamber was used
Measurement temperature
Comments

Figure 3 ICAT data file structure5

Journal of Synchrotron Radiation

research papers

One of the most important policies is compatibility. Although absolute angle of eachmonochromator can be determined by Pettier’s method or other{Pettifer, 1985 #2007}, it is moreconvenient to calibrate each data using foil measured at the same time. The data are uploaded withthe foil data measured at the same time. It benefit us to obtain the signal-to-noise ratio (S/N) and theenergy resolution of the XAFS measurement systems by comparison with the foil XAFS data in
addition to adjust the energy scale from different files by comparison with the foil XAFS spectra.
Another important policy is the guarantee of accuracy, that is, the quality of each XAFS spectrum.
One way to guarantee accuracy is to permit only highly qualified researchers to measure spectra undera strict, specific protocol and upload the data in a rigorously controlled way. However, this would
require more qualified researchers, time, and money than are not generally available. Also, theamount of data stored per day would be limited and it would be hard to construct a large database.
ICAT uses another strategy for data quality, that is, majority rule. The volunteers, who are expected
to have average skill for measuring XAFS spectra and preparing datasets, measure the spectra andupload the data with the metadata. When many volunteers randomly and independently upload spectra,
eventually different versions of the same reference spectra are collected. These data points are
statistically distributed so that the average spectra and their error bars can be determined. Data that lie
within the error bars are reliable, but a spectrum lying outside this range is either wrong or represents
a different phase . Thus, multiple spectra of the same compound improve the quality of the database.
Once the several spectra of the same compound available, users check the accuracy by comparing thespectra by themselves.
4. Problems with existing ICAT database

Despite its usefulness, the ICAT database has several drawbacks. The first problem is the small
number of data files in the database. This makes it difficult to apply majority rule and derive effective
relationships between spectral features and material properties. A way is needed to get more data
effectively. The second problem is that the database is not linked to other material databases, such as
X-ray diffraction, optical spectra, and other physical and chemical properties. The third problem isthe format. ICAT database uses simple the text-base format. Several data formats have been proposed,such as CIF XAFS, XDI (eXtensible Data Interchange), JASON(JavaScript Object Notation), NeXus,
and HDF5 (Ascone et al., 2012; Ravel & Newville, 2016; Konnecke et al., 2015 ). The NeXus andHDF5 formats can store and manage imaging data written in a binary format. Adoption of NeXus or
HDF5 may be a good choice for a flexible database, but it must first be designed well after longdeliberation. Nevertheless, the text format with only energy and t data is simple, easy to implement,
and transferrable to other formats. Although continued discussion of the XAFS database format isneeded, it might be expedient to start database construction in a text format and convert the data to aunified format later.
6

Journal of Synchrotron Radiation

research papers

5. Future database development – Bigger is betterIn the future, computers will be able to automatically evaluate the correctness of spectra based on
majority rule. Even if information about a sample is inadequate, the computer could classify the
samples into several subsets. For example, if the sample name is entered only as TiO2, the spectra
would need to be associated with one of the three different crystalline forms of TiO2 – Rutile, Anatase,and Brookite. Thus, the computer would need to assign the spectra to one of these crystal forms using
other spectra data. Some spectra may be located between two of the groups, indicating a mixture, so it
is better to have more data of the same compounds available for comparison. A large database will
reduce the probability of misinterpretation and improve our understanding of the spectra. The future
direction of the XAFS database is to be bigger and more open. The majority rule, in combination withadvanced computing, such as artificial intelligence(AI), can work to reinforce data quality andreliability and to elucidate meaningful new concepts through deep learning. The problem is how toconstruct a larger database as mentioned above. Since we collect data manually at the moment, theICAT database only contains a limited number of data files. If the data were automatically stored in
an appropriate way, all measured data could be included in the database. Manual input would be
limited to metadata and clarification and categorization of data into spectra for reference or unknown
compounds.
Since most XAFS spectra are measured at synchrotron radiation facilities, we propose thefollowing system:
Store all data measured at these facilities automatically in the facility’s computer inappropriate formats and with metadata. Thus, each facility can constructthe larger database.
Then combine the databases from each facility by connection to the internet. Before thatcan be done, however, we need to decide on rules for data disclosure. The fundamental
principle should be that all scientific data must be open to the public eventually, but thedata owner rights and originality should be reserved.
Using these basic ideas, the data can be made accessible to the public but only after the agreement of
the data owners. This will allow data owners choose to keep their data confidential, but it is hopedthat they would release the data after the associated studies are published in the literature.
Data disclosure would be beneficial to our society in two ways: (1) the quantity of data in the
XAFS database would increase, improving its quality and accessibility for everyone and (2) the
quality and transparency of published research would be improved by disclosing the raw data. The
cooperation of publishers would be important, and it is hoped that they would require disclosure of the
raw XAFS data when a paper is accepted. Facilities could provide further support by making data
7

Journal of Synchrotron Radiation

research papers

disclosure contracts with all users before they start experiments. The raw data should also be madeavailable when a patent is established. In addition to these rules, all data should be disclosed after acertain period (10 years for example). Facilities should retain responsibility for data security andprotection; otherwise, users would not allow facilities to store their data.
One more important suggestion is to define a unique digital data number, similar to the digital
object identifier (DOI) for a published paper. A data identifier would allow the data to be cited when
it is used in a publication. This would increase the incentive for owners to upload and to open theirdata. Like the citation index for a paper, a user could benefit from the number of citations of their data.
This would provide further motivation to perform precise measurements and develop higher-quality
data. A suggested format for the data identifier is as follows:
XAFS_ATOM_EDGE_Measure_Time_ContactPerson (Name & ResearcherID or
ORCID)_Facility_BeamLine.
Note that the identifier must be automatically determined and unique.
The linkage of facility databases will be another important task, since XAFS data are notstandalone. To derive structure-property relationships, XAFS data need to be considered in thecontext of the physical and chemical properties of the measured material. To do this, a clear sample
name must be determined uniquely and universally. If the sample is a standard reference compound,
this should be clearly conveyed by some unique sample identifier. The Chemical Abstracts Service(CAS) number is the best choice the sample identifier because it will be comprehensive and make iteasier to associate the sample with physical and chemical properties. Moreover, the majority rule will
work more effectively because different files for the same material can be linked easily, possibly
automatically. The facilities could encourage input of the CAS number into the metadata by providing
a CAS number dictionary to users. The data owner should provide their own data name according tosome rule, such as:
CAS_Number_ChemicalComposition_Phase_DataOwner (ResearcherID or ORCID)_Comment (Origin) (13463-67-7_TiO2_Rutile_G-6052-2010_PurchaseFromWakoLotNo0001).
6. What to Do Next

We believe that an open XAFS database is necessary but also very useful. Some issues should be
set aside for now, and each facility should start to construct a database or repository of its own data,with the goal of eventual linkage to a larger database. We propose the following actions:
1. Ask all facilities to start collecting XAFS data.
2. Decide on simple naming rules for linkage to other databases.
3. Decide on naming rules for data files, along the lines of the DOI.
8

Journal of Synchrotron Radiation

research papers

4. Start the discussion for determining data release rules.
We hope we can discuss my proposal at the next Q2XAFS and at other meetings.

Acknowledgment
This work was supported by MEXT Joint Usage/Research Center Program (2010-2015, 2016-2011)
and the Accelerator Science Support Fund from the High Energy Accelerator Research Organization(KEK) (2010-2017) and CREST JST “Resolution Catalyst”. One of the author (KA) thanks to

the fruitful discussion with Committee of manufacturing process innovation by materials
informatics( Chair : Prof.Toyohiro Chikyo in NIMS)

7. References

Asakura, K., Ikemoto, I., Kuroda, H., Kobayashi, T. & Shirakawa, H. (1985). Bull.Chem.Soc.Jpn. 58,
2113-2120.
Ascone, I., Asakura, K., George, G. N. & Wakatsuki, S. (2012). J.Synchro.Rad 19, 349-350.
Chantller, C., T,, Bunker , B. A., Abe, H., Kimura, M., Newville, M. & Weltere, E. (2018).
J.Synchro.Rad submitted to the same issue
Iwasawa, Y., Asakura, K. & Tada, M. (2016). Editor. XAFS techniques for catalysts, nanomaterials,
and surfaces, Springer.
Japan, C. S. o. (2008). Editor. Catalyst Handbook, 1 ed. Tokyo: Kodan-sha Scientific.
Kincaid, B. M. & Eisenberger, P. (1975). Phys. Rev. Lett. 34, 1361-1364.
Konnecke, M., Akeroyd, F. A., Bernstein, H. J., Brewster, A. S., Campbell, S. I., Clausen, B., Cottrell,S., Hoffmann, J. U., Jemian, P. R., Mannicke, D., Osborn, R., Peterson, P. F., Richter, T.,
Suzuki, J., Watts, B., Wintersberger, E. & Wuttke, J. (2015). J.Appl.Crystallo. 48, 301-305.
Lytle, F. W., Wei, P. S. P., Greegor, R. B., Via, G. H. & Sinfelt, J. H. (1979). J.Chem.Phys. 70, 4849.
Miyamoto , T., Kitajima, Y. & Asakura, K. (2012). e-J. Surf. Sci. Nanotech. 10, 609-612.
Miyamoto, T., Niimi, H., Kitajima, Y., Naito, T. & Asakura, K. (2010). J.Phys.Chem. A 114, 40934098.
Newville, M., Ravel, B., Sole, V. A. & Wellenreuther, G. (2015). XAS-DataInterchange/specification/spec.md, https://github.com/XraySpectroscopy/XAS-DataInterchange/blob/master/specification/spec.md.
Ravel, B. & Newville, M. (2016). J.Phys.Conf.Ser., pp. 12148-12151. IOP Publishing.
Shulman, G. R., Yafet, Y., Eisenberger, P. & Blumberg, W. E. (1976). Proc. Natl. Acad. Sci. USA 73,
1384-1388.
Takigawa, I., Shimizu, K.-i., Tsuda, K. & Takakusagi, S. (2016). RSC Adv. 6, 52587-52595.
Wong, J., Lytle, F. W., Messmer, R. P. & Maylotte, D. H. (1984). Phys. Rev. B 30, 5596.

9

Journal of Synchrotron Radiation

research papers

A Challenge of Constructing an International XAFS Database
Kiyotaka Asakuraa*, Hitoshi Abebc and Masao KimurabcaInstitute for Catalysis, Hokkaido University, Kita 21-10 Kita, Sapporo, Hokkaido, 001-0021, Japanb

Photon Factory, Institute of Materials' Structure Science, High Energy Accelerator Research

Organization, Oho 1-1, Tsukuba, Ibaraki, 305-0801, Japanc

Department of Materials' Structure Science, School of High Energy Accelerator Science,

SOKENDAI(The Graduate University for Advanced Studies), Oho 1-1, Tsukuba, Ibaraki, 305-0801,
Japan
Correspondence email: askr@cat.hokudai.ac.jp

Abstract

This paper describes the present state of XAFS databases, particularly in Japan, andproposes future directions. International
collaboration is important for enlarging the

FeCl – doped PA

database for further development of XAFS
spectroscopy.

[NEt ][FeCl ]Keywords: XAFS database; automatic data
deposition; data repository system

database

X-ray absorption fine structure (XAFS)[Co(NH ) ][FeCl ]t / arb. units

1. Why we need an international XAFS

[NEt ] [FeCl ]2040

spectroscopy is a powerful technique for0

determining local structure in metals with no

Photon Energy / eV

60

long-range order (Iwasawa et al., 2016).

Figure 2 Fe K-edge XANES spectra of selected Fe

Because a continuum X-ray source is required,

chlorides. The pre-edge peak is set at 0 eV. The Fe

XAFS spectroscopy became a practicalchloride dopant was characterized by XAFS

characterization technique only after

spectroscopy. By comparing with reference

synchrotron radiation sources were developed.

compounds, the Fe species in the PA could be
identified as [FeCl4]-.

and t are absorption

coefficient and thickness of the sample. (reproduced
from (Asakura et al., 1985) with permission
Chemical Society of Japan copyright (1985)).
IMPORTANT: this document contains embedded data - to preserve data integrity, please ensure where possible that the IUCr
Word tools (available from http://journals.iucr.org/services/docxtemplate/) are installed when editing this document.

1

Journal of Synchrotron Radiation

research papers

Since the first measurements were
Synchrotron Radiation Lightsource(Kincaid & Eisenberger, 1975), large
quantities of XAFS data have beencollected. These data can be divided
into two groups: (1) referencecompounds with known structures andproperties and (2)unknown target
materials under investigation. The data
for the former group are important formaterials scientists who wish to
analyse the XAFS spectra of unknown
compounds by comparing them withthose of reference compounds. Figure 1
shows the XAFS spectra of different Fe

Edge peak intensity / arb. units

made by Eisenberger at the Stanford
5
1.0
3
0.5

2
E
B

H

4
F

I
G

D

C
1 A
0
50
100
150
200
250
Exchange reaction enthalpy / kJ m ol-1

Figure 1 Relationship between edge peakintensity for Ag (I) compounds and covalence(Miyamoto et al., 2010; Miyamoto et al.,2012). Reproduced with permission from
(Miyamoto et al. 2010). Copyright (2010)
American Chemical Society.

chloride compounds. Some compounds produce a remarkable pre-edge peak that can be assigned to a
1s-to-3d transition, which is dipole forbidden , though it becomes stronger when centrosymmetry is
broken in a tetrahedral structure (Asakura et al., 1985) (Shulman et al., 1976). Thus, the Fe chloride
species in FeCl3-doped polyacetylene (PA) can be identified by comparing to XAFS spectra ofreference compounds. A collection of some XAFS spectra may be especially important when XAFS
spectroscopy is performed by non-specialists. Collections of typical XAFS spectra are published in apaper form such as books. The Catalysis Society of Japan has published the Catalyst Handbook,which includes XAFS spectra of reference compounds containing catalytically important elements(Japan, 2008).
An open-access, Internet-based database of XAFS spectra in a digital form is more convenient for
all researchers to update and search data. Such a large, comprehensive database would be useful not
only for XAFS non-specialists but also for specialists who want to elucidate general concepts fromXAFS spectra. Figure 2 shows the relationship between the intensity of edge-peak of Ag+ L3 X-ray
absorption near edge structure (XANES) and the covalence of Ag compounds (Miyamoto et al., 2010;
Miyamoto et al., 2012), which demonstrates a positive correlation. Such examples can be found inother studies, such as Lytle’s white line analysis and Wong’s V oxide pre-edge and edge shift analysis(Lytle et al., 1979; Wong et al., 1984). Eventually, deep learning methods could derive such relations
easily and automatically if a large database of XAFS spectra was available and related to othermaterial databases (Takigawa et al., 2016).
2. Overview of currently available XAFS databases

2

Journal of Synchrotron Radiation

research papers

Several databases of XAFS spectra have been developed, as shown in Table 1. These databases are
free, and they generally permit open access. F.W. Lytle database has a long history, which is thelargest and perhaps most well-known XAFS database. SPring-8 BL14 database, which requires a user
ID and password to view and search data, has ample data (more than 800) for reference compounds.
Recently, “Photon Beam Platform”, a national project in Japan to promote the collaboration among
synchrotron radiation and laser facilities is carrying out round robin tests for XAFS data in a data
format of XML(eXtensible Markup Language). International proposal of round robin tests of
XAFS data has also been proposed (Chantller et al., 2018)
This paper focuses on the XAFS database developed as a collaboration between the Hokkaido
University Institute for Catalysis (ICAT) and the Japanese XAFS Society (JXS). We would like topropose an international collaboration to make a new big and open database for XAFS.
Table 1 Available XAFS databases (as of Dec. 31, 2017)
Database
F.W. Lytle
database

URL
http://ixs.iit.edu/database/Features
Text format with periodic table interface
All data obtained by F.W. Lytle
19,307 records covering 74 elements

CARS

http://cars.uchicago.edu/
xaslib/search

Text (XDI) format with periodic table interface andgraphical output of spectra (Newville et al., 2015)
171 records covering 13 elements
Measured at the Advanced Photon Source, SSRL, andNational Synchrotron Light Source
Includes suites (tagging-related spectra) and user ratings

SPring-8 BL14

https://sp8dr.spring8.or.jp/
portal/dspace

Only available to SPring-8 users
725 records
Compressed text file (ZIP) format with metadata that
contains vendor and lot number

EuropeanSynchrotron
Radiation
Facility, ID21
group

http://www.esrf.eu/home/
UsersAndScience

Hokkaido
University ICAT
and JXS

https://www.cat.hokudai.ac.
jp/catdb/index.php?
action=xafs_login_form&
opnid=2/Experiments/XNP/ID21/
php.html

Sulphur database
41 (inorganic) and 26 (organic) records for S compounds
Graphical output, but text format is available
User name is included
209 records and 24 elements
Text format with metadata
Includes user name, beam line, and facility
Open access, but data uploading is restricted to users with
ID and password

3

Journal of Synchrotron Radiation

research papers

3. ICAT XAFS database in Japan
3.1. History

The Hokkaido University ICAT started to build the XAFS database in 2011 as a project of the Joint
Usage/Research Center for catalysis, in collaboration with JXS. The database is accessible to anyone
through the Internet. Volunteers working in the XAFS field can register for an ID and password to
upload their data to the database. For security and traceability, data files contain the name of theperson who uploaded the data. The website is managed by ICAT.
3.2. Fundamental ICAT data policies

The basic policies of the ICAT XAFS database are as follows:
Volunteer base – Anyone who is registered can upload their data.
Open-access database – Anyone can see and use the data. They are asked include a citation in
published work if they used the data.
Simple dataset format – The data have a text-based format, and only the energy and t of theraw spectrum are recorded, in addition to some metadata.
Compatibility – Foil XAFS data that are measured at the same beam time and beam line aredeposited simultaneously to make energy calibration possible. Consequently, we can compare
the data measured at different beam times, beam lines, and facilities.
Target – Dataset includes primarily standard compounds with known structures.
Guarantee of accuracy – A “majority rule” approach is used to improve accuracy. The
database allows deposition of multiple records for the same compounds.
Each data file has a metadata area and a data area, as shown in Fig. 3. Table 2 lists the available
metadata fields in the ICAT database. Although detailed metadata are helpful, too many required
inputs will reduce the motivation of volunteers, so the number of metadata fields are kept as small as
possible.

4

Journal of Synchrotron Radiation

Table 2

research papers

Available metadata fields in ICAT database

Sample name
Structural details (powder, foil, solution)
Absorption atom
Edge
Reference sample (usually foil)
Date of measurement
Monochromator (crystal)
Facility
Beam line

Beam current (mA)
Beam energy of storage ring (GeV)
Higher harmonics rejection method
Focus
Detection method
I｡ and I gases if ionization chamber was used
Measurement temperature
Comments

Figure 3 ICAT data file structure5

Journal of Synchrotron Radiation

research papers

One of the most important policies is compatibility. Although absolute angle of eachmonochromator can be determined by Pettier’s method or other{Pettifer, 1985 #2007}, it is moreconvenient to calibrate each data using foil measured at the same time. The data are uploaded withthe foil data measured at the same time. It benefit us to obtain the signal-to-noise ratio (S/N) and theenergy resolution of the XAFS measurement systems by comparison with the foil XAFS data in
addition to adjust the energy scale from different files by comparison with the foil XAFS spectra.
Another important policy is the guarantee of accuracy, that is, the quality of each XAFS spectrum.
One way to guarantee accuracy is to permit only highly qualified researchers to measure spectra undera strict, specific protocol and upload the data in a rigorously controlled way. However, this would
require more qualified researchers, time, and money than are not generally available. Also, theamount of data stored per day would be limited and it would be hard to construct a large database.
ICAT uses another strategy for data quality, that is, majority rule. The volunteers, who are expected
to have average skill for measuring XAFS spectra and preparing datasets, measure the spectra andupload the data with the metadata. When many volunteers randomly and independently upload spectra,
eventually different versions of the same reference spectra are collected. These data points are
statistically distributed so that the average spectra and their error bars can be determined. Data that lie
within the error bars are reliable, but a spectrum lying outside this range is either wrong or represents
a different phase . Thus, multiple spectra of the same compound improve the quality of the database.
Once the several spectra of the same compound available, users check the accuracy by comparing thespectra by themselves.
4. Problems with existing ICAT database

Despite its usefulness, the ICAT database has several drawbacks. The first problem is the small
number of data files in the database. This makes it difficult to apply majority rule and derive effective
relationships between spectral features and material properties. A way is needed to get more data
effectively. The second problem is that the database is not linked to other material databases, such as
X-ray diffraction, optical spectra, and other physical and chemical properties. The third problem isthe format. ICAT database uses simple the text-base format. Several data formats have been proposed,such as CIF XAFS, XDI (eXtensible Data Interchange), JASON(JavaScript Object Notation), NeXus,
and HDF5 (Ascone et al., 2012; Ravel & Newville, 2016; Konnecke et al., 2015 ). The NeXus andHDF5 formats can store and manage imaging data written in a binary format. Adoption of NeXus or
HDF5 may be a good choice for a flexible database, but it must first be designed well after longdeliberation. Nevertheless, the text format with only energy and t data is simple, easy to implement,
and transferrable to other formats. Although continued discussion of the XAFS database format isneeded, it might be expedient to start database construction in a text format and convert the data to aunified format later.
6

Journal of Synchrotron Radiation

research papers

5. Future database development – Bigger is betterIn the future, computers will be able to automatically evaluate the correctness of spectra based on
majority rule. Even if information about a sample is inadequate, the computer could classify the
samples into several subsets. For example, if the sample name is entered only as TiO2, the spectra
would need to be associated with one of the three different crystalline forms of TiO2 – Rutile, Anatase,and Brookite. Thus, the computer would need to assign the spectra to one of these crystal forms using
other spectra data. Some spectra may be located between two of the groups, indicating a mixture, so it
is better to have more data of the same compounds available for comparison. A large database will
reduce the probability of misinterpretation and improve our understanding of the spectra. The future
direction of the XAFS database is to be bigger and more open. The majority rule, in combination withadvanced computing, such as artificial intelligence(AI), can work to reinforce data quality andreliability and to elucidate meaningful new concepts through deep learning. The problem is how toconstruct a larger database as mentioned above. Since we collect data manually at the moment, theICAT database only contains a limited number of data files. If the data were automatically stored in
an appropriate way, all measured data could be included in the database. Manual input would be
limited to metadata and clarification and categorization of data into spectra for reference or unknown
compounds.
Since most XAFS spectra are measured at synchrotron radiation facilities, we propose thefollowing system:
Store all data measured at these facilities automatically in the facility’s computer inappropriate formats and with metadata. Thus, each facility can constructthe larger database.
Then combine the databases from each facility by connection to the internet. Before thatcan be done, however, we need to decide on rules for data disclosure. The fundamental
principle should be that all scientific data must be open to the public eventually, but thedata owner rights and originality should be reserved.
Using these basic ideas, the data can be made accessible to the public but only after the agreement of
the data owners. This will allow data owners choose to keep their data confidential, but it is hopedthat they would release the data after the associated studies are published in the literature.
Data disclosure would be beneficial to our society in two ways: (1) the quantity of data in the
XAFS database would increase, improving its quality and accessibility for everyone and (2) the
quality and transparency of published research would be improved by disclosing the raw data. The
cooperation of publishers would be important, and it is hoped that they would require disclosure of the
raw XAFS data when a paper is accepted. Facilities could provide further support by making data
7

Journal of Synchrotron Radiation

research papers

disclosure contracts with all users before they start experiments. The raw data should also be madeavailable when a patent is established. In addition to these rules, all data should be disclosed after acertain period (10 years for example). Facilities should retain responsibility for data security andprotection; otherwise, users would not allow facilities to store their data.
One more important suggestion is to define a unique digital data number, similar to the digital
object identifier (DOI) for a published paper. A data identifier would allow the data to be cited when
it is used in a publication. This would increase the incentive for owners to upload and to open theirdata. Like the citation index for a paper, a user could benefit from the number of citations of their data.
This would provide further motivation to perform precise measurements and develop higher-quality
data. A suggested format for the data identifier is as follows:
XAFS_ATOM_EDGE_Measure_Time_ContactPerson (Name & ResearcherID or
ORCID)_Facility_BeamLine.
Note that the identifier must be automatically determined and unique.
The linkage of facility databases will be another important task, since XAFS data are notstandalone. To derive structure-property relationships, XAFS data need to be considered in thecontext of the physical and chemical properties of the measured material. To do this, a clear sample
name must be determined uniquely and universally. If the sample is a standard reference compound,
this should be clearly conveyed by some unique sample identifier. The Chemical Abstracts Service(CAS) number is the best choice the sample identifier because it will be comprehensive and make iteasier to associate the sample with physical and chemical properties. Moreover, the majority rule will
work more effectively because different files for the same material can be linked easily, possibly
automatically. The facilities could encourage input of the CAS number into the metadata by providing
a CAS number dictionary to users. The data owner should provide their own data name according tosome rule, such as:
CAS_Number_ChemicalComposition_Phase_DataOwner (ResearcherID or ORCID)_Comment (Origin) (13463-67-7_TiO2_Rutile_G-6052-2010_PurchaseFromWakoLotNo0001).
6. What to Do Next

We believe that an open XAFS database is necessary but also very useful. Some issues should be
set aside for now, and each facility should start to construct a database or repository of its own data,with the goal of eventual linkage to a larger database. We propose the following actions:
1. Ask all facilities to start collecting XAFS data.
2. Decide on simple naming rules for linkage to other databases.
3. Decide on naming rules for data files, along the lines of the DOI.
8

Journal of Synchrotron Radiation

research papers

4. Start the discussion for determining data release rules.
We hope we can discuss my proposal at the next Q2XAFS and at other meetings.

Acknowledgment
This work was supported by MEXT Joint Usage/Research Center Program (2010-2015, 2016-2011)
and the Accelerator Science Support Fund from the High Energy Accelerator Research Organization(KEK) (2010-2017) and CREST JST “Resolution Catalyst”. One of the author (KA) thanks to

the fruitful discussion with Committee of manufacturing process innovation by materials
informatics( Chair : Prof.Toyohiro Chikyo in NIMS)

7. References

Asakura, K., Ikemoto, I., Kuroda, H., Kobayashi, T. & Shirakawa, H. (1985). Bull.Chem.Soc.Jpn. 58,
2113-2120.
Ascone, I., Asakura, K., George, G. N. & Wakatsuki, S. (2012). J.Synchro.Rad 19, 349-350.
Chantller, C., T,, Bunker , B. A., Abe, H., Kimura, M., Newville, M. & Weltere, E. (2018).
J.Synchro.Rad submitted to the same issue
Iwasawa, Y., Asakura, K. & Tada, M. (2016). Editor. XAFS techniques for catalysts, nanomaterials,
and surfaces, Springer.
Japan, C. S. o. (2008). Editor. Catalyst Handbook, 1 ed. Tokyo: Kodan-sha Scientific.
Kincaid, B. M. & Eisenberger, P. (1975). Phys. Rev. Lett. 34, 1361-1364.
Konnecke, M., Akeroyd, F. A., Bernstein, H. J., Brewster, A. S., Campbell, S. I., Clausen, B., Cottrell,S., Hoffmann, J. U., Jemian, P. R., Mannicke, D., Osborn, R., Peterson, P. F., Richter, T.,
Suzuki, J., Watts, B., Wintersberger, E. & Wuttke, J. (2015). J.Appl.Crystallo. 48, 301-305.
Lytle, F. W., Wei, P. S. P., Greegor, R. B., Via, G. H. & Sinfelt, J. H. (1979). J.Chem.Phys. 70, 4849.
Miyamoto , T., Kitajima, Y. & Asakura, K. (2012). e-J. Surf. Sci. Nanotech. 10, 609-612.
Miyamoto, T., Niimi, H., Kitajima, Y., Naito, T. & Asakura, K. (2010). J.Phys.Chem. A 114, 40934098.
Newville, M., Ravel, B., Sole, V. A. & Wellenreuther, G. (2015). XAS-DataInterchange/specification/spec.md, https://github.com/XraySpectroscopy/XAS-DataInterchange/blob/master/specification/spec.md.
Ravel, B. & Newville, M. (2016). J.Phys.Conf.Ser., pp. 12148-12151. IOP Publishing.
Shulman, G. R., Yafet, Y., Eisenberger, P. & Blumberg, W. E. (1976). Proc. Natl. Acad. Sci. USA 73,
1384-1388.
Takigawa, I., Shimizu, K.-i., Tsuda, K. & Takakusagi, S. (2016). RSC Adv. 6, 52587-52595.
Wong, J., Lytle, F. W., Messmer, R. P. & Maylotte, D. H. (1984). Phys. Rev. B 30, 5596.

9

Journal of Synchrotron Radiation

research papers

A Challenge of Constructing an International XAFS Database
Kiyotaka Asakuraa*, Hitoshi Abebc and Masao KimurabcaInstitute for Catalysis, Hokkaido University, Kita 21-10 Kita, Sapporo, Hokkaido, 001-0021, Japanb

Photon Factory, Institute of Materials' Structure Science, High Energy Accelerator Research

Organization, Oho 1-1, Tsukuba, Ibaraki, 305-0801, Japanc

Department of Materials' Structure Science, School of High Energy Accelerator Science,

SOKENDAI(The Graduate University for Advanced Studies), Oho 1-1, Tsukuba, Ibaraki, 305-0801,
Japan
Correspondence email: askr@cat.hokudai.ac.jp

Abstract

This paper describes the present state of XAFS databases, particularly in Japan, andproposes future directions. International
collaboration is important for enlarging the

FeCl – doped PA

database for further development of XAFS
spectroscopy.

[NEt ][FeCl ]Keywords: XAFS database; automatic data
deposition; data repository system

database

X-ray absorption fine structure (XAFS)[Co(NH ) ][FeCl ]t / arb. units

1. Why we need an international XAFS

[NEt ] [FeCl ]2040

spectroscopy is a powerful technique for0

determining local structure in metals with no

Photon Energy / eV

60

long-range order (Iwasawa et al., 2016).

Figure 2 Fe K-edge XANES spectra of selected Fe

Because a continuum X-ray source is required,

chlorides. The pre-edge peak is set at 0 eV. The Fe

XAFS spectroscopy became a practicalchloride dopant was characterized by XAFS

characterization technique only after

spectroscopy. By comparing with reference

synchrotron radiation sources were developed.

compounds, the Fe species in the PA could be
identified as [FeCl4]-.

and t are absorption

coefficient and thickness of the sample. (reproduced
from (Asakura et al., 1985) with permission
Chemical Society of Japan copyright (1985)).
IMPORTANT: this document contains embedded data - to preserve data integrity, please ensure where possible that the IUCr
Word tools (available from http://journals.iucr.org/services/docxtemplate/) are installed when editing this document.

1

Journal of Synchrotron Radiation

research papers

Since the first measurements were
Synchrotron Radiation Lightsource(Kincaid & Eisenberger, 1975), large
quantities of XAFS data have beencollected. These data can be divided
into two groups: (1) referencecompounds with known structures andproperties and (2)unknown target
materials under investigation. The data
for the former group are important formaterials scientists who wish to
analyse the XAFS spectra of unknown
compounds by comparing them withthose of reference compounds. Figure 1
shows the XAFS spectra of different Fe

Edge peak intensity / arb. units

made by Eisenberger at the Stanford
5
1.0
3
0.5

2
E
B

H

4
F

I
G

D

C
1 A
0
50
100
150
200
250
Exchange reaction enthalpy / kJ m ol-1

Figure 1 Relationship between edge peakintensity for Ag (I) compounds and covalence(Miyamoto et al., 2010; Miyamoto et al.,2012). Reproduced with permission from
(Miyamoto et al. 2010). Copyright (2010)
American Chemical Society.

chloride compounds. Some compounds produce a remarkable pre-edge peak that can be assigned to a
1s-to-3d transition, which is dipole forbidden , though it becomes stronger when centrosymmetry is
broken in a tetrahedral structure (Asakura et al., 1985) (Shulman et al., 1976). Thus, the Fe chloride
species in FeCl3-doped polyacetylene (PA) can be identified by comparing to XAFS spectra ofreference compounds. A collection of some XAFS spectra may be especially important when XAFS
spectroscopy is performed by non-specialists. Collections of typical XAFS spectra are published in apaper form such as books. The Catalysis Society of Japan has published the Catalyst Handbook,which includes XAFS spectra of reference compounds containing catalytically important elements(Japan, 2008).
An open-access, Internet-based database of XAFS spectra in a digital form is more convenient for
all researchers to update and search data. Such a large, comprehensive database would be useful not
only for XAFS non-specialists but also for specialists who want to elucidate general concepts fromXAFS spectra. Figure 2 shows the relationship between the intensity of edge-peak of Ag+ L3 X-ray
absorption near edge structure (XANES) and the covalence of Ag compounds (Miyamoto et al., 2010;
Miyamoto et al., 2012), which demonstrates a positive correlation. Such examples can be found inother studies, such as Lytle’s white line analysis and Wong’s V oxide pre-edge and edge shift analysis(Lytle et al., 1979; Wong et al., 1984). Eventually, deep learning methods could derive such relations
easily and automatically if a large database of XAFS spectra was available and related to othermaterial databases (Takigawa et al., 2016).
2. Overview of currently available XAFS databases

2

Journal of Synchrotron Radiation

research papers

Several databases of XAFS spectra have been developed, as shown in Table 1. These databases are
free, and they generally permit open access. F.W. Lytle database has a long history, which is thelargest and perhaps most well-known XAFS database. SPring-8 BL14 database, which requires a user
ID and password to view and search data, has ample data (more than 800) for reference compounds.
Recently, “Photon Beam Platform”, a national project in Japan to promote the collaboration among
synchrotron radiation and laser facilities is carrying out round robin tests for XAFS data in a data
format of XML(eXtensible Markup Language). International proposal of round robin tests of
XAFS data has also been proposed (Chantller et al., 2018)
This paper focuses on the XAFS database developed as a collaboration between the Hokkaido
University Institute for Catalysis (ICAT) and the Japanese XAFS Society (JXS). We would like topropose an international collaboration to make a new big and open database for XAFS.
Table 1 Available XAFS databases (as of Dec. 31, 2017)
Database
F.W. Lytle
database

URL
http://ixs.iit.edu/database/Features
Text format with periodic table interface
All data obtained by F.W. Lytle
19,307 records covering 74 elements

CARS

http://cars.uchicago.edu/
xaslib/search

Text (XDI) format with periodic table interface andgraphical output of spectra (Newville et al., 2015)
171 records covering 13 elements
Measured at the Advanced Photon Source, SSRL, andNational Synchrotron Light Source
Includes suites (tagging-related spectra) and user ratings

SPring-8 BL14

https://sp8dr.spring8.or.jp/
portal/dspace

Only available to SPring-8 users
725 records
Compressed text file (ZIP) format with metadata that
contains vendor and lot number

EuropeanSynchrotron
Radiation
Facility, ID21
group

http://www.esrf.eu/home/
UsersAndScience

Hokkaido
University ICAT
and JXS

https://www.cat.hokudai.ac.
jp/catdb/index.php?
action=xafs_login_form&
opnid=2/Experiments/XNP/ID21/
php.html

Sulphur database
41 (inorganic) and 26 (organic) records for S compounds
Graphical output, but text format is available
User name is included
209 records and 24 elements
Text format with metadata
Includes user name, beam line, and facility
Open access, but data uploading is restricted to users with
ID and password

3

Journal of Synchrotron Radiation

research papers

3. ICAT XAFS database in Japan
3.1. History

The Hokkaido University ICAT started to build the XAFS database in 2011 as a project of the Joint
Usage/Research Center for catalysis, in collaboration with JXS. The database is accessible to anyone
through the Internet. Volunteers working in the XAFS field can register for an ID and password to
upload their data to the database. For security and traceability, data files contain the name of theperson who uploaded the data. The website is managed by ICAT.
3.2. Fundamental ICAT data policies

The basic policies of the ICAT XAFS database are as follows:
Volunteer base – Anyone who is registered can upload their data.
Open-access database – Anyone can see and use the data. They are asked include a citation in
published work if they used the data.
Simple dataset format – The data have a text-based format, and only the energy and t of theraw spectrum are recorded, in addition to some metadata.
Compatibility – Foil XAFS data that are measured at the same beam time and beam line aredeposited simultaneously to make energy calibration possible. Consequently, we can compare
the data measured at different beam times, beam lines, and facilities.
Target – Dataset includes primarily standard compounds with known structures.
Guarantee of accuracy – A “majority rule” approach is used to improve accuracy. The
database allows deposition of multiple records for the same compounds.
Each data file has a metadata area and a data area, as shown in Fig. 3. Table 2 lists the available
metadata fields in the ICAT database. Although detailed metadata are helpful, too many required
inputs will reduce the motivation of volunteers, so the number of metadata fields are kept as small as
possible.

4

Journal of Synchrotron Radiation

Table 2

research papers

Available metadata fields in ICAT database

Sample name
Structural details (powder, foil, solution)
Absorption atom
Edge
Reference sample (usually foil)
Date of measurement
Monochromator (crystal)
Facility
Beam line

Beam current (mA)
Beam energy of storage ring (GeV)
Higher harmonics rejection method
Focus
Detection method
I｡ and I gases if ionization chamber was used
Measurement temperature
Comments

Figure 3 ICAT data file structure5

Journal of Synchrotron Radiation

research papers

One of the most important policies is compatibility. Although absolute angle of eachmonochromator can be determined by Pettier’s method or other{Pettifer, 1985 #2007}, it is moreconvenient to calibrate each data using foil measured at the same time. The data are uploaded withthe foil data measured at the same time. It benefit us to obtain the signal-to-noise ratio (S/N) and theenergy resolution of the XAFS measurement systems by comparison with the foil XAFS data in
addition to adjust the energy scale from different files by comparison with the foil XAFS spectra.
Another important policy is the guarantee of accuracy, that is, the quality of each XAFS spectrum.
One way to guarantee accuracy is to permit only highly qualified researchers to measure spectra undera strict, specific protocol and upload the data in a rigorously controlled way. However, this would
require more qualified researchers, time, and money than are not generally available. Also, theamount of data stored per day would be limited and it would be hard to construct a large database.
ICAT uses another strategy for data quality, that is, majority rule. The volunteers, who are expected
to have average skill for measuring XAFS spectra and preparing datasets, measure the spectra andupload the data with the metadata. When many volunteers randomly and independently upload spectra,
eventually different versions of the same reference spectra are collected. These data points are
statistically distributed so that the average spectra and their error bars can be determined. Data that lie
within the error bars are reliable, but a spectrum lying outside this range is either wrong or represents
a different phase . Thus, multiple spectra of the same compound improve the quality of the database.
Once the several spectra of the same compound available, users check the accuracy by comparing thespectra by themselves.
4. Problems with existing ICAT database

Despite its usefulness, the ICAT database has several drawbacks. The first problem is the small
number of data files in the database. This makes it difficult to apply majority rule and derive effective
relationships between spectral features and material properties. A way is needed to get more data
effectively. The second problem is that the database is not linked to other material databases, such as
X-ray diffraction, optical spectra, and other physical and chemical properties. The third problem isthe format. ICAT database uses simple the text-base format. Several data formats have been proposed,such as CIF XAFS, XDI (eXtensible Data Interchange), JASON(JavaScript Object Notation), NeXus,
and HDF5 (Ascone et al., 2012; Ravel & Newville, 2016; Konnecke et al., 2015 ). The NeXus andHDF5 formats can store and manage imaging data written in a binary format. Adoption of NeXus or
HDF5 may be a good choice for a flexible database, but it must first be designed well after longdeliberation. Nevertheless, the text format with only energy and t data is simple, easy to implement,
and transferrable to other formats. Although continued discussion of the XAFS database format isneeded, it might be expedient to start database construction in a text format and convert the data to aunified format later.
6

Journal of Synchrotron Radiation

research papers

5. Future database development – Bigger is betterIn the future, computers will be able to automatically evaluate the correctness of spectra based on
majority rule. Even if information about a sample is inadequate, the computer could classify the
samples into several subsets. For example, if the sample name is entered only as TiO2, the spectra
would need to be associated with one of the three different crystalline forms of TiO2 – Rutile, Anatase,and Brookite. Thus, the computer would need to assign the spectra to one of these crystal forms using
other spectra data. Some spectra may be located between two of the groups, indicating a mixture, so it
is better to have more data of the same compounds available for comparison. A large database will
reduce the probability of misinterpretation and improve our understanding of the spectra. The future
direction of the XAFS database is to be bigger and more open. The majority rule, in combination withadvanced computing, such as artificial intelligence(AI), can work to reinforce data quality andreliability and to elucidate meaningful new concepts through deep learning. The problem is how toconstruct a larger database as mentioned above. Since we collect data manually at the moment, theICAT database only contains a limited number of data files. If the data were automatically stored in
an appropriate way, all measured data could be included in the database. Manual input would be
limited to metadata and clarification and categorization of data into spectra for reference or unknown
compounds.
Since most XAFS spectra are measured at synchrotron radiation facilities, we propose thefollowing system:
Store all data measured at these facilities automatically in the facility’s computer inappropriate formats and with metadata. Thus, each facility can constructthe larger database.
Then combine the databases from each facility by connection to the internet. Before thatcan be done, however, we need to decide on rules for data disclosure. The fundamental
principle should be that all scientific data must be open to the public eventually, but thedata owner rights and originality should be reserved.
Using these basic ideas, the data can be made accessible to the public but only after the agreement of
the data owners. This will allow data owners choose to keep their data confidential, but it is hopedthat they would release the data after the associated studies are published in the literature.
Data disclosure would be beneficial to our society in two ways: (1) the quantity of data in the
XAFS database would increase, improving its quality and accessibility for everyone and (2) the
quality and transparency of published research would be improved by disclosing the raw data. The
cooperation of publishers would be important, and it is hoped that they would require disclosure of the
raw XAFS data when a paper is accepted. Facilities could provide further support by making data
7

Journal of Synchrotron Radiation

research papers

disclosure contracts with all users before they start experiments. The raw data should also be madeavailable when a patent is established. In addition to these rules, all data should be disclosed after acertain period (10 years for example). Facilities should retain responsibility for data security andprotection; otherwise, users would not allow facilities to store their data.
One more important suggestion is to define a unique digital data number, similar to the digital
object identifier (DOI) for a published paper. A data identifier would allow the data to be cited when
it is used in a publication. This would increase the incentive for owners to upload and to open theirdata. Like the citation index for a paper, a user could benefit from the number of citations of their data.
This would provide further motivation to perform precise measurements and develop higher-quality
data. A suggested format for the data identifier is as follows:
XAFS_ATOM_EDGE_Measure_Time_ContactPerson (Name & ResearcherID or
ORCID)_Facility_BeamLine.
Note that the identifier must be automatically determined and unique.
The linkage of facility databases will be another important task, since XAFS data are notstandalone. To derive structure-property relationships, XAFS data need to be considered in thecontext of the physical and chemical properties of the measured material. To do this, a clear sample
name must be determined uniquely and universally. If the sample is a standard reference compound,
this should be clearly conveyed by some unique sample identifier. The Chemical Abstracts Service(CAS) number is the best choice the sample identifier because it will be comprehensive and make iteasier to associate the sample with physical and chemical properties. Moreover, the majority rule will
work more effectively because different files for the same material can be linked easily, possibly
automatically. The facilities could encourage input of the CAS number into the metadata by providing
a CAS number dictionary to users. The data owner should provide their own data name according tosome rule, such as:
CAS_Number_ChemicalComposition_Phase_DataOwner (ResearcherID or ORCID)_Comment (Origin) (13463-67-7_TiO2_Rutile_G-6052-2010_PurchaseFromWakoLotNo0001).
6. What to Do Next

We believe that an open XAFS database is necessary but also very useful. Some issues should be
set aside for now, and each facility should start to construct a database or repository of its own data,with the goal of eventual linkage to a larger database. We propose the following actions:
1. Ask all facilities to start collecting XAFS data.
2. Decide on simple naming rules for linkage to other databases.
3. Decide on naming rules for data files, along the lines of the DOI.
8

Journal of Synchrotron Radiation

research papers

4. Start the discussion for determining data release rules.
We hope we can discuss my proposal at the next Q2XAFS and at other meetings.

Acknowledgment
This work was supported by MEXT Joint Usage/Research Center Program (2010-2015, 2016-2011)
and the Accelerator Science Support Fund from the High Energy Accelerator Research Organization(KEK) (2010-2017) and CREST JST “Resolution Catalyst”. One of the author (KA) thanks to

the fruitful discussion with Committee of manufacturing process innovation by materials
informatics( Chair : Prof.Toyohiro Chikyo in NIMS)

7. References

Asakura, K., Ikemoto, I., Kuroda, H., Kobayashi, T. & Shirakawa, H. (1985). Bull.Chem.Soc.Jpn. 58,
2113-2120.
Ascone, I., Asakura, K., George, G. N. & Wakatsuki, S. (2012). J.Synchro.Rad 19, 349-350.
Chantller, C., T,, Bunker , B. A., Abe, H., Kimura, M., Newville, M. & Weltere, E. (2018).
J.Synchro.Rad submitted to the same issue
Iwasawa, Y., Asakura, K. & Tada, M. (2016). Editor. XAFS techniques for catalysts, nanomaterials,
and surfaces, Springer.
Japan, C. S. o. (2008). Editor. Catalyst Handbook, 1 ed. Tokyo: Kodan-sha Scientific.
Kincaid, B. M. & Eisenberger, P. (1975). Phys. Rev. Lett. 34, 1361-1364.
Konnecke, M., Akeroyd, F. A., Bernstein, H. J., Brewster, A. S., Campbell, S. I., Clausen, B., Cottrell,S., Hoffmann, J. U., Jemian, P. R., Mannicke, D., Osborn, R., Peterson, P. F., Richter, T.,
Suzuki, J., Watts, B., Wintersberger, E. & Wuttke, J. (2015). J.Appl.Crystallo. 48, 301-305.
Lytle, F. W., Wei, P. S. P., Greegor, R. B., Via, G. H. & Sinfelt, J. H. (1979). J.Chem.Phys. 70, 4849.
Miyamoto , T., Kitajima, Y. & Asakura, K. (2012). e-J. Surf. Sci. Nanotech. 10, 609-612.
Miyamoto, T., Niimi, H., Kitajima, Y., Naito, T. & Asakura, K. (2010). J.Phys.Chem. A 114, 40934098.
Newville, M., Ravel, B., Sole, V. A. & Wellenreuther, G. (2015). XAS-DataInterchange/specification/spec.md, https://github.com/XraySpectroscopy/XAS-DataInterchange/blob/master/specification/spec.md.
Ravel, B. & Newville, M. (2016). J.Phys.Conf.Ser., pp. 12148-12151. IOP Publishing.
Shulman, G. R., Yafet, Y., Eisenberger, P. & Blumberg, W. E. (1976). Proc. Natl. Acad. Sci. USA 73,
1384-1388.
Takigawa, I., Shimizu, K.-i., Tsuda, K. & Takakusagi, S. (2016). RSC Adv. 6, 52587-52595.
Wong, J., Lytle, F. W., Messmer, R. P. & Maylotte, D. H. (1984). Phys. Rev. B 30, 5596.

9

Journal of Synchrotron Radiation

research papers

A Challenge of Constructing an International XAFS Database
Kiyotaka Asakuraa*, Hitoshi Abebc and Masao KimurabcaInstitute for Catalysis, Hokkaido University, Kita 21-10 Kita, Sapporo, Hokkaido, 001-0021, Japanb

Photon Factory, Institute of Materials' Structure Science, High Energy Accelerator Research

Organization, Oho 1-1, Tsukuba, Ibaraki, 305-0801, Japanc

Department of Materials' Structure Science, School of High Energy Accelerator Science,

SOKENDAI(The Graduate University for Advanced Studies), Oho 1-1, Tsukuba, Ibaraki, 305-0801,
Japan
Correspondence email: askr@cat.hokudai.ac.jp

Abstract

This paper describes the present state of XAFS databases, particularly in Japan, andproposes future directions. International
collaboration is important for enlarging the

FeCl – doped PA

database for further development of XAFS
spectroscopy.

[NEt ][FeCl ]Keywords: XAFS database; automatic data
deposition; data repository system

database

X-ray absorption fine structure (XAFS)[Co(NH ) ][FeCl ]t / arb. units

1. Why we need an international XAFS

[NEt ] [FeCl ]2040

spectroscopy is a powerful technique for0

determining local structure in metals with no

Photon Energy / eV

60

long-range order (Iwasawa et al., 2016).

Figure 2 Fe K-edge XANES spectra of selected Fe

Because a continuum X-ray source is required,

chlorides. The pre-edge peak is set at 0 eV. The Fe

XAFS spectroscopy became a practicalchloride dopant was characterized by XAFS

characterization technique only after

spectroscopy. By comparing with reference

synchrotron radiation sources were developed.

compounds, the Fe species in the PA could be
identified as [FeCl4]-.

and t are absorption

coefficient and thickness of the sample. (reproduced
from (Asakura et al., 1985) with permission
Chemical Society of Japan copyright (1985)).
IMPORTANT: this document contains embedded data - to preserve data integrity, please ensure where possible that the IUCr
Word tools (available from http://journals.iucr.org/services/docxtemplate/) are installed when editing this document.

1

Journal of Synchrotron Radiation

research papers

Since the first measurements were
Synchrotron Radiation Lightsource(Kincaid & Eisenberger, 1975), large
quantities of XAFS data have beencollected. These data can be divided
into two groups: (1) referencecompounds with known structures andproperties and (2)unknown target
materials under investigation. The data
for the former group are important formaterials scientists who wish to
analyse the XAFS spectra of unknown
compounds by comparing them withthose of reference compounds. Figure 1
shows the XAFS spectra of different Fe

Edge peak intensity / arb. units

made by Eisenberger at the Stanford
5
1.0
3
0.5

2
E
B

H

4
F

I
G

D

C
1 A
0
50
100
150
200
250
Exchange reaction enthalpy / kJ m ol-1

Figure 1 Relationship between edge peakintensity for Ag (I) compounds and covalence(Miyamoto et al., 2010; Miyamoto et al.,2012). Reproduced with permission from
(Miyamoto et al. 2010). Copyright (2010)
American Chemical Society.

chloride compounds. Some compounds produce a remarkable pre-edge peak that can be assigned to a
1s-to-3d transition, which is dipole forbidden , though it becomes stronger when centrosymmetry is
broken in a tetrahedral structure (Asakura et al., 1985) (Shulman et al., 1976). Thus, the Fe chloride
species in FeCl3-doped polyacetylene (PA) can be identified by comparing to XAFS spectra ofreference compounds. A collection of some XAFS spectra may be especially important when XAFS
spectroscopy is performed by non-specialists. Collections of typical XAFS spectra are published in apaper form such as books. The Catalysis Society of Japan has published the Catalyst Handbook,which includes XAFS spectra of reference compounds containing catalytically important elements(Japan, 2008).
An open-access, Internet-based database of XAFS spectra in a digital form is more convenient for
all researchers to update and search data. Such a large, comprehensive database would be useful not
only for XAFS non-specialists but also for specialists who want to elucidate general concepts fromXAFS spectra. Figure 2 shows the relationship between the intensity of edge-peak of Ag+ L3 X-ray
absorption near edge structure (XANES) and the covalence of Ag compounds (Miyamoto et al., 2010;
Miyamoto et al., 2012), which demonstrates a positive correlation. Such examples can be found inother studies, such as Lytle’s white line analysis and Wong’s V oxide pre-edge and edge shift analysis(Lytle et al., 1979; Wong et al., 1984). Eventually, deep learning methods could derive such relations
easily and automatically if a large database of XAFS spectra was available and related to othermaterial databases (Takigawa et al., 2016).
2. Overview of currently available XAFS databases

2

Journal of Synchrotron Radiation

research papers

Several databases of XAFS spectra have been developed, as shown in Table 1. These databases are
free, and they generally permit open access. F.W. Lytle database has a long history, which is thelargest and perhaps most well-known XAFS database. SPring-8 BL14 database, which requires a user
ID and password to view and search data, has ample data (more than 800) for reference compounds.
Recently, “Photon Beam Platform”, a national project in Japan to promote the collaboration among
synchrotron radiation and laser facilities is carrying out round robin tests for XAFS data in a data
format of XML(eXtensible Markup Language). International proposal of round robin tests of
XAFS data has also been proposed (Chantller et al., 2018)
This paper focuses on the XAFS database developed as a collaboration between the Hokkaido
University Institute for Catalysis (ICAT) and the Japanese XAFS Society (JXS). We would like topropose an international collaboration to make a new big and open database for XAFS.
Table 1 Available XAFS databases (as of Dec. 31, 2017)
Database
F.W. Lytle
database

URL
http://ixs.iit.edu/database/Features
Text format with periodic table interface
All data obtained by F.W. Lytle
19,307 records covering 74 elements

CARS

http://cars.uchicago.edu/
xaslib/search

Text (XDI) format with periodic table interface andgraphical output of spectra (Newville et al., 2015)
171 records covering 13 elements
Measured at the Advanced Photon Source, SSRL, andNational Synchrotron Light Source
Includes suites (tagging-related spectra) and user ratings

SPring-8 BL14

https://sp8dr.spring8.or.jp/
portal/dspace

Only available to SPring-8 users
725 records
Compressed text file (ZIP) format with metadata that
contains vendor and lot number

EuropeanSynchrotron
Radiation
Facility, ID21
group

http://www.esrf.eu/home/
UsersAndScience

Hokkaido
University ICAT
and JXS

https://www.cat.hokudai.ac.
jp/catdb/index.php?
action=xafs_login_form&
opnid=2/Experiments/XNP/ID21/
php.html

Sulphur database
41 (inorganic) and 26 (organic) records for S compounds
Graphical output, but text format is available
User name is included
209 records and 24 elements
Text format with metadata
Includes user name, beam line, and facility
Open access, but data uploading is restricted to users with
ID and password

3

Journal of Synchrotron Radiation

research papers

3. ICAT XAFS database in Japan
3.1. History

The Hokkaido University ICAT started to build the XAFS database in 2011 as a project of the Joint
Usage/Research Center for catalysis, in collaboration with JXS. The database is accessible to anyone
through the Internet. Volunteers working in the XAFS field can register for an ID and password to
upload their data to the database. For security and traceability, data files contain the name of theperson who uploaded the data. The website is managed by ICAT.
3.2. Fundamental ICAT data policies

The basic policies of the ICAT XAFS database are as follows:
Volunteer base – Anyone who is registered can upload their data.
Open-access database – Anyone can see and use the data. They are asked include a citation in
published work if they used the data.
Simple dataset format – The data have a text-based format, and only the energy and t of theraw spectrum are recorded, in addition to some metadata.
Compatibility – Foil XAFS data that are measured at the same beam time and beam line aredeposited simultaneously to make energy calibration possible. Consequently, we can compare
the data measured at different beam times, beam lines, and facilities.
Target – Dataset includes primarily standard compounds with known structures.
Guarantee of accuracy – A “majority rule” approach is used to improve accuracy. The
database allows deposition of multiple records for the same compounds.
Each data file has a metadata area and a data area, as shown in Fig. 3. Table 2 lists the available
metadata fields in the ICAT database. Although detailed metadata are helpful, too many required
inputs will reduce the motivation of volunteers, so the number of metadata fields are kept as small as
possible.

4

Journal of Synchrotron Radiation

Table 2

research papers

Available metadata fields in ICAT database

Sample name
Structural details (powder, foil, solution)
Absorption atom
Edge
Reference sample (usually foil)
Date of measurement
Monochromator (crystal)
Facility
Beam line

Beam current (mA)
Beam energy of storage ring (GeV)
Higher harmonics rejection method
Focus
Detection method
I｡ and I gases if ionization chamber was used
Measurement temperature
Comments

Figure 3 ICAT data file structure5

Journal of Synchrotron Radiation

research papers

One of the most important policies is compatibility. Although absolute angle of eachmonochromator can be determined by Pettier’s method or other{Pettifer, 1985 #2007}, it is moreconvenient to calibrate each data using foil measured at the same time. The data are uploaded withthe foil data measured at the same time. It benefit us to obtain the signal-to-noise ratio (S/N) and theenergy resolution of the XAFS measurement systems by comparison with the foil XAFS data in
addition to adjust the energy scale from different files by comparison with the foil XAFS spectra.
Another important policy is the guarantee of accuracy, that is, the quality of each XAFS spectrum.
One way to guarantee accuracy is to permit only highly qualified researchers to measure spectra undera strict, specific protocol and upload the data in a rigorously controlled way. However, this would
require more qualified researchers, time, and money than are not generally available. Also, theamount of data stored per day would be limited and it would be hard to construct a large database.
ICAT uses another strategy for data quality, that is, majority rule. The volunteers, who are expected
to have average skill for measuring XAFS spectra and preparing datasets, measure the spectra andupload the data with the metadata. When many volunteers randomly and independently upload spectra,
eventually different versions of the same reference spectra are collected. These data points are
statistically distributed so that the average spectra and their error bars can be determined. Data that lie
within the error bars are reliable, but a spectrum lying outside this range is either wrong or represents
a different phase . Thus, multiple spectra of the same compound improve the quality of the database.
Once the several spectra of the same compound available, users check the accuracy by comparing thespectra by themselves.
4. Problems with existing ICAT database

Despite its usefulness, the ICAT database has several drawbacks. The first problem is the small
number of data files in the database. This makes it difficult to apply majority rule and derive effective
relationships between spectral features and material properties. A way is needed to get more data
effectively. The second problem is that the database is not linked to other material databases, such as
X-ray diffraction, optical spectra, and other physical and chemical properties. The third problem isthe format. ICAT database uses simple the text-base format. Several data formats have been proposed,such as CIF XAFS, XDI (eXtensible Data Interchange), JASON(JavaScript Object Notation), NeXus,
and HDF5 (Ascone et al., 2012; Ravel & Newville, 2016; Konnecke et al., 2015 ). The NeXus andHDF5 formats can store and manage imaging data written in a binary format. Adoption of NeXus or
HDF5 may be a good choice for a flexible database, but it must first be designed well after longdeliberation. Nevertheless, the text format with only energy and t data is simple, easy to implement,
and transferrable to other formats. Although continued discussion of the XAFS database format isneeded, it might be expedient to start database construction in a text format and convert the data to aunified format later.
6

Journal of Synchrotron Radiation

research papers

5. Future database development – Bigger is betterIn the future, computers will be able to automatically evaluate the correctness of spectra based on
majority rule. Even if information about a sample is inadequate, the computer could classify the
samples into several subsets. For example, if the sample name is entered only as TiO2, the spectra
would need to be associated with one of the three different crystalline forms of TiO2 – Rutile, Anatase,and Brookite. Thus, the computer would need to assign the spectra to one of these crystal forms using
other spectra data. Some spectra may be located between two of the groups, indicating a mixture, so it
is better to have more data of the same compounds available for comparison. A large database will
reduce the probability of misinterpretation and improve our understanding of the spectra. The future
direction of the XAFS database is to be bigger and more open. The majority rule, in combination withadvanced computing, such as artificial intelligence(AI), can work to reinforce data quality andreliability and to elucidate meaningful new concepts through deep learning. The problem is how toconstruct a larger database as mentioned above. Since we collect data manually at the moment, theICAT database only contains a limited number of data files. If the data were automatically stored in
an appropriate way, all measured data could be included in the database. Manual input would be
limited to metadata and clarification and categorization of data into spectra for reference or unknown
compounds.
Since most XAFS spectra are measured at synchrotron radiation facilities, we propose thefollowing system:
Store all data measured at these facilities automatically in the facility’s computer inappropriate formats and with metadata. Thus, each facility can constructthe larger database.
Then combine the databases from each facility by connection to the internet. Before thatcan be done, however, we need to decide on rules for data disclosure. The fundamental
principle should be that all scientific data must be open to the public eventually, but thedata owner rights and originality should be reserved.
Using these basic ideas, the data can be made accessible to the public but only after the agreement of
the data owners. This will allow data owners choose to keep their data confidential, but it is hopedthat they would release the data after the associated studies are published in the literature.
Data disclosure would be beneficial to our society in two ways: (1) the quantity of data in the
XAFS database would increase, improving its quality and accessibility for everyone and (2) the
quality and transparency of published research would be improved by disclosing the raw data. The
cooperation of publishers would be important, and it is hoped that they would require disclosure of the
raw XAFS data when a paper is accepted. Facilities could provide further support by making data
7

Journal of Synchrotron Radiation

research papers

disclosure contracts with all users before they start experiments. The raw data should also be madeavailable when a patent is established. In addition to these rules, all data should be disclosed after acertain period (10 years for example). Facilities should retain responsibility for data security andprotection; otherwise, users would not allow facilities to store their data.
One more important suggestion is to define a unique digital data number, similar to the digital
object identifier (DOI) for a published paper. A data identifier would allow the data to be cited when
it is used in a publication. This would increase the incentive for owners to upload and to open theirdata. Like the citation index for a paper, a user could benefit from the number of citations of their data.
This would provide further motivation to perform precise measurements and develop higher-quality
data. A suggested format for the data identifier is as follows:
XAFS_ATOM_EDGE_Measure_Time_ContactPerson (Name & ResearcherID or
ORCID)_Facility_BeamLine.
Note that the identifier must be automatically determined and unique.
The linkage of facility databases will be another important task, since XAFS data are notstandalone. To derive structure-property relationships, XAFS data need to be considered in thecontext of the physical and chemical properties of the measured material. To do this, a clear sample
name must be determined uniquely and universally. If the sample is a standard reference compound,
this should be clearly conveyed by some unique sample identifier. The Chemical Abstracts Service(CAS) number is the best choice the sample identifier because it will be comprehensive and make iteasier to associate the sample with physical and chemical properties. Moreover, the majority rule will
work more effectively because different files for the same material can be linked easily, possibly
automatically. The facilities could encourage input of the CAS number into the metadata by providing
a CAS number dictionary to users. The data owner should provide their own data name according tosome rule, such as:
CAS_Number_ChemicalComposition_Phase_DataOwner (ResearcherID or ORCID)_Comment (Origin) (13463-67-7_TiO2_Rutile_G-6052-2010_PurchaseFromWakoLotNo0001).
6. What to Do Next

We believe that an open XAFS database is necessary but also very useful. Some issues should be
set aside for now, and each facility should start to construct a database or repository of its own data,with the goal of eventual linkage to a larger database. We propose the following actions:
1. Ask all facilities to start collecting XAFS data.
2. Decide on simple naming rules for linkage to other databases.
3. Decide on naming rules for data files, along the lines of the DOI.
8

Journal of Synchrotron Radiation

research papers

4. Start the discussion for determining data release rules.
We hope we can discuss my proposal at the next Q2XAFS and at other meetings.

Acknowledgment
This work was supported by MEXT Joint Usage/Research Center Program (2010-2015, 2016-2011)
and the Accelerator Science Support Fund from the High Energy Accelerator Research Organization(KEK) (2010-2017) and CREST JST “Resolution Catalyst”. One of the author (KA) thanks to

the fruitful discussion with Committee of manufacturing process innovation by materials
informatics( Chair : Prof.Toyohiro Chikyo in NIMS)

7. References

Asakura, K., Ikemoto, I., Kuroda, H., Kobayashi, T. & Shirakawa, H. (1985). Bull.Chem.Soc.Jpn. 58,
2113-2120.
Ascone, I., Asakura, K., George, G. N. & Wakatsuki, S. (2012). J.Synchro.Rad 19, 349-350.
Chantller, C., T,, Bunker , B. A., Abe, H., Kimura, M., Newville, M. & Weltere, E. (2018).
J.Synchro.Rad submitted to the same issue
Iwasawa, Y., Asakura, K. & Tada, M. (2016). Editor. XAFS techniques for catalysts, nanomaterials,
and surfaces, Springer.
Japan, C. S. o. (2008). Editor. Catalyst Handbook, 1 ed. Tokyo: Kodan-sha Scientific.
Kincaid, B. M. & Eisenberger, P. (1975). Phys. Rev. Lett. 34, 1361-1364.
Konnecke, M., Akeroyd, F. A., Bernstein, H. J., Brewster, A. S., Campbell, S. I., Clausen, B., Cottrell,S., Hoffmann, J. U., Jemian, P. R., Mannicke, D., Osborn, R., Peterson, P. F., Richter, T.,
Suzuki, J., Watts, B., Wintersberger, E. & Wuttke, J. (2015). J.Appl.Crystallo. 48, 301-305.
Lytle, F. W., Wei, P. S. P., Greegor, R. B., Via, G. H. & Sinfelt, J. H. (1979). J.Chem.Phys. 70, 4849.
Miyamoto , T., Kitajima, Y. & Asakura, K. (2012). e-J. Surf. Sci. Nanotech. 10, 609-612.
Miyamoto, T., Niimi, H., Kitajima, Y., Naito, T. & Asakura, K. (2010). J.Phys.Chem. A 114, 40934098.
Newville, M., Ravel, B., Sole, V. A. & Wellenreuther, G. (2015). XAS-DataInterchange/specification/spec.md, https://github.com/XraySpectroscopy/XAS-DataInterchange/blob/master/specification/spec.md.
Ravel, B. & Newville, M. (2016). J.Phys.Conf.Ser., pp. 12148-12151. IOP Publishing.
Shulman, G. R., Yafet, Y., Eisenberger, P. & Blumberg, W. E. (1976). Proc. Natl. Acad. Sci. USA 73,
1384-1388.
Takigawa, I., Shimizu, K.-i., Tsuda, K. & Takakusagi, S. (2016). RSC Adv. 6, 52587-52595.
Wong, J., Lytle, F. W., Messmer, R. P. & Maylotte, D. H. (1984). Phys. Rev. B 30, 5596.

9

Journal of Synchrotron Radiation

research papers

A Challenge of Constructing an International XAFS Database
Kiyotaka Asakuraa*, Hitoshi Abebc and Masao KimurabcaInstitute for Catalysis, Hokkaido University, Kita 21-10 Kita, Sapporo, Hokkaido, 001-0021, Japanb

Photon Factory, Institute of Materials' Structure Science, High Energy Accelerator Research

Organization, Oho 1-1, Tsukuba, Ibaraki, 305-0801, Japanc

Department of Materials' Structure Science, School of High Energy Accelerator Science,

SOKENDAI(The Graduate University for Advanced Studies), Oho 1-1, Tsukuba, Ibaraki, 305-0801,
Japan
Correspondence email: askr@cat.hokudai.ac.jp

Abstract

This paper describes the present state of XAFS databases, particularly in Japan, andproposes future directions. International
collaboration is important for enlarging the

FeCl – doped PA

database for further development of XAFS
spectroscopy.

[NEt ][FeCl ]Keywords: XAFS database; automatic data
deposition; data repository system

database

X-ray absorption fine structure (XAFS)[Co(NH ) ][FeCl ]t / arb. units

1. Why we need an international XAFS

[NEt ] [FeCl ]2040

spectroscopy is a powerful technique for0

determining local structure in metals with no

Photon Energy / eV

60

long-range order (Iwasawa et al., 2016).

Figure 2 Fe K-edge XANES spectra of selected Fe

Because a continuum X-ray source is required,

chlorides. The pre-edge peak is set at 0 eV. The Fe

XAFS spectroscopy became a practicalchloride dopant was characterized by XAFS

characterization technique only after

spectroscopy. By comparing with reference

synchrotron radiation sources were developed.

compounds, the Fe species in the PA could be
identified as [FeCl4]-.

and t are absorption

coefficient and thickness of the sample. (reproduced
from (Asakura et al., 1985) with permission
Chemical Society of Japan copyright (1985)).
IMPORTANT: this document contains embedded data - to preserve data integrity, please ensure where possible that the IUCr
Word tools (available from http://journals.iucr.org/services/docxtemplate/) are installed when editing this document.

1

Journal of Synchrotron Radiation

research papers

Since the first measurements were
Synchrotron Radiation Lightsource(Kincaid & Eisenberger, 1975), large
quantities of XAFS data have beencollected. These data can be divided
into two groups: (1) referencecompounds with known structures andproperties and (2)unknown target
materials under investigation. The data
for the former group are important formaterials scientists who wish to
analyse the XAFS spectra of unknown
compounds by comparing them withthose of reference compounds. Figure 1
shows the XAFS spectra of different Fe

Edge peak intensity / arb. units

made by Eisenberger at the Stanford
5
1.0
3
0.5

2
E
B

H

4
F

I
G

D

C
1 A
0
50
100
150
200
250
Exchange reaction enthalpy / kJ m ol-1

Figure 1 Relationship between edge peakintensity for Ag (I) compounds and covalence(Miyamoto et al., 2010; Miyamoto et al.,2012). Reproduced with permission from
(Miyamoto et al. 2010). Copyright (2010)
American Chemical Society.

chloride compounds. Some compounds produce a remarkable pre-edge peak that can be assigned to a
1s-to-3d transition, which is dipole forbidden , though it becomes stronger when centrosymmetry is
broken in a tetrahedral structure (Asakura et al., 1985) (Shulman et al., 1976). Thus, the Fe chloride
species in FeCl3-doped polyacetylene (PA) can be identified by comparing to XAFS spectra ofreference compounds. A collection of some XAFS spectra may be especially important when XAFS
spectroscopy is performed by non-specialists. Collections of typical XAFS spectra are published in apaper form such as books. The Catalysis Society of Japan has published the Catalyst Handbook,which includes XAFS spectra of reference compounds containing catalytically important elements(Japan, 2008).
An open-access, Internet-based database of XAFS spectra in a digital form is more convenient for
all researchers to update and search data. Such a large, comprehensive database would be useful not
only for XAFS non-specialists but also for specialists who want to elucidate general concepts fromXAFS spectra. Figure 2 shows the relationship between the intensity of edge-peak of Ag+ L3 X-ray
absorption near edge structure (XANES) and the covalence of Ag compounds (Miyamoto et al., 2010;
Miyamoto et al., 2012), which demonstrates a positive correlation. Such examples can be found inother studies, such as Lytle’s white line analysis and Wong’s V oxide pre-edge and edge shift analysis(Lytle et al., 1979; Wong et al., 1984). Eventually, deep learning methods could derive such relations
easily and automatically if a large database of XAFS spectra was available and related to othermaterial databases (Takigawa et al., 2016).
2. Overview of currently available XAFS databases

2

Journal of Synchrotron Radiation

research papers

Several databases of XAFS spectra have been developed, as shown in Table 1. These databases are
free, and they generally permit open access. F.W. Lytle database has a long history, which is thelargest and perhaps most well-known XAFS database. SPring-8 BL14 database, which requires a user
ID and password to view and search data, has ample data (more than 800) for reference compounds.
Recently, “Photon Beam Platform”, a national project in Japan to promote the collaboration among
synchrotron radiation and laser facilities is carrying out round robin tests for XAFS data in a data
format of XML(eXtensible Markup Language). International proposal of round robin tests of
XAFS data has also been proposed (Chantller et al., 2018)
This paper focuses on the XAFS database developed as a collaboration between the Hokkaido
University Institute for Catalysis (ICAT) and the Japanese XAFS Society (JXS). We would like topropose an international collaboration to make a new big and open database for XAFS.
Table 1 Available XAFS databases (as of Dec. 31, 2017)
Database
F.W. Lytle
database

URL
http://ixs.iit.edu/database/Features
Text format with periodic table interface
All data obtained by F.W. Lytle
19,307 records covering 74 elements

CARS

http://cars.uchicago.edu/
xaslib/search

Text (XDI) format with periodic table interface andgraphical output of spectra (Newville et al., 2015)
171 records covering 13 elements
Measured at the Advanced Photon Source, SSRL, andNational Synchrotron Light Source
Includes suites (tagging-related spectra) and user ratings

SPring-8 BL14

https://sp8dr.spring8.or.jp/
portal/dspace

Only available to SPring-8 users
725 records
Compressed text file (ZIP) format with metadata that
contains vendor and lot number

EuropeanSynchrotron
Radiation
Facility, ID21
group

http://www.esrf.eu/home/
UsersAndScience

Hokkaido
University ICAT
and JXS

https://www.cat.hokudai.ac.
jp/catdb/index.php?
action=xafs_login_form&
opnid=2/Experiments/XNP/ID21/
php.html

Sulphur database
41 (inorganic) and 26 (organic) records for S compounds
Graphical output, but text format is available
User name is included
209 records and 24 elements
Text format with metadata
Includes user name, beam line, and facility
Open access, but data uploading is restricted to users with
ID and password

3

Journal of Synchrotron Radiation

research papers

3. ICAT XAFS database in Japan
3.1. History

The Hokkaido University ICAT started to build the XAFS database in 2011 as a project of the Joint
Usage/Research Center for catalysis, in collaboration with JXS. The database is accessible to anyone
through the Internet. Volunteers working in the XAFS field can register for an ID and password to
upload their data to the database. For security and traceability, data files contain the name of theperson who uploaded the data. The website is managed by ICAT.
3.2. Fundamental ICAT data policies

The basic policies of the ICAT XAFS database are as follows:
Volunteer base – Anyone who is registered can upload their data.
Open-access database – Anyone can see and use the data. They are asked include a citation in
published work if they used the data.
Simple dataset format – The data have a text-based format, and only the energy and t of theraw spectrum are recorded, in addition to some metadata.
Compatibility – Foil XAFS data that are measured at the same beam time and beam line aredeposited simultaneously to make energy calibration possible. Consequently, we can compare
the data measured at different beam times, beam lines, and facilities.
Target – Dataset includes primarily standard compounds with known structures.
Guarantee of accuracy – A “majority rule” approach is used to improve accuracy. The
database allows deposition of multiple records for the same compounds.
Each data file has a metadata area and a data area, as shown in Fig. 3. Table 2 lists the available
metadata fields in the ICAT database. Although detailed metadata are helpful, too many required
inputs will reduce the motivation of volunteers, so the number of metadata fields are kept as small as
possible.

4

Journal of Synchrotron Radiation

Table 2

research papers

Available metadata fields in ICAT database

Sample name
Structural details (powder, foil, solution)
Absorption atom
Edge
Reference sample (usually foil)
Date of measurement
Monochromator (crystal)
Facility
Beam line

Beam current (mA)
Beam energy of storage ring (GeV)
Higher harmonics rejection method
Focus
Detection method
I｡ and I gases if ionization chamber was used
Measurement temperature
Comments

Figure 3 ICAT data file structure5

Journal of Synchrotron Radiation

research papers

One of the most important policies is compatibility. Although absolute angle of eachmonochromator can be determined by Pettier’s method or other{Pettifer, 1985 #2007}, it is moreconvenient to calibrate each data using foil measured at the same time. The data are uploaded withthe foil data measured at the same time. It benefit us to obtain the signal-to-noise ratio (S/N) and theenergy resolution of the XAFS measurement systems by comparison with the foil XAFS data in
addition to adjust the energy scale from different files by comparison with the foil XAFS spectra.
Another important policy is the guarantee of accuracy, that is, the quality of each XAFS spectrum.
One way to guarantee accuracy is to permit only highly qualified researchers to measure spectra undera strict, specific protocol and upload the data in a rigorously controlled way. However, this would
require more qualified researchers, time, and money than are not generally available. Also, theamount of data stored per day would be limited and it would be hard to construct a large database.
ICAT uses another strategy for data quality, that is, majority rule. The volunteers, who are expected
to have average skill for measuring XAFS spectra and preparing datasets, measure the spectra andupload the data with the metadata. When many volunteers randomly and independently upload spectra,
eventually different versions of the same reference spectra are collected. These data points are
statistically distributed so that the average spectra and their error bars can be determined. Data that lie
within the error bars are reliable, but a spectrum lying outside this range is either wrong or represents
a different phase . Thus, multiple spectra of the same compound improve the quality of the database.
Once the several spectra of the same compound available, users check the accuracy by comparing thespectra by themselves.
4. Problems with existing ICAT database

Despite its usefulness, the ICAT database has several drawbacks. The first problem is the small
number of data files in the database. This makes it difficult to apply majority rule and derive effective
relationships between spectral features and material properties. A way is needed to get more data
effectively. The second problem is that the database is not linked to other material databases, such as
X-ray diffraction, optical spectra, and other physical and chemical properties. The third problem isthe format. ICAT database uses simple the text-base format. Several data formats have been proposed,such as CIF XAFS, XDI (eXtensible Data Interchange), JASON(JavaScript Object Notation), NeXus,
and HDF5 (Ascone et al., 2012; Ravel & Newville, 2016; Konnecke et al., 2015 ). The NeXus andHDF5 formats can store and manage imaging data written in a binary format. Adoption of NeXus or
HDF5 may be a good choice for a flexible database, but it must first be designed well after longdeliberation. Nevertheless, the text format with only energy and t data is simple, easy to implement,
and transferrable to other formats. Although continued discussion of the XAFS database format isneeded, it might be expedient to start database construction in a text format and convert the data to aunified format later.
6

Journal of Synchrotron Radiation

research papers

5. Future database development – Bigger is betterIn the future, computers will be able to automatically evaluate the correctness of spectra based on
majority rule. Even if information about a sample is inadequate, the computer could classify the
samples into several subsets. For example, if the sample name is entered only as TiO2, the spectra
would need to be associated with one of the three different crystalline forms of TiO2 – Rutile, Anatase,and Brookite. Thus, the computer would need to assign the spectra to one of these crystal forms using
other spectra data. Some spectra may be located between two of the groups, indicating a mixture, so it
is better to have more data of the same compounds available for comparison. A large database will
reduce the probability of misinterpretation and improve our understanding of the spectra. The future
direction of the XAFS database is to be bigger and more open. The majority rule, in combination withadvanced computing, such as artificial intelligence(AI), can work to reinforce data quality andreliability and to elucidate meaningful new concepts through deep learning. The problem is how toconstruct a larger database as mentioned above. Since we collect data manually at the moment, theICAT database only contains a limited number of data files. If the data were automatically stored in
an appropriate way, all measured data could be included in the database. Manual input would be
limited to metadata and clarification and categorization of data into spectra for reference or unknown
compounds.
Since most XAFS spectra are measured at synchrotron radiation facilities, we propose thefollowing system:
Store all data measured at these facilities automatically in the facility’s computer inappropriate formats and with metadata. Thus, each facility can constructthe larger database.
Then combine the databases from each facility by connection to the internet. Before thatcan be done, however, we need to decide on rules for data disclosure. The fundamental
principle should be that all scientific data must be open to the public eventually, but thedata owner rights and originality should be reserved.
Using these basic ideas, the data can be made accessible to the public but only after the agreement of
the data owners. This will allow data owners choose to keep their data confidential, but it is hopedthat they would release the data after the associated studies are published in the literature.
Data disclosure would be beneficial to our society in two ways: (1) the quantity of data in the
XAFS database would increase, improving its quality and accessibility for everyone and (2) the
quality and transparency of published research would be improved by disclosing the raw data. The
cooperation of publishers would be important, and it is hoped that they would require disclosure of the
raw XAFS data when a paper is accepted. Facilities could provide further support by making data
7

Journal of Synchrotron Radiation

research papers

disclosure contracts with all users before they start experiments. The raw data should also be madeavailable when a patent is established. In addition to these rules, all data should be disclosed after acertain period (10 years for example). Facilities should retain responsibility for data security andprotection; otherwise, users would not allow facilities to store their data.
One more important suggestion is to define a unique digital data number, similar to the digital
object identifier (DOI) for a published paper. A data identifier would allow the data to be cited when
it is used in a publication. This would increase the incentive for owners to upload and to open theirdata. Like the citation index for a paper, a user could benefit from the number of citations of their data.
This would provide further motivation to perform precise measurements and develop higher-quality
data. A suggested format for the data identifier is as follows:
XAFS_ATOM_EDGE_Measure_Time_ContactPerson (Name & ResearcherID or
ORCID)_Facility_BeamLine.
Note that the identifier must be automatically determined and unique.
The linkage of facility databases will be another important task, since XAFS data are notstandalone. To derive structure-property relationships, XAFS data need to be considered in thecontext of the physical and chemical properties of the measured material. To do this, a clear sample
name must be determined uniquely and universally. If the sample is a standard reference compound,
this should be clearly conveyed by some unique sample identifier. The Chemical Abstracts Service(CAS) number is the best choice the sample identifier because it will be comprehensive and make iteasier to associate the sample with physical and chemical properties. Moreover, the majority rule will
work more effectively because different files for the same material can be linked easily, possibly
automatically. The facilities could encourage input of the CAS number into the metadata by providing
a CAS number dictionary to users. The data owner should provide their own data name according tosome rule, such as:
CAS_Number_ChemicalComposition_Phase_DataOwner (ResearcherID or ORCID)_Comment (Origin) (13463-67-7_TiO2_Rutile_G-6052-2010_PurchaseFromWakoLotNo0001).
6. What to Do Next

We believe that an open XAFS database is necessary but also very useful. Some issues should be
set aside for now, and each facility should start to construct a database or repository of its own data,with the goal of eventual linkage to a larger database. We propose the following actions:
1. Ask all facilities to start collecting XAFS data.
2. Decide on simple naming rules for linkage to other databases.
3. Decide on naming rules for data files, along the lines of the DOI.
8

Journal of Synchrotron Radiation

research papers

4. Start the discussion for determining data release rules.
We hope we can discuss my proposal at the next Q2XAFS and at other meetings.

Acknowledgment
This work was supported by MEXT Joint Usage/Research Center Program (2010-2015, 2016-2011)
and the Accelerator Science Support Fund from the High Energy Accelerator Research Organization(KEK) (2010-2017) and CREST JST “Resolution Catalyst”. One of the author (KA) thanks to

the fruitful discussion with Committee of manufacturing process innovation by materials
informatics( Chair : Prof.Toyohiro Chikyo in NIMS)

7. References

Asakura, K., Ikemoto, I., Kuroda, H., Kobayashi, T. & Shirakawa, H. (1985). Bull.Chem.Soc.Jpn. 58,
2113-2120.
Ascone, I., Asakura, K., George, G. N. & Wakatsuki, S. (2012). J.Synchro.Rad 19, 349-350.
Chantller, C., T,, Bunker , B. A., Abe, H., Kimura, M., Newville, M. & Weltere, E. (2018).
J.Synchro.Rad submitted to the same issue
Iwasawa, Y., Asakura, K. & Tada, M. (2016). Editor. XAFS techniques for catalysts, nanomaterials,
and surfaces, Springer.
Japan, C. S. o. (2008). Editor. Catalyst Handbook, 1 ed. Tokyo: Kodan-sha Scientific.
Kincaid, B. M. & Eisenberger, P. (1975). Phys. Rev. Lett. 34, 1361-1364.
Konnecke, M., Akeroyd, F. A., Bernstein, H. J., Brewster, A. S., Campbell, S. I., Clausen, B., Cottrell,S., Hoffmann, J. U., Jemian, P. R., Mannicke, D., Osborn, R., Peterson, P. F., Richter, T.,
Suzuki, J., Watts, B., Wintersberger, E. & Wuttke, J. (2015). J.Appl.Crystallo. 48, 301-305.
Lytle, F. W., Wei, P. S. P., Greegor, R. B., Via, G. H. & Sinfelt, J. H. (1979). J.Chem.Phys. 70, 4849.
Miyamoto , T., Kitajima, Y. & Asakura, K. (2012). e-J. Surf. Sci. Nanotech. 10, 609-612.
Miyamoto, T., Niimi, H., Kitajima, Y., Naito, T. & Asakura, K. (2010). J.Phys.Chem. A 114, 40934098.
Newville, M., Ravel, B., Sole, V. A. & Wellenreuther, G. (2015). XAS-DataInterchange/specification/spec.md, https://github.com/XraySpectroscopy/XAS-DataInterchange/blob/master/specification/spec.md.
Ravel, B. & Newville, M. (2016). J.Phys.Conf.Ser., pp. 12148-12151. IOP Publishing.
Shulman, G. R., Yafet, Y., Eisenberger, P. & Blumberg, W. E. (1976). Proc. Natl. Acad. Sci. USA 73,
1384-1388.
Takigawa, I., Shimizu, K.-i., Tsuda, K. & Takakusagi, S. (2016). RSC Adv. 6, 52587-52595.
Wong, J., Lytle, F. W., Messmer, R. P. & Maylotte, D. H. (1984). Phys. Rev. B 30, 5596.

9

Journal of Synchrotron Radiation

research papers

A Challenge of Constructing an International XAFS Database
Kiyotaka Asakuraa*, Hitoshi Abebc and Masao KimurabcaInstitute for Catalysis, Hokkaido University, Kita 21-10 Kita, Sapporo, Hokkaido, 001-0021, Japanb

Photon Factory, Institute of Materials' Structure Science, High Energy Accelerator Research

Organization, Oho 1-1, Tsukuba, Ibaraki, 305-0801, Japanc

Department of Materials' Structure Science, School of High Energy Accelerator Science,

SOKENDAI(The Graduate University for Advanced Studies), Oho 1-1, Tsukuba, Ibaraki, 305-0801,
Japan
Correspondence email: askr@cat.hokudai.ac.jp

Abstract

This paper describes the present state of XAFS databases, particularly in Japan, andproposes future directions. International
collaboration is important for enlarging the

FeCl – doped PA

database for further development of XAFS
spectroscopy.

[NEt ][FeCl ]Keywords: XAFS database; automatic data
deposition; data repository system

database

X-ray absorption fine structure (XAFS)[Co(NH ) ][FeCl ]t / arb. units

1. Why we need an international XAFS

[NEt ] [FeCl ]2040

spectroscopy is a powerful technique for0

determining local structure in metals with no

Photon Energy / eV

60

long-range order (Iwasawa et al., 2016).

Figure 2 Fe K-edge XANES spectra of selected Fe

Because a continuum X-ray source is required,

chlorides. The pre-edge peak is set at 0 eV. The Fe

XAFS spectroscopy became a practicalchloride dopant was characterized by XAFS

characterization technique only after

spectroscopy. By comparing with reference

synchrotron radiation sources were developed.

compounds, the Fe species in the PA could be
identified as [FeCl4]-.

and t are absorption

coefficient and thickness of the sample. (reproduced
from (Asakura et al., 1985) with permission
Chemical Society of Japan copyright (1985)).
IMPORTANT: this document contains embedded data - to preserve data integrity, please ensure where possible that the IUCr
Word tools (available from http://journals.iucr.org/services/docxtemplate/) are installed when editing this document.

1

Journal of Synchrotron Radiation

research papers

Since the first measurements were
Synchrotron Radiation Lightsource(Kincaid & Eisenberger, 1975), large
quantities of XAFS data have beencollected. These data can be divided
into two groups: (1) referencecompounds with known structures andproperties and (2)unknown target
materials under investigation. The data
for the former group are important formaterials scientists who wish to
analyse the XAFS spectra of unknown
compounds by comparing them withthose of reference compounds. Figure 1
shows the XAFS spectra of different Fe

Edge peak intensity / arb. units

made by Eisenberger at the Stanford
5
1.0
3
0.5

2
E
B

H

4
F

I
G

D

C
1 A
0
50
100
150
200
250
Exchange reaction enthalpy / kJ m ol-1

Figure 1 Relationship between edge peakintensity for Ag (I) compounds and covalence(Miyamoto et al., 2010; Miyamoto et al.,2012). Reproduced with permission from
(Miyamoto et al. 2010). Copyright (2010)
American Chemical Society.

chloride compounds. Some compounds produce a remarkable pre-edge peak that can be assigned to a
1s-to-3d transition, which is dipole forbidden , though it becomes stronger when centrosymmetry is
broken in a tetrahedral structure (Asakura et al., 1985) (Shulman et al., 1976). Thus, the Fe chloride
species in FeCl3-doped polyacetylene (PA) can be identified by comparing to XAFS spectra ofreference compounds. A collection of some XAFS spectra may be especially important when XAFS
spectroscopy is performed by non-specialists. Collections of typical XAFS spectra are published in apaper form such as books. The Catalysis Society of Japan has published the Catalyst Handbook,which includes XAFS spectra of reference compounds containing catalytically important elements(Japan, 2008).
An open-access, Internet-based database of XAFS spectra in a digital form is more convenient for
all researchers to update and search data. Such a large, comprehensive database would be useful not
only for XAFS non-specialists but also for specialists who want to elucidate general concepts fromXAFS spectra. Figure 2 shows the relationship between the intensity of edge-peak of Ag+ L3 X-ray
absorption near edge structure (XANES) and the covalence of Ag compounds (Miyamoto et al., 2010;
Miyamoto et al., 2012), which demonstrates a positive correlation. Such examples can be found inother studies, such as Lytle’s white line analysis and Wong’s V oxide pre-edge and edge shift analysis(Lytle et al., 1979; Wong et al., 1984). Eventually, deep learning methods could derive such relations
easily and automatically if a large database of XAFS spectra was available and related to othermaterial databases (Takigawa et al., 2016).
2. Overview of currently available XAFS databases

2

Journal of Synchrotron Radiation

research papers

Several databases of XAFS spectra have been developed, as shown in Table 1. These databases are
free, and they generally permit open access. F.W. Lytle database has a long history, which is thelargest and perhaps most well-known XAFS database. SPring-8 BL14 database, which requires a user
ID and password to view and search data, has ample data (more than 800) for reference compounds.
Recently, “Photon Beam Platform”, a national project in Japan to promote the collaboration among
synchrotron radiation and laser facilities is carrying out round robin tests for XAFS data in a data
format of XML(eXtensible Markup Language). International proposal of round robin tests of
XAFS data has also been proposed (Chantller et al., 2018)
This paper focuses on the XAFS database developed as a collaboration between the Hokkaido
University Institute for Catalysis (ICAT) and the Japanese XAFS Society (JXS). We would like topropose an international collaboration to make a new big and open database for XAFS.
Table 1 Available XAFS databases (as of Dec. 31, 2017)
Database
F.W. Lytle
database

URL
http://ixs.iit.edu/database/Features
Text format with periodic table interface
All data obtained by F.W. Lytle
19,307 records covering 74 elements

CARS

http://cars.uchicago.edu/
xaslib/search

Text (XDI) format with periodic table interface andgraphical output of spectra (Newville et al., 2015)
171 records covering 13 elements
Measured at the Advanced Photon Source, SSRL, andNational Synchrotron Light Source
Includes suites (tagging-related spectra) and user ratings

SPring-8 BL14

https://sp8dr.spring8.or.jp/
portal/dspace

Only available to SPring-8 users
725 records
Compressed text file (ZIP) format with metadata that
contains vendor and lot number

EuropeanSynchrotron
Radiation
Facility, ID21
group

http://www.esrf.eu/home/
UsersAndScience

Hokkaido
University ICAT
and JXS

https://www.cat.hokudai.ac.
jp/catdb/index.php?
action=xafs_login_form&
opnid=2/Experiments/XNP/ID21/
php.html

Sulphur database
41 (inorganic) and 26 (organic) records for S compounds
Graphical output, but text format is available
User name is included
209 records and 24 elements
Text format with metadata
Includes user name, beam line, and facility
Open access, but data uploading is restricted to users with
ID and password

3

Journal of Synchrotron Radiation

research papers

3. ICAT XAFS database in Japan
3.1. History

The Hokkaido University ICAT started to build the XAFS database in 2011 as a project of the Joint
Usage/Research Center for catalysis, in collaboration with JXS. The database is accessible to anyone
through the Internet. Volunteers working in the XAFS field can register for an ID and password to
upload their data to the database. For security and traceability, data files contain the name of theperson who uploaded the data. The website is managed by ICAT.
3.2. Fundamental ICAT data policies

The basic policies of the ICAT XAFS database are as follows:
Volunteer base – Anyone who is registered can upload their data.
Open-access database – Anyone can see and use the data. They are asked include a citation in
published work if they used the data.
Simple dataset format – The data have a text-based format, and only the energy and t of theraw spectrum are recorded, in addition to some metadata.
Compatibility – Foil XAFS data that are measured at the same beam time and beam line aredeposited simultaneously to make energy calibration possible. Consequently, we can compare
the data measured at different beam times, beam lines, and facilities.
Target – Dataset includes primarily standard compounds with known structures.
Guarantee of accuracy – A “majority rule” approach is used to improve accuracy. The
database allows deposition of multiple records for the same compounds.
Each data file has a metadata area and a data area, as shown in Fig. 3. Table 2 lists the available
metadata fields in the ICAT database. Although detailed metadata are helpful, too many required
inputs will reduce the motivation of volunteers, so the number of metadata fields are kept as small as
possible.

4

Journal of Synchrotron Radiation

Table 2

research papers

Available metadata fields in ICAT database

Sample name
Structural details (powder, foil, solution)
Absorption atom
Edge
Reference sample (usually foil)
Date of measurement
Monochromator (crystal)
Facility
Beam line

Beam current (mA)
Beam energy of storage ring (GeV)
Higher harmonics rejection method
Focus
Detection method
I｡ and I gases if ionization chamber was used
Measurement temperature
Comments

Figure 3 ICAT data file structure5

Journal of Synchrotron Radiation

research papers

One of the most important policies is compatibility. Although absolute angle of eachmonochromator can be determined by Pettier’s method or other{Pettifer, 1985 #2007}, it is moreconvenient to calibrate each data using foil measured at the same time. The data are uploaded withthe foil data measured at the same time. It benefit us to obtain the signal-to-noise ratio (S/N) and theenergy resolution of the XAFS measurement systems by comparison with the foil XAFS data in
addition to adjust the energy scale from different files by comparison with the foil XAFS spectra.
Another important policy is the guarantee of accuracy, that is, the quality of each XAFS spectrum.
One way to guarantee accuracy is to permit only highly qualified researchers to measure spectra undera strict, specific protocol and upload the data in a rigorously controlled way. However, this would
require more qualified researchers, time, and money than are not generally available. Also, theamount of data stored per day would be limited and it would be hard to construct a large database.
ICAT uses another strategy for data quality, that is, majority rule. The volunteers, who are expected
to have average skill for measuring XAFS spectra and preparing datasets, measure the spectra andupload the data with the metadata. When many volunteers randomly and independently upload spectra,
eventually different versions of the same reference spectra are collected. These data points are
statistically distributed so that the average spectra and their error bars can be determined. Data that lie
within the error bars are reliable, but a spectrum lying outside this range is either wrong or represents
a different phase . Thus, multiple spectra of the same compound improve the quality of the database.
Once the several spectra of the same compound available, users check the accuracy by comparing thespectra by themselves.
4. Problems with existing ICAT database

Despite its usefulness, the ICAT database has several drawbacks. The first problem is the small
number of data files in the database. This makes it difficult to apply majority rule and derive effective
relationships between spectral features and material properties. A way is needed to get more data
effectively. The second problem is that the database is not linked to other material databases, such as
X-ray diffraction, optical spectra, and other physical and chemical properties. The third problem isthe format. ICAT database uses simple the text-base format. Several data formats have been proposed,such as CIF XAFS, XDI (eXtensible Data Interchange), JASON(JavaScript Object Notation), NeXus,
and HDF5 (Ascone et al., 2012; Ravel & Newville, 2016; Konnecke et al., 2015 ). The NeXus andHDF5 formats can store and manage imaging data written in a binary format. Adoption of NeXus or
HDF5 may be a good choice for a flexible database, but it must first be designed well after longdeliberation. Nevertheless, the text format with only energy and t data is simple, easy to implement,
and transferrable to other formats. Although continued discussion of the XAFS database format isneeded, it might be expedient to start database construction in a text format and convert the data to aunified format later.
6

Journal of Synchrotron Radiation

research papers

5. Future database development – Bigger is betterIn the future, computers will be able to automatically evaluate the correctness of spectra based on
majority rule. Even if information about a sample is inadequate, the computer could classify the
samples into several subsets. For example, if the sample name is entered only as TiO2, the spectra
would need to be associated with one of the three different crystalline forms of TiO2 – Rutile, Anatase,and Brookite. Thus, the computer would need to assign the spectra to one of these crystal forms using
other spectra data. Some spectra may be located between two of the groups, indicating a mixture, so it
is better to have more data of the same compounds available for comparison. A large database will
reduce the probability of misinterpretation and improve our understanding of the spectra. The future
direction of the XAFS database is to be bigger and more open. The majority rule, in combination withadvanced computing, such as artificial intelligence(AI), can work to reinforce data quality andreliability and to elucidate meaningful new concepts through deep learning. The problem is how toconstruct a larger database as mentioned above. Since we collect data manually at the moment, theICAT database only contains a limited number of data files. If the data were automatically stored in
an appropriate way, all measured data could be included in the database. Manual input would be
limited to metadata and clarification and categorization of data into spectra for reference or unknown
compounds.
Since most XAFS spectra are measured at synchrotron radiation facilities, we propose thefollowing system:
Store all data measured at these facilities automatically in the facility’s computer inappropriate formats and with metadata. Thus, each facility can constructthe larger database.
Then combine the databases from each facility by connection to the internet. Before thatcan be done, however, we need to decide on rules for data disclosure. The fundamental
principle should be that all scientific data must be open to the public eventually, but thedata owner rights and originality should be reserved.
Using these basic ideas, the data can be made accessible to the public but only after the agreement of
the data owners. This will allow data owners choose to keep their data confidential, but it is hopedthat they would release the data after the associated studies are published in the literature.
Data disclosure would be beneficial to our society in two ways: (1) the quantity of data in the
XAFS database would increase, improving its quality and accessibility for everyone and (2) the
quality and transparency of published research would be improved by disclosing the raw data. The
cooperation of publishers would be important, and it is hoped that they would require disclosure of the
raw XAFS data when a paper is accepted. Facilities could provide further support by making data
7

Journal of Synchrotron Radiation

research papers

disclosure contracts with all users before they start experiments. The raw data should also be madeavailable when a patent is established. In addition to these rules, all data should be disclosed after acertain period (10 years for example). Facilities should retain responsibility for data security andprotection; otherwise, users would not allow facilities to store their data.
One more important suggestion is to define a unique digital data number, similar to the digital
object identifier (DOI) for a published paper. A data identifier would allow the data to be cited when
it is used in a publication. This would increase the incentive for owners to upload and to open theirdata. Like the citation index for a paper, a user could benefit from the number of citations of their data.
This would provide further motivation to perform precise measurements and develop higher-quality
data. A suggested format for the data identifier is as follows:
XAFS_ATOM_EDGE_Measure_Time_ContactPerson (Name & ResearcherID or
ORCID)_Facility_BeamLine.
Note that the identifier must be automatically determined and unique.
The linkage of facility databases will be another important task, since XAFS data are notstandalone. To derive structure-property relationships, XAFS data need to be considered in thecontext of the physical and chemical properties of the measured material. To do this, a clear sample
name must be determined uniquely and universally. If the sample is a standard reference compound,
this should be clearly conveyed by some unique sample identifier. The Chemical Abstracts Service(CAS) number is the best choice the sample identifier because it will be comprehensive and make iteasier to associate the sample with physical and chemical properties. Moreover, the majority rule will
work more effectively because different files for the same material can be linked easily, possibly
automatically. The facilities could encourage input of the CAS number into the metadata by providing
a CAS number dictionary to users. The data owner should provide their own data name according tosome rule, such as:
CAS_Number_ChemicalComposition_Phase_DataOwner (ResearcherID or ORCID)_Comment (Origin) (13463-67-7_TiO2_Rutile_G-6052-2010_PurchaseFromWakoLotNo0001).
6. What to Do Next

We believe that an open XAFS database is necessary but also very useful. Some issues should be
set aside for now, and each facility should start to construct a database or repository of its own data,with the goal of eventual linkage to a larger database. We propose the following actions:
1. Ask all facilities to start collecting XAFS data.
2. Decide on simple naming rules for linkage to other databases.
3. Decide on naming rules for data files, along the lines of the DOI.
8

Journal of Synchrotron Radiation

research papers

4. Start the discussion for determining data release rules.
We hope we can discuss my proposal at the next Q2XAFS and at other meetings.

Acknowledgment
This work was supported by MEXT Joint Usage/Research Center Program (2010-2015, 2016-2011)
and the Accelerator Science Support Fund from the High Energy Accelerator Research Organization(KEK) (2010-2017) and CREST JST “Resolution Catalyst”. One of the author (KA) thanks to

the fruitful discussion with Committee of manufacturing process innovation by materials
informatics( Chair : Prof.Toyohiro Chikyo in NIMS)

7. References

Asakura, K., Ikemoto, I., Kuroda, H., Kobayashi, T. & Shirakawa, H. (1985). Bull.Chem.Soc.Jpn. 58,
2113-2120.
Ascone, I., Asakura, K., George, G. N. & Wakatsuki, S. (2012). J.Synchro.Rad 19, 349-350.
Chantller, C., T,, Bunker , B. A., Abe, H., Kimura, M., Newville, M. & Weltere, E. (2018).
J.Synchro.Rad submitted to the same issue
Iwasawa, Y., Asakura, K. & Tada, M. (2016). Editor. XAFS techniques for catalysts, nanomaterials,
and surfaces, Springer.
Japan, C. S. o. (2008). Editor. Catalyst Handbook, 1 ed. Tokyo: Kodan-sha Scientific.
Kincaid, B. M. & Eisenberger, P. (1975). Phys. Rev. Lett. 34, 1361-1364.
Konnecke, M., Akeroyd, F. A., Bernstein, H. J., Brewster, A. S., Campbell, S. I., Clausen, B., Cottrell,S., Hoffmann, J. U., Jemian, P. R., Mannicke, D., Osborn, R., Peterson, P. F., Richter, T.,
Suzuki, J., Watts, B., Wintersberger, E. & Wuttke, J. (2015). J.Appl.Crystallo. 48, 301-305.
Lytle, F. W., Wei, P. S. P., Greegor, R. B., Via, G. H. & Sinfelt, J. H. (1979). J.Chem.Phys. 70, 4849.
Miyamoto , T., Kitajima, Y. & Asakura, K. (2012). e-J. Surf. Sci. Nanotech. 10, 609-612.
Miyamoto, T., Niimi, H., Kitajima, Y., Naito, T. & Asakura, K. (2010). J.Phys.Chem. A 114, 40934098.
Newville, M., Ravel, B., Sole, V. A. & Wellenreuther, G. (2015). XAS-DataInterchange/specification/spec.md, https://github.com/XraySpectroscopy/XAS-DataInterchange/blob/master/specification/spec.md.
Ravel, B. & Newville, M. (2016). J.Phys.Conf.Ser., pp. 12148-12151. IOP Publishing.
Shulman, G. R., Yafet, Y., Eisenberger, P. & Blumberg, W. E. (1976). Proc. Natl. Acad. Sci. USA 73,
1384-1388.
Takigawa, I., Shimizu, K.-i., Tsuda, K. & Takakusagi, S. (2016). RSC Adv. 6, 52587-52595.
Wong, J., Lytle, F. W., Messmer, R. P. & Maylotte, D. H. (1984). Phys. Rev. B 30, 5596.

9

Journal of Synchrotron Radiation

research papers

A Challenge of Constructing an International XAFS Database
Kiyotaka Asakuraa*, Hitoshi Abebc and Masao KimurabcaInstitute for Catalysis, Hokkaido University, Kita 21-10 Kita, Sapporo, Hokkaido, 001-0021, Japanb

Photon Factory, Institute of Materials' Structure Science, High Energy Accelerator Research

Organization, Oho 1-1, Tsukuba, Ibaraki, 305-0801, Japanc

Department of Materials' Structure Science, School of High Energy Accelerator Science,

SOKENDAI(The Graduate University for Advanced Studies), Oho 1-1, Tsukuba, Ibaraki, 305-0801,
Japan
Correspondence email: askr@cat.hokudai.ac.jp

Abstract

This paper describes the present state of XAFS databases, particularly in Japan, andproposes future directions. International
collaboration is important for enlarging the

FeCl – doped PA

database for further development of XAFS
spectroscopy.

[NEt ][FeCl ]Keywords: XAFS database; automatic data
deposition; data repository system

database

X-ray absorption fine structure (XAFS)[Co(NH ) ][FeCl ]t / arb. units

1. Why we need an international XAFS

[NEt ] [FeCl ]2040

spectroscopy is a powerful technique for0

determining local structure in metals with no

Photon Energy / eV

60

long-range order (Iwasawa et al., 2016).

Figure 2 Fe K-edge XANES spectra of selected Fe

Because a continuum X-ray source is required,

chlorides. The pre-edge peak is set at 0 eV. The Fe

XAFS spectroscopy became a practicalchloride dopant was characterized by XAFS

characterization technique only after

spectroscopy. By comparing with reference

synchrotron radiation sources were developed.

compounds, the Fe species in the PA could be
identified as [FeCl4]-.

and t are absorption

coefficient and thickness of the sample. (reproduced
from (Asakura et al., 1985) with permission
Chemical Society of Japan copyright (1985)).
IMPORTANT: this document contains embedded data - to preserve data integrity, please ensure where possible that the IUCr
Word tools (available from http://journals.iucr.org/services/docxtemplate/) are installed when editing this document.

1

Journal of Synchrotron Radiation

research papers

Since the first measurements were
Synchrotron Radiation Lightsource(Kincaid & Eisenberger, 1975), large
quantities of XAFS data have beencollected. These data can be divided
into two groups: (1) referencecompounds with known structures andproperties and (2)unknown target
materials under investigation. The data
for the former group are important formaterials scientists who wish to
analyse the XAFS spectra of unknown
compounds by comparing them withthose of reference compounds. Figure 1
shows the XAFS spectra of different Fe

Edge peak intensity / arb. units

made by Eisenberger at the Stanford
5
1.0
3
0.5

2
E
B

H

4
F

I
G

D

C
1 A
0
50
100
150
200
250
Exchange reaction enthalpy / kJ m ol-1

Figure 1 Relationship between edge peakintensity for Ag (I) compounds and covalence(Miyamoto et al., 2010; Miyamoto et al.,2012). Reproduced with permission from
(Miyamoto et al. 2010). Copyright (2010)
American Chemical Society.

chloride compounds. Some compounds produce a remarkable pre-edge peak that can be assigned to a
1s-to-3d transition, which is dipole forbidden , though it becomes stronger when centrosymmetry is
broken in a tetrahedral structure (Asakura et al., 1985) (Shulman et al., 1976). Thus, the Fe chloride
species in FeCl3-doped polyacetylene (PA) can be identified by comparing to XAFS spectra ofreference compounds. A collection of some XAFS spectra may be especially important when XAFS
spectroscopy is performed by non-specialists. Collections of typical XAFS spectra are published in apaper form such as books. The Catalysis Society of Japan has published the Catalyst Handbook,which includes XAFS spectra of reference compounds containing catalytically important elements(Japan, 2008).
An open-access, Internet-based database of XAFS spectra in a digital form is more convenient for
all researchers to update and search data. Such a large, comprehensive database would be useful not
only for XAFS non-specialists but also for specialists who want to elucidate general concepts fromXAFS spectra. Figure 2 shows the relationship between the intensity of edge-peak of Ag+ L3 X-ray
absorption near edge structure (XANES) and the covalence of Ag compounds (Miyamoto et al., 2010;
Miyamoto et al., 2012), which demonstrates a positive correlation. Such examples can be found inother studies, such as Lytle’s white line analysis and Wong’s V oxide pre-edge and edge shift analysis(Lytle et al., 1979; Wong et al., 1984). Eventually, deep learning methods could derive such relations
easily and automatically if a large database of XAFS spectra was available and related to othermaterial databases (Takigawa et al., 2016).
2. Overview of currently available XAFS databases

2

Journal of Synchrotron Radiation

research papers

Several databases of XAFS spectra have been developed, as shown in Table 1. These databases are
free, and they generally permit open access. F.W. Lytle database has a long history, which is thelargest and perhaps most well-known XAFS database. SPring-8 BL14 database, which requires a user
ID and password to view and search data, has ample data (more than 800) for reference compounds.
Recently, “Photon Beam Platform”, a national project in Japan to promote the collaboration among
synchrotron radiation and laser facilities is carrying out round robin tests for XAFS data in a data
format of XML(eXtensible Markup Language). International proposal of round robin tests of
XAFS data has also been proposed (Chantller et al., 2018)
This paper focuses on the XAFS database developed as a collaboration between the Hokkaido
University Institute for Catalysis (ICAT) and the Japanese XAFS Society (JXS). We would like topropose an international collaboration to make a new big and open database for XAFS.
Table 1 Available XAFS databases (as of Dec. 31, 2017)
Database
F.W. Lytle
database

URL
http://ixs.iit.edu/database/Features
Text format with periodic table interface
All data obtained by F.W. Lytle
19,307 records covering 74 elements

CARS

http://cars.uchicago.edu/
xaslib/search

Text (XDI) format with periodic table interface andgraphical output of spectra (Newville et al., 2015)
171 records covering 13 elements
Measured at the Advanced Photon Source, SSRL, andNational Synchrotron Light Source
Includes suites (tagging-related spectra) and user ratings

SPring-8 BL14

https://sp8dr.spring8.or.jp/
portal/dspace

Only available to SPring-8 users
725 records
Compressed text file (ZIP) format with metadata that
contains vendor and lot number

EuropeanSynchrotron
Radiation
Facility, ID21
group

http://www.esrf.eu/home/
UsersAndScience

Hokkaido
University ICAT
and JXS

https://www.cat.hokudai.ac.
jp/catdb/index.php?
action=xafs_login_form&
opnid=2/Experiments/XNP/ID21/
php.html

Sulphur database
41 (inorganic) and 26 (organic) records for S compounds
Graphical output, but text format is available
User name is included
209 records and 24 elements
Text format with metadata
Includes user name, beam line, and facility
Open access, but data uploading is restricted to users with
ID and password

3

Journal of Synchrotron Radiation

research papers

3. ICAT XAFS database in Japan
3.1. History

The Hokkaido University ICAT started to build the XAFS database in 2011 as a project of the Joint
Usage/Research Center for catalysis, in collaboration with JXS. The database is accessible to anyone
through the Internet. Volunteers working in the XAFS field can register for an ID and password to
upload their data to the database. For security and traceability, data files contain the name of theperson who uploaded the data. The website is managed by ICAT.
3.2. Fundamental ICAT data policies

The basic policies of the ICAT XAFS database are as follows:
Volunteer base – Anyone who is registered can upload their data.
Open-access database – Anyone can see and use the data. They are asked include a citation in
published work if they used the data.
Simple dataset format – The data have a text-based format, and only the energy and t of theraw spectrum are recorded, in addition to some metadata.
Compatibility – Foil XAFS data that are measured at the same beam time and beam line aredeposited simultaneously to make energy calibration possible. Consequently, we can compare
the data measured at different beam times, beam lines, and facilities.
Target – Dataset includes primarily standard compounds with known structures.
Guarantee of accuracy – A “majority rule” approach is used to improve accuracy. The
database allows deposition of multiple records for the same compounds.
Each data file has a metadata area and a data area, as shown in Fig. 3. Table 2 lists the available
metadata fields in the ICAT database. Although detailed metadata are helpful, too many required
inputs will reduce the motivation of volunteers, so the number of metadata fields are kept as small as
possible.

4

Journal of Synchrotron Radiation

Table 2

research papers

Available metadata fields in ICAT database

Sample name
Structural details (powder, foil, solution)
Absorption atom
Edge
Reference sample (usually foil)
Date of measurement
Monochromator (crystal)
Facility
Beam line

Beam current (mA)
Beam energy of storage ring (GeV)
Higher harmonics rejection method
Focus
Detection method
I｡ and I gases if ionization chamber was used
Measurement temperature
Comments

Figure 3 ICAT data file structure5

Journal of Synchrotron Radiation

research papers

One of the most important policies is compatibility. Although absolute angle of eachmonochromator can be determined by Pettier’s method or other{Pettifer, 1985 #2007}, it is moreconvenient to calibrate each data using foil measured at the same time. The data are uploaded withthe foil data measured at the same time. It benefit us to obtain the signal-to-noise ratio (S/N) and theenergy resolution of the XAFS measurement systems by comparison with the foil XAFS data in
addition to adjust the energy scale from different files by comparison with the foil XAFS spectra.
Another important policy is the guarantee of accuracy, that is, the quality of each XAFS spectrum.
One way to guarantee accuracy is to permit only highly qualified researchers to measure spectra undera strict, specific protocol and upload the data in a rigorously controlled way. However, this would
require more qualified researchers, time, and money than are not generally available. Also, theamount of data stored per day would be limited and it would be hard to construct a large database.
ICAT uses another strategy for data quality, that is, majority rule. The volunteers, who are expected
to have average skill for measuring XAFS spectra and preparing datasets, measure the spectra andupload the data with the metadata. When many volunteers randomly and independently upload spectra,
eventually different versions of the same reference spectra are collected. These data points are
statistically distributed so that the average spectra and their error bars can be determined. Data that lie
within the error bars are reliable, but a spectrum lying outside this range is either wrong or represents
a different phase . Thus, multiple spectra of the same compound improve the quality of the database.
Once the several spectra of the same compound available, users check the accuracy by comparing thespectra by themselves.
4. Problems with existing ICAT database

Despite its usefulness, the ICAT database has several drawbacks. The first problem is the small
number of data files in the database. This makes it difficult to apply majority rule and derive effective
relationships between spectral features and material properties. A way is needed to get more data
effectively. The second problem is that the database is not linked to other material databases, such as
X-ray diffraction, optical spectra, and other physical and chemical properties. The third problem isthe format. ICAT database uses simple the text-base format. Several data formats have been proposed,such as CIF XAFS, XDI (eXtensible Data Interchange), JASON(JavaScript Object Notation), NeXus,
and HDF5 (Ascone et al., 2012; Ravel & Newville, 2016; Konnecke et al., 2015 ). The NeXus andHDF5 formats can store and manage imaging data written in a binary format. Adoption of NeXus or
HDF5 may be a good choice for a flexible database, but it must first be designed well after longdeliberation. Nevertheless, the text format with only energy and t data is simple, easy to implement,
and transferrable to other formats. Although continued discussion of the XAFS database format isneeded, it might be expedient to start database construction in a text format and convert the data to aunified format later.
6

Journal of Synchrotron Radiation

research papers

5. Future database development – Bigger is betterIn the future, computers will be able to automatically evaluate the correctness of spectra based on
majority rule. Even if information about a sample is inadequate, the computer could classify the
samples into several subsets. For example, if the sample name is entered only as TiO2, the spectra
would need to be associated with one of the three different crystalline forms of TiO2 – Rutile, Anatase,and Brookite. Thus, the computer would need to assign the spectra to one of these crystal forms using
other spectra data. Some spectra may be located between two of the groups, indicating a mixture, so it
is better to have more data of the same compounds available for comparison. A large database will
reduce the probability of misinterpretation and improve our understanding of the spectra. The future
direction of the XAFS database is to be bigger and more open. The majority rule, in combination withadvanced computing, such as artificial intelligence(AI), can work to reinforce data quality andreliability and to elucidate meaningful new concepts through deep learning. The problem is how toconstruct a larger database as mentioned above. Since we collect data manually at the moment, theICAT database only contains a limited number of data files. If the data were automatically stored in
an appropriate way, all measured data could be included in the database. Manual input would be
limited to metadata and clarification and categorization of data into spectra for reference or unknown
compounds.
Since most XAFS spectra are measured at synchrotron radiation facilities, we propose thefollowing system:
Store all data measured at these facilities automatically in the facility’s computer inappropriate formats and with metadata. Thus, each facility can constructthe larger database.
Then combine the databases from each facility by connection to the internet. Before thatcan be done, however, we need to decide on rules for data disclosure. The fundamental
principle should be that all scientific data must be open to the public eventually, but thedata owner rights and originality should be reserved.
Using these basic ideas, the data can be made accessible to the public but only after the agreement of
the data owners. This will allow data owners choose to keep their data confidential, but it is hopedthat they would release the data after the associated studies are published in the literature.
Data disclosure would be beneficial to our society in two ways: (1) the quantity of data in the
XAFS database would increase, improving its quality and accessibility for everyone and (2) the
quality and transparency of published research would be improved by disclosing the raw data. The
cooperation of publishers would be important, and it is hoped that they would require disclosure of the
raw XAFS data when a paper is accepted. Facilities could provide further support by making data
7

Journal of Synchrotron Radiation

research papers

disclosure contracts with all users before they start experiments. The raw data should also be madeavailable when a patent is established. In addition to these rules, all data should be disclosed after acertain period (10 years for example). Facilities should retain responsibility for data security andprotection; otherwise, users would not allow facilities to store their data.
One more important suggestion is to define a unique digital data number, similar to the digital
object identifier (DOI) for a published paper. A data identifier would allow the data to be cited when
it is used in a publication. This would increase the incentive for owners to upload and to open theirdata. Like the citation index for a paper, a user could benefit from the number of citations of their data.
This would provide further motivation to perform precise measurements and develop higher-quality
data. A suggested format for the data identifier is as follows:
XAFS_ATOM_EDGE_Measure_Time_ContactPerson (Name & ResearcherID or
ORCID)_Facility_BeamLine.
Note that the identifier must be automatically determined and unique.
The linkage of facility databases will be another important task, since XAFS data are notstandalone. To derive structure-property relationships, XAFS data need to be considered in thecontext of the physical and chemical properties of the measured material. To do this, a clear sample
name must be determined uniquely and universally. If the sample is a standard reference compound,
this should be clearly conveyed by some unique sample identifier. The Chemical Abstracts Service(CAS) number is the best choice the sample identifier because it will be comprehensive and make iteasier to associate the sample with physical and chemical properties. Moreover, the majority rule will
work more effectively because different files for the same material can be linked easily, possibly
automatically. The facilities could encourage input of the CAS number into the metadata by providing
a CAS number dictionary to users. The data owner should provide their own data name according tosome rule, such as:
CAS_Number_ChemicalComposition_Phase_DataOwner (ResearcherID or ORCID)_Comment (Origin) (13463-67-7_TiO2_Rutile_G-6052-2010_PurchaseFromWakoLotNo0001).
6. What to Do Next

We believe that an open XAFS database is necessary but also very useful. Some issues should be
set aside for now, and each facility should start to construct a database or repository of its own data,with the goal of eventual linkage to a larger database. We propose the following actions:
1. Ask all facilities to start collecting XAFS data.
2. Decide on simple naming rules for linkage to other databases.
3. Decide on naming rules for data files, along the lines of the DOI.
8

Journal of Synchrotron Radiation

research papers

4. Start the discussion for determining data release rules.
We hope we can discuss my proposal at the next Q2XAFS and at other meetings.

Acknowledgment
This work was supported by MEXT Joint Usage/Research Center Program (2010-2015, 2016-2011)
and the Accelerator Science Support Fund from the High Energy Accelerator Research Organization(KEK) (2010-2017) and CREST JST “Resolution Catalyst”. One of the author (KA) thanks to

the fruitful discussion with Committee of manufacturing process innovation by materials
informatics( Chair : Prof.Toyohiro Chikyo in NIMS)

7. References

Asakura, K., Ikemoto, I., Kuroda, H., Kobayashi, T. & Shirakawa, H. (1985). Bull.Chem.Soc.Jpn. 58,
2113-2120.
Ascone, I., Asakura, K., George, G. N. & Wakatsuki, S. (2012). J.Synchro.Rad 19, 349-350.
Chantller, C., T,, Bunker , B. A., Abe, H., Kimura, M., Newville, M. & Weltere, E. (2018).
J.Synchro.Rad submitted to the same issue
Iwasawa, Y., Asakura, K. & Tada, M. (2016). Editor. XAFS techniques for catalysts, nanomaterials,
and surfaces, Springer.
Japan, C. S. o. (2008). Editor. Catalyst Handbook, 1 ed. Tokyo: Kodan-sha Scientific.
Kincaid, B. M. & Eisenberger, P. (1975). Phys. Rev. Lett. 34, 1361-1364.
Konnecke, M., Akeroyd, F. A., Bernstein, H. J., Brewster, A. S., Campbell, S. I., Clausen, B., Cottrell,S., Hoffmann, J. U., Jemian, P. R., Mannicke, D., Osborn, R., Peterson, P. F., Richter, T.,
Suzuki, J., Watts, B., Wintersberger, E. & Wuttke, J. (2015). J.Appl.Crystallo. 48, 301-305.
Lytle, F. W., Wei, P. S. P., Greegor, R. B., Via, G. H. & Sinfelt, J. H. (1979). J.Chem.Phys. 70, 4849.
Miyamoto , T., Kitajima, Y. & Asakura, K. (2012). e-J. Surf. Sci. Nanotech. 10, 609-612.
Miyamoto, T., Niimi, H., Kitajima, Y., Naito, T. & Asakura, K. (2010). J.Phys.Chem. A 114, 40934098.
Newville, M., Ravel, B., Sole, V. A. & Wellenreuther, G. (2015). XAS-DataInterchange/specification/spec.md, https://github.com/XraySpectroscopy/XAS-DataInterchange/blob/master/specification/spec.md.
Ravel, B. & Newville, M. (2016). J.Phys.Conf.Ser., pp. 12148-12151. IOP Publishing.
Shulman, G. R., Yafet, Y., Eisenberger, P. & Blumberg, W. E. (1976). Proc. Natl. Acad. Sci. USA 73,
1384-1388.
Takigawa, I., Shimizu, K.-i., Tsuda, K. & Takakusagi, S. (2016). RSC Adv. 6, 52587-52595.
Wong, J., Lytle, F. W., Messmer, R. P. & Maylotte, D. H. (1984). Phys. Rev. B 30, 5596.

9