OMEX metadata specification (version 1.2)
A standardized approach to annotating computational biomedical models and their associated files can facilitate model reuse and reproducibility among research groups, enhance search and retrieval of models and data, and enable semantic comparisons between models. Motivated by these potential benefit...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
De Gruyter
2021-10-01
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| Series: | Journal of Integrative Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1515/jib-2021-0020 |
| _version_ | 1811272412104228864 |
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| author | Gennari John H. König Matthias Misirli Goksel Neal Maxwell L. Nickerson David P. Waltemath Dagmar |
| author_facet | Gennari John H. König Matthias Misirli Goksel Neal Maxwell L. Nickerson David P. Waltemath Dagmar |
| author_sort | Gennari John H. |
| collection | DOAJ |
| description | A standardized approach to annotating computational biomedical models and their associated files can facilitate model reuse and reproducibility among research groups, enhance search and retrieval of models and data, and enable semantic comparisons between models. Motivated by these potential benefits and guided by consensus across the COmputational Modeling in BIology NEtwork (COMBINE) community, we have developed a specification for encoding annotations in Open Modeling and EXchange (OMEX)-formatted archives. This document details version 1.2 of the specification, which builds on version 1.0 published last year in this journal. In particular, this version includes a set of initial model-level annotations (whereas v 1.0 described exclusively annotations at a smaller scale). Additionally, this version uses best practices for namespaces, and introduces omex-library.org as a common root for all annotations. Distributing modeling projects within an OMEX archive is a best practice established by COMBINE, and the OMEX metadata specification presented here provides a harmonized, community-driven approach for annotating a variety of standardized model representations. This specification acts as a technical guideline for developing software tools that can support this standard, and thereby encourages broad advances in model reuse, discovery, and semantic analyses. |
| first_indexed | 2024-04-12T22:39:47Z |
| format | Article |
| id | doaj.art-cc6b53848d884b448b71f90b9561df1c |
| institution | Directory Open Access Journal |
| issn | 1613-4516 |
| language | English |
| last_indexed | 2024-04-12T22:39:47Z |
| publishDate | 2021-10-01 |
| publisher | De Gruyter |
| record_format | Article |
| series | Journal of Integrative Bioinformatics |
| spelling | doaj.art-cc6b53848d884b448b71f90b9561df1c2022-12-22T03:13:46ZengDe GruyterJournal of Integrative Bioinformatics1613-45162021-10-0118310.1515/jib-2021-0020OMEX metadata specification (version 1.2)Gennari John H.0König Matthias1Misirli Goksel2Neal Maxwell L.3Nickerson David P.4Waltemath Dagmar5University of Washington, Seattle, USAHumboldt University, Berlin, GermanyKeele University, Newcastle, UKSeattle Children’s Research Institute, Seattle, USAAuckland Bioengineering Institute, The University of Auckland, Auckland, New ZealandUniversity of Greifswald, Greifswald, GermanyA standardized approach to annotating computational biomedical models and their associated files can facilitate model reuse and reproducibility among research groups, enhance search and retrieval of models and data, and enable semantic comparisons between models. Motivated by these potential benefits and guided by consensus across the COmputational Modeling in BIology NEtwork (COMBINE) community, we have developed a specification for encoding annotations in Open Modeling and EXchange (OMEX)-formatted archives. This document details version 1.2 of the specification, which builds on version 1.0 published last year in this journal. In particular, this version includes a set of initial model-level annotations (whereas v 1.0 described exclusively annotations at a smaller scale). Additionally, this version uses best practices for namespaces, and introduces omex-library.org as a common root for all annotations. Distributing modeling projects within an OMEX archive is a best practice established by COMBINE, and the OMEX metadata specification presented here provides a harmonized, community-driven approach for annotating a variety of standardized model representations. This specification acts as a technical guideline for developing software tools that can support this standard, and thereby encourages broad advances in model reuse, discovery, and semantic analyses.https://doi.org/10.1515/jib-2021-0020biosimulation modelingcombine standardsmetadatasemantics |
| spellingShingle | Gennari John H. König Matthias Misirli Goksel Neal Maxwell L. Nickerson David P. Waltemath Dagmar OMEX metadata specification (version 1.2) Journal of Integrative Bioinformatics biosimulation modeling combine standards metadata semantics |
| title | OMEX metadata specification (version 1.2) |
| title_full | OMEX metadata specification (version 1.2) |
| title_fullStr | OMEX metadata specification (version 1.2) |
| title_full_unstemmed | OMEX metadata specification (version 1.2) |
| title_short | OMEX metadata specification (version 1.2) |
| title_sort | omex metadata specification version 1 2 |
| topic | biosimulation modeling combine standards metadata semantics |
| url | https://doi.org/10.1515/jib-2021-0020 |
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