• Something wrong with this record ?

DOME Registry: implementing community-wide recommendations for reporting supervised machine learning in biology

OA. Attafi, D. Clementel, K. Kyritsis, E. Capriotti, G. Farrell, SC. Fragkouli, LJ. Castro, A. Hatos, T. Lenaerts, S. Mazurenko, S. Mozaffari, F. Pradelli, P. Ruch, C. Savojardo, P. Turina, F. Zambelli, D. Piovesan, AM. Monzon, F. Psomopoulos,...

. 2024 ; 13 (-) : . [pub] 20240102

Language English Country United States

Document type Journal Article

Persistent link   https://www.medvik.cz/link/bmc25004182

Grant support
CA21160 European Cooperation in Science and Technology

Supervised machine learning (ML) is used extensively in biology and deserves closer scrutiny. The Data Optimization Model Evaluation (DOME) recommendations aim to enhance the validation and reproducibility of ML research by establishing standards for key aspects such as data handling and processing, optimization, evaluation, and model interpretability. The recommendations help to ensure that key details are reported transparently by providing a structured set of questions. Here, we introduce the DOME registry (URL: registry.dome-ml.org), a database that allows scientists to manage and access comprehensive DOME-related information on published ML studies. The registry uses external resources like ORCID, APICURON, and the Data Stewardship Wizard to streamline the annotation process and ensure comprehensive documentation. By assigning unique identifiers and DOME scores to publications, the registry fosters a standardized evaluation of ML methods. Future plans include continuing to grow the registry through community curation, improving the DOME score definition and encouraging publishers to adopt DOME standards, and promoting transparency and reproducibility of ML in the life sciences.

Artificial Intelligence Laboratory Vrije Universiteit Brussels Brussels 1050 Belgium

Department of Biology National and Kapodistrian University of Athens Athens 157 72 Greece

Department of Biomedical Sciences University of Padova Padova 35131 Italy

Department of Biosciences University of Milan Milan 20133 Italy

Department of Computational Biology University of Lausanne Lausanne 1015 Switzerland

Department of Information Engineering University of Padova Padova 35131 Italy

Department of Oncology Geneva University Hospitals Geneva 1205 Switzerland

Department of Pharmacy and Biotechnology University of Bologna Bologna 40126 Italy

ELIXIR Hub Hinxton Cambridge CB10 1SD UK

HES SO HEG Geneva Geneva 1227 Switzerland

Institute of Applied Biosciences Centre for Research and Technology Hellas Thessaloniki 570 01 Greece

Institute of Biomembranes Bioenergetics and Molecular Biotechnologies Bari 70126 Italy

Interuniversity Institute of Bioinformatics in Brussels Université Libre de Bruxelles Vrije Universiteit Brussels Brussels 1050 Belgium

Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of Science Brno 62500 Czech Republic

Machine Learning Group Université Libre de Bruxelles Brussels 1050 Belgium

Masaryk University Czech Republic International Clinical Research Centre St Anne's Hospital Brno 65690 Czech Republic

SIB Swiss Institute of Bioinformatics Geneva 1206 Switzerland

Swiss Cancer Center Léman Lausanne 1015 Switzerland

Swiss Institute of Bioinformatics Lausanne 1015 Switzerland

ZB Med Information Centre for Life Sciences Cologne 50931 Germany

References provided by Crossref.org

000      
00000naa a2200000 a 4500
001      
bmc25004182
003      
CZ-PrNML
005      
20250206110001.0
007      
ta
008      
250121e20240102xxu f 000 0|eng||
009      
AR
024    7_
$a 10.1093/gigascience/giae094 $2 doi
035    __
$a (PubMed)39661723
040    __
$a ABA008 $b cze $d ABA008 $e AACR2
041    0_
$a eng
044    __
$a xxu
100    1_
$a Attafi, Omar Abdelghani $u Department of Biomedical Sciences, University of Padova, Padova 35131, Italy $1 https://orcid.org/0009000223279430
245    10
$a DOME Registry: implementing community-wide recommendations for reporting supervised machine learning in biology / $c OA. Attafi, D. Clementel, K. Kyritsis, E. Capriotti, G. Farrell, SC. Fragkouli, LJ. Castro, A. Hatos, T. Lenaerts, S. Mazurenko, S. Mozaffari, F. Pradelli, P. Ruch, C. Savojardo, P. Turina, F. Zambelli, D. Piovesan, AM. Monzon, F. Psomopoulos, SCE. Tosatto
520    9_
$a Supervised machine learning (ML) is used extensively in biology and deserves closer scrutiny. The Data Optimization Model Evaluation (DOME) recommendations aim to enhance the validation and reproducibility of ML research by establishing standards for key aspects such as data handling and processing, optimization, evaluation, and model interpretability. The recommendations help to ensure that key details are reported transparently by providing a structured set of questions. Here, we introduce the DOME registry (URL: registry.dome-ml.org), a database that allows scientists to manage and access comprehensive DOME-related information on published ML studies. The registry uses external resources like ORCID, APICURON, and the Data Stewardship Wizard to streamline the annotation process and ensure comprehensive documentation. By assigning unique identifiers and DOME scores to publications, the registry fosters a standardized evaluation of ML methods. Future plans include continuing to grow the registry through community curation, improving the DOME score definition and encouraging publishers to adopt DOME standards, and promoting transparency and reproducibility of ML in the life sciences.
650    12
$a řízené strojové učení $7 D000069553
650    12
$a registrace $7 D012042
650    _2
$a reprodukovatelnost výsledků $7 D015203
650    _2
$a databáze faktografické $7 D016208
650    _2
$a lidé $7 D006801
655    _2
$a časopisecké články $7 D016428
700    1_
$a Clementel, Damiano $u Department of Biomedical Sciences, University of Padova, Padova 35131, Italy $1 https://orcid.org/0000000273952921
700    1_
$a Kyritsis, Konstantinos $u Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki 570 01, Greece $1 https://orcid.org/000000018035341X
700    1_
$a Capriotti, Emidio $u Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy $1 https://orcid.org/0000000223230963
700    1_
$a Farrell, Gavin $u ELIXIR Hub, Hinxton, Cambridge CB10 1SD, UK $1 https://orcid.org/0000000151668551
700    1_
$a Fragkouli, Styliani-Christina $u Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki 570 01, Greece $u Department of Biology, National and Kapodistrian University of Athens, Athens 157 72, Greece $1 https://orcid.org/0000000340677123
700    1_
$a Castro, Leyla Jael $u ZB Med Information Centre for Life Sciences, Cologne 50931, Germany $1 https://orcid.org/0000000339860510
700    1_
$a Hatos, András $u Department of Oncology, Geneva University Hospitals, Geneva 1205, Switzerland $u Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland $u Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland $u Swiss Cancer Center Léman, Lausanne 1015, Switzerland $1 https://orcid.org/0000000192249820
700    1_
$a Lenaerts, Tom $u Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussels, Brussels 1050, Belgium $u Machine Learning Group, Université Libre de Bruxelles, Brussels 1050, Belgium $u Artificial Intelligence Laboratory, Vrije Universiteit Brussels, Brussels 1050, Belgium $1 https://orcid.org/0000000336451455
700    1_
$a Mazurenko, Stanislav $u Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Brno 62500, Czech Republic $u Masaryk University, Czech Republic International Clinical Research Centre, St. Anne's Hospital, Brno 65690, Czech Republic $1 https://orcid.org/0000000336594819
700    1_
$a Mozaffari, Soroush $u Department of Biomedical Sciences, University of Padova, Padova 35131, Italy
700    1_
$a Pradelli, Franco $u Department of Biomedical Sciences, University of Padova, Padova 35131, Italy $1 https://orcid.org/0000000271525512
700    1_
$a Ruch, Patrick $u HES-SO-HEG Geneva, Geneva 1227, Switzerland $u SIB Swiss Institute of Bioinformatics, Geneva 1206, Switzerland $1 https://orcid.org/0000000233742962
700    1_
$a Savojardo, Castrense $u Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy $1 https://orcid.org/0000000273590633
700    1_
$a Turina, Paola $u Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy $1 https://orcid.org/000000019174511X
700    1_
$a Zambelli, Federico $u Department of Biosciences, University of Milan, Milan 20133, Italy $u Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari 70126, Italy $1 https://orcid.org/0000000334874331
700    1_
$a Piovesan, Damiano $u Department of Biomedical Sciences, University of Padova, Padova 35131, Italy $1 https://orcid.org/0000000182102390
700    1_
$a Monzon, Alexander Miguel $u Department of Information Engineering, University of Padova, Padova 35131, Italy $1 https://orcid.org/0000000303628218
700    1_
$a Psomopoulos, Fotis $u Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki 570 01, Greece $1 https://orcid.org/0000000202224273
700    1_
$a Tosatto, Silvio C E $u Department of Biomedical Sciences, University of Padova, Padova 35131, Italy $u Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari 70126, Italy $1 https://orcid.org/0000000345257793
773    0_
$w MED00186214 $t GigaScience $x 2047-217X $g Roč. 13 (20240102)
856    41
$u https://pubmed.ncbi.nlm.nih.gov/39661723 $y Pubmed
910    __
$a ABA008 $b sig $c sign $y - $z 0
990    __
$a 20250121 $b ABA008
991    __
$a 20250206105956 $b ABA008
999    __
$a ok $b bmc $g 2263736 $s 1240189
BAS    __
$a 3
BAS    __
$a PreBMC-MEDLINE
BMC    __
$a 2024 $b 13 $c - $e 20240102 $i 2047-217X $m GigaScience $n Gigascience $x MED00186214
GRA    __
$a CA21160 $p European Cooperation in Science and Technology
LZP    __
$a Pubmed-20250121

Find record

Citation metrics

Archiving options