FAIR and verifiable: The role of FAIR Digital Objects in trusted AI

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