Molecular Biophysics Database (MBDB) makes raw measurements findable and reusable
Status Publisher Jazyk angličtina Země Německo Médium print-electronic
Typ dokumentu časopisecké články
Grantová podpora
101004806
Horizon 2020 Framework Programme
LM2023042
Ministerstvo Školství, Mládeže a Tělovýchovy
CZ.02.01.01/00/23_014/0008787
Ministerstvo Školství, Mládeže a Tělovýchovy
86652036
Akademie Věd České Republiky
PubMed
40783896
DOI
10.1007/s00249-025-01789-1
PII: 10.1007/s00249-025-01789-1
Knihovny.cz E-zdroje
- Klíčová slova
- Database, FAIR principles, Metadata model, Molecular biophysics, Raw data, Repository,
- Publikační typ
- časopisecké články MeSH
Open science is now established as an important paradigm for publicly funded research. The main principle being that to ensure best use of research data and integrity of the scientific process the information from experiments should be made widely and freely available. However, dedicated technical infrastructure to enable useful access to comprehensive experimental information in molecular biophysics is lacking, in particular in regard to repositories for raw measurement data. The Molecular Biophysics Database (MBDB) was created to fill this gap. The MBDB provides a common and extensible framework to store and access raw measurement data from a growing number of biophysical methods, currently including bio-layer interferometry, isothermal titration calorimetry, surface plasmon resonance, and microscale thermophoresis, with additional methods planned for the future. Alongside the raw measurement data from these methods, a rich set of metadata to enable data reuse is captured in accordance with the FAIR data management principles. An overview of the data models and technologies that were used to create the MBDB is presented here.
Zobrazit více v PubMed
Bourne PE, Berman HM, McMahon B, Watenpaugh KD, Westbrook JD, Fitzgerald PMD (1997) Macromolecular crystallographic information file. Methods Enzymol 277:571–590. https://doi.org/10.1016/S0076-6879(97)77032-0 PubMed DOI
Burastero O, Niebling S, Defelipe LA, Günther C, Struve A, Garcia Alai MM (2021) eSPC: an online data-analysis platform for molecular biophysics. Acta Crystallogr Sect D Struct Biol. https://doi.org/10.1107/S2059798321008998 DOI
Cappannini A, Mosca K, Mukherjee S, Moafinejad SN, Sinden RR, Arluison V, Bujnicki J, Wien F (2023) NACDDB: nucleic acid circular dichroism database. Nucl Acids Res 51(D1):D226–D231. https://doi.org/10.1093/nar/gkac829 PubMed DOI
DataCite Metadata Working Group (2024) DataCite metadata schema documentation for the publication and citation of research data and other research outputs. Version 4.5. DataCite e.V. https://doi.org/10.14454/g8e5-6293
Dohnálek J, Stránský J, Malý M, Černý J (2022) MOSBRI survey—biophysical data standards and accessibility. Zenodo. https://doi.org/10.5281/zenodo.6604159
Grabowski M, Langner KM, Cymborowski M, Porebski PJ, Sroka P, Zheng H, Cooper DR, Zimmerman MD, Elsliger MA, Burley SK, Minor W (2016) A public database of macromolecular diffraction experiments. Acta Crystallogr Sect D Struct Biol 72(11):1181–1193. https://doi.org/10.1107/S2059798316014716 DOI
Heller SR, McNaught A, Pletnev I, Stein S, Tchekhovskoi D (2015) InChI, the IUPAC international chemical identifier. J Cheminform 7:23. https://doi.org/10.1186/s13321-015-0068-4 PubMed DOI PMC
Hoch JC, Baskaran K, Burr H, Chin J, Eghbalnia HR, Fujiwara T, Gryk MR, Iwata T, Kojima C, Kurisu G, Maziuk D, Miyanoiri Y, Wedell JR, Wilburn C, Yao H, Yokoch M (2023) Biological magnetic resonance data bank. Nucleic Acids Res 51(D1):D368–D376. https://doi.org/10.1093/nar/gkac1050 PubMed DOI
Jacobsen A, de MirandaAzevedo R, Juty N, Batista D, Coles S, Cornet R, Courtot M, Crosas M, Dumontier M, Evelo CT, Goble C, Guizzardi G, Hansen KK, Hasnain A, Hettne K, Heringa J, Hooft RWW, Imming M, Jeffery KG, Kaliyaperumal R, Kersloot MG, Kirkpatrick CR, Kuhn T, Labastida I, Magagna B, McQuilton P, Meyers N, Montesanti A, van Reisen M, Rocca-Serra P, Pergl R, Sansone SA, Santos LOB, Schneider J, Strawn G, Thompson M, Waagmeester A, Weigel T, Wilkinson MD, Willighagen EL, Wittenburg P, Roos M, Mons B, Schultes E (2020) FAIR Principles: Interpretations and Implementation Considerations. Data Intelligence 2:10–29. https://doi.org/10.1162/dint_r_00024 DOI
Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA, Thiessen PA, Yu B, Zaslavsky L, Zhang J, Bolton EE (2025) PubChem 2025 update, Nucleic Acids Res 53(D1):D1516–D1525. https://doi.org/10.1093/nar/gkae1059
Kim S, Thiessen PA, Cheng T, Yu B, Bolton EE (2018) An update on PUG-REST: restful interface for programmatic access to PubChem. Nucleic Acids Res 46(W1):W563–W570. https://doi.org/10.1093/nar/gky294 PubMed DOI PMC
Lingė D, Gedgaudas M, Merkys A, Petrauskas V, Vaitkus A, Grybauskas A, Paketurytė V, Zubrienė A, Zakšauskas A, Mickevičiūtė A, Smirnovienė J, Baranauskienė L, Čapkauskaitė E, Dudutienė V, Urniežius E, Konovalovas A, Kazlauskas E, Shubin K, Schiöth HB, Chen WY, Matulis D (2023) PLBD: protein-ligand binding database of thermodynamic and kinetic intrinsic parameters. Database 2023:baad040. https://doi.org/10.1093/database/baad040 PubMed DOI PMC
Morin A, Eisenbraun B, Key J, Sanschagrin PC, Timony MA, Ottaviano M, Sliz P (2013) Cutting edge: collaboration gets the most out of software. Elife 2:e01456. https://doi.org/10.7554/eLife.01456 PubMed DOI PMC
Perez-Riverol Y, Bandla C, Kundu DJ, Kamatchinathan S, Bai J, Hewapathirana S, John NS, Prakash A, Walzer M, Wang S, Vizcaíno JA (2025) The PRIDE database at 20 years: 2025 update. Nucleic Acids Res 53(D1):D543–D553. https://doi.org/10.1093/nar/gkae1011 PubMed DOI
Schneider J, Strawn G, Thompson M, Waagmeester A, Weigel T, Wilkinson MD, Willighagen EL, Wittenburg P, Roos M, Mons B, Schultes E (2020) Fair principles: interpretations and implementation considerations. Data Intell 2:10–29. https://doi.org/10.1162/dint_r_00024 DOI
Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, Leipe D, Mcveigh R, O’Neill K, Robbertse B, Sharma S, Soussov V, Sullivan JP, Sun L, Turner S, Karsch-Mizrachi I (2020) NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (Oxford) 2020:baaa062. https://doi.org/10.1093/database/baaa062 PubMed DOI
Stránský J, Williams M, Mas C (2022) Databases related to molecular biophysics 09–2022. Zenodo. https://doi.org/10.5281/zenodo.7114168
The UniProt Consortium (2025) UniProt: the universal protein knowledgebase in 2025. Nucleic Acids Res 53(D1):D609–D617. https://doi.org/10.1093/nar/gkae1010 DOI
The wwPDB Consortium (2024) EMDB—the electron microscopy data bank. Nucleic Acids Res 52(D1), D456–D465. https://doi.org/10.1093/nar/gkad1019
Whitmore L, Woollett B, Miles AJ, Klose DP, Janes RW, Wallace BA (2011) PCDDB: the protein circular dichroism data bank, a repository for circular dichroism spectral and metadata. Nucleic Acids Res 39(suppl_1):D480–D486. https://doi.org/10.1093/nar/gkq1026 PubMed DOI
Wilkinson MD, Dumontier M., Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJG, Groth P, Goble C, Grethe JS, Heringa J, 't Hoen PAC, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer, AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B (2016) The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3:160018. https://doi.org/10.1038/sdata.2016.18