Towards self-describing and FAIR bulk formats for biomedical data.
Towards self-describing and FAIR bulk formats for biomedical data.
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DOI：
10.1371/journal.pcbi.1010944
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发表时间：
2023-03
影响因子：
4.3
通讯作者：
中科院分区：
文献类型：
--
作者：
我们介绍了一个自我描述的批量生物医学数据的序列化格式，称为生物医学（PFB）数据的便携式格式。生物医学数据的可移植格式基于Avro，并封装了数据模型，数据字典，数据本身以及指向第三方控制词汇表的指针。通常，数据字典中的每个数据元素与第三方控制的词汇表相关联，以使应用程序更容易协调两个或更多个PFB文件。我们还介绍了一个名为PyPFB的开源软件开发工具包（SDK），用于创建，探索和修改PFB文件。我们描述了实验研究，显示了在PFB格式中导入和导出批量生物医学数据时与使用JSON和SQL格式相比的性能改进。许多生物医学数据集具有封装和描述数据的独特结构。当使用这些数据集时，很难跟踪定义各个属性的整体结构和本体。PFB的开发是为了使处理这种类型的数据变得更简单。这使得任何与数据交互的人都可以将这个完全自我描述的数据集放在一个文件中的任何地方，并对其中包含的表型和生物数据进行分析。PFB是在Avro序列化数据格式上开发的，该格式可以帮助研究人员和公共运营商进行数据模式更新以及更改对外部ontologies的引用。在这项工作中，我们展示了使用PFB作为生物信息学工具的优势，以及它如何用于快速共享大型生物医学研究数据集。结果还表明，PFB为存储和共享结构化生物医学数据集带来了显着的加速。
We introduce a self-describing serialized format for bulk biomedical data called the Portable Format for Biomedical (PFB) data. The Portable Format for Biomedical data is based upon Avro and encapsulates a data model, a data dictionary, the data itself, and pointers to third party controlled vocabularies. In general, each data element in the data dictionary is associated with a third party controlled vocabulary to make it easier for applications to harmonize two or more PFB files. We also introduce an open source software development kit (SDK) called PyPFB for creating, exploring and modifying PFB files. We describe experimental studies showing the performance improvements when importing and exporting bulk biomedical data in the PFB format versus using JSON and SQL formats. Many biomedical data sets have a unique structure that encapsulates and describes the data. When working with these datasets it can be difficult to keep track of the overall structure and ontologies that define the individual properties. PFB was developed so that working with this type of data is made simpler. This allows anyone interacting with the data to bring this fully self-describing dataset in one file anywhere and do analysis over the phenotypic and biological data contained within it. PFB was devleoped over the Avro serialized data format which helps researchers and commons operators to make data schema updates as well as change references to external ontolgies. In this work we show the advantages to using PFB as a bioinformatic tool and how it is used to enable fast sharing of large biomedical research data sets. The results also show that PFB is bringing significant speedups for storing and sharing structured biomedical datasets.
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影响因子：
14.9
作者：
Köhler S;Vasilevsky NA;Engelstad M;Foster E;McMurry J;Aymé S;Baynam G;Bello SM;Boerkoel CF;Boycott KM;Brudno M;Buske OJ;Chinnery PF;Cipriani V;Connell LE;Dawkins HJ;DeMare LE;Devereau AD;de Vries BB;Firth HV;Freson K;Greene D;Hamosh A;Helbig I;Hum C;Jähn JA;James R;Krause R;F Laulederkind SJ;Lochmüller H;Lyon GJ;Ogishima S;Olry A;Ouwehand WH;Pontikos N;Rath A;Schaefer F;Scott RH;Segal M;Sergouniotis PI;Sever R;Smith CL;Straub V;Thompson R;Turner C;Turro E;Veltman MW;Vulliamy T;Yu J;von Ziegenweidt J;Zankl A;Züchner S;Zemojtel T;Jacobsen JO;Groza T;Smedley D;Mungall CJ;Haendel M;Robinson PN
通讯作者：
Robinson PN
DOI：
10.1097/ppo.0000000000000318
发表时间：
2018
期刊：
Cancer journal (Sudbury, Mass.)
影响因子：
--
作者：
Grossman RL
通讯作者：
Grossman RL
DOI：
10.1093/jamia/ocv189
发表时间：
2016-09
期刊：
Journal of the American Medical Informatics Association : JAMIA
影响因子：
--
作者：
Mandel JC;Kreda DA;Mandl KD;Kohane IS;Ramoni RB
通讯作者：
Ramoni RB
影响因子：
9.8
作者：
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 AJ;Groth P;Goble C;Grethe JS;Heringa J;'t Hoen PA;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
通讯作者：
Mons B
影响因子：
14.9
作者：
Schriml LM;Arze C;Nadendla S;Chang YW;Mazaitis M;Felix V;Feng G;Kibbe WA
通讯作者：
Kibbe WA