PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology: PDBx/mmCIF Ecosystem: Foundational Semantic Tools

John Westbrook; Jasmine Y. Young; Chenghua Shao; Zukang Feng; Vladimir Guranovic; Catherine L. Lawson; Brinda Vallat; Paul D. Adams; John M. Berrisford; Gerard Bricogne; Kay Diederichs; Robbie P. Joosten; Peter Keller; Nigel W. Moriarty; Oleg V. Sobolev; Sameer Velankar; Clemens Vonrhein; David G. Waterman; Genji Kurisu; Helen M. Berman; Stephen K. Burley; Ezra Peisach

doi:https://doi.org/10.1016/j.jmb.2022.167599

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology: PDBx/mmCIF Ecosystem: Foundational Semantic Tools

John Westbrook, Jasmine Y. Young, Chenghua Shao, Zukang Feng, Vladimir Guranovic, Catherine L. Lawson, Brinda Vallat, Paul D. Adams, John M. Berrisford, Gerard Bricogne, Kay Diederichs, Robbie P. Joosten, Peter Keller, Nigel W. Moriarty, Oleg V. Sobolev, Sameer Velankar, Clemens Vonrhein, David G. Waterman, Genji Kurisu, Helen M. BermanStephen K. Burley, Ezra Peisach

Rutgers, The State University

Research output: Contribution to journal › Review article › peer-review

Abstract

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.

Original language	American English
Article number	167599
Journal	Journal of molecular biology
Volume	434
Issue number	11
DOIs	https://doi.org/10.1016/j.jmb.2022.167599
State	Published - Jun 15 2022

ASJC Scopus subject areas

Biophysics
Structural Biology
Molecular Biology

Keywords

biological data
data management
data standard
macromolecular structure
protein data bank (PDB)

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https://doi.org/10.1016/j.jmb.2022.167599

Cite this

Westbrook, J., Young, J. Y., Shao, C., Feng, Z., Guranovic, V., Lawson, C. L., Vallat, B., Adams, P. D., Berrisford, J. M., Bricogne, G., Diederichs, K., Joosten, R. P., Keller, P., Moriarty, N. W., Sobolev, O. V., Velankar, S., Vonrhein, C., Waterman, D. G., Kurisu, G., ... Peisach, E. (2022). PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology: PDBx/mmCIF Ecosystem: Foundational Semantic Tools. Journal of molecular biology, 434(11), [167599]. https://doi.org/10.1016/j.jmb.2022.167599

@article{87a5ed913b5b4f2dba4785364faee769,

title = "PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology: PDBx/mmCIF Ecosystem: Foundational Semantic Tools",

abstract = "PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.",

keywords = "biological data, data management, data standard, macromolecular structure, protein data bank (PDB)",

author = "John Westbrook and Young, {Jasmine Y.} and Chenghua Shao and Zukang Feng and Vladimir Guranovic and Lawson, {Catherine L.} and Brinda Vallat and Adams, {Paul D.} and Berrisford, {John M.} and Gerard Bricogne and Kay Diederichs and Joosten, {Robbie P.} and Peter Keller and Moriarty, {Nigel W.} and Sobolev, {Oleg V.} and Sameer Velankar and Clemens Vonrhein and Waterman, {David G.} and Genji Kurisu and Berman, {Helen M.} and Burley, {Stephen K.} and Ezra Peisach",

note = "Funding Information: RCSB PDB is funded by the National Science Foundation [DBI-1832184; P.I.: S.K.B.], the US Department of Energy [DE-SC0019749; P.I.: S.K.B.], and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health [R01GM133198; P.I.: S.K.B.]. Development of the PDBx/mmCIF data dictionary is funded in part by [DBI-2019297; P.I.: S.K.B.]. PDBe is funded by European Molecular Biology Laboratory-European Bioinformatics Institute; Wellcome Trust [104948]; Biotechnology and Biological Sciences Research Council [BB/N019172/1, BB/G022577/1, BB/J007471/1, BB/K016970/1, BB/K020013/1, BB/M013146/1, BB/M011674/1, BB/M020347/1, BB/M020428/1, BB/P024351/1]; European Union [284209]; ELIXIR; and Open Targets. PDBj is funded by the NBDC-JST [P.I.: G.K.], partially by BINDS-AMED [P.I.: G.K.]. The authors would like to acknowledge the early work by Syd Hall, Paula Fitzgerald, and Brian McMahon, Keith Watenpaugh, Phil Bourne and many others who were instrumental in the development of the original mmCIF data standard. Publisher Copyright: {\textcopyright} 2022 The Authors",

year = "2022",

month = jun,

day = "15",

doi = "https://doi.org/10.1016/j.jmb.2022.167599",

language = "American English",

volume = "434",

journal = "Journal of molecular biology",

issn = "0022-2836",

publisher = "Academic Press Inc.",

number = "11",

}

Westbrook, J, Young, JY, Shao, C, Feng, Z, Guranovic, V, Lawson, CL, Vallat, B, Adams, PD, Berrisford, JM, Bricogne, G, Diederichs, K, Joosten, RP, Keller, P, Moriarty, NW, Sobolev, OV, Velankar, S, Vonrhein, C, Waterman, DG, Kurisu, G, Berman, HM , Burley, SK & Peisach, E 2022, 'PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology: PDBx/mmCIF Ecosystem: Foundational Semantic Tools', Journal of molecular biology, vol. 434, no. 11, 167599. https://doi.org/10.1016/j.jmb.2022.167599

TY - JOUR

T1 - PDBx/mmCIF Ecosystem

T2 - Foundational Semantic Tools for Structural Biology: PDBx/mmCIF Ecosystem: Foundational Semantic Tools

AU - Westbrook, John

AU - Young, Jasmine Y.

AU - Shao, Chenghua

AU - Feng, Zukang

AU - Guranovic, Vladimir

AU - Lawson, Catherine L.

AU - Vallat, Brinda

AU - Adams, Paul D.

AU - Berrisford, John M.

AU - Bricogne, Gerard

AU - Diederichs, Kay

AU - Joosten, Robbie P.

AU - Keller, Peter

AU - Moriarty, Nigel W.

AU - Sobolev, Oleg V.

AU - Velankar, Sameer

AU - Vonrhein, Clemens

AU - Waterman, David G.

AU - Kurisu, Genji

AU - Berman, Helen M.

AU - Burley, Stephen K.

AU - Peisach, Ezra

N1 - Funding Information: RCSB PDB is funded by the National Science Foundation [DBI-1832184; P.I.: S.K.B.], the US Department of Energy [DE-SC0019749; P.I.: S.K.B.], and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health [R01GM133198; P.I.: S.K.B.]. Development of the PDBx/mmCIF data dictionary is funded in part by [DBI-2019297; P.I.: S.K.B.]. PDBe is funded by European Molecular Biology Laboratory-European Bioinformatics Institute; Wellcome Trust [104948]; Biotechnology and Biological Sciences Research Council [BB/N019172/1, BB/G022577/1, BB/J007471/1, BB/K016970/1, BB/K020013/1, BB/M013146/1, BB/M011674/1, BB/M020347/1, BB/M020428/1, BB/P024351/1]; European Union [284209]; ELIXIR; and Open Targets. PDBj is funded by the NBDC-JST [P.I.: G.K.], partially by BINDS-AMED [P.I.: G.K.]. The authors would like to acknowledge the early work by Syd Hall, Paula Fitzgerald, and Brian McMahon, Keith Watenpaugh, Phil Bourne and many others who were instrumental in the development of the original mmCIF data standard. Publisher Copyright: © 2022 The Authors

PY - 2022/6/15

Y1 - 2022/6/15

N2 - PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.

AB - PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.

KW - biological data

KW - data management

KW - data standard

KW - macromolecular structure

KW - protein data bank (PDB)

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U2 - https://doi.org/10.1016/j.jmb.2022.167599

DO - https://doi.org/10.1016/j.jmb.2022.167599

M3 - Review article

C2 - 35460671

SN - 0022-2836

VL - 434

JO - Journal of molecular biology

JF - Journal of molecular biology

IS - 11

M1 - 167599

ER -

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology: PDBx/mmCIF Ecosystem: Foundational Semantic Tools

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