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OMEX Metadata
libOMEXMeta

Metadata about COMBINE/OMEX archives should be annotated using triples of subjects, predicates, and objects in RDF XML files according to the OMEX Metadata guidelines.

On top of these guidelines, BioSimulations recommends the predicates and identifier namespaces described below. In addition, the URI for each object should be annotated using http://dublincore.org/specifications/dublin-core/dcmi-terms/identifier and a human-readable description of each object should be annotated using http://www.w3.org/2000/01/rdf-schema#label. Futhermore, alternative predictates should also be described using http://dublincore.org/specifications/dublin-core/dcmi-terms/description.

COMBINE/OMEX archives should be referenced using unique identifiers which begin with the prefix http://omex-library.org/ and end with the file extension .omex (e.g., http://omex-library.org/BioSimulations-0001.omex). We recommend using identifiers that are a concentation of http://omex-library.org/ and the filename of the COMBINE archive (e.g., BioSimulations-0001.omex).

Files in COMBINE archives should be referenced by concatenating the above identifiers with their location within their parent COMBINE archives (e.g., http://omex-library.org/BioSimulations-0001.omex/simulation.sedml).

Elements in SED-ML files in COMBINE archives should be referenced by concatenating the above identifiers with their id (e.g., http://omex-library.org/BioSimulations-0001.omex/simulation.sedml/Figure_3a).

BioSimulators recommends that COMBINE/OMEX archives be annotated using the predicates and objects below.

  • Title:
    • Predicate: http://dublincore.org/specifications/dublin-core/dcmi-terms/title
    • Object: Literal string
  • Abstract (short summary):
    • Predicate: http://dublincore.org/specifications/dublin-core/dcmi-terms/abstract
    • Object: Literal string
  • Description (long summary):
    • Predicate: http://dublincore.org/specifications/dublin-core/dcmi-terms/description
    • Object: Literal string
  • Keyword:
    • Predicate: http://prismstandard.org/namespaces/basic/2.0/keyword
    • Object: Literal string
  • Thumbnail image:
    • Predicate: http://www.collex.org/schema#thumbnail
    • Object: URI for a GIF, JPEG, PNG, or WEBP file inside the COMBINE/OMEX archive (e.g., http://omex-library.org/Ciliberto.omex/BioSim0001.png)
  • Organism captured by a modeling project:
    • Predicate: http://biomodels.net/biology-qualifiers/hasTaxon
    • Objects: Identifiers.org URI for an entry in NCBI Taxonomy (e.g., https://identifiers.org/taxonomy/9606), Literal string
  • Other biology (e.g., cell type, organ) captured by a modeling project:
    • Predicate: http://biomodels.net/biology-qualifiers/encodes
    • Objects: URI (e.g., https://www.uniprot.org/uniprot/P07527), Literal string
  • Source of a modeling project:
    • Predicate: http://dublincore.org/specifications/dublin-core/dcmi-terms/source
    • Objects: URI (e.g., https://github.com/org/repo), Literal string
  • Predecessor of a modeling project:
    • Predicate: http://biomodels.net/model-qualifiers/isDerivedFrom
    • Objects: URI (e.g., https://identifiers.org/biomodels.db:BIOMD0000000296), Literal string
  • Successor of a modeling project:
    • Predicate: http://purl.org/spar/scoro/successor
    • Objects: URI (e.g., https://identifiers.org/biomodels.db:BIOMD0000000298), Literal string
  • More information about a modeling project:
    • Predicate: http://www.w3.org/2000/01/rdf-schema#seeAlso
    • Objects: URI (e.g., http://mpf.biol.vt.edu/lab_website/), Literal string
  • Other identifier for a modeling project:
    • Predicate: http://biomodels.net/model-qualifiers/is
    • Objects: URI (e.g., https://identifiers.org/biomodels.db:BIOMD0000000297), Literal string
  • Citation for a modeling project:
    • Predicate: http://biomodels.net/model-qualifiers/isDescribedBy
    • Objects: Identifiers.org DOI URI (e.g., https://identifiers.org/doi:10.1083/jcb.200306139), Literal string
  • Author:
    • Predicate: http://dublincore.org/specifications/dublin-core/dcmi-terms/creator
    • Objects: ORCID Identifiers.org URI (e.g., https://identifiers.org/orcid:0000-0001-7560-6013), Literal string
  • Contributor (e.g., curator):
    • Predicate: http://dublincore.org/specifications/dublin-core/dcmi-terms/contributor
    • Objects: ORCID Identifiers.org URI (e.g., https://identifiers.org/orcid:0000-0001-7560-6013), Literal string
  • License for a modeling project:
    • Predicate: http://dublincore.org/specifications/dublin-core/dcmi-terms/identifier
    • Objects: SPDX Identifiers.org URI (e.g., https://identifiers.org/spdx:CCO), Literal string
  • Funder:
    • Predicate: http://purl.org/spar/scoro/funder
    • Objects: FunderRegistry Identifiers.org URI (e.g., https://identifiers.org/doi:10.13039/100000185), Literal string
  • Creation date:
    • Predicate: http://dublincore.org/specifications/dublin-core/dcmi-terms/created
    • Objects: WC3DTF-encoded literal string (e.g., 2021-06-01)
  • Modification date:
    • Predicate: http://dublincore.org/specifications/dublin-core/dcmi-terms/modified
    • Objects: WC3DTF-encoded literal string (e.g., 2021-06-01)

BioSimulators also provides the following recommendations:

  • The title, abstract, description, license, and creation date predicates should only be used once per subject.
  • Identifiers.org URIs should be used when possible because Identifiers.org can be used to validate URIs and map URIs to URLs. For example, https://identifiers.org/orcid:0000-0001-7560-6013 should be used rather than https://orcid.org/0000-0001-7560-6013.

Submissions to BioSimulations must include the following metadata:

  • Title (http://dublincore.org/specifications/dublin-core/dcmi-terms/title)
  • Abstract (http://dublincore.org/specifications/dublin-core/dcmi-terms/abstract)
  • Author (http://dublincore.org/specifications/dublin-core/dcmi-terms/creator)
  • License (http://dublincore.org/specifications/dublin-core/dcmi-terms/license)

BioSimulators recommends using the http://dublincore.org/specifications/dublin-core/dcmi-terms/identifier predicate and literal strings to describe the SED-ML files, reports, and plots responsible for tables and figures in articles.

As an example, below is a representation of metadata for the Ciliberto 2003 model of the budding yeast cell cycle .