XAFS Database in Japan
Kiyotaka AsakuraInstitute for Catalysis
ICAT, Hokkaido University

2Introduction
Why do we need database?
1. We can guess the structure
faster and more correctly.
Strong demand frombeginners and nonprofessionals
2. To create a new concept.
3. AI and DEEP LEARNING
will give us directly thestructure from the spectra
based on database in nearfuture.
Data-driven analysis

FeClଷ in PA

NEt ସ FeClସ NEt ସ ଶ FeClସ Co NHଷ ଺ FeCl଺ FeClସ ＝ FeCl? ଷ in PA

Kiyotaka, A.; Isao, I.; Haruo, K.; Takaaki, K.; Hideki, S.
Bulletin of the Chemical Society of Japan 1985, 58,2113.

3Introduction
Why do we need database?
1. We can guess the structure
faster and more correctly.
Strong demand frombeginners and nonprofessionals
2. To create a new concept.
3. AI and DEEP LEARNING
will give us directly thestructure from the spectra
based on database in nearfuture.
Data-driven analysis

Covalency and L3 edge peakhight of Ag(I) are in proportion.

Miyamoto, T.; Niimi, H.; Kitajima, Y.; Naito, T.; Asakura, K. The
Journal of Physical Chemistry A 2010, 114, 4093.

4Introduction
Why do we need database?
1. We can guess the structure
faster and more correctly.
Strong demand frombeginners and nonprofessionals
2. To create a new concept.
3. AI and DEEP LEARNING
will give us directly thestructure from the spectra
based on database in nearfuture.
Data-driven analysis

AI and DEEP LEARNING
Create knowledge
I. Takigawa, K.-i. Shimizu, K. Tsuda and S. Takakusagi, Machinelearning prediction of the d-band center for metals and bimetals.
RSC Advances. 6,52587-52595(2016).

5XAFS DATABASE
http://cars.uchicago.edu/xaslib/search
Graphical
http://ixs.iit.edu/database/
Text baseSPring-8 BL14 Data repository https://sp8dr.spring8.or.jp/portal/dspace
http://www.esrf.eu/home/UsersAndScience/Experiments/XNP/ID21/php.html
Sulfur database
https://www.cat.hokudai.ac.jp/catdb/index.php?action=xafs_login_form&o
pnid=2XAFS SOCIETY OF JAPAN DATABASE

6XAFS database in Japan
History
Catalysis Research Center(now ICAT) started to build the database of XAFS
for future usage of data science in 2011, collaborating with XAFS Societyof Japan(XSJ) .
SystemWeb is prepared by ICAT and XSJ members upload their data.
Fundamental principles• Volunteer base = anyone who is registered can deposit his/her data .
• Open database = anyone in the world can see and use it with citation.
• Low cost = no one manage the data because of no budget.
• Simple dataset =text base. Only energy and µt of raw spectrum.
• Compatibility = Foil data simultaneously measured should be deposited.
• Target = Mainly standard compounds. But some repository for thepublished data.
• Guarantee for accuracy = majority rule. We allowed the many data
depositions of the same samples.

Majority rule = basic idea of the XAFS Database in XSJQuantity overcomes quality
If we have 60 data with samequality(S/N ratio) of the same
standard compounds.
59 data sets are the same spectra
and one is different from theother. The one should berejected.
It requires number of data of thesame compounds.

7

Rh9Co1 foilThis one should be wrong.

Inside database

https://www.cat.hokudai.ac.jp/catdb/inde
x.php?action=xafs_login_form&opnid=2

SearchDownload

Click

8Inside database

https://www.cat.hokudai.ac.jp/catdb/inde
x.php?action=xafs_login_form&opnid=2

9Inside database

https://www.cat.hokudai.ac.jp/catdb/inde
x.php?action=xafs_login_form&opnid=2

SearchDownload

Click

10

Download

Inside database

https://www.cat.hokudai.ac.jp/catdb/inde
x.php?action=xafs_login_form&opnid=2

Click
11

12

Header area

Data area

MinimumDownloaded dataInside database

https://www.cat.hokudai.ac.jp/catdb/inde
x.php?action=xafs_login_form&opnid=214

Input data= registration is necessary. Send email.
Direct download from the original data(9801 format )15

16
Data region
Uploaded or copy (E, µt) of sample
Uploaded or copy (E, µt) of foil
measured imultaneously.

17
Web site and how to18
What are the problems?

• Now August 12 2017. We have 194 datasets
uploaded.
– Too small and too biased.
– Duplication and multiplication must be necessary.

• Sample name must be unified for easy link to other
Material data base.

• Local data file name but no universal
one.(Data DOI)19
What are the problems?

• Now August 12 2017. We have 194 datasetsuploaded.
– Too small and too biased.
– Duplication and multiplication must be necessary.

• Please help!!

• Sample name must be unified for easy link to other
Material data base.

• Local data file name but no universal
one.(Data DOI)

How to get more data = automatic depository andopen after publication with DOI

Users can access thedata with PWD

Data are automatically uploaded
to central computer and add their
DOI but strongly protected byPWD

20

How to get more data = automatic depository andopen after publication with DOI
Submission

Users canaccess the datawith PWD

Journals(publisher)

Data are automaticallyuploaded to centralcomputer and add their
DOI but strongly
protected by PWD

21

How to get more data = automatic depository andopen after publication with DOI

22Submission

Users canaccess the datawith PWD

Journals(publisher)
Open data requirement when the paper are accepted.
Open for public with DOI.

Data are automaticallyuploaded to centralcomputer and add their
DOI but strongly
protected by PWDHow to get more data = automatic depository andopen after publication with DOI

23

Submission

Users canaccess the datawith PWD

Journals(publisher)
Open data requirement when the paper are accepted.
Open for public with DOI.

Data are automaticallyuploaded to centralcomputer and add their
DOI but strongly
protected by PWD• All data
should have
DOI andshould becited byothers.
• But all data
published canfreely bereproducedwith DOI.

24
Proposals

To facilities stuffs. Please take action to store all datameasured at your facility in your central storage withstrong security with temporal local DOI.
To users. Please allow the facility to store your data.
To communities and Q2XAFS. Please discuss the rule
about the data format, DOI and rule for open thedata.
To journal editors or publishers. Please require theauthors to open their data when accepted.
To authors. Please open the data in paper and pleasecite all data DOI used.

25
But what format.

Any data are OK if they include the sample chemicalformula(+phase）, Date, Facility name, and raw data
(E, µt). We can make data convertors.
DOI
FacilityBeamLineYDTContactPersonName_BranchNo.
is given automatically.
For example. PFARNW10A20170505235959KiyotakaAsakura_1

26
I propose following as the Q2XAFS missions.

1. Decide rule for the data file name or DOI and startthe discussion for data opening.
2. Ask all facilities to start the collection of XAFS
data.
3. Decide the sample name rule to link otherdatabase.
4. Propose the action plan and send advice to IXAS
and XAFS Commission in IUCr.
5. The final decision in 2021(XAFS2021)

acknowledgement
The presentation is based on the discussion with following people
H. Abe(PF), M.Kimura(PF), Y.Niwa(PF), Y.Nitani(PF), Y.Tamenori(SP8),
T.Honma(SP8), S.Ito(NIMS), Tanaka(NIMS),
K.Takahashi(NIMS),T.Chigyo(NIMS), K.Funatsu(Univ. Tokyo),
J.Hasegawa(ICAT), M.Nishida(ICAT), J.Lauterbach(USC)
K.Shimizu(ICAT), W.Ueda(Kanagawa),H.Takaya(Kyoto U)
XAFS Society of Japan27

What next?

AI supported analysis or data driven analysis.
Compare the data and give the conclusions.
But the number of experiments are finite.
We still need more data.

28

29
We need more data.

Automated calculations using some theoreticalanalysis programs(FEFF,GNXAS, EXCURVE and so on.)
Theory Database should have input file and output
chi(k) which both are automatically deposited.
Provide the cloud service or hub for analysis programs,
where people freely access programs and calculate
their own structure but automatically results aredownloaded and stored. (Like nanoHub)

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How to construct and control the database

Company(-ies) run(s) the hub and database.
Government(s) control(s).
A NPO or A Universities Alliance.

“All knowledge is the knowledge of all of us,
controlled by all of us and used for happinessof all of us”

All data should be deposited on crowd and linked

All data have data nameand DOI.

All Data in the One
IoT;Robotics
EXAFS,XRD,XPS,and so on

Internet LaboNote
Metafile to connect all dataset.

IoT;Robotics

Crowd service

AI technology

Utilization Cite the data name or DATA DOI.
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