European Joint Programme on Rare Diseases

Deliverables

Fourth Public Call documents JTC2019-2022: call text, guidelines for applicants, proposal templates

Other lead beneficiaries ANR 11 FFRD 12 and ISCIII 44Public Call documents JTC20192022 call text guidelines for applicants proposal templates due at month 35

First Report on processed genome-phenome datasets and multi-omics use cases analysed, including description of new cloud and online analysis functionalities and tools

Other lead beneficiary UMCG (35) First Report on processed genome-phenome datasets and multi-omics use cases analysed, including description of new cloud and online analysis functionalities and tools due at month 12

Third Report on processed genome-phenome datasets and multi-omics use cases analysed, including description of new cloud and online analysis functionalities and tools

Other lead beneficiary UMCG 35Third Report on processed genomephenome datasets and multiomics use cases analysed including description of new cloud and online analysis functionalities and tools due at month 36

First Report on course on interpretation of genetic variants and quality standards

First Report on course on interpretation of genetic variants and quality standards due at month 12

Fourth Analysis of national state of play and alignment process with EJP RD

Other lead beneficiary MUW 38Analysis of national state of play and alignment process with EJP RD due at month 55

Second Public Call documents JTC2019-2022: call text, guidelines for applicants, proposal templates

Other lead beneficiaries: ANR (11), FFRD (12) and ISCIII (44) Public Call documents JTC2019-2022: call text, guidelines for applicants, proposal templates due at month 11

First Report on ExPRESS

First Report on ExPRESS EURORDIS Summer School due at month 12

Fifth report from the face-to-face ExCom and Policy Board meeting

Report from the facetoface ExCom and Policy Board meeting due at month 55

Public Call document for Networking scheme

Other lead beneficiary: CSO/MOH (78) Public Call document for Networking scheme

First Report on International course on undiagnosed diseases

First Report on International course on undiagnosed diseases due at month 24

Final list of prioritization criteria

Other lead beneficiary FTELE 25Final list of prioritization criteria

Second List of research and innovation needs requiring medium- or long-term approach and related Task Forces

List of research and innovation needs requiring medium- or long-term approach and related Task Forces due at month 18

Second Report on processed genome-phenome datasets and multi-omics use cases analysed, including description of new cloud and online analysis functionalities and tools

Other lead beneficiary UMCG (35) Second Report on processed genome-phenome datasets and multi-omics use cases analysed, including description of new cloud and online analysis functionalities and tools due at month 24

Third report from the face-to-face ExCom and Policy Board meeting

Report from the face-to-face ExCom and Policy Board meeting due at Month 31

Second List of funded networks in Networking scheme

List of funded networks in Networking scheme due at month 54

Fourth Annual strategic report and Action plan for Pillar 2, including: Systematic surveys reports, QMS of Pillar 2 description, GDPR compliance report and sustainability planning reporting

Annual strategic report and Action plan for Pillar 2 including Systematic surveys reports QMS of Pillar 2 description GDPR compliance report and sustainability planning reporting update at month 45

Second Report on training of patient representatives on scientific innovation and translational research in RD

Second Report on training of patient representatives on scientific innovation and translational research in RD due at month 60

Second Report on ExPRESS

Second Report on ExPRESS EURORDIS Summer School due at month 60

Collection of 20 curated (sub)Portal on WikiPathways

Collection of 20 curated subPortal on WikiPathways

Third List of research and innovation needs requiring medium- or long-term approach and related Task Forces

List of research and innovation needs requiring medium or longterm approach and related Task Forces due at month 30

Report on core set of unified FAIR data standards
Report from the Kick-off meeting
Dynamic catalogue of EJP-RD sustainable resources including Service Roadmap Database

Dynamic catalogue of EJPRD sustainable resources including Service Roadmap Database Lead beneficiary INSERM RADICO

First RE(ACT) Congress report

First RE(ACT) Congress report due at M16

Second Annual reports on implementation of training programs

Second Annual reports on implementation of training programs due at month 60

List of first phase projects financed
First List of research and innovation needs requiring medium- or long-term approach and related Task Forces

List of research and innovation needs requiring medium or longterm approach and related Task Forces due at month 6

Fourth Scoping paper

Other lead beneficiaries ISCIII 44 and INSERM 1Scoping paper due at month 43

Draft content of the online academic course
Set of template agreements for EJP RD website
Second Report on EURORDIS' Leadership Programme

Second Report on EURORDIS’ Leadership Programme due at month 48

Third Analysis of national state of play and alignment process with EJP RD

Other lead beneficiary MUW 38Analysis of national state of play and alignment process with EJP RD due at month 32

Third Public Call documents JTC2019-2022: call text, guidelines for applicants, proposal templates

Other lead beneficiaries: ANR (11), FFRD (12) and ISCIII (44) Public Call documents JTC2019-2022: call text, guidelines for applicants, proposal templates due at mont 23

Training plan for paediatric patients' in the EJP

Other beneficiary FSJDTraining plan for paediatric patients in the EJP

First Report on sample data management training workshops

First Report on sample data management training workshops due at month 12

EJP RD ERN training programmes
First Public Call documents JTC2019-2022: call text, guidelines for applicants, proposal templates

Other lead beneficiaries: ANR (11), FFRD (12) and ISCIII (44) Public Call documents JTC2019-2022: call text, guidelines for applicants, proposal templates due at month 1

Call documents for validation
Second Analysis of national state of play and alignment process with EJP RD

Other lead beneficiary MUW (38) Analysis of national state of play and alignment process with EJP RD due at month 21

First Scoping paper

Other lead beneficiaries: ISCIII (44) and INSERM (1) Scoping paper due at Month 7

Fourth Report on processed genome-phenome datasets and multi-omics use cases analysed, including description of new cloud and online analysis functionalities and tools

Other lead beneficiary UMCG 35Fourth Report on processed genomephenome datasets and multiomics use cases analysed including description of new cloud and online analysis functionalities and tools due at month 48

Second Annual strategic report and Action plan for Pillar 2, including: Systematic surveys reports, QMS of Pillar 2 description, GDPR compliance report and sustainability planning reporting

Annual strategic report and Action plan for Pillar 2, including: Systematic surveys reports, QMS of Pillar 2 description, GDPR compliance report and sustainability planning reporting update at month 21

Completed pathway analysis workflow (data analysis including both types of genetic variant linking and network creation)

Completed pathway analysis workflow data analysis including both types of genetic variant linking and network creation

Fourth report from the face-to-face ExCom and Policy Board meeting

Report from the facetoface ExCom and Policy Board meeting due at Month 43

Results of survey on preferences, needs and resources from the ERNs ecosystem
Report on paediatric patients' experts training courses

Other beneficiary: FSJDReport on paediatric patients’ experts training courses

First Report on core set of FAIR software tools and on extended set of unified FAIR data standards, applied in EJP RD

First Report on core set of FAIR software tools and on extended set of unified FAIR data standards applied in EJP RD due at month 30

Second Report on sample data management training workshops

Second Report on sample data management training workshops due at month 60

First Report of Orphanet nomenclature training for trainers and national trainings

First Report of Orphanet nomenclature training for trainers and national trainings due at month 14

First Report from strategic workshop with national policy makers

Other lead beneficiary MUW 38Report from strategic workshop with national policy makers due at month 34

Third Annual strategic report and Action plan for Pillar 2, including: Systematic surveys reports, QMS of Pillar 2 description, GDPR compliance report and sustainability planning reporting

Annual strategic report and Action plan for Pillar 2 including Systematic surveys reports QMS of Pillar 2 description GDPR compliance report and sustainability planning reporting update at month 33

Prioritization scheme including decision-making process

Other lead beneficiary FTELE 25Prioritization scheme including decisionmaking process

Second RE(ACT) Congress report

Second REACT Congress report due at Month 30

Report on the State of the Art of existing resources
First List of funded networks in Networking scheme

List of funded networks in Networking scheme due at month 21

First Analysis of national state of play and alignment process with EJP RD

Other lead beneficiary MUW (38) Analysis of national state of play and alignment process with EJP RD due at Month 9

First Report on International course on Rare Disease Registries and FAIRification of data at source

First Report on International course on Rare Disease Registries and FAIRification of data at source due at month 12

Second Report of Orphanet nomenclature training for trainers and national trainings

Second Report of Orphanet nomenclature training for trainers and national trainings due at month 60

Fifth Scoping paper

Other lead beneficiaries ISCIII (44) and INSERM (1)Scoping paper due at month 55

Second Scoping paper

Other lead beneficiaries ISCIII (44) and INSERM (1) Scoping paper due at month 19

Second Report on course on interpretation of genetic variants and quality standards

Second Report on course on interpretation of genetic variants and quality standards due at month 60

Second Report on International course on Rare Disease Registries and FAIRification of data at source

Second Report on International course on Rare Disease Registries and FAIRification of data at source due at month 60

First Annual strategic report and Action plan for Pillar 2, including: Systematic surveys reports, QMS of Pillar 2 description, GDPR compliance report and sustainability planning reporting

Annual strategic report and Action plan for Pillar 2, including: Systematic surveys reports, QMS of Pillar 2 description, GDPR compliance report and sustainability planning reporting due at M9

First Annual report on implementation of training programs

First Annual reports on implementation of training programs due at month 13

Second Report from strategic workshop with national policy makers

Other lead beneficiary MUW 38Report from strategic workshop with national policy makers due at month 58

Second Report on core set of FAIR software tools and on extended set of unified FAIR data standards, applied in EJP RD

Second Report on core set of FAIR software tools and on extended set of unified FAIR data standards applied in EJP RD due at month 48

Third Scoping paper

Other lead beneficiaries ISCIII (44) and INSERM (1) Scoping paper due at month 31

Completed network analysis workflow (active node detection, lifestyle factor network evaluation and extended network analysis for drugs and toxic compounds)

Completed network analysis workflow active node detection lifestyle factor network evaluation and extended network analysis for drugs and toxic compounds

Fourth List of research and innovation needs requiring medium- or long-term approach and related Task Forces

List of research and innovation needs requiring medium or longterm approach and related Task Forces due at month 42

First report from the face-to-face ExCom and Policy Board meeting

Report from the face-to-face ExCom and Policy Board meeting due at M7

First Report on EURORDIS’ Leadership Programme

First Report on EURORDIS’ Leadership Programme due at month 12

Final Report of funded demonstration projects

Other lead beneficiaries: AP-HP (54), IOR (61) and ERN EpiCAREFinal Report of funded demonstration projects

First Report on training of patient representatives on scientific innovation and translational research in RD

First Report on training of patient representatives on scientific innovation and translational research in RD due at month 24

Second report from the face-to-face ExCom and Policy Board meeting

Report from the face-to-face ExCom and Policy Board meeting due at M19

Third update Virtual platform of RD resources annotated with EJP ontological model

Third update of the Virtual platform of RD resources annotated with EJP ontological model due at month 48

Second update Virtual platform of RD resources annotated with EJP ontological model

Second update of the Virtual platform of RD resources annotated with EJP ontological model due at month 36

EJP RD website
EJP RD Newsletter
Virtual platform of RD resources annotated with EJP ontological model

First version of the Virtual platform of RD resources annotated with EJP ontological model due at month 12

First update Virtual platform of RD resources annotated with EJP ontological model

First update of the Virtual platform of RD resources annotated with EJP ontological model due at month 24

Fourth version Additional facilities integrated to resources regarding data deposition and access, including user guidelines and documentation

Other lead beneficiary: ELIXIR (76)Fourth version of the Additional facilities integrated to resources regarding data deposition and access, including user guidelines and documentation due at month 48

First Ontological model of resources metadata

First Ontological model of resources metadata due at mont 12

First version of Additional facilities integrated to resources regarding data deposition and access, including user guidelines and documentation

Other lead beneficiary ELIXIR (76) First version of Additional facilities integrated to resources regarding data deposition and access, including user guidelines and documentation due at month 12

Fifth version Additional facilities integrated to resources regarding data deposition and access, including user guidelines and documentation

Other lead beneficiary: ELIXIR (76)Fifth version of the Additional facilities integrated to resources regarding data deposition and access, including user guidelines and documentation due at month 60

Third version Additional facilities integrated to resources regarding data deposition and access, including user guidelines and documentation

Other lead beneficiary ELIXIR 76Third version of Additional facilities integrated to resources regarding data deposition and access including user guidelines and documentation due at month 36

Content of the first 5 online modules
Content of the full online course
Fifth Ontological model of resources metadata

Fifth Ontological model of resources metadata due at month 60

Second version Additional facilities integrated to resources regarding data deposition and access, including user guidelines and documentation

Other lead beneficiary: ELIXIR (76) Second version of Additional facilities integrated to resources regarding data deposition and access, including user guidelines and documentation due at month 24

Fourth Ontological model of resources metadata

Fourth Ontological model of resources metadata due at month 48

Second Ontological model of resources metadata

Second Ontological model of resources metadata due at month 24

Third Ontological model of resources metadata

Third Ontological model of resources metadata due at month 36

Publications

Common conditions of use elements. Atomic concepts for consistent and effective information governance

Author(s): Maria del Carmen Sanchez Gonzalez, Pim Kamerling, Mariapia Iermito, Sara Casati, Umar Riaz, Colin D. Veal, Monika Maini, Francis Jeanson, Oussama Mohammed Benhamed, Esther van Enckevort, Annalisa Landi, Yanis Mimouni, Clèmence Le Cornec, Domenico A. Coviello, Tiziana Franchin, Francesca Fusco, Jose Antonio Ramírez García, Loes F. M. van der Zanden, Alexander Bernier, Mark D. Wilkinson, Heimo Mu
Published in: Scientific Data, Issue 11, 2024, ISSN 2052-4463
Publisher: Springer Nature
DOI: 10.1038/s41597-024-03279-z

A FAIR catalog of ontology-driven conceptual models

Author(s): Tiago Prince Sales, Pedro Paulo F. Barcelos, Claudenir M. Fonseca, Isadora Valle Souza, Elena Romanenko, César Henrique Bernabé, Luiz Olavo Bonino da Silva Santos, Mattia Fumagalli, Joshua Kritz, João Paulo A. Almeida, Giancarlo Guizzardi
Published in: Data & Knowledge Engineering, Issue 147, 2023, Page(s) 102210, ISSN 0169-023X
Publisher: Elsevier BV
DOI: 10.1016/j.datak.2023.102210

Variant recurrence confirms the existence of a FBXO31 ‐related spastic‐dystonic cerebral palsy syndrome

Author(s): Ivana Dzinovic, Matej Škorvánek, Petra Pavelekova, Chen Zhao, Boris Keren, Sandra Whalen, Somayeh Bakhtiari, Sheng Chih Jin, Michael C. Kruer, Robert Jech, Juliane Winkelmann, Michael Zech
Published in: Annals of Clinical and Translational Neurology, 2021, ISSN 2328-9503
Publisher: Wiley
DOI: 10.1002/acn3.51335

Lissencephaly: Update on diagnostics and clinical management

Author(s): Matti Koenig, William B. Dobyns, Nataliya Di Donato
Published in: European Journal of Paediatric Neurology, Issue 35, 2022, Page(s) 147-152, ISSN 1090-3798
Publisher: W. B. Saunders Co., Ltd.
DOI: 10.1016/j.ejpn.2021.09.013

Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations

Author(s): Denise N. Slenter, Irene M. G. M. Hemel, Chris T. Evelo, Jörgen Bierau, Egon L. Willighagen, Laura K. M. Steinbusch
Published in: Orphanet Journal of Rare Diseases, Issue 18, 2023, ISSN 1750-1172
Publisher: BioMed Central
DOI: 10.1186/s13023-023-02683-9

Ensembl 2024

Author(s): Peter W Harrison, M Ridwan Amode, Olanrewaju Austine-Orimoloye, Andrey G Azov, Matthieu Barba, If Barnes, Arne Becker, Ruth Bennett, Andrew Berry, Jyothish Bhai, Simarpreet Kaur Bhurji, Sanjay Boddu, Paulo R Branco Lins, Lucy Brooks, Shashank Budhanuru Ramaraju, Lahcen I Campbell, Manuel Carbajo Martinez, Mehrnaz Charkhchi, Kapeel Chougule, Alexander Cockburn, Claire Davidson, Nishadi H De S
Published in: Nucleic Acids Research, Issue 52, 2024, Page(s) D891-D899, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkad1049

Remote visualization of large-scale genomic alignments for collaborative clinical research and diagnosis of rare diseases

Author(s): Alberto Corvò, Leslie Matalonga, Dylan Spalding, Alexander Senf, Steven Laurie, Daniel Picó-Amador, Marcos Fernandez-Callejo, Ida Paramonov, Anna Foix Romero, Emilio Garcia-Rios, Jorge Izquierdo Ciges, Anand Mohan, Coline Thomas, Andres Felipe Silva Valencia, Csaba Halmagyi, Mallory Ann Freeberg, Ana Töpf, Rita Horvath, Gary Saunders, Ivo Gut, Thomas Keane, Davide Piscia, Sergi Beltran
Published in: Cell Genomics, Issue 3, 2023, Page(s) 100246, ISSN 2666-979X
Publisher: Elsevier Inc.
DOI: 10.1016/j.xgen.2022.100246

Increasing phenotypic annotation improves the diagnostic rate of exome sequencing in a rare neuromuscular disorder

Author(s): Rachel Thompson, Anastasios Papakonstantinou Ntalis, Sergi Beltran, Ana Töpf, Eduardo Paula Estephan, Kiran Polavarapu, Peter A. C. ’t Hoen, Paolo Missier, Hanns Lochmüller
Published in: Human Mutation, Issue 40/10, 2019, Page(s) 1797-1812, ISSN 1059-7794
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/humu.23792

The phenotypic and genetic spectrum of patients with heterozygous mutations in cyclin M2 (CNNM2)

Author(s): Gijs A. C. Franken, Dominik Müller, Cyril Mignot, Boris Keren, Jonathan Lévy, Anne‐Claude Tabet, David Germanaud, María‐Isabel Tejada, Hester Y. Kroes, Rutger A. J. Nievelstein, Elise Brimble, Maria Ruzhnikov, Felix Claverie‐Martin, Maria Szczepańska, Martin Ćuk, Femke Latta, Martin Konrad, Luis A. Martínez‐Cruz, René J. M. Bindels, Joost G. J. Hoenderop, Karl‐Peter Schlingmann, J
Published in: Human Mutation, 2021, ISSN 1059-7794
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/humu.24182

Evaluating FAIR maturity through a scalable, automated, community-governed framework

Author(s): Mark D. Wilkinson, Michel Dumontier, Susanna-Assunta Sansone, Luiz Olavo Bonino da Silva Santos, Mario Prieto, Dominique Batista, Peter McQuilton, Tobias Kuhn, Philippe Rocca-Serra, Mercѐ Crosas, Erik Schultes
Published in: Scientific Data, Issue 6/1, 2019, ISSN 2052-4463
Publisher: Nature
DOI: 10.1038/s41597-019-0184-5

Ensembl 2021

Author(s): Kevin L Howe, Premanand Achuthan, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Andrey G Azov, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, Mehrnaz Charkhchi, Carla Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Bilal El Houdaigui, Reham Fatima, Astrid Gall, Carlos Garcia Giron, Tiago Grego, Cristina Guijarro-Clarke, Lea
Published in: Nucleic Acids Research, Issue 49/D1, 2020, Page(s) D884-D891, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa942

A neutral comparison of statistical methods for analyzing longitudinally measured ordinal outcomes in rare diseases

Author(s): Martin Geroldinger, Johan Verbeeck, Konstantin E. Thiel, Geert Molenberghs, Arne C. Bathke, Martin Laimer, Georg Zimmermann
Published in: Biometrical Journal, Issue 66, 2024, ISSN 0323-3847
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/bimj.202200236

Detection of Telomeric DNA:RNA Hybrids Using TeloDRIP-qPCR

Author(s): Ilaria Rosso, Fabrizio d’Adda di Fagagna
Published in: International Journal of Molecular Sciences, Issue 21/24, 2020, Page(s) 9774, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms21249774

orsum: A Python package for filtering and comparing enrichment analyses using comprehensible rules

Author(s): Ozan Ozisik, Morgane Térézol, Anaı̈s Baudot
Published in: BMC Bioinformatics, Issue 23(1), 2022, Page(s) 293, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-022-04828-2

Towards FAIRification of sensitive and fragmented rare disease patient data: challenges and solutions in European reference network registries.

Author(s): Bruna dos Santos Vieira, César H. Bernabé, Shuxin Zhang, Haitham Abaza, Nirupama Benis, Alberto Cámara, Ronald Cornet, Clémence M. A. Le Cornec, Peter A. C. ’t Hoen, Franz Schaefer, K. Joeri van der Velde, Morris A. Swertz, Mark D. Wilkinson, Annika Jacobsen & Marco Roos
Published in: Orphanet Journal of Rare Diseases, 2022, ISSN 1750-1172
Publisher: BioMed Central
DOI: 10.1186/s13023-022-02558-5

Assessing resolvability, parsability, and consistency of RDF resources: a use case in rare diseases

Author(s): Shuxin Zhang, Nirupama Benis, Ronald Cornet
Published in: Journal of Biomedical Semantics, Issue 14, 2023, ISSN 2041-1480
Publisher: BioMed Central
DOI: 10.1186/s13326-023-00299-3

Building Expertise on FAIR Through Evolving Bring Your Own Data (BYOD) Workshops: Describing the Data, Software, and Management-focused Approaches and Their Evolution

Author(s): César H. Bernabé, Lieze Thielemans, Rajaram Kaliyaperumal, Claudio Carta, Shuxin Zhang, Celia W.G. van Gelder, Nirupama Benis, Luiz Olavo Bonino da Silva Santos, Ronald Cornet, Bruna dos Santos Vieira, Nawel Lalout, Ines Henriques, Alberto Cámara Ballesteros, Kees Burger, Martijn G. Kersloot, Friederike Ehrhart, Esther van Enckevort, Chris T. Evelo, Alasdair J. G. Gray, Marc Hanauer, Kristina H
Published in: Data Intelligence, Issue 6, 2024, Page(s) 429-456, ISSN 2641-435X
Publisher: The MIT Press
DOI: 10.1162/dint_a_00236

The case for open science: rare diseases

Author(s): Yaffa R Rubinstein, Peter N Robinson, William A Gahl, Paul Avillach, Gareth Baynam, Helene Cederroth, Rebecca M Goodwin, Stephen C Groft, Mats G Hansson, Nomi L Harris, Vojtech Huser, Deborah Mascalzoni, Julie A McMurry, Matthew Might, Christoffer Nellaker, Barend Mons, Dina N Paltoo, Jonathan Pevsner, Manuel Posada, Alison P Rockett-Frase, Marco Roos, Tamar B Rubinstein, Domenica Taruscio, Esther
Published in: JAMIA Open, Issue 3/3, 2020, Page(s) 472-486, ISSN 2574-2531
Publisher: Oxford Academic
DOI: 10.1093/jamiaopen/ooaa030

Ten quick tips for building FAIR workflows

Author(s): Casper de Visser, Lennart F. Johansson, Purva Kulkarni, Hailiang Mei, Pieter Neerincx, K. Joeri van der Velde, Péter Horvatovich, Alain J. van Gool, Morris A. Swertz, Peter A. C. ‘t Hoen, Anna Niehues
Published in: PLOS Computational Biology, Issue 19, 2023, Page(s) e1011369, ISSN 1553-7358
Publisher: San Francisco, CA Public Library of Science
DOI: 10.1371/journal.pcbi.1011369

Ensembl 2023.

Author(s): Martin FJ et al
Published in: Nucleic Acids Research, 2022, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkac958

Recommendations from the IRDiRC Working Group on methodologies to assess the impact of diagnoses and therapies on rare disease patients

Author(s): Galliano Zanello; Chun-Hung Chan; David A. Pearce; IRDiRC Working Group
Published in: Orphanet Journal of Rare Diseases, Vol 17, Iss 1, Pp 1-10 (2022), Issue 1, 2022, ISSN 1750-1172
Publisher: BioMed Central
DOI: 10.1186/s13023-022-02337-2

The use of foundational ontologies in biomedical research

Author(s): César H. Bernabé; Núria Queralt-Rosinach; Vítor E. Silva Souza; Luiz Olavo Bonino da Silva Santos; Barend Mons; Annika Jacobsen; Marco Roos
Published in: Journal of Biomedical Semantics, Vol 14, Iss 1, Pp 1-14 (2023), Issue 8, 2023, ISSN 2041-1480
Publisher: Biomed Central
DOI: 10.1186/s13326-023-00300-z

Artificial intelligence-enhanced electrocardiography derived body mass index as a predictor of future cardiometabolic disease

Author(s): Libor Pastika, Arunashis Sau, Konstantinos Patlatzoglou, Ewa Sieliwonczyk, Antônio H. Ribeiro, Kathryn A. McGurk, Sadia Khan, Danilo Mandic, William R. Scott, James S. Ware, Nicholas S. Peters, Antonio Luiz P. Ribeiro, Daniel B. Kramer, Jonathan W. Waks, Fu Siong Ng
Published in: npj Digital Medicine, Issue 7, 2024, ISSN 2398-6352
Publisher: Nature
DOI: 10.1038/s41746-024-01170-0

The FAIR Data Point: Interfaces and Tooling

Author(s): Ousamma Mohammed Benhamed1, Kees Burger2, Rajaram Kaliyaperumal2, Luiz Olavo Bonino da Silva Santos2,3, Marek Suchánek4, Jan Slifka4, Mark D Wilkinson1*
Published in: Data Intelligence, 2022, ISSN 2641-435X
Publisher: MIT Press
DOI: 10.1162/dint_a_00161

De novo variants in neurodevelopmental disorders—experiences from a tertiary care center

Author(s): Theresa Brunet, Robert Jech, Melanie Brugger, Reka Kovacs, Bader Alhaddad, Gloria Leszinski, Korbinian M. Riedhammer, Dominik S. Westphal, Isabella Mahle, Katharina Mayerhanser, Matej Skorvanek, Sandrina Weber, Elisabeth Graf, Riccardo Berutti, Ján Necpál, Petra Havránková, Petra Pavelekova, Maja Hempel, Urania Kotzaeridou, Georg F. Hoffmann, Steffen Leiz, Christine Makowski, Timo Roser, Sebas
Published in: Clinical Genetics, 2021, ISSN 0009-9163
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/cge.13946

WikiPathways: connecting communities

Author(s): Marvin Martens, Ammar Ammar, Anders Riutta, Andra Waagmeester, Denise N Slenter, Kristina Hanspers, Ryan A. Miller, Daniela Digles, Elisson N Lopes, Friederike Ehrhart, Lauren J Dupuis, Laurent A Winckers, Susan L Coort, Egon L Willighagen, Chris T Evelo, Alexander R Pico, Martina Kutmon
Published in: Nucleic Acids Research, Issue 49/D1, 2020, Page(s) D613-D621, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa1024

Exploring pathway interactions to detect molecular mechanisms of disease: 22q11.2 deletion syndrome

Author(s): Woosub Shin, Martina Kutmon, Eleni Mina, Therese van Amelsvoort, Chris T Evelo, Friederike Ehrhart
Published in: Orphanet Journal of Rare Diseases, Issue 18, 2023, ISSN 1750-1172
Publisher: BioMed Central
DOI: 10.1186/s13023-023-02953-6

SUsPECT: a pipeline for variant effect prediction based on custom long-read transcriptomes for improved clinical variant annotation

Author(s): Renee Salz, Nuno Saraiva-Agostinho, Emil Vorsteveld, Caspar I. van der Made, Simone Kersten, Merel Stemerdink, Jamie Allen, Pieter-Jan Volders, Sarah E. Hunt, Alexander Hoischen, Peter A.C. ’t Hoen
Published in: BMC Genomics, Issue 24, 2023, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-023-09391-5

Overlap of vitamin A and vitamin D target genes with CAKUT-related processes [version 2; peer review: 2 approved, 2 approved with reservations]

Author(s): Chris T. Evelo; Alberto Mantovani; Anaı̈s Baudot; Friederike Ehrhart; Ozan Ozisik
Published in: F1000Research, Vol 10 (2022), Issue 1, 2021, ISSN 2046-1402
Publisher: F1000 Research Ltd.

ABCA4 Variant c.5714+5G&gt;A in Trans With Null Alleles Results in Primary RPE Damage

Author(s): Jana Sajovic, Andrej Meglič, Zelia Corradi, Mubeen Khan, Aleš Maver, Martina Jarc Vidmar, Marko Hawlina, Frans P. M. Cremers, Ana Fakin
Published in: Investigative Opthalmology & Visual Science, Issue 64, 2023, Page(s) 33, ISSN 1552-5783
Publisher: ARVO Journals
DOI: 10.1167/iovs.64.12.33

FAIR Data Point: A FAIR-Oriented Approach for Metadata Publication

Author(s): Luiz Olavo Bonino da Silva Santos, Kees Burger, Rajaram Kaliyaperumal, Mark D. Wilkinson
Published in: Data Intelligence, 2022, ISSN 2641-435X
Publisher: MIT Press
DOI: 10.1162/dint_a_00160

Comparing regression curves: an L1-point of view

Author(s): Patrick Bastian, Holger Dette, Lukas Koletzko, Kathrin Möllenhoff
Published in: Annals of the Institute of Statistical Mathematics, Issue 76, 2024, Page(s) 159-183, ISSN 0020-3157
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10463-023-00880-8

Establishing the first pan-European Registry for rare bone and mineral disorders: EuRR-Bone

Author(s): Corinna Grasemann, Marina Mordenti, Inês Alves, Rebecca Skarberg, Ondrej Soucek, Marco Roos, M. Kassim Javaid, S. Faisal Ahmed, Agnès Lignart, Klaus Mohnike, Wolfgang Högler, Luca Sangiorgi, Natasha M. Appelman-Dijkstra
Published in: Bone Reports, Issue 13, 2020, Page(s) 100318, ISSN 2352-1872
Publisher: Elsevier Inc.
DOI: 10.1016/j.bonr.2020.100318

The RD-Connect Genome-Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases

Author(s): Steven Laurie, Davide Piscia, Leslie Matalonga, Alberto Corvó, Marcos Fernández-Callejo, Carles Garcia-Linares, Carles Hernandez-Ferrer, Cristina Luengo, Inés Martínez, Anastasios Papakonstantinou, Daniel Picó-Amador, Joan Protasio, Rachel Thompson, Raul Tonda, Mònica Bayés, Gemma Bullich, Jordi Camps-Puchadas, Ida Paramonov, Jean-Rémi Trotta, Angel Alonso, Marcella Attimonelli, Christophe
Published in: Human Mutation, Issue Volume 43, Issue 6, 2022, Page(s) Pages 717-733, ISSN 1098-1004
Publisher: Hindawi
DOI: 10.1002/humu.24353

Getting your DUCs in a row - standardising the representation of Digital Use Conditions

Author(s): Francis Jeanson, Spencer J. Gibson, Pinar Alper, Alexander Bernier, J. Patrick Woolley, Daniel Mietchen, Andrzej Strug, Regina Becker, Pim Kamerling, Maria del Carmen Sanchez Gonzalez, Nancy Mah, Ann Novakowski, Mark D. Wilkinson, Oussama Mohammed Benhamed, Annalisa Landi, Georg Philip Krog, Heimo Müller, Umar Riaz, Colin Veal, Petr Holub, Esther van Enckevort, Anthony J. Brookes
Published in: Scientific Data, Issue 11, 2024, ISSN 2052-4463
Publisher: Springer Nature
DOI: 10.1038/s41597-024-03280-6

A catalogue of 863 Rett-syndrome-causing MECP2 mutations and lessons learned from data integration

Author(s): Friederike Ehrhart, Annika Jacobsen, Maria Rigau, Mattia Bosio, Rajaram Kaliyaperumal, Jeroen F. J. Laros, Egon L. Willighagen, Alfonso Valencia, Marco Roos, Salvador Capella-Gutierrez, Leopold M. G. Curfs, Chris T. Evelo
Published in: Scientific Data, Issue 8/1, 2021, Page(s) 10, ISSN 2052-4463
Publisher: Nature
DOI: 10.1038/s41597-020-00794-7

Targeting shared molecular etiologies to accelerate drug development for rare diseases

Author(s): Galliano Zanello; Macarena Garrido‐Estepa; Ana Crespo; Daniel O'Connor; Rima Nabbout; Christina Waters; Anthony Hall; Maurizio Taglialatela; Chun‐Hung Chan; David A Pearce; Marc Dooms; Philip John Brooks
Published in: EMBO Molecular Medicine, Vol 15, Iss 7, Pp n/a-n/a (2023), Issue 6, 2023, ISSN 1757-4684
Publisher: Wiley Europe
DOI: 10.15252/emmm.202217159

A Resource for Guiding Data Stewards to Make European Rare Disease Patient Registries FAIR

Author(s): Philip van Damme; Pablo Alarcón Moreno; César H. Bernabé; Alberto Cámara Ballesteros; Clémence M. A. Le Cornec; Bruna Dos Santos Vieira; K. Joeri van der Velde; Shuxin Zhang; Claudio Carta; Ronald Cornet; Peter A.C. ’t Hoen; Annika Jacobsen; Morris A. Swertz; Marco Roos; Nirupama Benis
Published in: instname:Consejo Superior de Investigaciones Científicas (CSIC), Issue 8, 2023, ISSN 1683-1470
Publisher: Committee on Data for Science and Technology (CODATA) International Council for Science (ICSU)
DOI: 10.5334/dsj-2023-012

Consensus recommendations on chewing, swallowing and gastrointestinal problems in Phelan-McDermid syndrome

Author(s): Ausra Matuleviciene; Kamile Siauryte; Els Kuiper; Andreas M. Grabrucker
Published in: European Journal of Medical Genetics, Issue 8, 2023, ISSN 1769-7212
Publisher: Elsevier BV
DOI: 10.1016/j.ejmg.2023.104763

A Generic Workflow for the Data FAIRification Process

Author(s): Annika Jacobsen, Rajaram Kaliyaperumal, Luiz Olavo Bonino da Silva Santos, Barend Mons, Erik Schultes, Marco Roos, Mark Thompson
Published in: Data Intelligence, Issue 2/1-2, 2020, Page(s) 56-65, ISSN 2641-435X
Publisher: The MIT PressJournals
DOI: 10.1162/dint_a_00028

FAIR Principles: Interpretations and Implementation Considerations

Author(s): Annika Jacobsen, Ricardo de Miranda Azevedo, Nick Juty, Dominique Batista, Simon Coles, Ronald Cornet, Mélanie Courtot, Mercè Crosas, Michel Dumontier, Chris T. Evelo, Carole Goble, Giancarlo Guizzardi, Karsten Kryger Hansen, Ali Hasnain, Kristina Hettne, Jaap Heringa, Rob W.W. Hooft, Melanie Imming, Keith G. Jeffery, Rajaram Kaliyaperumal, Martijn G. Kersloot, Christine R. Kirkpatrick, Tobias K
Published in: Data Intelligence, Issue 2/1-2, 2020, Page(s) 10-29, ISSN 2641-435X
Publisher: The MIT PressJournals
DOI: 10.1162/dint_r_00024

A pipeline‐friendly software tool for genome diagnostics to prioritize genes by matching patient symptoms to literature

Author(s): K. Joeri Velde, Sander Hoek, Freerk Dijk, Dennis Hendriksen, Cleo C. Diemen, Lennart F. Johansson, Kristin M. Abbott, Patrick Deelen, Birgit Sikkema‐Raddatz, Morris A. Swertz
Published in: Advanced Genetics, Issue 1/1, 2020, Page(s) e10023, ISSN 2641-6573
Publisher: Wiley
DOI: 10.1002/ggn2.10023

Composite endpoints, including patient reported outcomes, in rare diseases

Author(s): Johan Verbeeck; Maya Dirani; Johann W. Bauer; Ralf-Dieter Hilgers; Geert Molenberghs; Rima Nabbout
Published in: Orphanet Journal of Rare Diseases, Vol 18, Iss 1, Pp 1-11 (2023), Issue 8, 2023, ISSN 1750-1172
Publisher: BioMed Central
DOI: 10.1186/s13023-023-02819-x

Author(s): Ugo Sorrentino, Sylvia Boesch, Diane Doummar, Claudia Ravelli, Tereza Serranova, Elisabetta Indelicato, Juliane Winkelmann, Lydie Burglen, Robert Jech, Michael Zech
Published in: Journal of Neurology, Issue 271, 2024, Page(s) 2859-2865, ISSN 0340-5354
Publisher: Dr. Dietrich Steinkopff Verlag
DOI: 10.1007/s00415-024-12271-x

A Simple Standard for Sharing Ontological Mappings (SSSOM)

Author(s): Nicolas Matentzoglu, James P Balhoff, Susan M Bello, Chris Bizon, Matthew Brush, Tiffany J Callahan, Christopher G Chute, William D Duncan, Chris T Evelo, Davera Gabriel, John Graybeal, Alasdair Gray, Benjamin M Gyori, Melissa Haendel, Henriette Harmse, Nomi L Harris, Ian Harrow, Harshad B Hegde, Amelia L Hoyt, Charles T Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian
Published in: Database, Issue 2022, 2022, ISSN 1758-0463
Publisher: Oxford University Press
DOI: 10.1093/database/baac035

Corrigendum: Reactive astrogliosis in the era of single-cell transcriptomics

Author(s): Zuzana Matusova; Zuzana Matusova; Elly M. Hol; Milos Pekny; Milos Pekny; Milos Pekny; Mikael Kubista; Mikael Kubista; Lukas Valihrach; Lukas Valihrach
Published in: Frontiers in Cellular Neuroscience, Vol 17 (2023), Issue 2, 2023, ISSN 1662-5102
Publisher: Frontiers Research Foundation
DOI: 10.3389/fncel.2023.1212975

Automated approach for quality assessment of RDF resources

Author(s): Shuxin Zhang, Nirupama Benis, Ronald Cornet
Published in: BMC Medical Informatics and Decision Making, Issue 23, 2024, ISSN 1472-6947
Publisher: BioMed Central
DOI: 10.1186/s12911-023-02182-8

The GA4GH Phenopacket schema defines a computable representation of clinical data

Author(s): Julius O. B. Jacobsen, Michael Baudis, Gareth S. Baynam, Jacques S. Beckmann, Sergi Beltran, Orion J. Buske, Tiffany J. Callahan, Christopher G. Chute, Mélanie Courtot, Daniel Danis, Olivier Elemento, Andrea Essenwanger, Robert R. Freimuth, Michael A. Gargano, Tudor Groza, Ada Hamosh, Nomi L. Harris, Rajaram Kaliyaperumal, Kevin C. Kent Lloyd, Aly Khalifa, Peter M. Krawitz, Sebastian Köhler, Bri
Published in: Nature Biotechnology, Issue 40, 2022, Page(s) 817-820, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-022-01357-4

Machine learning in Huntington’s disease: exploring the Enroll-HD dataset for prognosis and driving capability prediction

Author(s): Jasper Ouwerkerk, Stephanie Feleus, Kasper F. van der Zwaan, Yunlei Li, Marco Roos, Willeke M. C. van Roon-Mom, Susanne T. de Bot, Katherine J. Wolstencroft, Eleni Mina
Published in: Orphanet Journal of Rare Diseases, Issue 18, 2023, ISSN 1750-1172
Publisher: BioMed Central
DOI: 10.1186/s13023-023-02785-4

Improved Diagnosis of Rare Disease Patients through Systematic Detection of Runs of Homozygosity

Author(s): Leslie Matalonga, Steven Laurie, Anastasios Papakonstantinou, Davide Piscia, Elisabetta Mereu, Gemma Bullich, Rachel Thompson, Rita Horvath, Luis Pérez-Jurado, Olaf Riess, Ivo Gut, Gert-Jan van Ommen, Hanns Lochmüller, Sergi Beltran, Alessandra Renieri, Ali Dursun, Antoni Matilla-Duenas, Bru Cormand, Carlo Rivolta, Carmen Ayuso, Carmen Espinós, Christian Scerri, Dilek Yalnizoglu, Doriette Soler
Published in: The Journal of Molecular Diagnostics, Issue 22/9, 2020, Page(s) 1205-1215, ISSN 1525-1578
Publisher: American Society for Investigative Pathology
DOI: 10.1016/j.jmoldx.2020.06.008

How to Analyze Continuous and Discrete Repeated Measures in Small-Sample Cross-Over Trials?

Author(s): Johan Verbeeck, Martin Geroldinger, Konstantin Thiel, Andrew Craig Hooker, Sebastian Ueckert, Mats Karlsson, Arne Cornelius Bathke, Johann Wolfgang Bauer, Geert Molenberghs, Georg Zimmermann
Published in: Biometrics, Issue 79, 2024, Page(s) 3998-4011, ISSN 0006-341X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/biom.13920

Ability of a polygenic risk score to refine colorectal cancer risk in Lynch syndrome

Author(s): Nuria Dueñas, Hannah Klinkhammer, Nuria Bonifaci, Isabel Spier, Andreas Mayr, Emadeldin Hassanin, Anna Diez-Villanueva, Victor Moreno, Marta Pineda, Carlo Maj, Gabriel Capellà, Stefan Aretz, Joan Brunet
Published in: Journal of Medical Genetics, Issue 60, 2023, Page(s) 1044-1051, ISSN 0022-2593
Publisher: British Medical Association
DOI: 10.1136/jmg-2023-109344

Beyond Pathway Analysis: Identification of Active Subnetworks in Rett Syndrome

Author(s): Ryan A. Miller, Friederike Ehrhart, Lars M. T. Eijssen, Denise N. Slenter, Leopold M. G. Curfs, Chris T. Evelo, Egon L. Willighagen, Martina Kutmon
Published in: Frontiers in Genetics, Issue 10, 2019, ISSN 1664-8021
Publisher: Frontiers Media
DOI: 10.3389/fgene.2019.00059

Statistical recommendations for count, binary, and ordinal data in rare disease cross-over trials

Author(s): Martin Geroldinger; Johan Verbeeck; Andrew C. Hooker; Konstantin E. Thiel; Geert Molenberghs; Joakim Nyberg; Johann Bauer; Martin Laimer; Verena Wally; Arne C. Bathke; Georg Zimmermann
Published in: Orphanet J Rare Dis, Issue 18(1):391, 2023, ISSN 1750-1172
Publisher: BioMed Central
DOI: 10.1186/s13023-023-02990-1

Semantic modelling of Common Data Elements for Rare Disease registries, and a prototype workflow for their deployment over registry data

Author(s): Rajaram Kaliyaperumal; Mark D Wilkinson; Pablo Alarcón Moreno; Nirupama Benis; Ronald Cornet; Bruna dos Santos Vieira; Michel Dumontier; César Henrique Bernabé; Annika Jacobsen; Clémence M. A. Le Cornec; Mario Prieto Godoy; Núria Queralt-Rosinach; Leo J Schultze Kool; Morris A Swertz; Philip van Damme; Joeri K van der Velde; Nawel van Lin; Shuxin Zhang; Marco Roos
Published in: Journal of Biomedical Semantics, 2022, ISSN 2041-1480
Publisher: BioMed Central
DOI: 10.1186/s13326-022-00264-6

SUsPECT: A pipeline for variant effect prediction based on custom long-read transcriptomes for improved clinical variant

Author(s): Renee Salz, Nuno Saraiva-Agostinho, Emil Vorsteveld, Caspar I. van der Made, Simone Kersten, Merel Stemerdink, Jamie Allen, Pieter-Jan Volders, Sarah E. Hunt, Alexander Hoischen, Peter A.C. ’t Hoen
Published in: BARI RD conference, 2022
Publisher: CSHL
DOI: 10.1101/2022.10.23.513417

A Systems Biology Workflow to Support the Diagnosis of Inherited Metabolic Disorders: a study on Pyrimidine and Urea Cycle disorders

Author(s): Denise N. Slenter, Irene M.G.M. Hemel, Chris T. Evelo, Jörgen Bierau, Egon L. Willighagen, Laura K.M. Steinbusch
Published in: medRxiv, 2022
Publisher: Cold Spring Harbour Laboratory
DOI: 10.1101/2022.01.31.21265847

Lightweight Distributed Provenance Model for Complex Real–world Environments

Author(s): Rudolf Wittner; Cecilia Mascia; Matej Gallo; Francesca Frexia; Heimo Müller; Markus Plass; Jörg Geiger; Petr Holub
Published in: Crossref, Issue 1, 2022
Publisher: Sci Data
DOI: 10.1038/s41597-022-01537-6

A polymorphic AT-repeat causes frequent allele dropout for an MME mutational hotspot exon

Author(s): Helle Høyer; Hilde T Hilmarsen; Raute Sunder-Plassmann; Geir J Braathen; Peter M Andersen; Christian Beetz; Sandra Hacker; Øystein L Holla; Ingo Kurth; Wolfgang N Löscher; Simone B C F Reiter; Sabine Rudnik-Schöneborn; Linda Strand; Reinhard Windhager; Martina Witsch-Baumgartner; Jan Senderek; Michaela Auer-Grumbach
Published in: Crossref, Issue Oct;59(10):1024-1026, 2022
Publisher: J Med Genet
DOI: 10.1136/jmedgenet-2021-108281

Alpha‐Synuclein is Involved in <scp>DYT1</scp> Dystonia Striatal Synaptic Dysfunction

Author(s): Giulia Ponterio; Gaia Faustini; Ilham El Atiallah; Giuseppe Sciamanna; Maria Meringolo; Annalisa Tassone; Paola Imbriani; Silvia Cerri; Giuseppina Martella; Paola Bonsi; Arianna Bellucci; Antonio Pisani
Published in: Crossref, Issue 37(5):949-961, 2022
Publisher: Mov Disord
DOI: 10.1002/mds.29024

The European Genome-phenome Archive in 2021.

Author(s): Mallory A. Freeberg; Lauren A Fromont; Teresa D’Altri; Anna Foix Romero; Jorge Izquierdo Ciges; Aina Jene; Giselle Kerry; Mauricio Moldes; Roberto Ariosa; Silvia Bahena; Daniel Barrowdale; Marcos Casado Barbero; Dietmar Fernandez-Orth; Carles Garcia-Linares; Emilio Garcia-Rios; Frédéric Haziza; Bela Juhasz; Oscar Martinez Llobet; Gemma Milla; Anand Mohan; Manuel Rueda; Aravind Sankar; Dona Sha
Published in: Nucleic Acids Research, Issue Volume 50, Issue D1, 7 January 2022, 2021, Page(s) Pages D980–D987
Publisher: Oxford Academic
DOI: 10.1093/nar/gkab1059

A mosaic PIK3CA variant in a young adult with diffuse gastric cancer: case report.

Author(s): te Paske, Iris B. A. W.; Garcia-Pelaez, José; Sommer, Anna K.; Matalonga, Leslie; Starzynska, Teresa; Jakubowska, Anna; Valle, Laura; Capella, Gabriel; Aretz, Stefan; Holinski-Feder, Elke; Steinke-Lange, Verena; Laner, Andreas; Schröck, Evelin; Rump, Andreas; Ligtenberg, Marjolijn; Hoischen, Alexander; Geverink, Nicoline; Evans, D. Gareth; Tischkowitz, Marc; Laurie, Steven; van der Post, Rachel
Published in: European Journal of Human Genetics ,, Issue vol. 29 , no. 9, 2021, Page(s) pp. 1354-1358
Publisher: European Journal of Genetics
DOI: 10.1038/s41431-021-00853-6

Isolation and transfection of myenteric neurons from mice for patch-clamp applications

Author(s): Samuel Kuehs; Laura Teege; Ann-Katrin Hellberg; Christina Stanke; Natja Haag; Ingo Kurth; Robert Blum; Carla Nau; Enrico Leipold
Published in: Crossref, Issue 1, 2022
Publisher: Front. Mol. Neurosci
DOI: 10.3389/fnmol.2022.1076187

De-novo FAIRification via an Electronic Data Capture system by automated transformation of filled electronic Case Report Forms into machine-readable data.

Author(s): Martijn G. Kersloot; Annika Jacobsen; Karlijn H. J. Groenen; Bruna dos Santos Vieira; Rajaram Kaliyaperumal; Ameen Abu-Hanna; Ronald Cornet; Peter A C 't Hoen; Marco Roos; Leo J. Schultze Kool; Derk L. Arts
Published in: VOLUME=122;TITLE=Journal of Biomedical Informatics, Issue 1, 2021
Publisher: Science direct
DOI: 10.1016/j.jbi.2021.103897

Variant recurrence confirms the existence of a FBXO31 ‐related spastic‐dystonic cerebral palsy syndrome

Author(s): Dzinovic, I.; Škorvánek, M.; Pavelekova, P.; Zhao, C.; Keren, B.; Whalen, S.; Bakhtiari, S.; Chih Jin, S.; Kruer, M.C.; Jech, R.; Winkelmann, J.; Zech, M.
Published in: Annals of Clinical and Translational Neurology, Vol 8, Iss 4, Pp 951-955 (2021), Issue 1, 2021
Publisher: Ann Clin Transl Neurol

Vesicular Acetylcholine Transporter Alters Cholinergic Tone and Synaptic Plasticity in DYT1 Dystonia.

Author(s): Annalisa Tassone; Giuseppina Martella; Maria Meringolo; Valentina Vanni; Giuseppe Sciamanna; Giulia Ponterio; Paola Imbriani; Paola Bonsi; Antonio Pisani
Published in: Movement disorders, Issue 1, 2021
Publisher: Movement disorders
DOI: 10.1002/mds.28698

FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research

Author(s): K. Joeri van der Velde; Gurnoor Singh; Rajaram Kaliyaperumal; XiaoFeng Liao; Sander de Ridder; Susanne Rebers; Hindrik H. D. Kerstens; Fernanda de Andrade; Jeroen van Reeuwijk; Fini E. De Gruyter; Saskia Hiltemann; Maarten Ligtvoet; Marjan M. Weiss; Hanneke W. M. van Deutekom; Anne M. L. Jansen; Andrew P. Stubbs; Lisenka E. L. M. Vissers; Jeroen F. J. Laros; Esther van Enckevort; Daphne Stemkens;
Published in: van der Velde , K J , Singh , G , Kaliyaperumal , R , Liao , X , de Ridder , S , Rebers , S , Kerstens , H H D , de Andrade , F , van Reeuwijk , J , de Gruyter , F E , Hiltemann , S , Ligtvoet , M , Weiss , M M , van Deutekom , H W M , Jansen , A M L , Stubbs , A P , Vissers , L E L M , Laros , J F J , van Enckevort , E , Stemkens , D , ‘t Hoen , P A C , Beliën , J A M , van Gijn , M E & Swertz, Issue 1, 2022
Publisher: Scientific data
DOI: 10.1038/s41597-022-01265-x

A formalization of one of the main claims of “Overlap of vitamin A and vitamin D target genes with CAKUT-related processes” by Ozisik et al. 2021.

Author(s): Friederike Ehrhart, Chris T. Evelo
Published in: Data Science, Issue 5(1), 2022, Page(s) 25-27
Publisher: IOS Press
DOI: 10.3233/ds-210041

Long-read technologies identify a hidden inverted duplication in a family with choroideremia

Author(s): Zeinab Fadaie; Kornelia Neveling; Tuomo Mantere; Ronny Derks; Lonneke Haer-Wigman; Amber den Ouden; Michael Kwint; Luke O’Gorman; Dyon Valkenburg; Carel B. Hoyng; Christian Gilissen; Lisenka E.L.M. Vissers; Marcel R. Nelen; Frans P.M. Cremers; Alexander Hoischen; Susanne Roosing
Published in: HGG Advances, 2, 1 - 11, Issue 1, 2022
Publisher: Science direct
DOI: 10.1016/j.xhgg.2021.100046

A Community-Driven, Openly Accessible Molecular Pathway Integrating Knowledge on Malignant Pleural Mesothelioma

Author(s): Marvin Martens; Franziska Kreidl; Friederike Ehrhart; Didier Jean; Merlin Mei; Holly M. Mortensen; Alistair Nash; Penny Nymark; Chris T. Evelo; Ferdinando Cerciello
Published in: "Frontiers in Oncology, Frontiers, 2022, 12, pp.849640. ⟨10.3389/fonc.2022.849640⟩", Issue 1, 2022
Publisher: Frontiers in oncology
DOI: 10.3389/fonc.2022.849640

Beacon v2 and Beacon networks: A “lingua franca” for federated data discovery in biomedical genomics, and beyond

Author(s): Jordi Rambla; Michael Baudis; Roberto Ariosa; Tim Beck; Lauren A. Fromont; Arcadi Navarro; Rahel Paloots; Manuel Rueda; Gary Saunders; Babita Singh; John D. Spalding; Juha Törnroos; Claudia Vasallo; Colin D. Veal; Anthony J. Brookes
Published in: instname:, Issue 1, 2022
Publisher: Zurich Open Repository and Archive, University of Zurich
DOI: 10.1002/humu.24369

Gitelman-Like Syndrome Caused by Pathogenic Variants in mtDNA.

Author(s): Daan H H M Viering; Karl-Peter Schlingmann; Marguerite Hureaux; Tom Nijenhuis; Andrew Mallett; Melanie Chan; André P van Beek; Albertien M. van Eerde; Jean-Marie Coulibaly; Marion Vallet; Stéphane Decramer; Solenne Pelletier; Günter Klaus; Martin Kömhoff; Rolf Beetz; Chirag Patel; Mohan Shenoy; Eric J. Steenbergen; Glenn Anderson; Ernie M.H.F. Bongers; Carsten Bergmann; Daan M. Panneman; Richa
Published in: VOLUME=33;STARTPAGE=305;ENDPAGE=325;ISSN=1046-6673;TITLE=Journal of the American Society of Nephrology, Issue 1, 2022
Publisher: JASN
DOI: 10.1681/asn.2021050596

Systematic Collaborative Reanalysis of Genomic Data Improves Diagnostic Yield in Neurologic Rare Diseases

Author(s): Gemma Bullich; Leslie Matalonga; Montserrat Pujadas; Anastasios Papakonstantinou; Davide Piscia; Raúl Tonda; Rafael Artuch; Pia Gallano; Glòria Garrabou; Juan R. González; Daniel Grinberg; Míriam Guitart; Steven Laurie; Conxi Lázaro; Cristina Luengo; Ramon Martí; Montserrat Milà; David Ovelleiro; Genís Parra; Aurora Pujol; Eduardo Tizzano; Alfons Macaya; Francesc Palau; Antònia Ribes; Lui
Published in: reponame:r-IIB SANT PAU. Repositorio Institucional de Producción Científica del Instituto de Investigación Biomédica Sant Pau, Issue 1, 2022
Publisher: The journal of molecular diagnostics
DOI: 10.1016/j.jmoldx.2022.02.003

Frameshift mutation S368fs in the gene encoding cytoskeletal β-actin leads to ACTB-associated syndromic thrombocytopenia by impairing actin dynamics

Author(s): Johannes N. Greve; Frederic V. Schwäbe; Thomas Pokrant; Jan Faix; Nataliya Di Donato; Manuel H. Taft; Dietmar J. Manstein
Published in: Crossref, Issue 1, 2022
Publisher: Elsevier GmbH
DOI: 10.1016/j.ejcb.2022.151216

Goal-models to support communication, planning and guiding of FAIRification

Author(s): Bernab��, C��sar Henrique; Jacobsen, Annika; Queralt Rosinach, N��ria; Bonino da Silva Santos, Luiz Olavo; Silva Souza, V��tor E.; Mons, Barend; Roos, Marco
Published in: Zenodo, Issue 1, 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5784628

Applying the FAIR Data Principles to the Registry of Vascular Anomalies (VASCA)

Author(s): Bruna dos Santos Vieira, Karlijn Groenen, P.A.C. ‘t Hoen, Annika Jacobsen, Marco Roos, Rajaram Kaliyaperumal, Martijn Kersloot, Ronald Cornet, Leo Schultze Kool
Published in: Studies in Health Technology and Informatics, Issue Volume 271: dHealth 2020 – Biomedical Informatics for Health and Care, 2020, Page(s) 115 - 116, ISSN 0926-9630
Publisher: IOS Press
DOI: 10.3233/shti200085

A FAIR data model for PRISMA (Personalised RISk-based MAmmascreening) Study

Author(s): Liao, Xiaofeng; de Jong, Milou; van Damme, Philip; Cornet, Ronald; Dos Santos Vieira, Bruna; Lutomski, Jennifer; Brullemans-Spansier, Mirjam; 't Hoen, Peter
Published in: Zenodo, Issue 1, 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7029267

Converging pathways found in copy number variation syndromes with high schizophrenia risk

Author(s): Friederike Ehrhart, Ana Silva, Therese van Amelsvoort, Emma von Scheibler, Chris Evelo, David E.J. Linden
Published in: bioRxiv, 2022, Page(s) United States
Publisher: Cold Spring Harbour Laboratory
DOI: 10.1101/2022.02.07.479370

Rare disease education in Europe and beyond: time to act

Author(s): Birute Tumiene 1, Harm Peters 2 3, Bela Melegh 4, Borut Peterlin 5, Algirdas Utkus 1 3, Natalja Fatkulina 6, György Pfliegler 7, Holm Graessner 8 9, Sanja Hermanns 8 9, Maurizio Scarpa 10, Jean-Yves Blay 11, Sharon Ashton 12, Lucy McKay 13, Gareth Baynam 14 15 16
Published in: Orphanet Journal of Rare disease, Issue 19;17(1):441, 2022
Publisher: BMC
DOI: 10.1186/s13023-022-02527-y

Solving patients with rare diseases through programmatic reanalysis of genome-phenome data

Author(s): Matalonga, Leslie; Hernández-Ferrer, Carles; Piscia, Davide; Schüle, Rebecca; Synofzik, Matthis; Töpf, Ana; Vissers, Lisenka E. L. M.; de Voer, Richarda; Tonda, Raul; Laurie, Steven; Fernandez-Callejo, Marcos; Picó, Daniel; Garcia-Linares, Carles; Papakonstantinou, Anastasios; Corvó, Alberto; Joshi, Ricky; Diez, Hector; Gut, Ivo; Hoischen, Alexander; Graessner, Holm; Beltran, Sergi; Cohen, En
Published in: European journal of human genetics, Issue 1, 2021
Publisher: Eur J Hum Genet
DOI: 10.1038/s41431-021-00852-7

Performance assessment of ontology matching systems for FAIR data

Author(s): Philip van Damme; Jesualdo Tomás Fernández-Breis; Nirupama Benis; Jose Antonio Miñarro-Gimenez; Nicolette F. de Keizer; Ronald Cornet
Published in: Journal of Biomedical Semantics, 13(1):19. BioMed Central Ltd., Issue 1, 2022, ISSN 2041-1480
Publisher: Journal of biomedical semantics
DOI: 10.1186/s13326-022-00273-5

Solving unsolved rare neurological diseases—a Solve-RD viewpoint

Author(s): Schüle, Rebecca; Timmann, Dagmar; Erasmus, Corrie E.; Reichbauer, Jennifer; Wayand, Melanie; van de Warrenburg, Bart; Schöls, Ludger; Wilke, Carlo; Bevot, Andrea; Zuchner, Stephan; Beltran, Sergi; Laurie, Steven; Matalonga, Leslie; Graessner, Holm; Synofzik, Matthis; Baets, Jonathan; Balicza, Peter; Chinnery, Patrick; Dürr, Alexandra; Haack, Tobias; Hengel, Holger; Horvath, Rita; Houlden, Henry
Published in: European journal of human genetics, Issue 1, 2021, ISSN 1476-5438
Publisher: European Journal of Human Genetics
DOI: 10.1038/s41431-021-00901-1

Possible role for rare TRPM7 variants in patients with hypomagnesaemia with secondary hypocalcaemia

Author(s): Rosa Vargas-Poussou; Felix Claverie-Martin; Caroline Prot-Bertoye; Valentina Carotti; Jenny van der Wijst; Ana Perdomo-Ramirez; Gloria M Fraga-Rodriguez; Marguerite Hureaux; Caro Bos; Femke Latta; Pascal Houillier; Joost G J Hoenderop; Jeroen H F de Baaij
Published in: reponame:r-IIB SANT PAU. Repositorio Institucional de Producción Científica del Instituto de Investigación Biomédica Sant Pau, Issue 1, 2022, ISSN 0931-0509
Publisher: Oxford University Press
DOI: 10.1093/ndt/gfac182

Applying the FAIR principles to data in a hospital: challenges and opportunities in a pandemic

Author(s): Queralt Rosinach, N.; Kaliyaperumal, R.; Bernabe, C.H.; Long, Q.Q.; Joosten, S.A.; Wijk, H.J. van der; Flikkenschild, E.L.A.; Burger, K.; Jacobsen, A.; Mons, B.; Roos, M.; BEAT COVID Grp; COVID-19 LUMC Grp
Published in: Journal of Biomedical Semantics, 13(1). BMC, Issue 1, 2022, ISSN 2041-1480
Publisher: BMC
DOI: 10.1186/s13326-022-00263-7

DMD – BIOMARKERS & OUTCOME MEASURES

Author(s): I. Verhaart, P. 'tHoen, M. Roos, E. Vroom
Published in: Neuromuscular Disorders, Issue 30, 2020, Page(s) S86, ISSN 0960-8966
Publisher: Elsevier BV
DOI: 10.1016/j.nmd.2020.08.137

The de novo FAIRification process of a registry for vascular anomalies

Author(s): Karlijn H.J. Groenen, Annika Jacobsen, Martijn G. Kersloot, Bruna Vieira, Esther van Enckevort, Rajaram Kaliyaperumal, Derk L. Arts, Peter A.C. ‘t Hoen, Ronald Cornet, Marco Roos, Leo Schultze Kool
Published in: Orphanet Journal of Rare Diseases, Issue 16(1), 2021, Page(s) 376, ISSN 1750-1172
Publisher: BioMed Central
DOI: 10.1186/s13023-021-02004-y

Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions

Author(s): Ryan A. Miller; Martina Kutmon; Anwesha Bohler; Andra Waagmeester; Chris T. Evelo; Egon Willighagen
Published in: Plos one, Issue 1, 2022, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1101/2020.07.31.230599

The “A” of FAIR – As Open as Possible, as Closed as Necessary

Author(s): Annalisa Landi, Mark Thompson, Viviana Giannuzzi, Fedele Bonifazi, Ignasi Labastida, Luiz Olavo Bonino da Silva Santos, Marco Roos
Published in: Data Intelligence, Issue 2/1-2, 2020, Page(s) 47-55, ISSN 2641-435X
Publisher: The MIT PressJournals
DOI: 10.1162/dint_a_00027

10th European Conference on Rare Diseases & Orphan Products (ECRD 2020)

Author(s): Marco Roos, Mark D. Wilkinson, Ronald Cornet, Deborah Mascalzoni, Veronica Popa, Ian Harrow,Claudio Carta, Yaffa R. Rubinstein, Dipak Kalra, Ana Rath, Victoria Hedley, Gülçin Gümüş
Published in: Orphanet Journal of Rare Diseases, Issue 15/S1, 2020, ISSN 1750-1172
Publisher: BioMed Central
DOI: 10.1186/s13023-020-01550-1

Recommendations for whole genome sequencing in diagnostics for rare diseases

Author(s): Erika Souche Sergi Beltran, Erwin Brosens, John W Belmont, Magdalena Fossum, Olaf Riess, Christian Gilissen, Amin Ardeshirdavani, Gunnar Houge, Marielle van Gijn , Jill Clayton-Smith , Matthis Synofzik , Nicole de Leeuw, Zandra C Deans, Yasemin Dincer, Sebastian H Eck, Saskia van der Crabben, Meena Balasubramanian, Holm Graessner , Marc Sturm, Helen Firth, Alessandra Ferlini, Rima Nabbout, Elfrid
Published in: Eur. J. Hum. Genet., Issue Sep;30(9), 2022, Page(s) 1017-1021, ISSN 1476-5438
Publisher: European Journal of Human Genetics
DOI: 10.1038/s41431-022-01113-x

Whole genome sequencing and in vitro splice assays reveal genetic causes for inherited retinal diseases.

Author(s): Zeinab Fadaie; Laura Whelan; Tamar Ben-Yosef; Adrian Dockery; Zelia Corradi; Christian Gilissen; Lonneke Haer-Wigman; Jordi Corominas; Galuh D.N. Astuti; Galuh D.N. Astuti; Laura de Rooij; L. Ingeborgh van den Born; Caroline C W Klaver; Caroline C W Klaver; Carel B. Hoyng; Niamh Wynne; Emma Duignan; Paul F. Kenna; Paul F. Kenna; Frans P.M. Cremers; G. Jane Farrar; Susanne Roosing
Published in: NPJ Genomic Medicine, 6, Issue 1, 2021, ISSN 2056-7944
Publisher: Genomic medicine
DOI: 10.1038/s41525-021-00261-1

The Data Use Ontology to streamline responsible access to human biomedical datasets.

Author(s): Jonathan Lawson; Moran N. Cabili; Giselle Kerry; Tiffany Boughtwood; Adrian Thorogood; Adrian Thorogood; Pinar Alper; Sarion R. Bowers; Rebecca R. Boyles; Anthony J. Brookes; Matthew Brush; Tony Burdett; Hayley L. Clissold; Stacey Donnelly; Stephanie O. M. Dyke; Mallory A. Freeberg; Melissa Haendel; Chihiro Hata; Petr Holub; Francis Jeanson; Aina Jene; Minae Kawashima; Shuichi Kawashima; Melissa A
Published in: Cell genome, Issue 1, 2021, ISSN 2666-979X
Publisher: Cell genome
DOI: 10.1016/j.xgen.2021.100028

Myopathic mitochondrial DNA depletion syndrome associated with biallelic variants in LIG3.

Author(s): Federica Invernizzi; Andrea Legati; Alessia Nasca; Eleonora Lamantea; Barbara Garavaglia; Mirjana Gusic; Robert Kopajtich; Holger Prokisch; Massimo Zeviani; Costanza Lamperti; Daniele Ghezzi
Published in: Brain, Issue Volume 144, Issue 9, 2021, Page(s) e74, ISSN 1460-2156
Publisher: Oxford academic
DOI: 10.1093/brain/awab238

Adenine base editing efficiently restores the function of Fanconi anemia hematopoietic stem and progenitor cells

Author(s): Sebastian M. Siegner; Laura Ugalde; Alexandra Clemens; Laura Garcia-Garcia; Juan A. Bueren; Paula Rio; Mehmet E. Karasu; Jacob E. Corn
Published in: Nature Communications, 13 (1), Issue 1, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.3929/ethz-b-000582242

Identifying obstacles hindering the conduct of academic-sponsored trials for drug repurposing on rare-diseases: an analysis of six use cases

Author(s): Marta del Álamo; Christoph Bührer; Dirk Fisher; Matthias Griese; Paul Lingor; Giovanni Palladini; Nicolas Sireau; Virginie Hivert; Luca Sangiorgi; Florence Guillot; Juliane Halftermeyer; Lenka Soucková; Kristýna Nosková; Regina Demlová
Published in: Crossref, Issue 1, 2022, ISSN 1745-6215
Publisher: BioMed Central
DOI: 10.1186/s13063-022-06713-y

The COVID-19 epidemiology and monitoring ontology

Author(s): Queralt-Rosinach, Núria; Schofield, Paul N.; Hoehndorf, Robert; Weiland, Claus; Schultes, Erik; Bernabé, César H.; Roos, Marco
Published in: BioHackrXiv, Issue 6, 2021
Publisher: BioHackrXiv
DOI: 10.37044/osf.io/n6tcz

Reuse of design pattern measurements for health data.

Author(s): Núria Queralt-Rosinach1, Mark Wilkinson2, Rajaram Kaliyaperumal1,César H. Bernabé1, Qinqin Long1, Michel Dumontier3, Paul N. Schofield4andMarco Roos
Published in: CEUR Workshop Proceedings, 2021, ISSN 1613-0073
Publisher: University of Cambridge
DOI: 10.17863/cam.77969

Proceedings of the 20th International Vasculitis and ANCA workshop 3-6th April 2022

Author(s): Michael Clarkson; Allyson Egan; Mark A Little
Published in: Zenodo, Issue 58, 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7154405

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