PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata.
| العنوان: | PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata. |
|---|---|
| المؤلفون: | LeRoy NJ; Center for Public Health Genomics, School of Medicine, University of Virginia, 22908, Charlottesville VA.; Department of Biomedical Engineering, School of Medicine, University of Virginia, 22904, Charlottesville VA., Khoroshevskyi O; Center for Public Health Genomics, School of Medicine, University of Virginia, 22908, Charlottesville VA., O'Brien A; Center for Public Health Genomics, School of Medicine, University of Virginia, 22908, Charlottesville VA., Stepień R; Center for Public Health Genomics, School of Medicine, University of Virginia, 22908, Charlottesville VA., Arslan A; Department of Computer Science, School of Engineering, University of Virginia, 22908, Charlottesville VA., Sheffield NC; Center for Public Health Genomics, School of Medicine, University of Virginia, 22908, Charlottesville VA.; School of Data Science, University of Virginia, Charlottesville VA 22904, Charlottesville VA.; Department of Biomedical Engineering, School of Medicine, University of Virginia, 22904, Charlottesville VA.; Department of Public Health Sciences, School of Medicine, University of Virginia, 22908, Charlottesville VA.; Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, 22908, Charlottesville VA.; Child Health Research Center, School of Medicine, University of Virginia, 22908, Charlottesville VA. |
| المصدر: | BioRxiv : the preprint server for biology [bioRxiv] 2024 May 11. Date of Electronic Publication: 2024 May 11. |
| نوع المنشور: | Preprint |
| اللغة: | English |
| بيانات الدورية: | Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE |
| مستخلص: | Background: As biological data increases, we need additional infrastructure to share it and promote interoperability. While major effort has been put into sharing data, relatively less emphasis is placed on sharing metadata. Yet, sharing metadata is also important, and in some ways has a wider scope than sharing data itself. Results: Here, we present PEPhub, an approach to improve sharing and interoperability of biological metadata. PEPhub provides an API, natural language search, and user-friendly web-based sharing and editing of sample metadata tables. We used PEPhub to process more than 100,000 published biological research projects and index them with fast semantic natural language search. PEPhub thus provides a fast and user-friendly way to finding existing biological research data, or to share new data. Availability: https://pephub.databio.org. Competing Interests: Conflict of interest statement NCS is a consultant for InVitro Cell Research, LLC. |
| التعليقات: | Update in: Gigascience. 2024 Jan 2;13:giae033. doi: 10.1093/gigascience/giae033. (PMID: 38991851) |
| References: | Am Soc Clin Oncol Educ Book. 2017;37:746-752. (PMID: 28561664) Nucleic Acids Res. 2002 Jan 1;30(1):207-10. (PMID: 11752295) BMC Bioinformatics. 2019 Jan 7;20(1):8. (PMID: 30612540) J Am Med Inform Assoc. 2015 Nov;22(6):1114. (PMID: 26555016) Sci Data. 2016 Mar 15;3:160018. (PMID: 26978244) Bioinformatics. 2015 Jun 15;31(12):1881-8. (PMID: 25649616) Front Genet. 2023 Mar 20;14:1155809. (PMID: 37020996) Bioinformatics. 2023 Mar 1;39(3):. (PMID: 36857584) Database (Oxford). 2019 Jan 1;2019:. (PMID: 31820804) Bioinformatics. 2007 Jul 15;23(14):1846-7. (PMID: 17496320) Database (Oxford). 2022 Jun 3;2022:. (PMID: 35657113) Bioinformatics. 2015 Dec 15;31(24):4038-40. (PMID: 26323714) Nucleic Acids Res. 2016 Jan 4;44(D1):D726-32. (PMID: 26527727) BMC Bioinformatics. 2020 Sep 3;21(1):378. (PMID: 32883210) Sci Data. 2022 Sep 8;9(1):553. (PMID: 36075919) Gigascience. 2021 Dec 6;10(12):. (PMID: 34890448) IEEE Trans Pattern Anal Mach Intell. 2020 Apr;42(4):824-836. (PMID: 30602420) Patterns (N Y). 2021 Sep 10;2(9):100322. (PMID: 34553169) Gigascience. 2022 Jun 14;11:. (PMID: 35701374) J Biomed Inform. 2017 May;69:115-117. (PMID: 28366789) Front Genet. 2023 May 23;14:1154198. (PMID: 37287537) Database (Oxford). 2021 Sep 29;2021:. (PMID: 34585726) |
| معلومات مُعتمدة: | R01 HG012558 United States HG NHGRI NIH HHS; R35 GM128636 United States GM NIGMS NIH HHS; T32 GM145443 United States GM NIGMS NIH HHS |
| تواريخ الأحداث: | Date Created: 20230830 Latest Revision: 20240722 |
| رمز التحديث: | 20240722 |
| مُعرف محوري في PubMed: | PMC10462087 |
| DOI: | 10.1101/2023.08.15.551388 |
| PMID: | 37645717 |
| قاعدة البيانات: | MEDLINE |
| تدمد: | 2692-8205 |
|---|---|
| DOI: | 10.1101/2023.08.15.551388 |