Questions&Answers

Seek

What links are used by the seek-users to link their models?

• Answered on 16.09.2020 by SO

  • there is no restriction on this field, the user can link the model directly or link a website

• impact

  • MaSeMiWa must check the target and try to find the model file in the content_blobs field

What SEEK-ID in json is persistent?

• Answered on 03.09.2020 by SO

  • SEEK-id(20) and version(1) (i.e. https://fairdomhub.org/models/20.json?version=1) is bound to domain name

    • domain change → force recreate DB

  • the uuid is persistent per model

• Overview of the if-related fields (issue)

  • data.id

    • points to the model, ignoring the version (model id)
    • i.e. 24

  • data.meta.uuid

    • points to the model, ignoring the version (model uuid)
    • i.e. 67bb3ce0-caa7-0138-f7f7-0242ac120004

  • data.links.self

    • points to the model + version without domain dependency (model relative link)
    • i.e. /models/24?version=3

  • data.attributes.version

    • provides the current version number (model version)
    • i.e. 3

  • data.attributes.versions.?.url (? is version number)

    • provides the model + version with domain dependency (model absolute link)
    • i.e. https://sandbox2.fairdomhub.org/models/24.json?version=3

Are SEEK-ids reused?

• Answered on 03.09.2020 by SO

• question was: Is it in any case possible, that Model Y gets the ID of a deleted Model X? (database reorganisation)

  • no, the ID stays unique, new models get the next free, never before used ID

Working with SEEK-versions

• Answered on 03.09.2020 by SO

• Has SEEK some kind of active version (use version 2 instead of version 3 as current version)

  • no

• Is it possible to delete versions in SEEK?

  • no

• Versioning is linear, right?

  • yes

MaSyMoS Morre

Supported Model Types: SBML, CELLML, SEDML

• Answered on 30.09.2020 by RH

• Description

  • SBML < Level 3, namespaces:

    • http://www.sbml.org/sbml/level1/*
    • http://www.sbml.org/sbml/level2/*
    • SBML versions have no big impact

  • SEDML < Level 1 Version 3

    • http://sed-ml.org

  • CELLML <= Version 1.1

    • http://www.cellml.org/cellml/1.0
    • http://www.cellml.org/cellml/1.1

Check of the SEEK Model data - numbers

The small python scripts for reproduction can be found here.

Results (30.09.2020 fairdomhub.org)

• Counters: Versions by namespace for "valid MIME" ('application/sbml+xml', 'application/xml', 'text/xml')

  'http://www.sbml.org/sbml/level2/version4'       →    71
  'http://www.sbml.org/sbml/level3/version1/core'  →    40
  'http://www.sbml.org/sbml/level2'                →    17
  'http://www.copasi.org/static/schema'            →    13
  'http://www.sbml.org/sbml/level2/version3'       →    13
  'http://sbgn.org/libsbgn/pd/0.1'                 →    5
  'http://www.sbml.org/sbml/level2/version2'       →    1
  

• Counters: Metadata from json

  Number of public models: 334
  Number of models with fairdomhub.org-content in link-field: 333
  Number of models with non-fairdomhub.org-content in link-field: 0
  Number of models without fairdomhub.org-content in any link-field: 0
  Number of models without content_blobs: 1
  Number of models with valid MIME¹: 187
  Number of models with maybe MIME¹: 0
  Number of models with invalid MIME¹: 146
  Number of models with more then one MIME-valid content: 6: ['225', '231', '269', '325', '326', '734']
  Number of MIME-valid models (usable by MaSyMoS): 187
  
  ¹MIME-overview:
  - valid MIME: ('application/sbml+xml', 'application/xml', 'text/xml')
  - maybe MIME: ()
  - invalid MIME: ('namespace', 'application/gzip', 'application/json', 'application/mathematica', 'application/matlab', 'application/octet-stream', 'application/pdf', 'application/x-compressed-tar', 'application/x-rar', 'application/x-ruby', 'application/x-tar', 'application/xhtml+xml', 'application/zip', 'image/png', 'text/html', 'text/plain', 'text/x-python', 'text/x-uuencode', 'text/nlogo')
  

• All Mime Types

  application/gzip
  application/json
  application/mathematica
  application/matlab
  application/octet-stream
  application/pdf
  application/sbml+xml
  application/x-compressed-tar
  application/xhtml+xml
  application/xml
  application/x-rar
  application/x-ruby
  application/x-tar
  application/zip
  image/png
  text/html
  text/nlogo
  text/plain
  text/xml
  text/x-python
  text/x-uuencode