Skip to content

Class: Study

General information about the study

URI: bia_mifa_models:Study

classDiagram class Study PublicationsCollection <|-- Study AuthorCollection <|-- Study Links <|-- Study GrantReferenceCollection <|-- Study Study : acknowledgements Study : ai_models_trained Study : authors Study --> Author : authors Study : description Study : funding_statement Study : grants Study --> GrantReference : grants Study : keywords Study : license Study --> LicenseType : license Study : link_description Study : link_url Study : publications Study --> Publications : publications Study : title

Inheritance

Slots

Name Cardinality and Range Description Inheritance
title 1..1
String		 The title for your dataset direct
description 1..1
String		 Brief description of the detaset direct
keywords 1..*
String		 Keywords or tags used to describe the dataset direct
license 1..1
LicenseType		 The license under which the data are available direct
ai_models_trained 0..*
Uriorcurie		 Link to the models that have been trained with this dataset (if any) direct
acknowledgements 0..1
String		 Any people or groups that should be acknowledged as part of the dataset direct
funding_statement 1..1
String		 Description of how the study was funded direct
publications 0..*
Publications		 a collection of publications associated with a study PublicationsCollection
authors 0..*
Author		 a collection of the authors of a study AuthorCollection
link_url 1..*
Uriorcurie		 URL of relevant link Links
link_description 0..*
String		 The description of the linked content Links
grants 0..*
GrantReference		 a collection of grant ids and funder names associated with the study GrantReferenceCollection

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/BioImage-Archive/bia-mifa-models

Mappings

Mapping Type Mapped Value
self bia_mifa_models:Study
native bia_mifa_models:Study

LinkML Source

Direct

name: Study
description: General information about the study
from_schema: https://w3id.org/BioImage-Archive/bia-mifa-models
mixins:
- PublicationsCollection
- AuthorCollection
- Links
- GrantReferenceCollection
slots:
- title
- description
- keywords
- license
- ai_models_trained
- acknowledgements
- funding_statement

Induced

name: Study
description: General information about the study
from_schema: https://w3id.org/BioImage-Archive/bia-mifa-models
mixins:
- PublicationsCollection
- AuthorCollection
- Links
- GrantReferenceCollection
attributes:
  title:
    name: title
    description: The title for your dataset. This will be displayed when search results
      including your data are shown. Often this will be the same as an associated
      publication.
    examples:
    - value: An annotated fluorescence image dataset for training nuclear segmentation
        methods
    - value: Embryonic mice ultrasound volumes with body and brain volume segmentation
        masks
    from_schema: https://w3id.org/BioImage-Archive/bia-mifa-models
    rank: 1000
    slot_uri: schema:title
    alias: title
    owner: Study
    domain_of:
    - Study
    range: string
    required: true
  description:
    name: description
    description: Brief description of the detaset. Must contain the biological application
      of the dataset
    examples:
    - value: Accurate quantification of nuclear features is critical for the characterization
        of tumours.  This dataset contains annotated fluorescent images of cell nuclei
        from a normal human skin cell line, and from different tumour samples from
        cancer patients.  This dataset can be used to train nuclear image segmentation
        algorithms.
    - value: The number of cells in an embryo at early stages of development can be
        used to understand its viability, however counting cells on DIC images is
        a challenging task.  This dataset contains annotated DIC images of mouse embryos
        to train machine learning models.
    from_schema: https://w3id.org/BioImage-Archive/bia-mifa-models
    rank: 1000
    slot_uri: schema:description
    alias: description
    owner: Study
    domain_of:
    - Study
    range: string
    required: true
  keywords:
    name: keywords
    description: Keywords or tags used to describe the dataset
    examples:
    - value: '[''segmentation'', ''nuclei'', ''cancer'']'
    - value: '[''image segmentation'', ''high-frequency ultrasound'', ''mouse embryo'',
        ''volumetric deep learning'']'
    from_schema: https://w3id.org/BioImage-Archive/bia-mifa-models
    rank: 1000
    slot_uri: schema:keywords
    multivalued: true
    alias: keywords
    owner: Study
    domain_of:
    - Study
    range: string
    required: true
  license:
    name: license
    description: The license under which the data are available
    examples:
    - value: CC0
    - value: CC_BY
    from_schema: https://w3id.org/BioImage-Archive/bia-mifa-models
    rank: 1000
    slot_uri: schema:license
    alias: license
    owner: Study
    domain_of:
    - Study
    range: LicenseType
    required: true
  ai_models_trained:
    name: ai_models_trained
    description: Link to the models that have been trained with this dataset (if any).
      This could be links to GitHub or repositories like the BioImage Zoo.
    examples:
    - value: https://github.com/BIIFSweden/MariaUlvmar2020-1
    - value: '[''https://github.com/perlfloccri/NuclearSegmentationPipeline'', ''https://bioimage.io/#/?id=10.5281%2Fzenodo.6028097'']'
    from_schema: https://w3id.org/BioImage-Archive/bia-mifa-models
    rank: 1000
    multivalued: true
    alias: ai_models_trained
    owner: Study
    domain_of:
    - Study
    range: uriorcurie
  acknowledgements:
    name: acknowledgements
    description: Any people or groups that should be acknowledged as part of the dataset
    examples:
    - value: We thank the Institute microscopy facility for support with image acquisition.  Flybase
        provided important information for this study.
    - value: 'We are grateful to Y. Papadopoulos for providing reagents and access
        to her confocal microscope.  We thank J. Dupont and E. Mustermann for comments
        on the manuscript, and G. Hong for useful discussions. '
    from_schema: https://w3id.org/BioImage-Archive/bia-mifa-models
    rank: 1000
    alias: acknowledgements
    owner: Study
    domain_of:
    - Study
    range: string
  funding_statement:
    name: funding_statement
    description: Description of how the study was funded
    examples:
    - value: T.G. was supported by an EMBO Long-Term Fellowship (ALTF 1234-5678),
        and the European Union Horizon 2020 research and innovation programme  under
        the Marie Sklodowska-Curie grant agreement No 12345. This work was supported
        by a Cancer Research UK Programme Grant (DRCNPG-123\123456) to J.C.
    - value: This work was facilitated by an EraSME grant (project TisQuant) under
        the grant no. 844198 and by a COIN grant (project VISIOMICS)  under the grant
        no. 861750, both grants kindly provided by the Austrian Research Promotion
        Agency (FFG), and the St. Anna Kinderkrebsforschung.  Partial funding was
        further provided by BMK, BMDW, and the Province of Upper Austria in the frame
        of the COMET Programme managed by FFG.
    from_schema: https://w3id.org/BioImage-Archive/bia-mifa-models
    rank: 1000
    alias: funding_statement
    owner: Study
    domain_of:
    - Study
    range: string
    required: true
  publications:
    name: publications
    description: a collection of publications associated with a study
    from_schema: https://w3id.org/BioImage-Archive/bia-mifa-models
    rank: 1000
    multivalued: true
    alias: publications
    owner: Study
    domain_of:
    - PublicationsCollection
    range: Publications
    inlined: true
  authors:
    name: authors
    description: a collection of the authors of a study
    from_schema: https://w3id.org/BioImage-Archive/bia-mifa-models
    rank: 1000
    multivalued: true
    alias: authors
    owner: Study
    domain_of:
    - AuthorCollection
    range: Author
    inlined_as_list: true
  link_url:
    name: link_url
    description: URL of relevant link
    examples:
    - value: '[''https://github.com/BioImage-Archive'', ''https://www.ebi.ac.uk/empiar/EMPIAR-10459/'']'
    from_schema: https://w3id.org/BioImage-Archive/bia-mifa-models
    rank: 1000
    multivalued: true
    alias: link_url
    owner: Study
    domain_of:
    - Links
    range: uriorcurie
    required: true
  link_description:
    name: link_description
    description: The description of the linked content
    examples:
    - value: '[''Image analysis code'', ''FIB SEM dataset matching the light microscopy
        data'']'
    from_schema: https://w3id.org/BioImage-Archive/bia-mifa-models
    rank: 1000
    multivalued: true
    alias: link_description
    owner: Study
    domain_of:
    - Links
    range: string
  grants:
    name: grants
    description: a collection of grant ids and funder names associated with the study
    from_schema: https://w3id.org/BioImage-Archive/bia-mifa-models
    rank: 1000
    multivalued: true
    alias: grants
    owner: Study
    domain_of:
    - GrantReferenceCollection
    range: GrantReference
    inlined_as_list: true