Internet Archive Scholar

ISA API: An open platform for interoperable life science experimental metadata

David Johnson, Dominique Batista, Keeva Cochrane, Robert P Davey, Anthony Etuk, Alejandra Gonzalez-Beltran, Kenneth Haug, Massimiliano Izzo, Martin Larralde, Thomas N Lawson, Alice Minotto, Pablo Moreno (+9 others)
2021 GigaScience  

Preserved Fulltext

fulltext thumbnail
Web Archive Capture PDF (4.1 MB)
https://web.archive.org/web/20211010141047/https://watermark.silverchair.com/giab060.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAtwwggLYBgkqhkiG9w0BBwagggLJMIICxQIBADCCAr4GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM1CvW5te20dARa62gAgEQgIICj9M9puNfmSWq8X78zbpDFjSRWJSNmcwIH_rct-VaVmNax86ST01C2aYaa8ZQInmNnZysQPEv9ysmuy3CC21smz0B1wDmBWEogmkY6h2UtrUBkebw5eiI7OKNiopdaLyg2eTBkF0cvjz4iEasatf_BAHzltzMq3CN801Pk5NSAjwc88djJn83lnR9ZTvZyDoX5QxrHo68QEKzBi8gAC8zaVb9k5BUrnGoXadAXt3e0WqMm1niryu45nXlL2OC5CMVv6M95NJOsm3SmYntCTL69bAmmP7oJ9MRx7pGrIxsA0l3s3-xeKJfaQjR3CdSm4GhYOBHejtM7ywATvUmXBY6AF44UwoKDj0KbzHPRX_FscTKbPwdBN5qvF7B62Mr-QlkGghomYuzK_1tkyPd3r0l6oziwWCRnwDrauQlSKh3_xkC0nu5Ilr0jE847GqO7dtwMmvW4m1eITf-jI76Gh796-IxKWmuYYfClFuwqtjTEZXPT6uQ_np7maxyjBAeLvC83aZYmtGMD1UyjqpDxhdbnNswoTGeQhVp338UEO6HwYMsBZI_kib_KKgwAVd3fmw_3l-ZgXHMfKEc0f0A7WPiGkxFN8EPGkPAh7hlPCU7VHojL0yFycOhHg4TmaGRFiY2bBVUjwhVh5MUEVx-wEZQkklkZ5Rhh_Lb6g8Y-6eA9hkPVpBc4Psrh_N76TCT_0IoHuk6KQCJgG-p_kTsXrDRNGmKqt0Jr-qJeam4wkdYY8fKkWtVg7oLKvY3Vw57fX5q6o6IsYur0lSTTtH5VHnDLeOCKV4u0ovOXvYgD230zdQ3Ag8KmWGeAHVdT5xZYVr50d68o95Vax9BIwfu4h4vmJ6Qyz8bTJWDrKfzYT2NtDw

A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL. The file type is application/pdf.

Background The Investigation/Study/Assay (ISA) Metadata Framework is an established and widely used set of open source community specifications and software tools for enabling discovery, exchange, and publication of metadata from experiments in the life sciences. The original ISA software suite provided a set of user-facing Java tools for creating and manipulating the information structured in ISA-Tab—a now widely used tabular format. To make the ISA framework more accessible to machines and
more » ... ble programmatic manipulation of experiment metadata, the JSON serialization ISA-JSON was developed. Results In this work, we present the ISA API, a Python library for the creation, editing, parsing, and validating of ISA-Tab and ISA-JSON formats by using a common data model engineered as Python object classes. We describe the ISA API feature set, early adopters, and its growing user community. Conclusions The ISA API provides users with rich programmatic metadata-handling functionality to support automation, a common interface, and an interoperable medium between the 2 ISA formats, as well as with other life science data formats required for depositing data in public databases.
doi:10.1093/gigascience/giab060 pmid:34528664 pmcid:PMC8444265 fatcat:emisaswturffta4b6bv7rlu5by
DOAJ
Citation

David Johnson, Dominique Batista, Keeva Cochrane, Robert P Davey, Anthony Etuk, Alejandra Gonzalez-Beltran, Kenneth Haug, Massimiliano Izzo, Martin Larralde, Thomas N Lawson, Alice Minotto, Pablo Moreno, Venkata Chandrasekhar Nainala, Claire O'Donovan, Luca Pireddu, Pierrick Roger, Felix Shaw, Christoph Steinbeck, Ralf J M Weber, Susanna-Assunta Sansone, Philippe Rocca-Serra. "ISA API: An open platform for interoperable life science experimental metadata." GigaScience 10.9 (2021)