E ik Schul es
ORCID: h p://o cid.o g/0000-0001-8888-635X
Email: e.a.schul es@lacd .leidenuni .nl
Da e: Oc obe 8, 2025
DOI: h ps://doi.o g/10.5281/zenodo.17257168
h ps://www.open-science-con e ence.eu
FAIR and e i iable:
The ole o FAIR Digi al Objec s in us ed AI
FAIR
Find me all known low molecula weigh
inhibi o s o he Human p65 P o ein.
Sepa a e he lis based on hose ha
we e ound in cu a ed da abases, om
hose ha we e ound in sel -deposi ed
da a a chi es. Keep ack o he license
and ci a ion in o ma ion o each one. I
da a is ele an , bu no public, please
p o ide he con ac in o ma ion o he
pe son I need so I can eques he da a.
Hypo he ical sea ch applica ion on FAIR da a.
Ma k Wilkinson, CBGP-UPM/INIA, Mad id
2017
In a wo ld ha was FAIR…
…you would ge a lis o inhibi o s!
…you would ge a lis o inhibi o s!
No a lis
pape s
No a lis
da ase s
{
"inhibi o ": {
"name": "Example Inhibi o ",
"desc ip ion": "A small molecule ha inhibi s he ac i i y o he NF-κB p65 subuni .",
"iden i ie s": {
"CHEBI": "CHEBI:XXXXX",
"PubChem": "12345678",
"InChIKey": "ABCDABCDABCDAB-UHFFFAOYSA-N",
"SMILES": "C1=CC=CC=C1C(=O)NC2=CC=CC=C2",
"molecula _weigh ": 321.36
},
" a ge ": {
"name": "NF-κB p65 subuni ",
"unip o _id": "Q04206",
"gene_symbol": "RELA",
"mechanism_o _ac ion": "Blocks DNA binding o p65 in he nucleus"
},
"o ganism": {
"name": "Homo sapiens",
" axonomy_id": "9606"
},
"sou ces": {
"cu a ed_da abase": {
"name": "ChEMBL",
" eco d_u l": "h ps://www.ebi.ac.uk/chembl/compound/inspec /CHEMBLXXXXX",
"access": "open"
},
"sel _deposi ed_da a": {
" eposi o y": "Zenodo",
" eco d_u l": "h ps://zenodo.o g/ eco d/1234567",
"access": " es ic ed",
"access_condi ions": "A ailable upon eques o non-comme cial use"
}
},
"license": {
" ype": "CC BY-NC 4.0",
"license_u l": "h ps://c ea i ecommons.o g/licenses/by-nc/4.0/"
},
"ci a ion": {
" i le": "Iden i ica ion o inhibi o s a ge ing NF-κB p65 in human cance cells",
"doi": "10.1234/example.doi",
"au ho s": ["Doe, J.", "Smi h, A."],
"jou nal": "Jou nal o Molecula Biology",
"yea ": 2022
},
" es ic ed_access_con ac ": {
"name": "D . Jane Doe",
"email": "[email p o ec ed]",
"a ilia ion": "Depa men o Molecula Biology, Example Uni e si y"
}
}
}
Hypo he ical JSON
E ik Schul es, LACDR 2025
FAIR
Find me all known low molecula weigh
inhibi o s o he Human p65 P o ein.
Sepa a e he lis based on hose ha
we e ound in cu a ed da abases, om
hose ha we e ound in sel -deposi ed
da a a chi es. Keep ack o he license
and ci a ion in o ma ion o each one. I
da a is ele an , bu no public, please
p o ide he con ac in o ma ion o he
pe son I need so I can eques he da a.
Hypo he ical sea ch applica ion on FAIR da a.
Ma k Wilkinson, CBGP-UPM/INIA, Mad id
2017

Finding known low molecula weigh inhibi o s o he Human p65 p o ein (also known as RelA, pa o he NF-κB
complex) can be sou ced om cu a ed da abases and sel -deposi ed da a a chi es.
### Cu a ed Da abases:
1. **ChEMBL**: A well-es ablished da abase o bioac i e molecules, ChEMBL includes se e al small molecule inhibi o s
a ge ing p65/RelA. These molecules a e indexed based on hei in e ac ion da a, ac i i y, and ele ance in d ug
disco e y. You can access and download compound da a unde an open license om he ChEMBL si e (EMBL-EBI).
2. **PubChem**: This public esou ce houses chemical compounds, including hose wi h inhibi o y ac ion on p65.
De ailed molecula p ope ies, including s uc u e and bioac i i y, a e a ailable. Licensing o da a is open o academic
use.
3. **SMMDB**: The SMMDB (Small Molecule Modula o Da abase) con ains de ailed in o ma ion on small molecules
modula ing a ge s like p65 in neu ological and o he diseases. I is a manually cu a ed esou ce, p o iding PubMed
links and compound de ails, including molecula weigh , 3D s uc u es, and inhibi ion da a【15†sou ce】
【18†sou ce】.
### Sel -deposi ed Da a A chi es:
1. **ZINC Da abase**: This includes use -submi ed and cu a ed molecules, many o which a ge NF-κB, including p65.
Resea che s can deposi hei indings he e, making i a mix u e o communi y-con ibu ed da a. Usage o he da abase
is open, bu some en ies may equi e con ac ing he deposi o o u he licensing de ails.
2. **IPAD-DB**: Al hough p ima ily ocused on Alzheime ’s disease, he IPAD-DB con ains da a on molecules ha
modula e ela ed in lamma o y pa hways, including NF-κB. Licensing de ails a y, bu access is gene ally open
【17†sou ce】.
### Ci a ion and License In o ma ion:
- Mos cu a ed da abases like **ChEMBL** and **PubChem** o e open access wi h clea academic use licenses.
**SMMDB** is simila ly eely accessible o non-comme cial esea ch, while da a in **ZINC** may ha e di e en
licensing based on indi idual submissions.
- Fo di ec inqui ies o eques ing non-public da a, each da abase ypically p o ides he deposi o 's con ac , especially
in **ZINC** and **IPAD-DB**, whe e sel -deposi ed en ies may ha e es ic ed access.
Fo he mos comp ehensi e se o inhibi o s a ge ing p65, I ecommend s a ing wi h **ChEMBL** and **PubChem**
o licensed, pee - e iewed da a, and explo ing **ZINC** o **IPAD-DB** o communi y-deposi ed esou ces.
OpenAI’s Cha GPT-4, Oc obe 2024
FAIR
Find me all known low molecula weigh
inhibi o s o he Human p65 P o ein.
Sepa a e he lis based on hose ha
we e ound in cu a ed da abases, om
hose ha we e ound in sel -deposi ed
da a a chi es. Keep ack o he license
and ci a ion in o ma ion o each one. I
da a is ele an , bu no public, please
p o ide he con ac in o ma ion o he
pe son I need so I can eques he da a.
Hypo he ical sea ch applica ion on FAIR da a.
Ma k Wilkinson, CBGP-UPM/INIA, Mad id
2017
OpenAI’s GPT-5
OpenAI’s GPT-5, Sep embe 2025
OpenAI’s GPT-5
OpenAI’s GPT-5, Sep embe 2025
The FAIR Guiding P inciples enhance he abili y o machines o do F, A, I and R.
Wha does FAIR mean o AI?
h ps://www.na u e.com/a icles/sda a201618
h ps://www.senscience.ai/
Open Da a
A icle
h ps://doi.o g/
10.3389/
bin .2025.16341
11
In e ac i e da a
explo e
h ps://
www.doi.o g/
10.71728/hw56-
j34
Pod cas
h ps://
open.subs ack.co
m/pub/
senscience/p/
s aying-ahead-o -
sa s-co -2-
inside?
=58b36l&u m_c
ampaign=pos &u
m_medium=we
b&showWelcome
OnSha e= alse
AI d i en FAIRi ica ion pipelines
AI-Ready Da a is o AI inpu s
FAIR-Ready AI will c ea e AI ou pu s
P oposal:
FAIR da a as he s anda d o
bo h AI inpu and ou pu .
T us ed AI will consume and
p oduce FAIR Da a

Yoda
iRODs
FAIR
Da a
Poin
Reposi o y Resea ch
Objec
C a e
ReBo n
A icle
DeSci
Publish
CORDRA Nanopub
Se e
Ne wo k
FAIR^2
Da a Po al
Eme ging echnologies suppo ing FAIR Da a O ches a ion
Yoda
iRODs
FAIR
Da a
Poin
Reposi o y Resea ch
Objec
C a e
ReBo n
A icle
DeSci
Publish
CORDRA Nanopub
Se e
Ne wo k
FAIR^2
Da a Po al
Eme ging echnologies suppo ing FAIR Da a O ches a ion
P oposal:
Nanopub-based FDOs as
s anda d I/O o T us ed AI
Leiden Labo a o y
o Nanopublica ion
LLN
Leiden Labo a o y
o Nanopublica ion
LLN
AI-Ready Da a is o AI inpu s
h ps://www.uni e si ei leiden.nl/en/science/d ug- esea ch/me abolomics-and-analy ics-cen e
Me abolomics is he comp ehensi e, high- h oughpu
analysis o small-molecule me aboli es in cells,
issues, bio luids, o o ganisms unde speci ic physiological
o pa hological condi ions. I aims o iden i y, quan i y, and
cha ac e ize he dynamic me abolic changes associa ed wi h
gene ic, en i onmen al, o he apeu ic ac o s.
Cha GPT5, 30 Sep embe 2025
WikiPedia, C ea i e Commons CC0 1.0 Uni e sal
Public Domain Dedica ion
(MAC)
Mass Spec ome y

Wha is a nanopublica ion?
Wha is a nanopublica ion?
S anda dized in o ma ion o ma
Wha is a nanopublica ion?
• Open s anda ds (HTTP)
• Machine- eadable (RDF)
• FAIR is o ches a ed on a global
se e ne wo k (decen alised)
• publish
• au hen ica ion (ORCID)
• ime/da e
• Pe sis en Iden i ie s
•s o e
•sea ch
S anda dized in o ma ion o ma
Wha is a nanopublica ion?
Low le els o 25-hyd oxy i amin D a e
linked o hype ension and diabe es.
S anda dized in o ma ion o ma
• Open s anda ds (HTTP)
• Machine- eadable (RDF)
• FAIR is o ches a ed on a global
se e ne wo k (decen alised)
• publish
• au hen ica ion (ORCID)
• ime/da e
• Pe sis en Iden i ie s
•s o e
•sea ch
Me ada a
PID
By esea che
MAC
Nanopubs as FAIR Me ada a Tags
S anda dized in o ma ion o ma
• Open s anda ds (HTTP)
• Machine- eadable (RDF)
• FAIR is o ches a ed on a global
se e ne wo k (decen alised)
• publish
• au hen ica ion (ORCID)
• ime/da e
• Pe sis en Iden i ie s
•s o e
•sea ch
1. has ype
2. has loca ion
3. has ype-speci ic me ada a
h ps://zenodo.o g/ eco ds/7782262

Me ada a
PID
By esea che
MAC
Nanopubs as FAIR Me ada a Tags
S anda dized in o ma ion o ma
• Open s anda ds (HTTP)
• Machine- eadable (RDF)
• FAIR is o ches a ed on a global
se e ne wo k (decen alised)
• publish
• au hen ica ion (ORCID)
• ime/da e
• Pe sis en Iden i ie s
•s o e
•sea ch
1. has ype
2. has loca ion
3. has ype-speci ic me ada a
h ps://zenodo.o g/ eco ds/7782262
Single, a omic,
seman ic uni
Nanopubs as FAIR Me ada a Tags
S anda dized in o ma ion o ma
Me ada a o
Digi ial Objec s
o ype
da ase
• has ype - da ase
• has loca ion - PID
• has au ho - esea che
• has con ibu o (s)
• has con ac poin
• uses language - English
• has domain - me abolomics, hype ension
• has publishe - MAC, LACDR, LU
• has publica ion da e - xx/xx/xx
• has e sion - x.x.x.
• has unde - ZonMw
• has p ojec - Hype ma ke
Nanopubs as FAIR Me ada a Tags
S anda dized in o ma ion o ma
• has ype - me hod
• has loca ion - PID
• has au ho - esea che
• has con ibu o (s)
• has con ac poin
• uses language - English
• has domain - me abolomics, hype ension
• has publishe - MAC, LACDR, LU
• has publica ion da e - xx/xx/xx
• has e sion - x.x.x.
• has unde - ZonMw
• has p ojec - Hype ma ke
Me ada a o
Digi ial Objec s
o ype
me hod
Nanopubs as FAIR Me ada a Tags
S anda dized in o ma ion o ma
• has ype - a icle
• has loca ion - DOI
• has au ho - esea che
• has con ibu o (s)
• has con ac poin
• uses language - English
• has jou nal - Na u e
• has domain - me abolomics, hype ension
• has publishe - MAC, LACDR, LU
• has publica ion da e - xx/xx/xx
• has e sion - x.x.x.
• has unde - ZonMw
• has p ojec - Hype ma ke
Me ada a o
Digi ial Objec s
o ype
a icle
Nanopubs as FAIR Me ada a Tags
S anda dized in o ma ion o ma
• has ype - a icle
• has loca ion - DOI
• has au ho - esea che
• has con ibu o (s)
• has con ac poin
• uses language - English
• has jou nal - Na u e
• has domain - me abolomics, hype ension
• has publishe - MAC, LACDR, LU
• has publica ion da e - xx/xx/xx
• has e sion - x.x.x.
• has unde - ZonMw
• has p ojec - Hype ma ke
Me ada a o
Digi ial Objec s
o ype
a icle
MAC FAIR Go e nance G oup
• Main ain MAC me ada a
• Main ain MAC ocabula y
• Main ain MAC FIP

How o make a Nanopub
h ps://nanodash.knowledgepixels.com/p ojec ?21&id=h ps://w3id.o g/kpxl/cus om/p ojec / e ms/MAC-FDO
• Seman ic modeling
• C ea ing nanopub empla es
• Min ing new FAIR ocabula ies
• Cu a ing in o ma ion
• “Filling in he o m”
• Publishing o he se e ne wo k
How o make a Nanopub
How o ind Nanopub
h ps://nanodash.knowledgepixels.com/p ojec ?21&id=h ps://w3id.o g/kpxl/cus om/p ojec / e ms/MAC-FDO
Nanopubs as FAIR Me ada a Tags
Resea ch P og amme
Call o P oposals
P ojec s
Da ase
So wa e
DMP
P oposal
E hical Clea ance
Conso ium Ag eemen A icle
PI and con ibu o s
Budge
Me hod
FAIR Funde F amewo k
Ma g ee Bloeme s
GO FAIR Founda ion Fellow
ZonMw. h ps://os .io/nx cj/
Wednesday Nanopub Club
K is ina He ne
Aslessa Gamba della
Kim Elsink
Ma hijs Sloep
Max an den Boom
Elham Mema ian
E ik Schul es
When MAC is FAIR
FAIR
Find me all A icles published by Amy
Ha ms.

When MAC is FAIR
FAIR
Find me all Me hods de eloped unde
he Hype ma ke p ojec .
• Including me hods de eloped by
o he conso ium membe s
When MAC is FAIR
FAIR
Find me all Ins umen Logs ela ed o
da ase s published in 2025 eal ed o
S ayAhead.
When MAC is FAIR
FAIR
Find me all DMPs o p ojec s ela ed o
hype ension.
• Including DMPs de eloped
anywhe e
When MAC is FAIR, MAC is AI-Ready
Sc eensho o MATSU lab Discou se G aph, h ps://discou seg aphs.com/
LeiBi s
h ps://nanodash.knowledgepixels.com/p ojec ?13&id=h ps://w3id.o g/kpxl/cus om/p ojec / e ms/LEIbi s
h ps://www.lib a y.uni e si ei leiden.nl/e en s/2025/05/connec --in e link

LeiBi s
FAIR
Find me all Da ase s published a
Leiden Uni i e si y in 2025.
Leiden Labo a o y
o Nanopublica ion
LLN
FAIR-Ready AI will c ea e AI ou pu s
Mos o he web is AI gene a ed - and ha s a big p oblem.
A amewo k o me ada a
disclosing he ole o AI in
con en c ea ion.
Se ice p o ide s:
•Au ho ing a scale
•Regis a ion a scale
•Sea ch a scale
Human-!
Gene a ed
AI-!
Assis eded
AI-!
Gene a ed
h ps:// aia.liccium.com/
h ps://www.sidn onds.nl/
FDOs as AI ou pu : FAIR AI A ibu ion (FAIA)
ISCC S anda d - ISO 24138
MAC S o age Reposi o ies
h ps://os .io/ 625a/ iles/os s o age h ps://os .io/q9xcu/ iles/os s o age
Da ase
Call o P oposals
Resea ch P og amme
A icle
Da ase
Me hod
P ojec
DMP
Me hod
Me hod

Nanopubs o Heal h-Holland S ayAhead
Heal h~Holland’s public–p i a e pa ne ship subsidy
h ps://w3id.o g/np/RAo 6kN_keiB675cM6GwHmqqlX47ekF-yZ5jKowZs zSE
Resea ch P og amme
PPP_Allowance_Call_ o _P oposals
h ps://w3id.o g/np/RA J3YwHg1L lbDkHmz3I1BT JeSuoh sJy4p mCFnN7w
Call o P oposals
STAYAHEAD
h ps://w3id.o g/np/RAFPOe4OIl_u s-U_7-Fos jzcUo8 a6Las S GplO o
P ojec
Da a Managemen Plan o STAYAHEAD
h ps://w3id.o g/np/RAU1Mo98h2lw3zWADMKx8V7Q03uQNyu2mkTJkRjRQQUOE
DMP

Me hods o p ojec STAYAHEAD
h ps://w3id.o g/np/RAjV 8HI8gn9WJwSVIeRR yVLixF0yKx258RRDM1S2sKI
Me hods
AphaFold2 Da ase STAYAHEAD
h ps://w3id.o g/np/RA 6JJe-l oadhNwml8pzSLs5aO bU1xbHT5qgF gwQ-s
Da ase
ESM Da ase STAYAHEAD
h ps://w3id.o g/np/RA9YxiABPRNy3 Jm20p1oanJchBcI22IPpSu36zj2MLs
Da ase
STAYAHEAD esea ch a icle
h ps://w3id.o g/np/RAnQSVXSx Y3 IdW4 25K_j4im J_ijyigLI S907R8c
A icle
Me hods Measu emen s o Global Pola analysis in p ojec Hype ma ke
h ps://w3id.o g/np/RAhpepqj9IWw8uiQMIs 9hlpU-zGSUJGpC7xGeZGulZPc